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| Center for Biomolecular and Tissue Engineering : Publications since January 2023List all publications in the database. :chronological alphabetical combined listing:%% Barr, Roger C. @article{2573262, Author = {DiPersio, D.A. and Barr, R.C.}, Title = {Evaluation of the fan method of adaptive sampling on human electrocardiograms}, Journal = {Med. Biol. Eng. Comput. (UK)}, Volume = {23}, Number = {5}, Pages = {401 - 10}, Keywords = {electrocardiography;}, Abstract = {The fan is a method of adaptive sampling that selects samples from electrocardiograms more rapidly during periods of rapid waveform change and more slowly otherwise. One attribute of the fan is the guarantee that the original waveform can be reconstructed within tolerance ε. Many questions about the particulars of the fan's performance on human ECGs have been undocumented, e.g, what ε choice leads to good quality recording, how does the choice of ε effect visual quality, and what average sampling rates occur? The paper provides answers to these and other questions. It is based on retrospective analysis of 20700 human ECG waveforms from subjects of all ages. The results show, for example, that ε=10 μV leads to high quality waveforms sampled at an average rate of 266 samples s<sup>-1</sup> with maximum errors only 1/24 th the maximum errors using uniform sampling at 250 samples s<sup>-1</sup>, and that ε=30 μV leads to waveforms showing all deflections at an average rate of 45 samples s<sup>-1</sup> with maximum errors only 1/57 th of the maximum errors from uniform sampling at 45 samples s<sup>-1</sup>}, Key = {2573262} } @article{4035817, Author = {Plonsey, R. and Barr, R.C. and Witkowski, F.X.}, Title = {One-dimensional model of cardiac defibrillation}, Journal = {Med. Biol. Eng. Comput. (UK)}, Volume = {29}, Number = {5}, Pages = {465 - 9}, Keywords = {bioelectric phenomena;biomembranes;cardiology;cellular biophysics;physiological models;}, Abstract = {The response of a single strand of cardiac cells to a uniform defibrillatory shock assuming steady-state linear conditions is examined. It is argued that the effect of this current is quantitatively described by the induced transmembrane potential even under passive conditions. The characteristics of the single strand are those that would exist if the heart was a system of equivalent parallel pathways from apex to base. It is shown that essentially every cell is both hyperpolarised and depolarised from the shock by an amount proportional to the stimulus intensity and the intercellular junctional resistance. For physiological values of model parameters the evaluated depolarisations are consistent with levels necessary to affect electrophysiological behaviour}, Key = {4035817} } @article{3042774, Author = {Di Persio and D.A. and Barr, R.C.}, Title = {A prototype inverse solution in one-dimension to find the origin of excitation, strand radius, intracellular resistivity, or distance from the surface}, Journal = {IEEE Trans. Biomed. Eng. (USA)}, Volume = {BME-34}, Number = {9}, Pages = {681 - 91}, Keywords = {bioelectric phenomena;cardiology;cellular biophysics;}, Abstract = {A computer simulation of a strand 11.8 mm long was used to examine whether extracellular waveforms from a one-dimensional strand can be used to find the site of origin of excitation (<i>x</i><sub>s0</sub>), strand radius (<i>a</i><sub>0</sub>), intracellular resistivity (<i>R</i><sub>i0</sub>), or distance of the electrodes from the strand (<i>b</i><sub>0</sub>). The Ebihara-Johnson equations were used to model the membrane's behavior. Extracellular waveforms simulated at two of 60 points along the strand were used as `measurements'. The inverse calculations had the objective of finding one or two of the variables <i>x</i><sub>s0</sub>, <i>a</i><sub>0</sub>, <i>R</i><sub>i0</sub>, or <i>b</i><sub>0</sub> with the others known. The solution procedure compared the `measured' waveforms to trial waveforms obtained by varying all unknown parameters through their physiological range. The error curves were frequently found to have several relative minima. In general, however, no combination of unknowns other than the correct one led to rms errors within experimental noise levels, a result in marked contrast to that of most other inverse calculations in electrocardiography}, Key = {3042774} } @article{1266888, Author = {Hersh, L.T. and Barr, R.C. and Spach, M.S.}, Title = {An analysis of transfer coefficients calculated directly from epicardial and body surface potential measurements in the intact dog}, Journal = {IEEE Trans. Biomed. Eng. (USA)}, Volume = {BME-25}, Number = {5}, Pages = {446 - 61}, Keywords = {bioelectric potentials;biological techniques and instruments;electrocardiography;}, Abstract = {The study considered the feasibility of obtaining transfer coefficients directly from sequences of epicardial and body surface measurements of ventricular excitation and repolarisation potential distributions, rather than from measurements of the geometry of the volume conductor. The transfer coefficients were calculated from the measured potentials via the mathematical method of using a Bayes estimator. The merit of this approach was that it offered the possibility of accurately representing the characteristics of the volume conductor without directly measuring either the volume conductor's geometry or its inhomogeneities. The experimental protocol made use of measurements from two dogs}, Key = {1266888} } @article{8123233, Author = {Mossop, B.J. and Barr, R.C. and Zaharoff, D.A. and Fan Yuan}, Title = {Electric fields within cells as a function of membrane resistivity-a model study}, Journal = {IEEE Trans. Nanobiosc. (USA)}, Volume = {3}, Number = {3}, Pages = {225 - 31}, url = {http://dx.doi.org/10.1109/TNB.2004.833703}, Keywords = {bioelectric potentials;biological effects of fields;biomembranes;cellular effects of radiation;physiological models;}, Abstract = {Externally applied electric fields play an important role in many therapeutic modalities, but the fields they produce inside cells remain largely unknown. This study makes use of a three-dimensional model to determine the electric field that exists in the intracellular domain of a 10-μm spherical cell exposed to an applied field of 100 V/cm. The transmembrane potential resulting from the applied field was also determined and its change was compared to those of the intracellular field. The intracellular field increased as the membrane resistance decreased over a wide range of values. The results showed that the intracellular electric field was about 1.1 mV/cm for R<sub>m</sub> of 10 000 Ω·cm<sup>2</sup>, increasing to about 111 mV/cm as R<sub>m</sub> decreased to 100 Ω·cm<sup>2</sup>. Over this range of R<sub>m</sub> the transmembrane potential was nearly constant. The transmembrane potential declined only as R<sub>m</sub> decreased below 1 Ω·cm<sup>2</sup>. The simulation results suggest that intracellular electric field depends on R<sub>m</sub> in its physiologic range, and may not be negligible in understanding some mechanisms of electric field-mediated therapies}, Key = {8123233} } %% Chilkoti, Ashutosh @article{fds376860, Author = {Li, Z and Shen, Q and Usher, ET and Anderson, AP and Iburg, M and Lin, R and Zimmer, B and Meyer, MD and Holehouse, AS and You, L and Chilkoti, A and Dai, Y and Lu, GJ}, Title = {Phase transition of GvpU regulates gas vesicle clustering in bacteria.}, Journal = {Nature microbiology}, Volume = {9}, Number = {4}, Pages = {1021-1035}, Year = {2024}, Month = {April}, url = {http://dx.doi.org/10.1038/s41564-024-01648-3}, Abstract = {Gas vesicles (GVs) are microbial protein organelles that support cellular buoyancy. GV engineering has multiple applications, including reporter gene imaging, acoustic control and payload delivery. GVs often cluster into a honeycomb pattern to minimize occupancy of the cytosol. The underlying molecular mechanism and the influence on cellular physiology remain unknown. Using genetic, biochemical and imaging approaches, here we identify GvpU from Priestia megaterium as a protein that regulates GV clustering in vitro and upon expression in Escherichia coli. GvpU binds to the C-terminal tail of the core GV shell protein and undergoes a phase transition to form clusters in subsaturated solution. These properties of GvpU tune GV clustering and directly modulate bacterial fitness. GV variants can be designed with controllable sensitivity to GvpU-mediated clustering, enabling design of genetically tunable biosensors. Our findings elucidate the molecular mechanisms and functional roles of GV clustering, enabling its programmability for biomedical applications.}, Doi = {10.1038/s41564-024-01648-3}, Key = {fds376860} } @article{fds376746, Author = {Walter, V and Schmatko, T and Muller, P and Schroder, AP and MacEwan, SR and Chilkoti, A and Marques, CM}, Title = {Negative lipid membranes enhance the adsorption of TAT-decorated elastin-like polypeptide micelles.}, Journal = {Biophysical journal}, Volume = {123}, Number = {7}, Pages = {901-908}, Year = {2024}, Month = {April}, url = {http://dx.doi.org/10.1016/j.bpj.2024.03.001}, Abstract = {A cell-penetrating peptide (CPP) is a short amino-acid sequence capable of efficiently translocating across the cellular membrane of mammalian cells. However, the potential of CPPs as a delivery vector is hampered by the strong reduction of its translocation efficiency when it bears an attached molecular cargo. To overcome this problem, we used previously developed diblock copolymers of elastin-like polypeptides (ELP<sub>BC</sub>s), which we end functionalized with TAT (transactivator of transcription), an archetypal CPP built from a positively charged amino acid sequence of the HIV-1 virus. These ELP<sub>BC</sub>s self-assemble into micelles at a specific temperature and present the TAT peptide on their corona. These micelles can recover the lost membrane affinity of TAT and can trigger interactions with the membrane despite the presence of a molecular cargo. Herein, we study the influence of membrane surface charge on the adsorption of TAT-functionalized ELP micelles onto giant unilamellar vesicles (GUVs). We show that the TAT-ELP<sub>BC</sub> micelles show an increased binding constant toward negatively charged membranes compared to neutral membranes, but no translocation is observed. The affinity of the TAT-ELP<sub>BC</sub> micelles for the GUVs displays a stepwise dependence on the lipid charge of the GUV, which, to our knowledge, has not been reported previously for interactions between peptides and lipid membranes. By unveiling the key steps controlling the interaction of an archetypal CPP with lipid membranes, through regulation of the charge of the lipid bilayer, our results pave the way for a better design of delivery vectors based on CPPs.}, Doi = {10.1016/j.bpj.2024.03.001}, Key = {fds376746} } @article{fds375503, Author = {Strader, RL and Shmidov, Y and Chilkoti, A}, Title = {Encoding Structure in Intrinsically Disordered Protein Biomaterials.}, Journal = {Accounts of chemical research}, Volume = {57}, Number = {3}, Pages = {302-311}, Year = {2024}, Month = {February}, url = {http://dx.doi.org/10.1021/acs.accounts.3c00624}, Abstract = {ConspectusIn nature, proteins range from those with highly ordered secondary and tertiary structures to those that completely lack a well-defined three-dimensional structure, termed intrinsically disordered proteins (IDPs). IDPs are generally characterized by one or more segments that have a compositional bias toward small hydrophilic amino acids and proline residues that promote structural disorder and are called intrinsically disordered regions (IDRs). The combination of IDRs with ordered regions and the interactions between the two determine the phase behavior, structure, and function of IDPs. Nature also diversifies the structure of proteins and thereby their functions by hybridization of the proteins with other moieties such as glycans and lipids; for instance, post-translationally glycosylated and lipidated proteins are important cell membrane components. Additionally, diversity in protein structure and function is achieved in nature through cross-linking proteins within themselves or with other domains to create various topologies. For example, an essential characteristic of the extracellular matrix (ECM) is the cross-linking of its network components, including proteins such as collagen and elastin, as well as polysaccharides such as hyaluronic acid (HA). Inspired by nature, synthetic IDP (SynIDP)-based biomaterials can be designed by employing similar strategies with the goal of introducing structural diversity and hence unique physiochemical properties. This Account describes such materials produced over the past decade and following one or more of the following approaches: (1) incorporating highly ordered domains into SynIDPs, (2) conjugating SynIDPs to other moieties through either genetically encoded post-translational modification or chemical conjugation, and (3) engineering the topology of SynIDPs via chemical modification. These approaches introduce modifications to the primary structure of SynIDPs, which are then translated to unique three-dimensional secondary and tertiary structures. Beginning with completely disordered SynIDPs as the point of origin, structure may be introduced into SynIDPs by each of these three unique approaches individually along orthogonal axes or by combinations of the three, enabling bioinspired designs to theoretically span the entire range of three-dimensional structural possibilities. Furthermore, the resultant structures span a wide range of length scales, from nano- to meso- to micro- and even macrostructures. In this Account, emphasis is placed on the physiochemical properties and structural features of the described materials. Conjugates of SynIDPs to synthetic polymers and materials achieved by simple mixing of components are outside the scope of this Account. Related biomedical applications are described briefly. Finally, we note future directions for the design of functional SynIDP-based biomaterials.}, Doi = {10.1021/acs.accounts.3c00624}, Key = {fds375503} } @article{fds376124, Author = {Albarghouthi, FM and Semeniak, D and Khanani, I and Doherty, JL and Smith, BN and Salfity, M and MacFarlane, Q and Karappur, A and Noyce, SG and Williams, NX and Joh, DY and Andrews, JB and Chilkoti, A and Franklin, AD}, Title = {Addressing Signal Drift and Screening for Detection of Biomarkers with Carbon Nanotube Transistors.}, Journal = {ACS nano}, Year = {2024}, Month = {February}, url = {http://dx.doi.org/10.1021/acsnano.3c11679}, Abstract = {Electrical biosensors, including transistor-based devices (i.e., BioFETs), have the potential to offer versatile biomarker detection in a simple, low-cost, scalable, and point-of-care manner. Semiconducting carbon nanotubes (CNTs) are among the most explored nanomaterial candidates for BioFETs due to their high electrical sensitivity and compatibility with diverse fabrication approaches. However, when operating in solutions at biologically relevant ionic strengths, CNT-based BioFETs suffer from debilitating levels of signal drift and charge screening, which are often unaccounted for or sidestepped (but not addressed) by testing in diluted solutions. In this work, we present an ultrasensitive CNT-based BioFET called the D4-TFT, an immunoassay with an electrical readout, which overcomes charge screening and drift-related limitations of BioFETs. In high ionic strength solution (1X PBS), the D4-TFT repeatedly and stably detects subfemtomolar biomarker concentrations in a point-of-care form factor by increasing the sensing distance in solution (Debye length) and mitigating signal drift effects. Debye length screening and biofouling effects are overcome using a poly(ethylene glycol)-like polymer brush interface (POEGMA) above the device into which antibodies are printed. Simultaneous testing of a control device having no antibodies printed over the CNT channel confirms successful detection of the target biomarker via an on-current shift caused by antibody sandwich formation. Drift in the target signal is mitigated by a combination of: (1) maximizing sensitivity by appropriate passivation alongside the polymer brush coating; (2) using a stable electrical testing configuration; and (3) enforcing a rigorous testing methodology that relies on infrequent DC sweeps rather than static or AC measurements. These improvements are realized in a relatively simple device using printed CNTs and antibodies for a low-cost, versatile platform for the ongoing pursuit of point-of-care BioFETs.}, Doi = {10.1021/acsnano.3c11679}, Key = {fds376124} } @article{fds374925, Author = {Deshpande, S and Yang, Y and Zauscher, S and Chilkoti, A}, Title = {Enzymatic Synthesis of Aptamer-Polynucleotide Nanoparticles with High Anticancer Drug Loading for Targeted Delivery.}, Journal = {Biomacromolecules}, Volume = {25}, Number = {1}, Pages = {155-164}, Year = {2024}, Month = {January}, url = {http://dx.doi.org/10.1021/acs.biomac.3c00888}, Abstract = {We report a targeted prodrug delivery platform that can deliver a cytostatic nucleobase analog with high drug loading. We chose fluorouracil (5FU), a drug used to treat various cancers, whose active metabolite 5-fluorodeoxyuridine monophosphate (5-FdUMP) is the antineoplastic agent. We use terminal deoxynucleotidyl transferase (TdT) to polymerize 5-fluorodeoxyuridine triphosphate (5-FdUTP) onto the 3'-end of an aptamer. We find that (i) addition of hydrophobic, unnatural nucleotides at the 3'-end of the 5-FdU polynucleotide by TdT leads to their spontaneous self-assembly into nuclease resistant micelles, (ii) aptamers presented on the micelle corona retain specificity for their cognate receptor on tumor cells, and (iii) the micelles deliver 5FU to tumor cells and exhibit greater cytotoxicity than the free drug. The modular design of our platform, consisting of a targeting moiety, a polynucleotide drug, and a self-assembly domain, can be adapted to encompass a range of polymerizable therapeutic nucleotides and targeting units.}, Doi = {10.1021/acs.biomac.3c00888}, Key = {fds374925} } @article{fds376263, Author = {Subramaniam, S and Akay, M and Anastasio, MA and Bailey, V and Boas, D and Bonato, P and Chilkoti, A and Cochran, JR and Colvin, V and Desai, TA and Duncan, JS and Epstein, FH and Fraley, S and Giachelli, C and Grande-Allen, KJ and Green, J and Guo, XE and Hilton, IB and Humphrey, JD and Johnson, CR and Karniadakis, G and King, MR and Kirsch, RF and Kumar, S and Laurencin, CT and Li, S and Lieber, RL and Lovell, N and Mali, P and Margulies, SS and Meaney, DF and Ogle, B and Palsson, B and A Peppas, N and Perreault, EJ and Rabbitt, R and Setton, LA and Shea, LD and Shroff, SG and Shung, K and Tolias, AS and van der Meulen, MCH and Varghese, S and Vunjak-Novakovic, G and White, JA and Winslow, R and Zhang, J and Zhang, K and Zukoski, C and Miller, MI}, Title = {Grand Challenges at the Interface of Engineering and Medicine.}, Journal = {IEEE Open J Eng Med Biol}, Volume = {5}, Pages = {1-13}, Year = {2024}, url = {http://dx.doi.org/10.1109/OJEMB.2024.3351717}, Abstract = {Over the past two decades Biomedical Engineering has emerged as a major discipline that bridges societal needs of human health care with the development of novel technologies. Every medical institution is now equipped at varying degrees of sophistication with the ability to monitor human health in both non-invasive and invasive modes. The multiple scales at which human physiology can be interrogated provide a profound perspective on health and disease. We are at the nexus of creating "avatars" (herein defined as an extension of "digital twins") of human patho/physiology to serve as paradigms for interrogation and potential intervention. Motivated by the emergence of these new capabilities, the IEEE Engineering in Medicine and Biology Society, the Departments of Biomedical Engineering at Johns Hopkins University and Bioengineering at University of California at San Diego sponsored an interdisciplinary workshop to define the grand challenges that face biomedical engineering and the mechanisms to address these challenges. The Workshop identified five grand challenges with cross-cutting themes and provided a roadmap for new technologies, identified new training needs, and defined the types of interdisciplinary teams needed for addressing these challenges. The themes presented in this paper include: 1) accumedicine through creation of avatars of cells, tissues, organs and whole human; 2) development of smart and responsive devices for human function augmentation; 3) exocortical technologies to understand brain function and treat neuropathologies; 4) the development of approaches to harness the human immune system for health and wellness; and 5) new strategies to engineer genomes and cells.}, Doi = {10.1109/OJEMB.2024.3351717}, Key = {fds376263} } @article{fds374612, Author = {Sethi, V and Cohen-Gerassi, D and Meir, S and Ney, M and Shmidov, Y and Koren, G and Adler-Abramovich, L and Chilkoti, A and Beck, R}, Title = {Modulating hierarchical self-assembly in thermoresponsive intrinsically disordered proteins through high-temperature incubation time.}, Journal = {Scientific reports}, Volume = {13}, Number = {1}, Pages = {21688}, Year = {2023}, Month = {December}, url = {http://dx.doi.org/10.1038/s41598-023-48483-w}, Abstract = {The cornerstone of structural biology is the unique relationship between protein sequence and the 3D structure at equilibrium. Although intrinsically disordered proteins (IDPs) do not fold into a specific 3D structure, breaking this paradigm, some IDPs exhibit large-scale organization, such as liquid-liquid phase separation. In such cases, the structural plasticity has the potential to form numerous self-assembled structures out of thermal equilibrium. Here, we report that high-temperature incubation time is a defining parameter for micro and nanoscale self-assembly of resilin-like IDPs. Interestingly, high-resolution scanning electron microscopy micrographs reveal that an extended incubation time leads to the formation of micron-size rods and ellipsoids that depend on the amino acid sequence. More surprisingly, a prolonged incubation time also induces amino acid composition-dependent formation of short-range nanoscale order, such as periodic lamellar nanostructures. We, therefore, suggest that regulating the period of high-temperature incubation, in the one-phase regime, can serve as a unique method of controlling the hierarchical self-assembly mechanism of structurally disordered proteins.}, Doi = {10.1038/s41598-023-48483-w}, Key = {fds374612} } @article{fds372990, Author = {Lazar, KM and Shetty, S and Chilkoti, A and Collier, JH}, Title = {Immune-active polymeric materials for the treatment of inflammatory diseases}, Journal = {Current Opinion in Colloid and Interface Science}, Volume = {67}, Year = {2023}, Month = {October}, url = {http://dx.doi.org/10.1016/j.cocis.2023.101726}, Abstract = {In recent years, a growing understanding of the underlying mechanisms of autoinflammatory and autoimmune disease has enabled significant advances in biomaterial therapeutics for their treatment and prevention. Drug-free or immune-active polymeric materials are of particular interest due to their chemical tunability, multifaceted mechanisms of action, and potential to offer alternatives to conventional treatments. While in many cases the relationships between polymer physicochemical properties and the immune processes they influence are context-dependent and require further clarity, several concepts are emerging that can be applied in the design of anti-inflammatory materials. This review highlights recent work that investigates these relationships, as well as work that applies them to immunomodulatory biomaterials for the treatment or prevention of autoimmune and autoinflammatory diseases.}, Doi = {10.1016/j.cocis.2023.101726}, Key = {fds372990} } @article{fds363245, Author = {Semeniak, D and Cruz, DF and Chilkoti, A and Mikkelsen, MH}, Title = {Plasmonic Fluorescence Enhancement in Diagnostics for Clinical Tests at Point-of-Care: A Review of Recent Technologies.}, Journal = {Advanced materials (Deerfield Beach, Fla.)}, Volume = {35}, Number = {34}, Pages = {e2107986}, Year = {2023}, Month = {August}, url = {http://dx.doi.org/10.1002/adma.202107986}, Abstract = {Fluorescence-based biosensors have widely been used in the life-sciences and biomedical applications due to their low limit of detection and a diverse selection of fluorophores that enable simultaneous measurements of multiple biomarkers. Recent research effort has been made to implement fluorescent biosensors into the exploding field of point-of-care testing (POCT), which uses cost-effective strategies for rapid and affordable diagnostic testing. However, fluorescence-based assays often suffer from their feeble signal at low analyte concentrations, which often requires sophisticated, costly, and bulky instrumentation to maintain high detection sensitivity. Metal- and metal oxide-based nanostructures offer a simple solution to increase the output signal from fluorescent biosensors due to the generation of high field enhancements close to a metal or metal oxide surface, which has been shown to improve the excitation rate, quantum yield, photostability, and radiation pattern of fluorophores. This article provides an overview of existing biosensors that employ various strategies for fluorescence enhancement via nanostructures and have demonstrated the potential for use as POCT. Biosensors using nanostructures such as planar substrates, freestanding nanoparticles, and metal-dielectric-metal nanocavities are discussed with an emphasis placed on technologies that have shown promise towards POCT applications without the need for centralized laboratories.}, Doi = {10.1002/adma.202107986}, Key = {fds363245} } @article{fds376100, Author = {Vahabi, H and Liu, J and Dai, Y and Joh, DY and Britton, R and Heggestad, J and Kinnamon, D and Rajput, S and Chilkoti, A}, Title = {A gravity-driven droplet fluidic point-of-care test.}, Journal = {Device}, Volume = {1}, Number = {1}, Pages = {100009}, Year = {2023}, Month = {July}, url = {http://dx.doi.org/10.1016/j.device.2023.100009}, Abstract = {We report a simple droplet fluidic point-of-care test (POCT) that uses gravity to manipulate the sequence, timing, and motion of droplets on a surface. To fabricate this POCT, we first developed a surface coating toolbox of nine different coatings with three levels of wettability and three levels of slipperiness that can be independently tailored. We then fabricated a device that has interconnected fluidic elements-pumps, flow resistors and flow guides-on a highly slippery solid surface to precisely control the timing and sequence of motion of multiple droplets and their interactions on the surface. We then used this device to carry out a multi-step enzymatic assay of a clinically relevant analyte-lactate dehydrogenase (LDH)-to demonstrate the application of this technology for point-of-care diagnosis.}, Doi = {10.1016/j.device.2023.100009}, Key = {fds376100} } @article{fds371663, Author = {Kinnamon, DS and Heggestad, JT and Liu, J and Nguyen, T and Ly, V and Hucknall, AM and Fontes, CM and Britton, RJ and Cai, J-P and Chan, JF-W and Yuen, K-Y and Le, T and Chilkoti, A}, Title = {Environmentally Resilient Microfluidic Point-of-Care Immunoassay Enables Rapid Diagnosis of Talaromycosis.}, Journal = {ACS Sens}, Volume = {8}, Number = {6}, Pages = {2228-2236}, Year = {2023}, Month = {June}, url = {http://dx.doi.org/10.1021/acssensors.3c00209}, Abstract = {Point-of-care tests (POCTs) are increasingly being used in field settings, particularly outdoors. The performance of current POCTs─most commonly the lateral flow immunoassay─can be adversely affected by ambient temperature and humidity. We developed a self-contained immunoassay platform─the D4 POCT─that can be conducted at the POC by integrating all reagents in a capillary-driven passive microfluidic cassette that minimizes user intervention. The assay can be imaged and analyzed on a portable fluorescence reader─the D4Scope─and provide quantitative outputs. Here, we systematically investigated the resilience of our D4 POCT to varied temperature and humidity and to physiologically diverse human whole blood samples that span a wide range of physiological hematocrit (30-65%). For all conditions, we showed that the platform maintained high sensitivity (0.05-0.41 ng/mL limits of detection). The platform also demonstrated good accuracy in reporting true analyte concentration across environmental extremes when compared to the manually operated format of the same test to detect a model analyte─ovalbumin. Additionally, we engineered an improved version of the microfluidic cassette that improved the ease-of-use of the device and shortened the time-to-result. We implemented this new cassette to create a rapid diagnostic test to detect talaromycosis infection in patients with advanced HIV disease at the POC, demonstrating comparable sensitivity and specificity to the laboratory test for the disease.}, Doi = {10.1021/acssensors.3c00209}, Key = {fds371663} } @article{fds371273, Author = {Dai, Y and Chamberlayne, CF and Messina, MS and Chang, CJ and Zare, RN and You, L and Chilkoti, A}, Title = {Interface of biomolecular condensates modulates redox reactions.}, Journal = {Chem}, Volume = {9}, Number = {6}, Pages = {1594-1609}, Year = {2023}, Month = {June}, url = {http://dx.doi.org/10.1016/j.chempr.2023.04.001}, Abstract = {Biomolecular condensates mediate diverse cellular processes. The density transition process of condensate formation results in selective partitioning of molecules, which define a distinct chemical environment within the condensates. However, the fundamental features of the chemical environment and the mechanisms by which such environment can contribute to condensate functions have not been revealed. Here, we report that an electric potential gradient, thereby an electric field, is established at the liquid-liquid interface between the condensate and the bulk environment due to the density transition of ions and molecules brought about by phase separation. We find that the interface of condensates can drive spontaneous redox reactions in vitro and in living cells. Our results uncover a fundamental physicochemical property of the interface of condensates and the mechanism by which the interface can modulate biochemical activities.}, Doi = {10.1016/j.chempr.2023.04.001}, Key = {fds371273} } @article{fds371664, Author = {Burrow, DT and Heggestad, JT and Kinnamon, DS and Chilkoti, A}, Title = {Engineering Innovative Interfaces for Point-of-Care Diagnostics.}, Journal = {Current opinion in colloid & interface science}, Pages = {101718}, Year = {2023}, Month = {June}, url = {http://dx.doi.org/10.1016/j.cocis.2023.101718}, Abstract = {The ongoing Coronavirus disease 2019 (COVID-19) pandemic illustrates the need for sensitive and reliable tools to diagnose and monitor diseases. Traditional diagnostic approaches rely on centralized laboratory tests that result in long wait times to results and reduce the number of tests that can be given. Point-of-care tests (POCTs) are a group of technologies that miniaturize clinical assays into portable form factors that can be run both in clinical areas --in place of traditional tests-- and outside of traditional clinical settings --to enable new testing paradigms. Hallmark examples of POCTs are the pregnancy test lateral flow assay and the blood glucose meter. Other uses for POCTs include diagnostic assays for diseases like COVID-19, HIV, and malaria but despite some successes, there are still unsolved challenges for fully translating these lower cost and more versatile solutions. To overcome these challenges, researchers have exploited innovations in colloid and interface science to develop various designs of POCTs for clinical applications. Herein, we provide a review of recent advancements in lateral flow assays, other paper based POCTs, protein microarray assays, microbead flow assays, and nucleic acid amplification assays. Features that are desirable to integrate into future POCTs, including simplified sample collection, end-to-end connectivity, and machine learning, are also discussed in this review.}, Doi = {10.1016/j.cocis.2023.101718}, Key = {fds371664} } @article{fds370381, Author = {Heggestad, JT and Britton, RJ and Kinnamon, DS and Liu, J and Anderson, JG and Joh, DY and Quinn, Z and Fontes, CM and Hucknall, AM and Parks, R and Sempowski, GD and Denny, TN and Burke, TW and Haynes, BF and Woods, CW and Chilkoti, A}, Title = {COVID-19 Diagnosis and SARS-CoV-2 Strain Identification by a Rapid, Multiplexed, Point-of-Care Antibody Microarray.}, Journal = {Anal Chem}, Volume = {95}, Number = {13}, Pages = {5610-5617}, Year = {2023}, Month = {April}, url = {http://dx.doi.org/10.1021/acs.analchem.2c05180}, Abstract = {Antigen tests to detect SARS-CoV-2 have emerged as a promising rapid diagnostic method for COVID-19, but they are unable to differentiate between variants of concern (VOCs). Here, we report a rapid point-of-care test (POC-T), termed CoVariant-SPOT, that uses a set of antibodies that are either tolerant or intolerant to spike protein mutations to identify the likely SARS-CoV-2 strain concurrent with COVID-19 diagnosis using antibodies targeting the nucleocapsid protein. All reagents are incorporated into a portable, multiplexed, and sensitive diagnostic platform built upon a nonfouling polymer brush. To validate CoVariant-SPOT, we tested recombinant SARS-CoV-2 proteins, inactivated viruses, and nasopharyngeal swab samples from COVID-19 positive and negative individuals and showed that CoVariant-SPOT can readily distinguish between two VOCs: Delta and Omicron. We believe that CoVariant-SPOT can serve as a valuable adjunct to next-generation sequencing to rapidly identify variants using a scalable and deployable POC-T, thereby enhancing community surveillance efforts worldwide and informing treatment selection.}, Doi = {10.1021/acs.analchem.2c05180}, Key = {fds370381} } @article{fds369362, Author = {Dai, Y and Farag, M and Lee, D and Zeng, X and Kim, K and Son, H-I and Guo, X and Su, J and Peterson, N and Mohammed, J and Ney, M and Shapiro, DM and Pappu, RV and Chilkoti, A and You, L}, Title = {Programmable synthetic biomolecular condensates for cellular control.}, Journal = {Nature chemical biology}, Volume = {19}, Number = {4}, Pages = {518-528}, Year = {2023}, Month = {April}, url = {http://dx.doi.org/10.1038/s41589-022-01252-8}, Abstract = {The formation of biomolecular condensates mediated by a coupling of associative and segregative phase transitions plays a critical role in controlling diverse cellular functions in nature. This has inspired the use of phase transitions to design synthetic systems. While design rules of phase transitions have been established for many synthetic intrinsically disordered proteins, most efforts have focused on investigating their phase behaviors in a test tube. Here, we present a rational engineering approach to program the formation and physical properties of synthetic condensates to achieve intended cellular functions. We demonstrate this approach through targeted plasmid sequestration and transcription regulation in bacteria and modulation of a protein circuit in mammalian cells. Our approach lays the foundation for engineering designer condensates for synthetic biology applications.}, Doi = {10.1038/s41589-022-01252-8}, Key = {fds369362} } @article{fds368928, Author = {Ozer, I and Slezak, A and Sirohi, P and Li, X and Zakharov, N and Yao, Y and Everitt, JI and Spasojevic, I and Craig, SL and Collier, JH and Campbell, JE and D'Alessio, DA and Chilkoti, A}, Title = {An injectable PEG-like conjugate forms a subcutaneous depot and enables sustained delivery of a peptide drug.}, Journal = {Biomaterials}, Volume = {294}, Pages = {121985}, Year = {2023}, Month = {March}, url = {http://dx.doi.org/10.1016/j.biomaterials.2022.121985}, Abstract = {Many biologics have a short plasma half-life, and their conjugation to polyethylene glycol (PEG) is commonly used to solve this problem. However, the improvement in the plasma half-life of PEGylated drugs' is at an asymptote because the development of branched PEG has only had a modest impact on pharmacokinetics and pharmacodynamics. Here, we developed an injectable PEG-like conjugate that forms a subcutaneous depot for the sustained delivery of biologics. The PEG-like conjugate consists of poly[oligo(ethylene glycol) methyl ether methacrylate] (POEGMA) conjugated to exendin, a peptide drug used in the clinic to treat type 2 diabetes. The depot-forming exendin-POEGMA conjugate showed greater efficacy than a PEG conjugate of exendin as well as Bydureon, a clinically approved sustained-release formulation of exendin. The injectable depot-forming exendin-POEGMA conjugate did not elicit an immune response against the polymer, so that it remained effective and safe for long-term management of type 2 diabetes upon chronic administration. In contrast, the PEG conjugate induced an anti-PEG immune response, leading to early clearance and loss of efficacy upon repeat dosing. The exendin-POEGMA depot also showed superior long-term efficacy compared to Bydureon. Collectively, these results suggest that an injectable POEGMA conjugate of biologic drugs that forms a drug depot under the skin, providing favorable pharmacokinetic properties and sustained efficacy while remaining non-immunogenic, offers significant advantages over other commonly used drug delivery technologies.}, Doi = {10.1016/j.biomaterials.2022.121985}, Key = {fds368928} } @booklet{Pyhtila06, Author = {J. W. Pyhtila and H. W. Ma and A. J. Simnick and A. Chilkoti and A. Wax}, Title = {Analysis of long range correlations due to coherent light scattering from in-vitro cell arrays using angle-resolved low coherence interferometry}, Journal = {Journal Of Biomedical Optics}, Volume = {11}, Number = {3}, Year = {2006}, ISSN = {1083-3668}, Abstract = {Angle-resolved low coherence interferometry (a/LCl) enables depth-resolved measurements of scattered light that can be used to recover subsurface structural information, such as the size of cell nuclei. Measurements of nuclear morphology, however, can be complicated by coherent scattering between adjacent cell nuclei. Previous studies have eliminated this component by applying a window filter to Fourier transformed angular data, based on the justification that the coherent scattering must necessarily occur over length scales greater than the cell size. To fully study this effect, results of experiments designed to test the validity of this approach are now presented. The a/LCl technique is used to examine light scattered by regular cell arrays, created using stamped adhesive micropatterned substrates. By varying the array spacing, it is demonstrated that cell-to-cell correlations have a predictable effect on light scattering distributions. These results are compared to image analysis of fluorescence micrographs of the cell array samples. The a/LCI results show that the impact of coherent scattering on nuclear morphology measurements can be eliminated through data filtering. (c) 2006 Society of Photo-Optical Instrumentation Engineers.}, Key = {Pyhtila06} } %% Craig, Stephen L @article{fds370028, Author = {Wang, J and Kouznetsova, TB and Xia, J and Ángeles, FJ and de la Cruz, MO and Craig, SL}, Title = {A polyelectrolyte handle for single-molecule force spectroscopy}, Journal = {Journal of Polymer Science}, Volume = {62}, Number = {7}, Pages = {1277-1286}, Year = {2024}, Month = {April}, url = {http://dx.doi.org/10.1002/pol.20230051}, Abstract = {Single-molecule force spectroscopy is a powerful tool for the quantitative investigation of the biophysics, polymer physics and mechanochemistry of individual polymer strands. One limitation of this technique is that the attachment between the tip of the atomic force microscope and the covalent or noncovalent analyte in a given pull is typically not strong enough to sustain the force at which the event of interest occurs, which makes the experiments time-consuming and inhibits throughput. Here we report a polyelectrolyte handle for single-molecule force spectroscopy that offers a combination of high (several hundred pN) attachment forces, good (~4%) success in obtaining a high-force (>200 pN) attachment, a non-fouling detachment process that allows for repetition, and specific attachment locations along the polymer analyte.}, Doi = {10.1002/pol.20230051}, Key = {fds370028} } @article{fds376825, Author = {Sun, Y and Neary, WJ and Huang, X and Kouznetsova, TB and Ouchi, T and Kevlishvili, I and Wang, K and Chen, Y and Kulik, HJ and Craig, SL and Moore, JS}, Title = {A Thermally Stable SO2-Releasing Mechanophore: Facile Activation, Single-Event Spectroscopy, and Molecular Dynamic Simulations.}, Journal = {Journal of the American Chemical Society}, Year = {2024}, Month = {April}, url = {http://dx.doi.org/10.1021/jacs.4c02139}, Abstract = {Polymers that release small molecules in response to mechanical force are promising candidates as next-generation on-demand delivery systems. Despite advancements in the development of mechanophores for releasing diverse payloads through careful molecular design, the availability of scaffolds capable of discharging biomedically significant cargos in substantial quantities remains scarce. In this report, we detail a nonscissile mechanophore built from an 8-thiabicyclo[3.2.1]octane 8,8-dioxide (<b>TBO</b>) motif that releases one equivalent of sulfur dioxide (SO<sub>2</sub>) from each repeat unit. The <b>TBO</b> mechanophore exhibits high thermal stability but is activated mechanochemically using solution ultrasonication in either organic solvent or aqueous media with up to 63% efficiency, equating to 206 molecules of SO<sub>2</sub> released per 143.3 kDa chain. We quantified the mechanochemical reactivity of <b>TBO</b> by single-molecule force spectroscopy and resolved its single-event activation. The force-coupled rate constant for <b>TBO</b> opening reaches ∼9.0 s<sup>-1</sup> at ∼1520 pN, and each reaction of a single <b>TBO</b> domain releases a stored length of ∼0.68 nm. We investigated the mechanism of <b>TBO</b> activation using ab initio steered molecular dynamic simulations and rationalized the observed stereoselectivity. These comprehensive studies of the <b>TBO</b> mechanophore provide a mechanically coupled mechanism of multi-SO<sub>2</sub> release from one polymer chain, facilitating the translation of polymer mechanochemistry to potential biomedical applications.}, Doi = {10.1021/jacs.4c02139}, Key = {fds376825} } @article{fds376826, Author = {Hu, Y and Wang, L and Kevlishvili, I and Wang, S and Chiou, C-Y and Shieh, P and Lin, Y and Kulik, HJ and Johnson, JA and Craig, SL}, Title = {Self-Amplified HF Release and Polymer Deconstruction Cascades Triggered by Mechanical Force.}, Journal = {Journal of the American Chemical Society}, Volume = {146}, Number = {14}, Pages = {10115-10123}, Year = {2024}, Month = {April}, url = {http://dx.doi.org/10.1021/jacs.4c01402}, Abstract = {Hydrogen fluoride (HF) is a versatile reagent for material transformation, with applications in self-immolative polymers, remodeled siloxanes, and degradable polymers. The responsive <i>in situ</i> generation of HF in materials therefore holds promise for new classes of adaptive material systems. Here, we report the mechanochemically coupled generation of HF from alkoxy-<i>gem</i>-difluorocyclopropane (<i>g</i>DFC) mechanophores derived from the addition of difluorocarbene to enol ethers. Production of HF involves an initial mechanochemically assisted rearrangement of <i>g</i>DFC mechanophore to α-fluoro allyl ether whose regiochemistry involves preferential migration of fluoride to the alkoxy-substituted carbon, and ab initio steered molecular dynamics simulations reproduce the observed selectivity and offer insights into the mechanism. When the alkoxy <i>g</i>DFC mechanophore is derived from poly(dihydrofuran), the α-fluoro allyl ether undergoes subsequent hydrolysis to generate 1 equiv of HF and cleave the polymer chain. The hydrolysis is accelerated via acid catalysis, leading to self-amplifying HF generation and concomitant polymer degradation. The mechanically generated HF can be used in combination with fluoride indicators to generate an optical response and to degrade polybutadiene with embedded HF-cleavable silyl ethers (11 mol %). The alkoxy-<i>g</i>DFC mechanophore thus provides a mechanically coupled mechanism of releasing HF for polymer remodeling pathways that complements previous thermally driven mechanisms.}, Doi = {10.1021/jacs.4c01402}, Key = {fds376826} } @article{fds375389, Author = {Duan, C and Malek, JC and Craig, SL and Widenhoefer, RA}, Title = {Modulating Transition Metal Reactivity with Force}, Journal = {ChemCatChem}, Volume = {16}, Number = {5}, Year = {2024}, Month = {March}, url = {http://dx.doi.org/10.1002/cctc.202301479}, Abstract = {The reactivity and selectivity of a transition metal catalyst is intimately related to its ligand-sphere geometry, and, in many cases, the ideal ligand geometry for one step of a catalytic cycle is poorly matched to the ideal ligand geometry for another. For this reason, methods for reversibly modulating ligand geometry on the time scale of catalytic turnover or monomer enchainment are highly desirable. Mechanical force represents a heretofore untapped approach to modulate catalyst geometry and/or reactivity, with the potential to do so on the timescale of catalytic turnover or monomer enchainment. Macroscopic mechanical forces are large, directional and localized to an extent that differentiates them from other forms of energy input such as heat or light. In this Concept, we describe our efforts to address the fundamental challenges associated with force-modulated transition metal catalysis by employing molecular force probe ligands comprising a stiff stilbene photoswitch tethered to rotationally flexible biaryl bisphosphine ligand. Our efforts to date include the modulation of catalytic activity through force-mediated ligand perturbations, quantification of the force-coupled ligand effects on the energetics of elementary organometallic transformations, and evaluation of the mechanisms of force transduction in these systems.}, Doi = {10.1002/cctc.202301479}, Key = {fds375389} } @article{fds375839, Author = {Wu, Z and Bayón, JL and Kouznetsova, TB and Ouchi, T and Barkovich, KJ and Hsu, SK and Craig, SL and Steinmetz, NF}, Title = {Virus-like Particles Armored by an Endoskeleton.}, Journal = {Nano letters}, Volume = {24}, Number = {10}, Pages = {2989-2997}, Year = {2024}, Month = {March}, url = {http://dx.doi.org/10.1021/acs.nanolett.3c03806}, Abstract = {Many virus-like particles (VLPs) have good chemical, thermal, and mechanical stabilities compared to those of other biologics. However, their stability needs to be improved for the commercialization and use in translation of VLP-based materials. We developed an endoskeleton-armored strategy for enhancing VLP stability. Specifically, the VLPs of physalis mottle virus (PhMV) and Qβ were used to demonstrate this concept. We built an internal polymer "backbone" using a maleimide-PEG<sub>15</sub>-maleimide cross-linker to covalently interlink viral coat proteins inside the capsid cavity, while the native VLPs are held together by only noncovalent bonding between subunits. Endoskeleton-armored VLPs exhibited significantly improved thermal stability (95 °C for 15 min), increased resistance to denaturants (i.e., surfactants, pHs, chemical denaturants, and organic solvents), and enhanced mechanical performance. Single-molecule force spectroscopy demonstrated a 6-fold increase in rupture distance and a 1.9-fold increase in rupture force of endoskeleton-armored PhMV. Overall, this endoskeleton-armored strategy provides more opportunities for the development and applications of materials.}, Doi = {10.1021/acs.nanolett.3c03806}, Key = {fds375839} } @article{fds375324, Author = {Hu, Y and Lin, Y and Craig, SL}, Title = {Mechanically Triggered Polymer Deconstruction through Mechanoacid Generation and Catalytic Enol Ether Hydrolysis.}, Journal = {Journal of the American Chemical Society}, Volume = {146}, Number = {5}, Pages = {2876-2881}, Year = {2024}, Month = {February}, url = {http://dx.doi.org/10.1021/jacs.3c10153}, Abstract = {Polymers that amplify a transient external stimulus into changes in their morphology, physical state, or properties continue to be desirable targets for a range of applications. Here, we report a polymer comprising an acid-sensitive, hydrolytically unstable enol ether backbone onto which is embedded <i>gem</i>-dichlorocyclopropane (<i>g</i>DCC) mechanophores through a single postsynthetic modification. The <i>g</i>DCC mechanophore releases HCl in response to large forces of tension along the polymer backbone, and the acid subsequently catalyzes polymer deconstruction at the enol ether sites. Pulsed sonication of a 61 kDa PDHF with 77% <i>g</i>DCC on the backbone in THF with 100 mM H<sub>2</sub>O for 10 min triggers the subsequent degradation of the polymer to a final molecular weight of less than 3 kDa after 24 h of standing, whereas controls lacking either the <i>g</i>DCC or the enol ether reach final molecular weights of 38 and 27 kDa, respectively. The process of sonication, along with the presence of water and the existence of <i>g</i>DCC on the backbone, significantly accelerates the rate of polymer chain deconstruction. Both acid generation and the resulting triggered polymer deconstruction are translated to bulk, cross-linked polymer networks. Networks formed via thiol-ene cross-linking and subjected to unconstrained quasi-static uniaxial compression dissolve on time scales that are at least 3 times faster than controls where the mechanophore is not covalently coupled to the network. We anticipate that this concept can be extended to other acid-sensitive polymer networks for the stress-responsive deconstruction of gels and solvent-free elastomers.}, Doi = {10.1021/jacs.3c10153}, Key = {fds375324} } @article{fds375838, Author = {Lin, Y and Kouznetsova, TB and Foret, AG and Craig, SL}, Title = {Solvent Polarity Effects on the Mechanochemistry of Spiropyran Ring Opening.}, Journal = {Journal of the American Chemical Society}, Volume = {146}, Number = {6}, Pages = {3920-3925}, Year = {2024}, Month = {February}, url = {http://dx.doi.org/10.1021/jacs.3c11621}, Abstract = {The spiropyran mechanophore (SP) is employed as a reporter of molecular tension in a wide range of polymer matrices, but the influence of surrounding environment on the force-coupled kinetics of its ring opening has not been quantified. Here, we report single-molecule force spectroscopy studies of SP ring opening in five solvents that span normalized Reichardt solvent polarity factors (<i>E</i><sub>T</sub><sup>N</sup>) of 0.1-0.59. Individual multimechanophore polymers were activated under increasing tension at constant 300 nm s<sup>-1</sup> displacement in an atomic force microscope. The extension results in a plateau in the force-extension curve, whose midpoint occurs at a transition force <i>f</i>* that corresponds to the force required to increase the rate constant of SP activation to approximately 30 s<sup>-1</sup>. More polar solvents lead to mechanochemical reactions that are easier to trigger; <i>f</i>* decreases across the series of solvents, from a high of 415 ± 13 pN in toluene to a low of 234 ± 9 pN in <i>n</i>-butanol. The trend in mechanochemical reactivity is consistent with the developing zwitterionic character on going from SP to the ring-opened merocyanine product. The force dependence of the rate constant (Δ<i>x</i><sup>‡</sup>) was calculated for all solvent cases and found to increase with <i>E</i><sub>T</sub><sup>N</sup>, which is interpreted to reflect a shift in the transition state to a later and more productlike position. The inferred shift in the transition state position is consistent with a double-well (two-step) reaction potential energy surface, in which the second step is rate determining, and the intermediate is more polar than the product.}, Doi = {10.1021/jacs.3c11621}, Key = {fds375838} } @article{fds374905, Author = {Horst, M and Meisner, J and Yang, J and Kouznetsova, TB and Craig, SL and Martínez, TJ and Xia, Y}, Title = {Mechanochemistry of Pterodactylane.}, Journal = {Journal of the American Chemical Society}, Volume = {146}, Number = {1}, Pages = {884-891}, Year = {2024}, Month = {January}, url = {http://dx.doi.org/10.1021/jacs.3c11293}, Abstract = {Pterodactylane is a [4]-ladderane with substituents on the central rung. Comparing the mechanochemistry of the [4]-ladderane structure when pulled from the central rung versus the end rung revealed a striking difference in the threshold force of mechanoactivation: the threshold force is dramatically lowered from 1.9 nN when pulled on the end rung to 0.7 nN when pulled on the central rung. We investigated the bicyclic products formed from the mechanochemical activation of pterodactylane experimentally and computationally, which are distinct from the mechanochemical products of ladderanes being activated from the end rung. We compared the products of pterodactylane's mechanochemical and thermal activation to reveal differences and similarities in the mechanochemical and thermal pathways of pterodactylane transformation. Interestingly, we also discovered the presence of elementary steps that are accelerated or suppressed by force within the same mechanochemical reaction of pterodactylane, suggesting rich mechanochemical manifolds of multicyclic structures. We rationalized the greatly enhanced mechanochemical reactivity of the central rung of pterodactylane and discovered force-free ground state bond length to be a good low-cost predictor of the threshold force for cyclobutane-based mechanophores. These findings advance our understanding of mechanochemical reactivities and pathways, and they will guide future designs of mechanophores with low threshold forces to facilitate their applications in force-responsive materials.}, Doi = {10.1021/jacs.3c11293}, Key = {fds374905} } @article{fds375520, Author = {Barrat, JL and Del Gado and E and Egelhaaf, SU and Mao, X and Dijkstra, M and Pine, DJ and Kumar, SK and Bishop, K and Gang, O and Obermeyer, A and Papadakis, CM and Tsitsilianis, C and Smalyukh, II and Hourlier-Fargette, A and Andrieux, S and Drenckhan, W and Wagner, N and Murphy, RP and Weeks, ER and Cerbino, R and Han, Y and Cipelletti, L and Ramos, L and Poon, WCK and Richards, JA and Cohen, I and Furst, EM and Nelson, A and Craig, SL and Ganapathy, R and Sood, AK and Sciortino, F and Mungan, M and Sastry, S and Scheibner, C and Fruchart, M and Vitelli, V and Ridout, SA and Stern, M and Tah, I and Zhang, G and Liu, AJ and Osuji, CO and Xu, Y and Shewan, HM and Stokes, JR and Merkel, M and Ronceray, P and Rupprecht, JF and Matsarskaia, O and Schreiber, F and Roosen-Runge, F and Aubin-Tam, ME and Koenderink, GH and Espinosa-Marzal, RM and Yus, J and Kwon, J}, Title = {Soft matter roadmap}, Journal = {JPhys Materials}, Volume = {7}, Number = {1}, Year = {2024}, Month = {January}, url = {http://dx.doi.org/10.1088/2515-7639/ad06cc}, Abstract = {Soft materials are usually defined as materials made of mesoscopic entities, often self-organised, sensitive to thermal fluctuations and to weak perturbations. Archetypal examples are colloids, polymers, amphiphiles, liquid crystals, foams. The importance of soft materials in everyday commodity products, as well as in technological applications, is enormous, and controlling or improving their properties is the focus of many efforts. From a fundamental perspective, the possibility of manipulating soft material properties, by tuning interactions between constituents and by applying external perturbations, gives rise to an almost unlimited variety in physical properties. Together with the relative ease to observe and characterise them, this renders soft matter systems powerful model systems to investigate statistical physics phenomena, many of them relevant as well to hard condensed matter systems. Understanding the emerging properties from mesoscale constituents still poses enormous challenges, which have stimulated a wealth of new experimental approaches, including the synthesis of new systems with, e.g. tailored self-assembling properties, or novel experimental techniques in imaging, scattering or rheology. Theoretical and numerical methods, and coarse-grained models, have become central to predict physical properties of soft materials, while computational approaches that also use machine learning tools are playing a progressively major role in many investigations. This Roadmap intends to give a broad overview of recent and possible future activities in the field of soft materials, with experts covering various developments and challenges in material synthesis and characterisation, instrumental, simulation and theoretical methods as well as general concepts.}, Doi = {10.1088/2515-7639/ad06cc}, Key = {fds375520} } @article{fds374348, Author = {Beech, HK and Wang, S and Sen, D and Rota, D and Kouznetsova, TB and Arora, A and Rubinstein, M and Craig, SL and Olsen, BD}, Title = {Reactivity-Guided Depercolation Processes Determine Fracture Behavior in End-Linked Polymer Networks.}, Journal = {ACS macro letters}, Volume = {12}, Number = {12}, Pages = {1685-1691}, Year = {2023}, Month = {December}, url = {http://dx.doi.org/10.1021/acsmacrolett.3c00559}, Abstract = {The fracture of polymer networks is tied to the molecular behavior of strands within the network, yet the specific molecular-level processes that determine the mechanical limits of a network remain elusive. Here, the question of reactivity-guided fracture is explored in otherwise indistinguishable end-linked networks by tuning the relative composition of strands with two different mechanochemical reactivities. Increasing the substitution of less mechanochemically reactive ("strong") strands into a network comprising more reactive ("weak") strands has a negligible impact on the fracture energy until the strong strand content reaches approximately 45%, at which point the fracture energy sharply increases with strong strand content. This aligns with the measured strong strand percolation threshold of 48 ± 3%, revealing that depercolation, or the loss of a percolated network structure, is a necessary criterion for crack propagation in a polymer network. Coarse-grained fracture simulations agree closely with the tearing energy trend observed experimentally, confirming that weak strand scissions dominate the failure until the strong strands approach percolation. The simulations further show that twice as many strands break in a mixture than in a pure network.}, Doi = {10.1021/acsmacrolett.3c00559}, Key = {fds374348} } @article{fds371955, Author = {Ritter, VC and McDonald, SM and Dobrynin, AV and Craig, SL and Becker, ML}, Title = {Mechanochromism and Strain-Induced Crystallization in Thiol-yne-Derived Stereoelastomers.}, Journal = {Advanced materials (Deerfield Beach, Fla.)}, Volume = {35}, Number = {41}, Pages = {e2302163}, Year = {2023}, Month = {October}, url = {http://dx.doi.org/10.1002/adma.202302163}, Abstract = {Most elastomers undergo strain-induced crystallization (SIC) under tension; as individual chains are held rigidly in a fixed position by an applied strain, their alignment along the strain field results in a shift from strain-hardening (SH) to SIC. A similar degree of stretching is associated with the tension necessary to accelerate mechanically coupled, covalent chemical responses of mechanophores in overstretched chains, raising the possibility of an interplay between the macroscopic response of SIC and the molecular response of mechanophore activation. Here, thiol-yne-derived stereoelastomers doped covalently with a dipropiolate-derivatized spiropyran (SP) mechanophore (0.25-0.38 mol%) are reported. The material properties of SP-containing films are consistent with undoped controls, indicating that the SP is a reporter of the mechanical state of the polymer. Uniaxial tensile tests reveal correlations between mechanochromism and SIC, which are strain-rate-dependent. When mechanochromic films are stretched slowly to the point of mechanophore activation, the covalently tethered mechanophore remains trapped in a force-activated state, even after the applied stress is removed. Mechanophore reversion kinetics correlate with the applied strain rate, resulting in highly tunable decoloration rates. Because these polymers are not covalently crosslinked, they are recyclable by melt-pressing into new films, increasing their potential range of strain-sensing, morphology-sensing, and shape-memory applications.}, Doi = {10.1002/adma.202302163}, Key = {fds371955} } @article{fds372950, Author = {Zhao, J and Bobylev, EO and Lundberg, DJ and Oldenhuis, NJ and Wang, H and Kevlishvili, I and Craig, SL and Kulik, HJ and Li, X and Johnson, JA}, Title = {Polymer Networks with Cubic, Mixed Pd(II) and Pt(II) M6L12 Metal-Organic Cage Junctions: Synthesis and Stress Relaxation Behavior.}, Journal = {Journal of the American Chemical Society}, Volume = {145}, Number = {40}, Pages = {21879-21885}, Year = {2023}, Month = {October}, url = {http://dx.doi.org/10.1021/jacs.3c06029}, Abstract = {Metal-organic cages/polyhedra (MOCs) are versatile building blocks for advanced polymer networks with properties that synergistically blend those of traditional polymers and crystalline frameworks. Nevertheless, constructing polyMOCs from very stable Pt(II)-based MOCs or mixtures of metal ions such as Pd(II) and Pt(II) has not, to our knowledge, been demonstrated, nor has exploration of how the dynamics of metal-ligand exchange at the MOC level may impact bulk polyMOC energy dissipation. Here, we introduce a new class of polymer metal-organic cage (polyMOC) gels featuring polyethylene glycol (PEG) strands of varied length cross-linked through bis-pyridyl-carbazole-based M<sub>6</sub>L<sub>12</sub> cubes, where M is Pd(II), Pt(II), or mixtures thereof. We show that, while polyMOCs with varied Pd(II) content have similar network structures, their average stress-relaxation rates are tunable over 3 orders of magnitude due to differences in Pd(II)- and Pt(II)-ligand exchange rates at the M<sub>6</sub>L<sub>12</sub> junction level. Moreover, mixed-metal polyMOCs display relaxation times indicative of intrajunction cooperative interactions, which stands in contrast to previous materials based on point metal junctions. Altogether, this work (1) introduces a novel MOC architecture for polyMOC design, (2) shows that polyMOCs can be prepared from mixtures of Pd(II)/Pt(II), and (3) demonstrates that polyMOCs display unique relaxation behavior due to their multivalent junctions, offering a strategy for controlling polyMOC properties independently of their polymer components.}, Doi = {10.1021/jacs.3c06029}, Key = {fds372950} } @article{fds372653, Author = {Wentz, KE and Yao, Y and Kevlishvili, I and Kouznetsova, TB and Mediavilla, BA and Kulik, HJ and Craig, SL and Klausen, RS}, Title = {Systematic Investigation of Silicon Substitution on Single Macromolecule Mechanics}, Journal = {Macromolecules}, Volume = {56}, Number = {17}, Pages = {6776-6782}, Year = {2023}, Month = {September}, url = {http://dx.doi.org/10.1021/acs.macromol.3c01066}, Abstract = {Four unsaturated poly(carbooligosilane)s (P1-P4) were prepared via acyclic diene metathesis polycondensation of new oligosilane diene monomers (1-4). These novel polymers with varying main-chain Si incorporation have high trans internal olefin stereochemistry (ca. 80%) and molecular weights (9500-21,700 g mol-1). Postpolymerization epoxidation converted all alkene moieties to epoxides and rendered the polymers (P5-P8) more electrophilic, which allowed for single-molecule force spectroscopy studies via a modified atomic force microscope setup with a silicon tip and cantilever. The single-chain elasticity of the polycarbooligosilanes decreased with increasing numbers of Si-Si bonds, a finding reproduced by quantum chemical calculations.}, Doi = {10.1021/acs.macromol.3c01066}, Key = {fds372653} } @article{fds371593, Author = {Duan, C and Zheng, X and Craig, SL and Widenhoefer, RA}, Title = {Force-Modulated C-C Reductive Elimination from Nickel Bis(polyfluorophenyl) Complexes}, Journal = {Organometallics}, Volume = {42}, Number = {15}, Pages = {1918-1926}, Publisher = {American Chemical Society (ACS)}, Year = {2023}, Month = {August}, url = {http://dx.doi.org/10.1021/acs.organomet.3c00168}, Abstract = {We have analyzed the rate of C(sp2)-C(sp2) reductive elimination from nickel(II) bis(2,4,6-trifluorophenyl) complexes (P-P)Ni(2,4,6-C6H2F3)2 containing either MeOBiPhep (3a) or a macrocyclic bisphosphine ligand (3b-3e) as a function of force applied to the biaryl backbone of these ligands through intramolecular tension generated by a molecular force probe. Nickel complexes 3 were isolated in 22-60% yield from the reaction of bisphosphine with the bis(tetrahydrofuranyl) complex (THF)2Ni(2,4,6-C6H2F3)2 followed by chromatography. Thermolysis of complexes 3 in C6D6 at 68 °C leads to first-order decay through >3 half-lives to the form 2,2′,4,4′,6,6′-hexafluorobiphenyl as the exclusive fluorine-containing product in ≥93% yield. Whereas compressive forces up to −65 pN have no significant effect on the rate of reductive elimination, extension forces increase the rate of reductive elimination by a factor of 3 over an ∼230 pN range of restoring forces relative to the strain-free MeOBiphep complex. The rate response of reductive elimination from nickel(II) bis(trifluorophenyl) complexes as a function of extension force is similar to the previously reported 2.8-fold increase in the rate of reductive elimination from platinum diaryl complexes (P-P)Pt(4-C6H4NMe2)2 over the same range of forces.}, Doi = {10.1021/acs.organomet.3c00168}, Key = {fds371593} } @article{fds372356, Author = {Yu, Y and O'Neill, RT and Boulatov, R and Widenhoefer, RA and Craig, SL}, Title = {Allosteric control of olefin isomerization kinetics via remote metal binding and its mechanochemical analysis.}, Journal = {Nature communications}, Volume = {14}, Number = {1}, Pages = {5074}, Year = {2023}, Month = {August}, url = {http://dx.doi.org/10.1038/s41467-023-40842-5}, Abstract = {Allosteric control of reaction thermodynamics is well understood, but the mechanisms by which changes in local geometries of receptor sites lower activation reaction barriers in electronically uncoupled, remote reaction moieties remain relatively unexplored. Here we report a molecular scaffold in which the rate of thermal E-to-Z isomerization of an alkene increases by a factor of as much as 10<sup>4</sup> in response to fast binding of a metal ion to a remote receptor site. A mechanochemical model of the olefin coupled to a compressive harmonic spring reproduces the observed acceleration quantitatively, adding the studied isomerization to the very few reactions demonstrated to be sensitive to extrinsic compressive force. The work validates experimentally the generalization of mechanochemical kinetics to compressive loads and demonstrates that the formalism of force-coupled reactivity offers a productive framework for the quantitative analysis of the molecular basis of allosteric control of reaction kinetics. Important differences in the effects of compressive vs. tensile force on the kinetic stabilities of molecules are discussed.}, Doi = {10.1038/s41467-023-40842-5}, Key = {fds372356} } @article{fds375521, Author = {Caballero, RM and González-Gamboa, I and Craig, SL and Steinmetz, NF}, Title = {Linear and multivalent PEGylation of the tobacco mosaic virus and the effects on its biological properties}, Journal = {Frontiers in Virology}, Volume = {3}, Publisher = {Frontiers Media SA}, Year = {2023}, Month = {June}, url = {http://dx.doi.org/10.3389/fviro.2023.1184095}, Abstract = {<jats:p>Plant virus-based nanoparticles (VNPs) offer a bioinspired approach to the delivery of drugs and imaging agents. The chemical addressability, biocompatibility, and scalable manufacturability of VNPs make them a promising alternative to synthetic delivery platforms. However, VNPs, just like other proteinaceous or synthetic nanoparticles (NPs), are readily recognized and cleared by the immune system and mechanisms such as opsonization and phagocytosis. Shielding strategies, such as PEGylation, are commonly used to mitigate premature NP clearance. Here, we investigated polyethylene glycol (PEG) coatings on the tobacco mosaic virus (TMV), which was used as a model nanocarrier system. Specifically, we evaluated the effects of linear and multivalent PEG coatings at varying chain lengths on serum protein adsorption, antibody recognition, and macrophage uptake. Linear and multivalent PEGs of molecular weights 2,000 and 5,000 Da were successfully grafted onto the TMV at ≈ 20%–60% conjugation efficiencies, and the degree of cross-linking as a function of PEG valency and length was determined. PEGylation resulted in the modulation of TMV–macrophage interactions and reduced corona formation as well as antibody recognition. Linear and multivalent PEG 5,000 formulations (but not PEG 2,000 formulations) reduced α-TMV antibody recognition, whereas shorter, multivalent PEG coatings significantly reduced α-PEG recognition—this highlights an interesting interplay between the NP and the PEG itself in potential antigenicity and should be an important consideration in PEGylation strategies. This work provides insight into the PEGylation of VNPs, which may improve the possibility of their implementation in clinical applications.</jats:p>}, Doi = {10.3389/fviro.2023.1184095}, Key = {fds375521} } @article{fds371309, Author = {Wang, S and Hu, Y and Kouznetsova, TB and Sapir, L and Chen, D and Herzog-Arbeitman, A and Johnson, JA and Rubinstein, M and Craig, SL}, Title = {Facile mechanochemical cycloreversion of polymer cross-linkers enhances tear resistance.}, Journal = {Science (New York, N.Y.)}, Volume = {380}, Number = {6651}, Pages = {1248-1252}, Year = {2023}, Month = {June}, url = {http://dx.doi.org/10.1126/science.adg3229}, Abstract = {The mechanical properties of covalent polymer networks often arise from the permanent end-linking or cross-linking of polymer strands, and molecular linkers that break more easily would likely produce materials that require less energy to tear. We report that cyclobutane-based mechanophore cross-linkers that break through force-triggered cycloreversion lead to networks that are up to nine times as tough as conventional analogs. The response is attributed to a combination of long, strong primary polymer strands and cross-linker scission forces that are approximately fivefold smaller than control cross-linkers at the same timescales. The enhanced toughness comes without the hysteresis associated with noncovalent cross-linking, and it is observed in two different acrylate elastomers, in fatigue as well as constant displacement rate tension, and in a gel as well as elastomers.}, Doi = {10.1126/science.adg3229}, Key = {fds371309} } @article{fds370191, Author = {Wakefield, H and Kevlishvili, I and Wentz, KE and Yao, Y and Kouznetsova, TB and Melvin, SJ and Ambrosius, EG and Herzog-Arbeitman, A and Siegler, MA and Johnson, JA and Craig, SL and Kulik, HJ and Klausen, RS}, Title = {Synthesis and Ring-Opening Metathesis Polymerization of a Strained trans-Silacycloheptene and Single-Molecule Mechanics of Its Polymer.}, Journal = {Journal of the American Chemical Society}, Volume = {145}, Number = {18}, Pages = {10187-10196}, Year = {2023}, Month = {May}, url = {http://dx.doi.org/10.1021/jacs.3c01004}, Abstract = {The <i>cis</i>- and <i>trans</i>-isomers of a silacycloheptene were selectively synthesized by the alkylation of a silyl dianion, a novel approach to strained cycloalkenes. The <i>trans</i>-silacycloheptene (<i>trans</i>-SiCH) was significantly more strained than the <i>cis</i> isomer, as predicted by quantum chemical calculations and confirmed by crystallographic signatures of a twisted alkene. Each isomer exhibited distinct reactivity toward ring-opening metathesis polymerization (ROMP), where only <i>trans</i>-SiCH afforded high-molar-mass polymer under enthalpy-driven ROMP. Hypothesizing that the introduction of silicon might result in increased molecular compliance at large extensions, we compared poly(<i>trans</i>-SiCH) to organic polymers by single-molecule force spectroscopy (SMFS). Force-extension curves from SMFS showed that poly(<i>trans</i>-SiCH) is more easily overstretched than two carbon-based analogues, polycyclooctene and polybutadiene, with stretching constants that agree well with the results of computational simulations.}, Doi = {10.1021/jacs.3c01004}, Key = {fds370191} } @article{fds370029, Author = {Wang, S and Panyukov, S and Craig, SL and Rubinstein, M}, Title = {Contribution of Unbroken Strands to the Fracture of Polymer Networks}, Journal = {Macromolecules}, Volume = {56}, Number = {6}, Pages = {2309-2318}, Year = {2023}, Month = {March}, url = {http://dx.doi.org/10.1021/acs.macromol.2c02139}, Abstract = {We present a modified Lake-Thomas theory that accounts for the molecular details of network connectivity upon crack propagation in polymer networks. This theory includes not only the energy stored in the breaking network strands (bridging strands) but also the energy stored in the tree-like structure of the strands connecting the bridging strands to the network continuum, which remains intact as the crack propagates. The energy stored in each of the generations of this tree depends nonmonotonically on the generation index due to the nonlinear elasticity of the stretched network strands. Further, the energy required to break a single bridging strand is not necessarily dominated by the energy stored in the bridging strand itself but in the higher generations of the tree. We describe the effect of mechanophores with stored length on the energy stored in the tree-like structure. In comparison with the “strong” mechanophores that can only be activated in the bridging strand, “weak” mechanophores that can be activated both in the bridging strand and in other generations could provide more energy dissipation due to their larger contribution to higher generations of the tree.}, Doi = {10.1021/acs.macromol.2c02139}, Key = {fds370029} } @article{fds370192, Author = {Ouchi, T and Wang, W and Silverstein, BE and Johnson, JA and Craig, SL}, Title = {Effect of strand molecular length on mechanochemical transduction in elastomers probed with uniform force sensors}, Journal = {Polymer Chemistry}, Volume = {14}, Number = {14}, Pages = {1646-1655}, Year = {2023}, Month = {March}, url = {http://dx.doi.org/10.1039/d3py00065f}, Abstract = {The mechanical properties of a polymer network reflect the collective behavior of all of the constituent strands within the network. These strands comprise a distribution of states, and a central question is how the deformation and tension experienced by a strand is influenced by strand length. Here, we address this question through the use of mechanophore force probes with discrete molecular weights. Probe strands, each bearing a mechanochromic spiropyran (SP), were prepared through an iterative synthetic strategy, providing uniform PDMS-functionalized SP force probes with molecular weights of 578, 1170, and 2356 g mol−1. The probes were each doped (9 mM) into the same silicone elastomer matrix. Upon stretching, the materials change color, consistent with the expected conversion of SP to merocyanine (MC). The critical strain at which measurable mechanochromism is observed is correlated with the strain hardening of the matrix, but it is independent of the molecular length of the probe strand. When a network with activated strands is relaxed, the color dissipates, and the rate of decoloration varies as a function of the relaxing strain (= r); faster decoloration occurs at lower r. The dependence of decoloration rate on r is taken to reflect the effect of residual tension in the once-activated strands on the reversion reaction of MC to SP, and the effect of that residual tension is indistinguishable across the three molecular lengths examined. The combination of discrete strand synthesis and mechanochromism provides a foundation to further test and develop molecular-based theories of elasticity and fracture in polymer networks.}, Doi = {10.1039/d3py00065f}, Key = {fds370192} } @article{fds369053, Author = {Ozer, I and Slezak, A and Sirohi, P and Li, X and Zakharov, N and Yao, Y and Everitt, JI and Spasojevic, I and Craig, SL and Collier, JH and Campbell, JE and D'Alessio, DA and Chilkoti, A}, Title = {An injectable PEG-like conjugate forms a subcutaneous depot and enables sustained delivery of a peptide drug.}, Journal = {Biomaterials}, Volume = {294}, Pages = {121985}, Year = {2023}, Month = {March}, url = {http://dx.doi.org/10.1016/j.biomaterials.2022.121985}, Abstract = {Many biologics have a short plasma half-life, and their conjugation to polyethylene glycol (PEG) is commonly used to solve this problem. However, the improvement in the plasma half-life of PEGylated drugs' is at an asymptote because the development of branched PEG has only had a modest impact on pharmacokinetics and pharmacodynamics. Here, we developed an injectable PEG-like conjugate that forms a subcutaneous depot for the sustained delivery of biologics. The PEG-like conjugate consists of poly[oligo(ethylene glycol) methyl ether methacrylate] (POEGMA) conjugated to exendin, a peptide drug used in the clinic to treat type 2 diabetes. The depot-forming exendin-POEGMA conjugate showed greater efficacy than a PEG conjugate of exendin as well as Bydureon, a clinically approved sustained-release formulation of exendin. The injectable depot-forming exendin-POEGMA conjugate did not elicit an immune response against the polymer, so that it remained effective and safe for long-term management of type 2 diabetes upon chronic administration. In contrast, the PEG conjugate induced an anti-PEG immune response, leading to early clearance and loss of efficacy upon repeat dosing. The exendin-POEGMA depot also showed superior long-term efficacy compared to Bydureon. Collectively, these results suggest that an injectable POEGMA conjugate of biologic drugs that forms a drug depot under the skin, providing favorable pharmacokinetic properties and sustained efficacy while remaining non-immunogenic, offers significant advantages over other commonly used drug delivery technologies.}, Doi = {10.1016/j.biomaterials.2022.121985}, Key = {fds369053} } @article{fds368039, Author = {Ouchi, T and Bowser, BH and Kouznetsova, TB and Zheng, X and Craig, SL}, Title = {Strain-triggered acidification in a double-network hydrogel enabled by multi-functional transduction of molecular mechanochemistry.}, Journal = {Materials horizons}, Volume = {10}, Number = {2}, Pages = {585-593}, Year = {2023}, Month = {February}, url = {http://dx.doi.org/10.1039/d2mh01105k}, Abstract = {Recent work has demonstrated that force-triggered mechanochemical reactions within a polymeric material are capable of inducing measurable changes in macroscopic material properties, but examples of bulk property changes without irreversible changes in shape or structure are rare. Here, we report a double-network hydrogel that undergoes order-of-magnitude increases in acidity when strained, while recovering its initial shape after large deformation. The enabling mechanophore design is a 2-methoxy-<i>gem</i>-dichlorocyclopropane mechanoacid that is gated within a fused methyl methoxycyclobutene carboxylate mechanophore structure. This gated mechanoacid is incorporated <i>via</i> radical co-polymerization into linear and network polymers. Sonication experiments confirm the mechanical release of HCl, and single-molecule force spectroscopy reveals enhanced single-molecular toughness in the covalent strand. These mechanochemical functions are incorporated into a double-network hydrogel, leading to mechanically robust and thermally stable materials that undergo strain-triggered acid release. Both quasi-static stretching and high strain rate uniaxial compression result in substantial acidification of the hydrogel, from pH ∼ 7 to ∼5.}, Doi = {10.1039/d2mh01105k}, Key = {fds368039} } @article{fds368041, Author = {Craig, SL}, Title = {Concluding remarks: Fundamentals, applications and future of mechanochemistry.}, Journal = {Faraday discussions}, Volume = {241}, Pages = {485-491}, Year = {2023}, Month = {January}, url = {http://dx.doi.org/10.1039/d2fd00141a}, Abstract = {This paper provides a summary of the <i>Faraday Discussions</i> meeting on "Mechanochemistry: fundamentals, applications, and future" in the context of broad themes whose exploration might contribute to a unified framework of mechanochemical phenomena.}, Doi = {10.1039/d2fd00141a}, Key = {fds368041} } @article{fds368878, Author = {Lloyd, EM and Vakil, JR and Yao, Y and Sottos, NR and Craig, SL}, Title = {Covalent Mechanochemistry and Contemporary Polymer Network Chemistry: A Marriage in the Making.}, Journal = {Journal of the American Chemical Society}, Volume = {145}, Number = {2}, Pages = {751-768}, Year = {2023}, Month = {January}, url = {http://dx.doi.org/10.1021/jacs.2c09623}, Abstract = {Over the past 20 years, the field of polymer mechanochemistry has amassed a toolbox of mechanophores that translate mechanical energy into a variety of functional responses ranging from color change to small-molecule release. These productive chemical changes typically occur at the length scale of a few covalent bonds (Å) but require large energy inputs and strains on the micro-to-macro scale in order to achieve even low levels of mechanophore activation. The minimal activation hinders the translation of the available chemical responses into materials and device applications. The mechanophore activation challenge inspires core questions at yet another length scale of chemical control, namely: What are the molecular-scale features of a polymeric material that determine the extent of mechanophore activation? Further, how do we marry advances in the chemistry of polymer networks with the chemistry of mechanophores to create stress-responsive materials that are well suited for an intended application? In this Perspective, we speculate as to the potential match between covalent polymer mechanochemistry and recent advances in polymer network chemistry, specifically, topologically controlled networks and the hierarchical material responses enabled by multi-network architectures and mechanically interlocked polymers. Both fundamental and applied opportunities unique to the union of these two fields are discussed.}, Doi = {10.1021/jacs.2c09623}, Key = {fds368878} } @article{fds372763, Author = {Johnson, PN and Yao, Y and Huang, X and Kevlishvili, I and Schrettl, S and Weder, C and Kulik, HJ and Craig, SL}, Title = {Metal identity effects in the fracture behavior of coordinatively crosslinked elastomers}, Journal = {POLYMER}, Volume = {285}, Year = {2023}, url = {http://dx.doi.org/10.1016/j.polymer.2023.126337}, Abstract = {Polymers comprising polybutadiene backbones with 2,6-bis(1′-methyl-benzimidazolyl)pyridine (MeBip) sidechains were crosslinked by complexation with two different metal salts, either with copper(II) trifluoromethanosulfonate or with iron(II) trifluoromethanosulfonate. Dynamic mechanical analysis (DMA) and small-angle X-ray scattering (SAXS) data indicate that the crosslinking density and topology of the two materials are the same. The material crosslinked with copper ions, however, exhibits a higher extensibility and fracture energy than the polymer crosslinked with iron. These differences are attributed to differing mechanochemical responses of the metal complexes to applied stress. Computational results further indicate that the copper complexes are more labile, both in the stress-free state as well as upon application of force, and that the “open” complex in which only one MeBip ligand coordinates copper binds fewer counter-ions than the iron-coordinated analog. Both these factors enable easier re-binding of a second MeBip ligand. The computations further suggest that mechanochemically coupled spin-crossover behavior must be considered to fully understand the response of these metal-ligand complexes to mechanical stimuli. The data presented here furthers the facile manipulation of a material's strain response via metal species modulation, and the results offer a way to understand the relationship between bulk and molecular strain response.}, Doi = {10.1016/j.polymer.2023.126337}, Key = {fds372763} } %% Derbyshire, Emily R. @article{fds376675, Author = {Mansfield, CR and Quan, B and Chirgwin, ME and Eduful, B and Hughes, PF and Neveu, G and Sylvester, K and Ryan, DH and Kafsack, BFC and Haystead, TAJ and Leahy, JW and Fitzgerald, MC and Derbyshire, ER}, Title = {Selective targeting of Plasmodium falciparum Hsp90 disrupts the 26S proteasome.}, Journal = {Cell Chem Biol}, Pages = {S2451-9456(24)00082-5}, Year = {2024}, Month = {March}, url = {http://dx.doi.org/10.1016/j.chembiol.2024.02.008}, Abstract = {The molecular chaperone heat shock protein 90 (Hsp90) has an essential but largely undefined role in maintaining proteostasis in Plasmodium falciparum, the most lethal malaria parasite. Herein, we identify BX-2819 and XL888 as potent P. falciparum (Pf)Hsp90 inhibitors. Derivatization of XL888's scaffold led to the development of Tropane 1, as a PfHsp90-selective binder with nanomolar affinity. Hsp90 inhibitors exhibit anti-Plasmodium activity against the liver, asexual blood, and early gametocyte life stages. Thermal proteome profiling was implemented to assess PfHsp90-dependent proteome stability, and the proteasome-the main site of cellular protein recycling-was enriched among proteins with perturbed stability upon PfHsp90 inhibition. Subsequent biochemical and cellular studies suggest that PfHsp90 directly promotes proteasome hydrolysis by chaperoning the active 26S complex. These findings expand our knowledge of the PfHsp90-dependent proteome and protein quality control mechanisms in these pathogenic parasites, as well as further characterize this chaperone as a potential antimalarial drug target.}, Doi = {10.1016/j.chembiol.2024.02.008}, Key = {fds376675} } @article{fds376016, Author = {Schroeder, EA and Toro-Moreno, M and Raphemot, R and Sylvester, K and Colón, IC and Derbyshire, ER}, Title = {Toxoplasma and Plasmodium associate with host Arfs during infection.}, Journal = {mSphere}, Volume = {9}, Number = {3}, Pages = {e0077023}, Publisher = {American Society for Microbiology}, Editor = {Blader, IJ}, Year = {2024}, Month = {March}, url = {http://dx.doi.org/10.1128/msphere.00770-23}, Abstract = {The apicomplexans <i>Toxoplasma gondii</i> and <i>Plasmodium</i> are intracellular parasites that reside within a host-derived compartment termed the parasitophorous vacuole (PV). During infection, the parasites must acquire critical host resources and transport them across their PV for development. However, the mechanism by which host resources are trafficked to and across the PV remains uncertain. Here, we investigated host ADP ribosylation factors (Arfs), a class of proteins involved in vesicular trafficking that may be exploited by <i>T. gondii</i> and <i>Plasmodium berghei</i> for nutrient acquisition. Using overexpressed Arf proteins coupled with immunofluorescence microscopy, we found that all Arfs were internalized into the <i>T. gondii</i> PV, with most vacuoles containing at least one punctum of Arf protein by the end of the lytic cycle. We further characterized Arf1, the most abundant Arf inside the <i>T. gondii</i> PV, and observed that active recycling between its GDP/GTP-bound state influenced Arf1 internalization independent of host guanine nucleotide exchange factors (GEFs). In addition, Arf1 colocalized with vesicle coat complexes and exogenous sphingolipids, suggesting a role in nutrient acquisition. While Arf1 and Arf4 were not observed inside the PV during <i>P. berghei</i> infection, our gene depletion studies showed that liver stage development and survival depended on the expression of Arf4 and the host GEF, GBF1. Collectively, these observations indicate that apicomplexans use distinct mechanisms to subvert the host vesicular trafficking network and efficiently replicate. The findings also pave the way for future studies to identify parasite proteins critical to host vesicle recruitment and the components of vesicle cargo.<h4>Importance</h4>The parasites <i>Toxoplasma gondii</i> and <i>Plasmodium</i> live complex intracellular lifestyles where they must acquire essential host nutrients while avoiding recognition. Although previous work has sought to identify the specific nutrients scavenged by apicomplexans, the mechanisms by which host materials are transported to and across the parasite vacuole membrane are largely unknown. Here, we examined members of the host vesicular trafficking network to identify specific pathways subverted by <i>T. gondii</i> and <i>Plasmodium berghei</i>. Our results indicate that <i>T. gondii</i> selectively internalizes host Arfs, a class of proteins involved in intracellular trafficking. For <i>P. berghei</i>, host Arfs were restricted by the parasite's vacuole membrane, but proteins involved in vesicular trafficking were identified as essential for liver stage development. A greater exploration into how and why apicomplexans subvert host vesicular trafficking could help identify targets for host-directed therapeutics.}, Doi = {10.1128/msphere.00770-23}, Key = {fds376016} } @article{fds374540, Author = {Ong, HW and de Silva, C and Avalani, K and Kwarcinski, F and Mansfield, CR and Chirgwin, M and Truong, A and Derbyshire, ER and Zutshi, R and Drewry, DH}, Title = {Characterization of 2,4-Dianilinopyrimidines Against Five P. falciparum Kinases PfARK1, PfARK3, PfNEK3, PfPK9, and PfPKB.}, Journal = {ACS medicinal chemistry letters}, Volume = {14}, Number = {12}, Pages = {1774-1784}, Year = {2023}, Month = {December}, url = {http://dx.doi.org/10.1021/acsmedchemlett.3c00354}, Abstract = {<i>Plasmodium</i> kinases are increasingly recognized as potential novel antiplasmodial targets for the treatment of malaria, but only a small subset of these kinases have had structure-activity relationship (SAR) campaigns reported. Herein we report the discovery of CZC-54252 (<b>1</b>) as an inhibitor of five <i>P. falciparum</i> kinases PfARK1, PfARK3, PfNEK3, PfPK9, and PfPKB. 39 analogues were evaluated against all five kinases to establish SAR at three regions of the kinase active site. Nanomolar inhibitors of each kinase were discovered. We identified common and divergent SAR trends across all five kinases, highlighting substituents in each region that improve potency and selectivity for each kinase. Potent analogues were evaluated against the <i>P. falciparum</i> blood stage. Eight submicromolar inhibitors were discovered, of which <b>37</b> demonstrated potent antiplasmodial activity (EC<sub>50</sub> = 0.16 μM). Our results provide an understanding of features needed to inhibit each individual kinase and lay groundwork for future optimization efforts toward novel antimalarials.}, Doi = {10.1021/acsmedchemlett.3c00354}, Key = {fds374540} } @article{fds371885, Author = {D'Ambrosio, HK and Keeler, AM and Derbyshire, ER}, Title = {Examination of Secondary Metabolite Biosynthesis in Apicomplexa.}, Journal = {Chembiochem : a European journal of chemical biology}, Volume = {24}, Number = {17}, Pages = {e202300263}, Year = {2023}, Month = {September}, url = {http://dx.doi.org/10.1002/cbic.202300263}, Abstract = {Natural product discovery has traditionally relied on the isolation of small molecules from producing species, but genome-sequencing technology and advances in molecular biology techniques have expanded efforts to a wider array of organisms. Protists represent an underexplored kingdom for specialized metabolite searches despite bioinformatic analysis that suggests they harbor distinct biologically active small molecules. Specifically, pathogenic apicomplexan parasites, responsible for billions of global infections, have been found to possess multiple biosynthetic gene clusters, which hints at their capacity to produce polyketide metabolites. Biochemical studies have revealed unique features of apicomplexan polyketide synthases, but to date, the identity and function of the polyketides synthesized by these megaenzymes remains unknown. Herein, we discuss the potential for specialized metabolite production in protists and the possible evolution of polyketide biosynthetic gene clusters in apicomplexan parasites. We then focus on a polyketide synthase from the apicomplexan Toxoplasma gondii to discuss the unique domain architecture and properties of these proteins when compared to previously characterized systems, and further speculate on the possible functions for polyketides in these pathogenic parasites.}, Doi = {10.1002/cbic.202300263}, Key = {fds371885} } @article{fds372209, Author = {Keeler, AM and Petruzziello, PE and Boger, EG and D'Ambrosio, HK and Derbyshire, ER}, Title = {Exploring the Chain Release Mechanism from an Atypical Apicomplexan Polyketide Synthase.}, Journal = {Biochemistry}, Volume = {62}, Number = {17}, Pages = {2677-2688}, Year = {2023}, Month = {September}, url = {http://dx.doi.org/10.1021/acs.biochem.3c00272}, Abstract = {Polyketide synthases (PKSs) are megaenzymes that form chemically diverse polyketides and are found within the genomes of nearly all classes of life. We recently discovered the type I PKS from the apicomplexan parasite <i>Toxoplasma gondii</i>, <i>Tg</i>PKS2, which contains a unique putative chain release mechanism that includes ketosynthase (KS) and thioester reductase (TR) domains. Our bioinformatic analysis of the thioester reductase of <i>Tg</i>PKS2, <i>Tg</i>TR, suggests differences compared to other systems and hints at a possibly conserved release mechanism within the apicomplexan subclass Coccidia. To evaluate this release module, we first isolated <i>Tg</i>TR and observed that it is capable of 4 electron (4e<sup>-</sup>) reduction of octanoyl-CoA to the primary alcohol, octanol, utilizing NADH. <i>Tg</i>TR was also capable of generating octanol in the presence of octanal and NADH, but no reactions were observed when NADPH was supplied as a cofactor. To biochemically characterize the protein, we measured the catalytic efficiency of <i>Tg</i>TR using a fluorescence assay and determined the <i>Tg</i>TR binding affinity for cofactor and substrates using isothermal titration calorimetry (ITC). We additionally show that <i>Tg</i>TR is capable of reducing an acyl carrier protein (ACP)-tethered substrate by liquid chromatography mass spectrometry and determine that <i>Tg</i>TR binds to holo-<i>Tg</i>ACP4, its predicted cognate ACP, with a <i>K</i><sub>D</sub> of 5.75 ± 0.77 μM. Finally, our transcriptional analysis shows that <i>Tg</i>PKS2 is upregulated ∼4-fold in the parasite's cyst-forming bradyzoite stage compared to tachyzoites. Our study identifies features that distinguish <i>Tg</i>PKS2 from well-characterized systems in bacteria and fungi and suggests it aids the <i>T. gondii</i> cyst stage.}, Doi = {10.1021/acs.biochem.3c00272}, Key = {fds372209} } @article{fds370851, Author = {Mansfield, CR and Chirgwin, ME and Derbyshire, ER}, Title = {Labeling strategies to track protozoan parasite proteome dynamics.}, Journal = {Current opinion in chemical biology}, Volume = {75}, Pages = {102316}, Year = {2023}, Month = {August}, url = {http://dx.doi.org/10.1016/j.cbpa.2023.102316}, Abstract = {Intracellular protozoan parasites are responsible for wide-spread infectious diseases. These unicellular pathogens have complex, multi-host life cycles, which present challenges for investigating their basic biology and for discovering vulnerabilities that could be exploited for disease control. Throughout development, parasite proteomes are dynamic and support stage-specific functions, but detection of these proteins is often technically challenging and complicated by the abundance of host proteins. Thus, to elucidate key parasite processes and host-pathogen interactions, labeling strategies are required to track pathogen proteins during infection. Herein, we discuss the application of bioorthogonal non-canonical amino acid tagging and proximity-dependent labeling to broadly study protozoan parasites and include outlooks for future applications to study Plasmodium, the causative agent of malaria. We highlight the potential of these technologies to provide spatiotemporal labeling with selective parasite protein enrichment, which could enable previously unattainable insight into the biology of elusive developmental stages.}, Doi = {10.1016/j.cbpa.2023.102316}, Key = {fds370851} } @article{fds371861, Author = {Viswanathan, NK and Chirgwin, ME and Gibbs, J and Kalaj, BN and Durham, S and Tran, J and Gomez, M and Lazaro, H and Chen, M and Mansfield, CR and Derbyshire, ER and Eagon, S}, Title = {Synthesis and activity of β-carboline antimalarials targeting the Plasmodium falciparum heat shock 90 protein.}, Journal = {Bioorganic & medicinal chemistry letters}, Volume = {92}, Pages = {129410}, Year = {2023}, Month = {August}, url = {http://dx.doi.org/10.1016/j.bmcl.2023.129410}, Abstract = {A collection of β-carbolines based on the natural product harmine, a compound known to target the heat shock 90 protein of Plasmodium falciparum, was synthesized and tested for antimalarial activity and potential toxicity. Several of these novel compounds display promising bioactivity, providing a new potential therapeutic with a mode of action that differs versus any currently available clinical treatment.}, Doi = {10.1016/j.bmcl.2023.129410}, Key = {fds371861} } @article{fds369836, Author = {Keeler, AM and D'Ambrosio, HK and Ganley, JG and Derbyshire, ER}, Title = {Characterization of Unexpected Self-Acylation Activity of Acyl Carrier Proteins in a Modular Type I Apicomplexan Polyketide Synthase.}, Journal = {ACS chemical biology}, Volume = {18}, Number = {4}, Pages = {785-793}, Year = {2023}, Month = {April}, url = {http://dx.doi.org/10.1021/acschembio.2c00783}, Abstract = {Natural products play critical roles as antibiotics, anticancer therapeutics, and biofuels. Polyketides are a distinct natural product class of structurally diverse secondary metabolites that are synthesized by polyketide synthases (PKSs). The biosynthetic gene clusters that encode PKSs have been found across nearly all realms of life, but those from eukaryotic organisms are relatively understudied. A type I PKS from the eukaryotic apicomplexan parasite <i>Toxoplasma gondii</i>,<i>Tg</i>PKS2, was recently discovered through genome mining, and the functional acyltransferase (AT) domains were found to be selective for malonyl-CoA substrates. To further characterize <i>Tg</i>PKS2, we resolved assembly gaps within the gene cluster, which confirmed that the encoded protein consists of three distinct modules. We subsequently isolated and biochemically characterized the four acyl carrier protein (ACP) domains within this megaenzyme. We observed self-acylation─or substrate acylation without an AT domain─for three of the four <i>Tg</i>PKS2 ACP domains with CoA substrates. Furthermore, CoA substrate specificity and kinetic parameters were determined for all four unique ACPs. <i>Tg</i>ACP2-4 were active with a wide scope of CoA substrates, while <i>Tg</i>ACP1 from the loading module was found to be inactive for self-acylation. Previously, self-acylation has only been observed in type II systems, which are enzymes that act <i>in-trans</i> with one another, and this represents the first report of this activity in a modular type I PKS whose domains function <i>in-cis</i>. Site-directed mutagenesis of specific <i>Tg</i>PKS2 ACP3 acidic residues near the phosphopantetheinyl arm demonstrated that they influence self-acylation activity and substrate specificity, possibly by influencing substrate coordination or phosphopantetheinyl arm activation. Further, the lack of <i>Tg</i>PKS2 ACP self-acylation with acetoacetyl-CoA, which is utilized by previously characterized type II PKS systems, suggests that the substrate carboxyl group may be critical for <i>Tg</i>PKS2 ACP self-acylation. The unexpected properties observed from <i>T. gondii</i> PKS ACP domains highlight their distinction from well-characterized microbial and fungal systems. This work expands our understanding of ACP self-acylation beyond type II systems and helps pave the way for future studies on biosynthetic enzymes from eukaryotes.}, Doi = {10.1021/acschembio.2c00783}, Key = {fds369836} } @article{fds369322, Author = {Ong, HW and Truong, A and Kwarcinski, F and de Silva, C and Avalani, K and Havener, TM and Chirgwin, M and Galal, KA and Willis, C and Krämer, A and Liu, S and Knapp, S and Derbyshire, ER and Zutshi, R and Drewry, DH}, Title = {Discovery of potent Plasmodium falciparum protein kinase 6 (PfPK6) inhibitors with a type II inhibitor pharmacophore.}, Journal = {European journal of medicinal chemistry}, Volume = {249}, Pages = {115043}, Year = {2023}, Month = {March}, url = {http://dx.doi.org/10.1016/j.ejmech.2022.115043}, Abstract = {Malaria is a devastating disease that causes significant global morbidity and mortality. The rise of drug resistance against artemisinin-based combination therapy demonstrates the necessity to develop alternative antimalarials with novel mechanisms of action. We report the discovery of Ki8751 as an inhibitor of essential kinase PfPK6. 79 derivatives were designed, synthesized and evaluated for PfPK6 inhibition and antiplasmodial activity. Using group efficiency analyses, we established the importance of key groups on the scaffold consistent with a type II inhibitor pharmacophore. We highlight modifications on the tail group that contribute to antiplasmodial activity, cumulating in the discovery of compound 67, a PfPK6 inhibitor (IC<sub>50</sub> = 13 nM) active against the P. falciparum blood stage (EC<sub>50</sub> = 160 nM), and compound 79, a PfPK6 inhibitor (IC<sub>50</sub> < 5 nM) with dual-stage antiplasmodial activity against P. falciparum blood stage (EC<sub>50</sub> = 39 nM) and against P. berghei liver stage (EC<sub>50</sub> = 220 nM).}, Doi = {10.1016/j.ejmech.2022.115043}, Key = {fds369322} } %% Dewhirst, Mark W. @article{3072705, Author = {Engler, M.J. and Dewhirst, M.W. and Winget, J.M. and Oleson, J.R.}, Title = {Automated temperature scanning for hyperthermia treatment monitoring}, Journal = {Int. J. Radiat. Oncol. Biol. Phys. (UK)}, Volume = {13}, Number = {9}, Pages = {1377 - 82}, Keywords = {biomedical equipment;biothermics;computerised monitoring;patient monitoring;patient treatment;}, Abstract = {Ideal descriptors of hyperthermia treatments will most likely depend on complete target temperature distributions. Although these distributions can be modeled numerically, the accuracy of models is limited by the sparseness of temperatures measured in vivo. Thus, the strategy of monitoring temperatures may play a key role in improving hyperthermia therapy. Scanning temperatures by manual translations of thermometers was found to be excessively time consuming. Consequently an automated system was developed consisting of linear actuators, outriggers, guide tubes, thermometry catheters, personal computer, and dedicated hardware and software. During treatments, scan patterns were created with algorithms using temperatures measured preceding each thermometer translation. Measurement position had a noteworthy influence on thermal dose estimated by current models. Relative to manual scanning, automated scanning increased measurement efficiency, reduced probe position uncertainty, reduced operator time, and provided improved data for modeling bioheat transfer and thermal dose}, Key = {3072705} } @article{3735541, Author = {Samulski, T.V. and Grant, W.J. and Oleson, J.R. and Leopold, K.A. and Dewhirst, M.W. and Vallario, P. and Blivin, J.}, Title = {Clinical experience with a multi-element ultrasonic hyperthermia system: analysis of treatment temperatures}, Journal = {Int. J. Hyperth. (UK)}, Volume = {6}, Number = {5}, Pages = {909 - 22}, Keywords = {biomedical ultrasonics;biothermics;radiation therapy;}, Abstract = {A summary of tumour temperature data obtained from 31 patients who underwent 147 hyperthermia treatments with the Sonotherm 1000 ultrasonic system is presented. The treatment goal was to achieve a minimum of 42.0°C in tumour for 60 min duration with normal tissues remaining below 43.0°C. In 83% of treatments at least one measured tumour temperature reached or exceeded 42.0°C at some time during the treatment. Nineteen per cent of these treatments had a time- and spatial-averaged temperature (measured in tumour)⩾42.0°C. A variety of anatomical sites were treated and these were grouped into four categories: groin/trunk, axilla, breast/chest wall and head/neck. Measured temperatures in tumours located in the groin and trunk sites were significantly higher (22%⩾42°C) than other locations. The head and neck treatment temperatures were significantly lower (8% of measured points ⩾42°C)}, Key = {3735541} } @article{6712701, Author = {Thrall, D.E. and Rosner, G.L. and Azuma, C. and Larue, S.M. and Case, B.C. and Samulski, T. and Dewhirst, M.W.}, Title = {Using units of CEM 43°C T90, local hyperthermia thermal dose can be delivered as prescribed}, Journal = {Int. J. Hyperth. (UK)}, Volume = {16}, Number = {5}, Pages = {415 - 28}, url = {http://dx.doi.org/10.1080/026567300416712}, Keywords = {hyperthermia;tumours;units (measurement);}, Abstract = {A randomized study was designed in dogs with spontaneous soft tissue sarcomas to gain information about the relationship between hyperthermia dose and outcome. The study compared two levels of thermal dose applied to dogs with heatable tumours, so it was necessary to deliver either a low (2-5 CEM 43°C T<sub>90</sub>) or high (20-50 CEM 43°C T<sub>90</sub>) thermal dose as precisely as possible. It was also desirable to have similar numbers of hyperthermia treatments in each thermal dose group. Identification of heatable tumours and randomization to: high or low heat dose group was done during the first hyperthermia treatment. This was readily accomplished using mapping of temperatures in thermometry catheters, manual recording of thermal data, and visual inspection of raw thermal data with subsequent adjustment of the duration of the hyperthermia treatment. An analysis of precision of thermal dose delivery was conducted after approximately 50% of projected accrual had been met in a randomized phase III assessment of thermal dose effect. Fifty-four dogs were eligible for randomization; in 48 dogs the tumour was deemed heatable according to predetermined temperature criteria applied during the first heat treatment. Twenty-four dogs were randomized to the high heat dose group, and 24 to the low heat dose group. Median (range) total thermal dose for dogs in the high dose group was 43.5 CEM 43°C T<sub>90</sub> (16.4-66.6) compared to 3.2 CEM 43°C T<sub>90</sub> (2.1-4.6) for dogs in the low dose group. There was no overlap of thermal doses between groups. Thus, thermal dose could be delivered accurately, being within the predetermined range in 47 of the 48 dogs. Thermal dose quantified as CEM 43°C T50, however, did overlap between groups and the clinical significance of this finding will not be known until outcome data are analysed. Most dogs in both groups received five hyperthermia treatments. Median (range) treatment duration for dogs in the high dose group was 300 min (147-692) compared to 111 min (51-381) for dogs in the low dose group. Relatively simple but accurate methods of delivering prescribed thermal dose as described herein will aid the translation of clinical hyperthermia from the research setting into more general practice once the characteristics of the relationship between hyperthermia dose and outcome are understood}, Key = {6712701} } @article{7918178, Author = {Vujaskovic, Z. and Rosen, E.L. and Blackwell, K.L. and Jones, E.L. and Brizel, D.M. and Prosnitz, L.R. and Samulski, T.V. and Dewhirst, M.W.}, Title = {Ultrasound guided pO2 measurement of breast cancer reoxygenation after neoadjuvant chemotherapy and hyperthermia treatment}, Journal = {Int. J. Hyperth. (UK)}, Volume = {19}, Number = {5}, Pages = {498 - 506}, url = {http://dx.doi.org/10.1080/0265673031000121517}, Keywords = {biomedical electrodes;biomedical measurement;biomedical optical imaging;biomedical ultrasonics;blood vessels;cancer;hyperthermia;mammography;oxygen;polarography;surgery;tumours;}, Abstract = {The objective of this study was to determine whether neoadjuvant chemotherapy in combination with hyperthermia (HT) would improve oxygenation in locally advanced breast tumours. The study describes a new optimized ultrasound guided technique of pO<sub>2</sub> measurement using Eppendorf polarographic oxygen probes in 18 stage IIB-III breast cancer patients. Prior to treatment, tumour hypoxia (median pO<sub>2</sub><10mmHg) was present in 11/18 patients (average median pO<sub>2</sub>=3.2 mmHg). Seven patients had well oxygenated tumours (median pO<sub>2</sub> of 48.3 mmHg). Eight patients with hypoxic tumours prior to treatment had a significant improvement (p=0.0008) in tumour pO<sub>2</sub>after treatment (pO<sub>2</sub> increased to 19.2 mmHg). In three patients, tumours remained hypoxic (average median pO<sub>2</sub>=4.5mmHg). The advantages of the ultrasound guided pO<sub>2</sub> probe are in the accuracy of the Eppendorf electrode placement in tumour tissue, the ability to monitor electrode movement through the tumour tissue during the measurement and the ability to avoid electrode placement near or in large blood vessels by using colour Doppler imaging. The results of this preliminary study suggest that the combination of neoadjuvant chemotherapy and hyperthermia improves oxygenation in locally advanced breast tumours that are initially hypoxic}, Key = {7918178} } @article{6406702, Author = {Kong, G. and Dewhirst, M.W.}, Title = {Hyperthermia and liposomes}, Journal = {Int. J. Hyperth. (UK)}, Volume = {15}, Number = {5}, Pages = {345 - 70}, url = {http://dx.doi.org/10.1080/026567399285558}, Keywords = {biomembranes;cancer;hyperthermia;reviews;tumours;}, Abstract = {Hyperthermia and liposomal drug delivery are treatment modalities that have been used to treat cancer over the last two decades. More recently, the two therapies have been used together in an attempt to exploit their mutual interactions against cancer. The goal of this review is to explore the literature related to combined hyperthermia and liposomal drug delivery for cancer therapy. The motivation behind combining hyperthermia and liposomal drug delivery is discussed from a physical chemical and physiological standpoint. Two types of therapeutic ratios were calculated for in vivo studies from across the literature. These ratios compared the results obtained from hyperthermia and liposomes to hyperthermia and free drug as well as to liposomes without hyperthermia. These two therapeutic ratios were applied to both tumour drug uptake and tumour growth delay studies. In all studies reviewed, hyperthermia in combination with liposomal drug showed an enhanced therapeutic effect compared to either treatment modality alone or hyperthermia and free drug. Future work needs to be focused on optimizing thermosensitive liposomes and understanding the effect of thermal dose on liposomal drug delivery. Though not currently used in the clinic, this combination therapy seems to hold great promise towards improving current cancer therapeutic regimens}, Key = {6406702} } @article{6406703, Author = {Thrall, D.E. and Larue, S.M. and Powers, B.E. and Page, R.L. and Johnson, J. and George, S.L. and Kornegay, J.N. and McEntee, M.C. and Levesque, D.C. and Smith, M. and Case, B.C. and Dewhirst, M.W. and Gillette, E.L.}, Title = {Use of whole body hyperthermia as a method to heat inaccessible tumours uniformly: a phase III trial in canine brain masses}, Journal = {Int. J. Hyperth. (UK)}, Volume = {15}, Number = {5}, Pages = {383 - 98}, url = {http://dx.doi.org/10.1080/026567399285576}, Keywords = {brain;hyperthermia;tumours;}, Abstract = {In this study, whole body hyperthermia (WBH) was assessed as a means of heating intracranial tumours uniformly. Twenty-five dogs received radiation therapy and 20 the combination of radiation and WBH. Total radiation dose was randomly assigned and was either 44, 48, 52, 56 or 60 Gy. Because of WBH toxicity, intercurrent disease or tumour progression, 7 of the 45 dogs received less than the prescribed radiation dose. For WBH, the target rectal temperature was 42°C for 2 h and 3 treatments were planned. In 5 of the 20 dogs randomized to receive WBH, only one WBH treatment was given because of toxicity. WBH toxicity was severe in 6 dogs, and resulted in death or interruption in treatment. Most tumours did not undergo a complete response, making it impossible to differentiate tumour recurrence from brain necrosis as a cause of progressive neuropathy. Therefore, survival was the major study endpoint. There was no survival difference between groups. One-year survival probability (95% CI) for dogs receiving radiation therapy alone was 0.44 (0.25, 0.63) versus 0.40 (0.19, 0.63) for dogs receiving radiation and WBH. There was no difference in the incidence of brain necrosis in the 2 treatment groups. Results suggest that use of WBH alone to increase the temperature of intracranial tumours as a means to improve radiation therapy outcome is not a successful strategy}, Key = {6406703} } @article{4496016, Author = {Prescott, D.M. and Charles, H.C. and Sostman, H.D. and Page, R.L. and Thrall, D.E. and Moore, D. and Oleson, J.R. and Dewhirst, M.W.}, Title = {Manipulation of intra- and extracellular pH in spontaneous canine tumours by use of hyperglycaemia [hyperthermia efficacy improvement]}, Journal = {Int. J. Hyperth. (UK)}, Volume = {9}, Number = {5}, Pages = {745 - 54}, Keywords = {biothermics;cellular biophysics;pH;}, Abstract = {The authors evaluated the use of hyperglycaemia to reduce tumour pH in dogs with spontaneous tumours. Dogs were randomized to two groups: control and glucose. Intravenous administration of 20% glucose was used to induce and maintain hyperglycaemia. Extra and intracellular tumour pH were measured using interstitial pH microelectrodes and <sup>31</sup>P-MRS, respectively. During the administration of glucose, the mean (± SEM) blood glucose concentration was 419.8 (±32.8) and 121.1 (±8.0) mg/dI for the glucose and control groups, respectively. The mean extracellular tumour pH before and following 90 min of hyperglycaemia was 7.15 (±0.08) and 7.15 (±0.09). During consecutive measurements, intracellular tumour pH did not change significantly for the control group or the group subjected to hyperglycaemic manipulation. In contradistinction to previous rodent studies, the authors' results demonstrate that hyperglycaemia alone is not sufficient to manipulate either intra- (pH<sub>i</sub>) or extracellular (pH<sub>e</sub>) hydrogen ion concentration in spontaneous canine soft tissue tumours}, Key = {4496016} } %% Fitzgerald, Michael C. @article{fds376762, Author = {Mansfield, CR and Quan, B and Chirgwin, ME and Eduful, B and Hughes, PF and Neveu, G and Sylvester, K and Ryan, DH and Kafsack, BFC and Haystead, TAJ and Leahy, JW and Fitzgerald, MC and Derbyshire, ER}, Title = {Selective targeting of Plasmodium falciparum Hsp90 disrupts the 26S proteasome.}, Journal = {Cell Chem Biol}, Year = {2024}, Month = {March}, url = {http://dx.doi.org/10.1016/j.chembiol.2024.02.008}, Abstract = {The molecular chaperone heat shock protein 90 (Hsp90) has an essential but largely undefined role in maintaining proteostasis in Plasmodium falciparum, the most lethal malaria parasite. Herein, we identify BX-2819 and XL888 as potent P. falciparum (Pf)Hsp90 inhibitors. Derivatization of XL888's scaffold led to the development of Tropane 1, as a PfHsp90-selective binder with nanomolar affinity. Hsp90 inhibitors exhibit anti-Plasmodium activity against the liver, asexual blood, and early gametocyte life stages. Thermal proteome profiling was implemented to assess PfHsp90-dependent proteome stability, and the proteasome-the main site of cellular protein recycling-was enriched among proteins with perturbed stability upon PfHsp90 inhibition. Subsequent biochemical and cellular studies suggest that PfHsp90 directly promotes proteasome hydrolysis by chaperoning the active 26S complex. These findings expand our knowledge of the PfHsp90-dependent proteome and protein quality control mechanisms in these pathogenic parasites, as well as further characterize this chaperone as a potential antimalarial drug target.}, Doi = {10.1016/j.chembiol.2024.02.008}, Key = {fds376762} } @article{fds375840, Author = {Bailey, MA and Martyr, JG and Hargrove, AE and Fitzgerald, MC}, Title = {Stability-Based Proteomics for Investigation of Structured RNA-Protein Interactions.}, Journal = {Analytical chemistry}, Year = {2024}, Month = {February}, url = {http://dx.doi.org/10.1021/acs.analchem.3c04978}, Abstract = {RNA-protein interactions are essential to RNA function throughout biology. Identifying the protein interactions associated with a specific RNA, however, is currently hindered by the need for RNA labeling or costly tiling-based approaches. Conventional strategies, which commonly rely on affinity pull-down approaches, are also skewed to the detection of high affinity interactions and frequently miss weaker interactions that may be biologically important. Reported here is the first adaptation of stability-based mass spectrometry methods for the global analysis of RNA-protein interactions. The stability of proteins from rates of oxidation (SPROX) and thermal protein profiling (TPP) methods are used to identify the protein targets of three RNA ligands, the MALAT1 triple helix (<b>TH</b>), a viral stem loop (<b>SL</b>), and an unstructured RNA (<b>PolyU</b>), in LNCaP nuclear lysate. The 315 protein hits with RNA-induced conformational and stability changes detected by TPP and/or SPROX were enriched in previously annotated RNA-binding proteins and included new proteins for hypothesis generation. Also demonstrated are the orthogonality of the SPROX and TPP approaches and the utility of the domain-specific information available with SPROX. This work establishes a novel platform for the global discovery and interrogation of RNA-protein interactions that is generalizable to numerous biological contexts and RNA targets.}, Doi = {10.1021/acs.analchem.3c04978}, Key = {fds375840} } @article{fds370948, Author = {Quan, B and Bailey, MA and Mantyh, J and Hsu, DS and Fitzgerald, MC}, Title = {Protein Folding Stability Profiling of Colorectal Cancer Chemoresistance Identifies Functionally Relevant Biomarkers.}, Journal = {Journal of proteome research}, Volume = {22}, Number = {6}, Pages = {1923-1935}, Year = {2023}, Month = {June}, url = {http://dx.doi.org/10.1021/acs.jproteome.3c00045}, Abstract = {Reported here is the application of three protein folding stability profiling techniques (including the stability of proteins from rates of oxidation, thermal protein profiling, and limited proteolysis approaches) to identify differentially stabilized proteins in six patient-derived colorectal cancer (CRC) cell lines with different oxaliplatin sensitivities and eight CRC patient-derived xenografts (PDXs) derived from two of the patient derived cell lines with different oxaliplatin sensitivities. Compared to conventional protein expression level analyses, which were also performed here, the stability profiling techniques identified both unique and novel proteins and cellular components that differentiated the sensitive and resistant samples including 36 proteins that were differentially stabilized in at least two techniques in both the cell line and PDX studies of oxaliplatin resistance. These 36 differentially stabilized proteins included 10 proteins previously connected to cancer chemoresistance. Two differentially stabilized proteins, fatty acid synthase and elongation factor 2, were functionally validated <i>in vitro</i> and found to be druggable protein targets with biological functions that can be modulated to improve the efficacy of CRC chemotherapy. These results add to our understanding of CRC oxaliplatin resistance, suggest biomarker candidates for predicting oxaliplatin sensitivity in CRC, and inform new strategies for overcoming chemoresistance in CRC.}, Doi = {10.1021/acs.jproteome.3c00045}, Key = {fds370948} } @article{fds369833, Author = {Bailey, MA and Tang, Y and Park, H-J and Fitzgerald, MC}, Title = {Comparative Analysis of Protein Folding Stability-Based Profiling Methods for Characterization of Biological Phenotypes.}, Journal = {Journal of the American Society for Mass Spectrometry}, Volume = {34}, Number = {3}, Pages = {383-393}, Year = {2023}, Month = {March}, url = {http://dx.doi.org/10.1021/jasms.2c00248}, Abstract = {Recently, a new suite of mass spectrometry-based proteomic methods has been developed that enables evaluation of protein folding stability on the proteomic scale. These methods utilize chemical and thermal denaturation approaches (SPROX and TPP, respectively) as well as proteolysis strategies (DARTS, LiP, and PP) to assess protein folding stability. The analytical capabilities of these technique have been well-established for protein target discovery applications. However, less is known about the relative advantages and disadvantages of using these different strategies to characterize biological phenotypes. Reported here is a comparative study of SPROX, TPP, LiP, and conventional protein expression level measurements using both a mouse model of aging and a mammalian cell culture model of breast cancer. Analyses on proteins in brain tissue cell lysates derived from 1- and 18-month-old mice (<i>n</i> = 4-5 at each time point) and on proteins in cell lysates derived from the MCF-7 and MCF-10A cell lines revealed a majority of the differentially stabilized protein hits in each phenotype analysis had unchanged expression levels. In both phenotype analyses, TPP generated the largest number and fraction of differentially stabilized protein hits. Only a quarter of all the protein hits identified in each phenotype analysis had a differential stability that was detected using multiple techniques. This work also reports the first peptide-level analysis of TPP data, which was required for the correct interpretation of the phenotype analyses performed here. Studies on selected protein stability hits also uncovered phenotype-related functional changes.}, Doi = {10.1021/jasms.2c00248}, Key = {fds369833} } @article{fds369126, Author = {Robison, ATR and Sturrock, GR and Zaengle-Barone, JM and Wiebelhaus, N and Dharani, A and Williams, IG and Fitzgerald, MC and Franz, KJ}, Title = {Analysis of copper-induced protein precipitation across the E. coli proteome.}, Journal = {Metallomics : integrated biometal science}, Volume = {15}, Number = {1}, Pages = {mfac098}, Year = {2023}, Month = {January}, url = {http://dx.doi.org/10.1093/mtomcs/mfac098}, Abstract = {Metal cations have been exploited for their precipitation properties in a wide variety of studies, ranging from differentiating proteins from serum and blood to identifying the protein targets of drugs. Despite widespread recognition of this phenomenon, the mechanisms of metal-induced protein aggregation have not been fully elucidated. Recent studies have suggested that copper's (Cu) ability to induce protein aggregation may be a main contributor to Cu-induced cell death. Here, we provide the first proteome-wide analysis of the relative sensitivities of proteins across the Escherichia coli proteome to Cu-induced aggregation. We utilize a metal-induced protein precipitation (MiPP) methodology that relies on quantitative bottom-up proteomics to define the metal concentration-dependent precipitation properties of proteins on a proteomic scale. Our results establish that Cu far surpasses other metals in promoting protein aggregation and that the protein aggregation is reversible upon metal chelation. The bulk of the Cu bound in the protein aggregates is Cu1+, regardless of the Cu2+ source. Analysis of our MiPP data allows us to investigate underlying biophysical characteristics that determine a protein's sensitivity to Cu-induced aggregation, which is independent of the relative concentration of protein in the lysate. Overall, this analysis provides new insights into the mechanism behind Cu cytotoxicity, as well as metal cation-induced protein aggregation.}, Doi = {10.1093/mtomcs/mfac098}, Key = {fds369126} } %% Gordan, Raluca M. @article{fds375871, Author = {Duan, M and Song, S and Wasserman, H and Lee, P-H and Liu, KJ and Gordân, R and He, Y and Mao, P}, Title = {High UV damage and low repair, but not cytosine deamination, stimulate mutation hotspots at ETS binding sites in melanoma.}, Journal = {Proc Natl Acad Sci U S A}, Volume = {121}, Number = {4}, Pages = {e2310854121}, Year = {2024}, Month = {January}, url = {http://dx.doi.org/10.1073/pnas.2310854121}, Abstract = {Noncoding mutation hotspots have been identified in melanoma and many of them occur at the binding sites of E26 transformation-specific (ETS) proteins; however, their formation mechanism and functional impacts are not fully understood. Here, we used UV (Ultraviolet) damage sequencing data and analyzed cyclobutane pyrimidine dimer (CPD) formation, DNA repair, and CPD deamination in human cells at single-nucleotide resolution. Our data show prominent CPD hotspots immediately after UV irradiation at ETS binding sites, particularly at sites with a conserved TTCCGG motif, which correlate with mutation hotspots identified in cutaneous melanoma. Additionally, CPDs are repaired slower at ETS binding sites than in flanking DNA. Cytosine deamination in CPDs to uracil is suggested as an important step for UV mutagenesis. However, we found that CPD deamination is significantly suppressed at ETS binding sites, particularly for the CPD hotspot on the 5' side of the ETS motif, arguing against a role for CPD deamination in promoting ETS-associated UV mutations. Finally, we analyzed a subset of frequently mutated promoters, including the ribosomal protein genes RPL13A and RPS20, and found that mutations in the ETS motif can significantly reduce the promoter activity. Thus, our data identify high UV damage and low repair, but not CPD deamination, as the main mechanism for ETS-associated mutations in melanoma and uncover important roles of often-overlooked mutation hotspots in perturbing gene transcription.}, Doi = {10.1073/pnas.2310854121}, Key = {fds375871} } @article{fds375075, Author = {Martin, V and Zhuang, F and Zhang, Y and Pinheiro, K and Gordân, R}, Title = {High-throughput data and modeling reveal insights into the mechanisms of cooperative DNA-binding by transcription factor proteins.}, Journal = {Nucleic acids research}, Volume = {51}, Number = {21}, Pages = {11600-11612}, Year = {2023}, Month = {November}, url = {http://dx.doi.org/10.1093/nar/gkad872}, Abstract = {Cooperative DNA-binding by transcription factor (TF) proteins is critical for eukaryotic gene regulation. In the human genome, many regulatory regions contain TF-binding sites in close proximity to each other, which can facilitate cooperative interactions. However, binding site proximity does not necessarily imply cooperative binding, as TFs can also bind independently to each of their neighboring target sites. Currently, the rules that drive cooperative TF binding are not well understood. In addition, it is oftentimes difficult to infer direct TF-TF cooperativity from existing DNA-binding data. Here, we show that in vitro binding assays using DNA libraries of a few thousand genomic sequences with putative cooperative TF-binding events can be used to develop accurate models of cooperativity and to gain insights into cooperative binding mechanisms. Using factors ETS1 and RUNX1 as our case study, we show that the distance and orientation between ETS1 sites are critical determinants of cooperative ETS1-ETS1 binding, while cooperative ETS1-RUNX1 interactions show more flexibility in distance and orientation and can be accurately predicted based on the affinity and sequence/shape features of the binding sites. The approach described here, combining custom experimental design with machine-learning modeling, can be easily applied to study the cooperative DNA-binding patterns of any TFs.}, Doi = {10.1093/nar/gkad872}, Key = {fds375075} } @article{fds373653, Author = {Horton, CA and Alexandari, AM and Hayes, MGB and Marklund, E and Schaepe, JM and Aditham, AK and Shah, N and Suzuki, PH and Shrikumar, A and Afek, A and Greenleaf, WJ and Gordân, R and Zeitlinger, J and Kundaje, A and Fordyce, PM}, Title = {Short tandem repeats bind transcription factors to tune eukaryotic gene expression.}, Journal = {Science}, Volume = {381}, Number = {6664}, Pages = {eadd1250}, Year = {2023}, Month = {September}, url = {http://dx.doi.org/10.1126/science.add1250}, Abstract = {Short tandem repeats (STRs) are enriched in eukaryotic cis-regulatory elements and alter gene expression, yet how they regulate transcription remains unknown. We found that STRs modulate transcription factor (TF)-DNA affinities and apparent on-rates by about 70-fold by directly binding TF DNA-binding domains, with energetic impacts exceeding many consensus motif mutations. STRs maximize the number of weakly preferred microstates near target sites, thereby increasing TF density, with impacts well predicted by statistical mechanics. Confirming that STRs also affect TF binding in cells, neural networks trained only on in vivo occupancies predicted effects identical to those observed in vitro. Approximately 90% of TFs preferentially bound STRs that need not resemble known motifs, providing a cis-regulatory mechanism to target TFs to genomic sites.}, Doi = {10.1126/science.add1250}, Key = {fds373653} } @article{fds373601, Author = {Glasscock, CJ and Pecoraro, R and McHugh, R and Doyle, LA and Chen, W and Boivin, O and Lonnquist, B and Na, E and Politanska, Y and Haddox, HK and Cox, D and Norn, C and Coventry, B and Goreshnik, I and Vafeados, D and Lee, GR and Gordan, R and Stoddard, BL and DiMaio, F and Baker, D}, Title = {Computational design of sequence-specific DNA-binding proteins.}, Journal = {bioRxiv}, Year = {2023}, Month = {September}, url = {http://dx.doi.org/10.1101/2023.09.20.558720}, Abstract = {Sequence-specific DNA-binding proteins (DBPs) play critical roles in biology and biotechnology, and there has been considerable interest in the engineering of DBPs with new or altered specificities for genome editing and other applications. While there has been some success in reprogramming naturally occurring DBPs using selection methods, the computational design of new DBPs that recognize arbitrary target sites remains an outstanding challenge. We describe a computational method for the design of small DBPs that recognize specific target sequences through interactions with bases in the major groove, and employ this method in conjunction with experimental screening to generate binders for 5 distinct DNA targets. These binders exhibit specificity closely matching the computational models for the target DNA sequences at as many as 6 base positions and affinities as low as 30-100 nM. The crystal structure of a designed DBP-target site complex is in close agreement with the design model, highlighting the accuracy of the design method. The designed DBPs function in both Escherichia coli and mammalian cells to repress and activate transcription of neighboring genes. Our method is a substantial step towards a general route to small and hence readily deliverable sequence-specific DBPs for gene regulation and editing.}, Doi = {10.1101/2023.09.20.558720}, Key = {fds373601} } @article{fds370130, Author = {Mielko, Z and Zhang, Y and Sahay, H and Liu, Y and Schaich, MA and Schnable, B and Morrison, AM and Burdinski, D and Adar, S and Pufall, M and Van Houten and B and Gordân, R and Afek, A}, Title = {UV irradiation remodels the specificity landscape of transcription factors.}, Journal = {Proc Natl Acad Sci U S A}, Volume = {120}, Number = {11}, Pages = {e2217422120}, Year = {2023}, Month = {March}, url = {http://dx.doi.org/10.1073/pnas.2217422120}, Abstract = {Somatic mutations are highly enriched at transcription factor (TF) binding sites, with the strongest trend being observed for ultraviolet light (UV)-induced mutations in melanomas. One of the main mechanisms proposed for this hypermutation pattern is the inefficient repair of UV lesions within TF-binding sites, caused by competition between TFs bound to these lesions and the DNA repair proteins that must recognize the lesions to initiate repair. However, TF binding to UV-irradiated DNA is poorly characterized, and it is unclear whether TFs maintain specificity for their DNA sites after UV exposure. We developed UV-Bind, a high-throughput approach to investigate the impact of UV irradiation on protein-DNA binding specificity. We applied UV-Bind to ten TFs from eight structural families, and found that UV lesions significantly altered the DNA-binding preferences of all the TFs tested. The main effect was a decrease in binding specificity, but the precise effects and their magnitude differ across factors. Importantly, we found that despite the overall reduction in DNA-binding specificity in the presence of UV lesions, TFs can still compete with repair proteins for lesion recognition, in a manner consistent with their specificity for UV-irradiated DNA. In addition, for a subset of TFs, we identified a surprising but reproducible effect at certain nonconsensus DNA sequences, where UV irradiation leads to a high increase in the level of TF binding. These changes in DNA-binding specificity after UV irradiation, at both consensus and nonconsensus sites, have important implications for the regulatory and mutagenic roles of TFs in the cell.}, Doi = {10.1073/pnas.2217422120}, Key = {fds370130} } %% Guilak, Farshid @article{7435933, Author = {Flahiff, C.M. and Narmoneva, D.A. and Huebner, J.L. and Kraus, V.B. and Guilak, F. and Setton, L.A.}, Title = {Osmotic loading to determine the intrinsic material properties of guinea pig knee cartilage}, Journal = {J. Biomech. (UK)}, Volume = {35}, Number = {9}, Pages = {1285 - 90}, url = {http://dx.doi.org/10.1016/S0021-9290(02)00079-9}, Keywords = {biochemistry;biological techniques;biological tissues;biomechanics;elastic moduli;fluorescence;optical microscopy;osmosis;swelling;}, Abstract = {Few methods exist to study cartilage mechanics in small animal joints due to the difficulties associated with handling small tissue samples. In this study, we apply an osmotic loading method to quantify the intrinsic material properties of articular cartilage in small animal joints. Cartilage samples were studied from the femoral condyle and tibial plateau of two-month old guinea pigs. Swelling strains were measured using confocal fluorescence scanning microscopy in samples subjected to osmotic loading. A histochemical staining method was developed and calibrated for quantification of negative fixed charge density in guinea pig cartilage. Site-matched swelling strain data and fixed charge density values were then used with a triphasic theoretical model for cartilage swelling to determine the uniaxial modulus of the cartilage solid matrix. Moduli obtained in this study (7.2 MPa femoral condyle; 10.8 MPa, tibial plateau) compare well with previously reported values for the tensile moduli of human and other animal cartilages determined from uniaxial tension experiments. This study provides the first available data for material properties and fixed charge density in cartilage from the guinea pig knee and suggests a promising method for tracking changes in cartilage mechanics in small animal models of degeneration}, Key = {7435933} } %% Hargrove, Amanda @article{fds375841, Author = {Bailey, MA and Martyr, JG and Hargrove, AE and Fitzgerald, MC}, Title = {Stability-Based Proteomics for Investigation of Structured RNA-Protein Interactions.}, Journal = {Analytical chemistry}, Year = {2024}, Month = {February}, url = {http://dx.doi.org/10.1021/acs.analchem.3c04978}, Abstract = {RNA-protein interactions are essential to RNA function throughout biology. Identifying the protein interactions associated with a specific RNA, however, is currently hindered by the need for RNA labeling or costly tiling-based approaches. Conventional strategies, which commonly rely on affinity pull-down approaches, are also skewed to the detection of high affinity interactions and frequently miss weaker interactions that may be biologically important. Reported here is the first adaptation of stability-based mass spectrometry methods for the global analysis of RNA-protein interactions. The stability of proteins from rates of oxidation (SPROX) and thermal protein profiling (TPP) methods are used to identify the protein targets of three RNA ligands, the MALAT1 triple helix (<b>TH</b>), a viral stem loop (<b>SL</b>), and an unstructured RNA (<b>PolyU</b>), in LNCaP nuclear lysate. The 315 protein hits with RNA-induced conformational and stability changes detected by TPP and/or SPROX were enriched in previously annotated RNA-binding proteins and included new proteins for hypothesis generation. Also demonstrated are the orthogonality of the SPROX and TPP approaches and the utility of the domain-specific information available with SPROX. This work establishes a novel platform for the global discovery and interrogation of RNA-protein interactions that is generalizable to numerous biological contexts and RNA targets.}, Doi = {10.1021/acs.analchem.3c04978}, Key = {fds375841} } @article{fds374306, Author = {Hymon, D and Martins, J and Richter, C and Sreeramulu, S and Wacker, A and Ferner, J and Patwardhan, NN and Hargrove, AE and Schwalbe, H}, Title = {NMR 1H,19F-based screening of the four stem-looped structure 5_SL1-SL4 located in the 5'-untranslated region of SARS-CoV 2 RNA.}, Journal = {RSC medicinal chemistry}, Volume = {15}, Number = {1}, Pages = {165-177}, Publisher = {Royal Society of Chemistry (RSC)}, Year = {2024}, Month = {January}, url = {http://dx.doi.org/10.1039/d3md00322a}, Abstract = {Development of new antiviral medication against the beta-coronavirus SARS-CoV-2 (SCoV2) is actively being pursued. Both NMR spectroscopy and crystallography as structural screening technologies have been utilised to screen the viral proteome for binding to fragment libraries. Here, we report on NMR screening of elements of the viral RNA genome with two different ligand libraries using <sup>1</sup>H-NMR-screening experiments and <sup>1</sup>H and <sup>19</sup>F NMR-screening experiments for fluorinated compounds. We screened against the 5'-terminal 119 nucleotides located in the 5'-untranslated region of the RNA genome of SCoV2 and further dissected the four stem-loops into its constituent RNA elements to test specificity of binding of ligands to shorter and longer viral RNA stretches. The first library (DRTL-F library) is enriched in ligands binding to RNA motifs, while the second library (DSI-poised library) represents a fragment library originally designed for protein screening. Conducting screens with two different libraries allows us to compare different NMR screening methodologies, describe NMR screening workflows, validate the two different fragment libraries, and derive initial leads for further downstream medicinal chemistry optimisation.}, Doi = {10.1039/d3md00322a}, Key = {fds374306} } @article{fds373361, Author = {Vögele, J and Hymon, D and Martins, J and Ferner, J and Jonker, HRA and Hargrove, AE and Weigand, JE and Wacker, A and Schwalbe, H and Wöhnert, J and Duchardt-Ferner, E}, Title = {High-resolution structure of stem-loop 4 from the 5'-UTR of SARS-CoV-2 solved by solution state NMR.}, Journal = {Nucleic acids research}, Volume = {51}, Number = {20}, Pages = {11318-11331}, Year = {2023}, Month = {November}, url = {http://dx.doi.org/10.1093/nar/gkad762}, Abstract = {We present the high-resolution structure of stem-loop 4 of the 5'-untranslated region (5_SL4) of the severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) genome solved by solution state nuclear magnetic resonance spectroscopy. 5_SL4 adopts an extended rod-like structure with a single flexible looped-out nucleotide and two mixed tandem mismatches, each composed of a G•U wobble base pair and a pyrimidine•pyrimidine mismatch, which are incorporated into the stem-loop structure. Both the tandem mismatches and the looped-out residue destabilize the stem-loop structure locally. Their distribution along the 5_SL4 stem-loop suggests a role of these non-canonical elements in retaining functionally important structural plasticity in particular with regard to the accessibility of the start codon of an upstream open reading frame located in the RNA's apical loop. The apical loop-although mostly flexible-harbors residual structural features suggesting an additional role in molecular recognition processes. 5_SL4 is highly conserved among the different variants of SARS-CoV-2 and can be targeted by small molecule ligands, which it binds with intermediate affinity in the vicinity of the non-canonical elements within the stem-loop structure.}, Doi = {10.1093/nar/gkad762}, Key = {fds373361} } @article{fds369054, Author = {Bagnolini, G and Luu, TB and Hargrove, AE}, Title = {Recognizing the power of machine learning and other computational methods to accelerate progress in small molecule targeting of RNA.}, Journal = {RNA (New York, N.Y.)}, Volume = {29}, Number = {4}, Pages = {473-488}, Publisher = {Cold Spring Harbor Laboratory}, Year = {2023}, Month = {April}, url = {http://dx.doi.org/10.1261/rna.079497.122}, Abstract = {RNA structures regulate a wide range of processes in biology and disease, yet small molecule chemical probes or drugs that can modulate these functions are rare. Machine learning and other computational methods are well poised to fill gaps in knowledge and overcome the inherent challenges in RNA targeting, such as the dynamic nature of RNA and the difficulty of obtaining RNA high-resolution structures. Successful tools to date include principal component analysis, linear discriminate analysis, k-nearest neighbor, artificial neural networks, multiple linear regression, and many others. Employment of these tools has revealed critical factors for selective recognition in RNA:small molecule complexes, predictable differences in RNA- and protein-binding ligands, and quantitative structure activity relationships that allow the rational design of small molecules for a given RNA target. Herein we present our perspective on the value of using machine learning and other computation methods to advance RNA:small molecule targeting, including select examples and their validation as well as necessary and promising future directions that will be key to accelerate discoveries in this important field.}, Doi = {10.1261/rna.079497.122}, Key = {fds369054} } @article{fds369679, Author = {Davila-Calderon, J and Li, M-L and Penumutchu, SR and Haddad, C and Malcolm, L and Hargrove, AE and Brewer, G and Tolbert, BS}, Title = {Enterovirus Evolution Reveals the Mechanism of an RNA-Targeted Antiviral and Determinants of Viral Replication}, Volume = {10}, Number = {7}, Pages = {eadg3060}, Booktitle = {Cold Spring Harbor Laboratory}, Publisher = {American Association for the Advancement of Science (AAAS)}, Year = {2023}, Month = {February}, url = {http://dx.doi.org/10.1101/2023.02.20.529064}, Abstract = {Selective pressures on viruses provide opportunities to establish target site specificity and mechanisms of antivirals. Enterovirus (EV)-A71 with resistant mutations in the stem loop (SL) II internal ribosome entry site (IRES) (SLII<sup>resist</sup>) were selected at low doses of the antiviral dimethylamiloride (DMA)-135. The EV-A71 mutants were resistant to DMA-135 at concentrations that inhibit replication of wild-type virus. EV-A71 IRES structures harboring resistant mutations induced efficient expression of Luciferase messenger RNA in the presence of noncytotoxic doses of DMA-135. Nuclear magnetic resonance indicates that the mutations change the structure of SLII at the binding site of DMA-135 and at the surface recognized by the host protein AU-rich element/poly(U)-binding/degradation factor 1 (AUF1). Biophysical studies of complexes formed between AUF1, DMA-135, and either SLII or SLII<sup>resist</sup> show that DMA-135 stabilizes a ternary complex with AUF1-SLII but not AUF1-SLII<sup>resist</sup>. This work demonstrates how viral evolution elucidates the (DMA-135)-RNA binding site specificity in cells and provides insights into the viral pathways inhibited by the antiviral.}, Doi = {10.1101/2023.02.20.529064}, Key = {fds369679} } %% Izatt, Joseph A. @article{5728487, Author = {Izatt, J.A. and Kulkami, M.D. and Yazdanfar, S. and Barton, J.K. and Welch, A.J.}, Title = {In vivo bidirectional color Doppler flow imaging of picoliter blood volumes using optical coherence tomography}, Journal = {Opt. Lett. (USA)}, Volume = {22}, Number = {18}, Pages = {1439 - 41}, Year = {15}, Keywords = {biomedical imaging;blood flow measurement;Doppler measurement;light coherence;light interferometry;optical tomography;}, Abstract = {The authors describe a novel optical system for bidirectional color Doppler imaging of flow in biological tissues with micrometer-scale resolution and demonstrate its use for in vivo imaging of blood flow in an animal model. The authors' technique, color Doppler optical coherence tomography (CDOCT), performs spatially localized optical Doppler velocimetry by use of scanning low-coherence interferometry. CDOCT is an extension of optical coherence tomography (OCT), employing coherent signal-acquisition electronics and joint time-frequency analysis algorithms to perform flow imaging simultaneous with conventional OCT imaging. Cross-sectional maps of blood flow velocity with <50-μm spatial resolution and <0.6-mm/s velocity precision were obtained through intact skin in living hamster subdermal tissue. This technology has several potential medical applications}, Key = {5728487} } @article{6049791, Author = {Barton, J.K. and Welch, A.J. and Izatt, J.A.}, Title = {Investigating pulsed dye laser-blood vessel interaction with color Doppler optical coherence tomography}, Journal = {Opt. Express (USA)}, Volume = {3}, Number = {6}, Year = {14}, Keywords = {backscatter;biological effects of laser radiation;biological techniques;blood;Doppler measurement;dye lasers;light coherence;optical tomography;reflectivity;skin;}, Abstract = {A noninvasive method of imaging laser irradiated blood vessels has been achieved using Color Doppler Optical Coherence Tomography (CDOCT). This method may increase understanding of the mechanisms behind treatment of vascular disorders. The CDOCT system used a 1280 nm center wavelength superluminescent diode. A 585 nm, 360 μs pulsed dye laser was used to irradiate hamster dorsal skin flap window preparations. Irradiation sites were imaged with CDOCT prior to, immediately after, and 24 hours after laser irradiation. The processed CDOCT signal provided an estimate of the blood flow velocity. An increase in the blood vessel backscattered signal was observed as blood or vessel walls were coagulated. A decrease in damaged blood vessel reflectivity occurred after twenty four hours}, Key = {6049791} } @article{6049788, Author = {Rollins, A.M. and Kulkarni, M.D. and Yazdanfar, S. and Ung-arunyawee, R. and Izatt, J.A.}, Title = {In vivo video rate optical coherence tomography}, Journal = {Opt. Express (USA)}, Volume = {3}, Number = {6}, Year = {14}, Keywords = {biological techniques;biomedical imaging;eye;Fourier transform optics;light coherence;light interferometry;optical tomography;skin;}, Abstract = {An optical coherence tomography system is described which can image up to video rate. The system utilizes a high power broadband source and real time image acquisition hardware and features a high speed scanning delay line in the reference arm based on Fourier-transform pulse shaping technology. The theory of low coherence interferometry with a dispersive delay line, and the operation of the delay line are detailed and the design equations of the system are presented. Real time imaging is demonstrated in vivo in tissues relevant to early human disease diagnosis (skin, eye) and in an important model in developmental biology (Xenopus laevis)}, Key = {6049788} } @article{7909781, Author = {Choma, M.A. and Sarunic, M.V. and Changhuei Yang and Izatt, J.A.}, Title = {Sensitivity advantage of swept source and Fourier domain optical coherence tomography}, Journal = {Opt. Express (USA)}, Volume = {11}, Number = {18}, Year = {8}, Keywords = {biomedical optical imaging;Fourier transform optics;optical fibre theory;optical noise;optical tomography;photodiodes;sensitivity;superluminescent diodes;}, Abstract = {We present theoretical and experimental results which demonstrate the superior sensitivity of swept source (SS) and Fourier domain (FD) optical coherence tomography (OCT) techniques over the conventional time domain (TD) approach. We show that SS- and FD-OCT have equivalent expressions for system signal-to-noise ratio which result in a typical sensitivity advantage of 20 to 30 dB over TD-OCT. Experimental verification is provided using two novel spectral discrimination (SD) OCT systems: a differential fiber-based 800 nm FD-OCT system which employs deep-well photodiode arrays, and a differential 1300 nm SS-OCT system based on a swept laser with an 87 nm tuning range}, Key = {7909781} } @article{8379200, Author = {Changhuei Yang and McGuckin, L.E.L. and Simon, J.D. and Choma, M.A. and Applegate, B.E. and Izatt, J.A.}, Title = {Spectral triangulation molecular contrast optical coherence tomography with indocyanine green as the contrast agent}, Journal = {Opt. Lett. (USA)}, Volume = {29}, Number = {17}, Pages = {2016 - 18}, Year = {1}, url = {http://dx.doi.org/10.1364/OL.29.002016}, Keywords = {bio-optics;biomedical optical imaging;dyes;light scattering;molecular biophysics;optical tomography;}, Abstract = {We report a new molecular contrast optical coherence tomography (MCOCT) implementation that profiles the contrast agent distribution in a sample by measuring the agent's spectral differential absorption. The method, spectra triangulation MCOCT, can effectively suppress contributions from spectrally dependent scatterings from the sample without a priori knowledge of the scattering properties. We demonstrate molecular imaging with this new MCOCT modality by mapping the distribution of indocyanine green, a FDA-approved infrared red dye, within a stage 54 Xenopus laeuis}, Key = {8379200} } %% Katz, David F. @booklet{Braun06, Author = {K. E. Braun and J. D. Boyer and M. H. Henderson and D. F. Katz and A. Wax}, Title = {Label-free measurement of microbicidal gel thickness using low-coherence interferometry}, Journal = {Journal Of Biomedical Optics}, Volume = {11}, Number = {2}, Year = {2006}, ISSN = {1083-3668}, Abstract = {Spectral-domain low-coherence interferometry (LCI) was used to measure the thickness of microbicidal gels applied to a cylindrical calibration test socket. Microbicides are topical formulations containing active ingredients targeted to inhibit specific pathogens that are currently under development for application to the epithelial lining of the lower female reproductive tract to combat sexually transmitted infections such as HIV. Understanding the deployment and drug delivery of these formulations is vital to maximizing their effectiveness. Previously, in vivo measurements of microbicidal formulation thickness were assessed using fluorescence measurements of fluorescein-labeled gels via an optical endoscope-based device. Here we present an LCI-based device that measures the thickness of a formulation without the use of any exogenous agents by analyzing the interference pattern generated between the reflections from the front and back surface of the sample. Results are presented that validate the effectiveness and performance of the LCI measurement in a clinically relevant system as compared to an existing fluorescence-based method. The impact of the new LCI-based design on in vivo measurements is discussed. (c) 2006 Society of Photo-Optical Instrumentation Engineers.}, Key = {Braun06} } @booklet{Owen05, Author = {D. H. Owen and D. F. Katz}, Title = {A review of the physical and chemical properties of human semen and the formulation of a semen simulant}, Journal = {Journal Of Andrology}, Volume = {26}, Number = {4}, Pages = {459 -- 469}, Year = {2005}, ISSN = {0196-3635}, Abstract = {A fluid medium was developed to simulate the salient physical and chemical properties of human semen. The composition of the medium was based upon an extensive review of the literature on constituents of human semen. In choosing the ingredients for this medium, the goal was to emphasize properties that influence interactions of human semen with topical contraceptive, prophylactic, or therapeutic products. Among these properties, pH and buffering capacity, osmolarity, ionic strength, and rheological properties play dominant roles in the physico-chemical processes that govern drug release kinetics and delivery vehicle distribution.}, Key = {Owen05} } @booklet{Amann04, Author = {R. P. Amann and D. F. Katz}, Title = {Reflections on CASA after 25 years}, Journal = {Journal Of Andrology}, Volume = {25}, Number = {3}, Pages = {317 -- 325}, Year = {2004}, ISSN = {0196-3635}, Key = {Amann04} } @booklet{Fulford98, Author = {G. R. Fulford and D. F. Katz and R. L. Powell}, Title = {Swimming of spermatozoa in a linear viscoelastic fluid}, Journal = {Biorheology}, Volume = {35}, Number = {4-5}, Pages = {295 -- 309}, Year = {1998}, ISSN = {0006-355X}, Abstract = {A modified resistive force theory is developed for a spermatozoon swimming in a general linear viscoelastic fluid. The theory is based on a Fourier decomposition of the flagellar velocity, which leads to solving the Stokes flow equations with a complex viscosity. We use a model spermatozoon with a spherical head which propagates small amplitude sinusoidal waves along its flagellum. Results are obtained for the velocity of propulsion and the rate of working for a free swimming spermatozoon and the thrust on a fixed spermatozoon. There is no change in propulsive velocity for a viscoelastic fluid compared to a Newtonian fluid. The rate of working does change however, decreasing with increasing elasticity of the fluid, for a Maxwell fluid. Thus the theory predicts that a spermatozoon can swim faster in a Maxwell fluid with the same expenditure of energy for a Newtonian fluid.}, Key = {Fulford98} } @booklet{Katz97, Author = {D. F. Katz and D. A. Slade and S. T. Nakajima}, Title = {Analysis of pre-ovulatory changes in cervical mucus hydration and sperm penetrability}, Journal = {Advances In Contraception}, Volume = {13}, Number = {2-3}, Pages = {143 -- 151}, Year = {1997}, ISSN = {0267-4874}, Abstract = {Changes in cervical mucus occur during the proliferative phase of the menstrual cycle and are known to correlate with receptivity to sperm and to the endocrine milieu. Prior studies, however, have often lacked biological incisiveness and technical objectivity and precision. This study analyzed daily changes in mucus water content (hydration) prior to the LH surge (LH+0) in normal women, in relation to daily levels of serum LH, FSH, estradiol and progesterone, and to daily tests of sperm penetration of the mucus. Cervical mucus was studied for 12 cycles in 10 ovulating women. Three to ten mucus specimens were collected per cycle, over the days LH-8 to LH+0. Each specimen was subjected to measurement of both water content (hydration) and penetration by spermatozoa from fresh specimens of normal human semen. For the latter, a new microscale assay was developed and applied, which was amenable to very small volumes of mucus. The new technique determines objective measures of both the numbers of penetrating sperm (motile and non-motile) and the distance penetrated by the forwardmost vanguard sperm. In these experiments, variations in semen quality were controlled by performing a companion penetration assay in an artificial 1.5\% polyacrylamide gel. The patterns of change in mucus hydration varied quantitatively among women, with preovulatory baseline levels ranging from 93.8-96.5\%. All normal cycles (as defined by endocrine profiles) displayed a significant increase in hydration over a one-day period occurring 3-4 days before the LH peak. The magnitude of this shift varied among women between 2 and 3\% (absolute hydration), a distinction well within the precision of the hydration assay. This quantum increase in hydration was more pronounced than the corresponding increase in serum estradiol on the same day. The change in mucus hydration, and the associated increase in sperm penetrability, were more consistent among cycles than the changes in reproductive hormones. There was a strong but non-linear correlation between mucus hydration and sperm penetrability. Once the value of hydration rose above approximately 97.5\%, there was a substantial increase in penetrability. This 'cut-off point' in sperm penetrability was in the middle of the range of hydration values (across women) which preceded the quantum jump in hydration - which, itself, preceded the surge of LH. Hydration began to increase approximately 2 days before measurable increases in sperm penetration of the mucus in vitro. These results demonstrate that mucus hydration may be a valuable marker of the approach to ovulation and delineation of the fertile period. They also provide new methods for assessing sperm penetration into both large periovulatory and very small samples of collected mucus.}, Key = {Katz97} } @booklet{Fenster97, Author = {L. Fenster and D. F. Katz and A. J. Wyrobek and C. Pieper and D. M. Rempel and D. Oman and S. H. Swan}, Title = {Effects of psychological stress on human semen quality}, Journal = {Journal Of Andrology}, Volume = {18}, Number = {2}, Pages = {194 -- 202}, Year = {1997}, ISSN = {0196-3635}, Abstract = {We investigated the relationship between psychological stress and sperm concentration, motility, and morphometry in a prospective study of 157 volunteers who were enrolled in a prepaid health plan. We measured psychological job stress and life-event stress by telephone interview. Sperm-kinematic and nuclear-morphometric variables were measured using computer-assisted image analyses. Sperm concentration, percent motility, and semen volume were determined by objective visual methods. We performed multiple linear regression for each semen variable to examine its relationship to stress, controlling for potential confounders. Stress at work and total number of life events were not related to differences in semen quality. However, the recent death of a close family member was associated with a reduction in straight-line velocity (P = 0.002) and percent of progressively motile sperm (P = 0.02); it was also marginally associated with an increase in the fraction of sperm with larger and more tapered nuclei. These findings suggest that the fecundity of men experiencing the stress of a family member's death might be temporarily diminished.}, Key = {Fenster97} } @booklet{Wyrobek97, Author = {A. J. Wyrobek and S. M. Schrader and S. D. Perreault and L. Fenster and G. Huszar and D. F. Katz and A. M. Osorio and V. Sublet and D. Evenson}, Title = {Assessment of reproductive disorders and birth defects in communities near hazardous chemical sites .3. Guidelines for field studies of male reproductive disorders}, Journal = {Reproductive Toxicology}, Volume = {11}, Number = {2-3}, Pages = {243 -- 259}, Year = {1997}, ISSN = {0890-6238}, Abstract = {Exposures to environmental toxicants can have detrimental effects on several aspects of human male reproduction: fertility, sexual function, hormone status, and pregnancy/birth outcomes. However, no simple prescreening methods are available for reliably identifying potential hazards; questionnaires alone are relatively imprecise and inefficient in the absence of field data. Multidisciplinary field studies are required that include detailed exposure information, health and reproductive histories, physical examinations, semen analyses, and possibly, hormone analyses. Semen analysis is a critical component of field studies for evaluating two aspects of male reproduction: 1) changes in sperm or seminal content, which may be indicative of adverse effects on the male reproductive system with possible implications for fertility potential; and 2) defects in sperm DNA or chromosomes, which may be associated with subsequent changes in viability during embryonic development and health risks to the offspring. Semen analyses may be tiered: 1) initially, each semen study may include conventional semen assays (concentration, motility, and morphology) as well as specific biomarkers indicated by the health effect of concern in the study cohort; and 2) archived samples (i.e., frozen, videotaped, or smeared) mag be utilized in later second-tier analyses to further characterize specific findings. Before initiating any field study, it is cost effective to critically evaluate the suitability of the cohort by confirming exposure and determining that there are adequate numbers of male participants in each exposure category. Such evaluations must be based on the statistical sensitivities of the specific tissue biomarkers and health endpoints for detecting changes. This article summarizes the components of the ideal field study and identifies research needs for improving field studies of mate effects and for understanding the mechanisms of male reproductive toxicity. Several promising semen methods currently under development are also discussed. (C) 1997 Elsevier Science Inc.}, Key = {Wyrobek97} } %% Lazarides, Anne A @article{3747324, Author = {Lazarides, A.A. and Rabitz, H.}, Title = {On the relation between electronic structure and molecular dynamics}, Journal = {J. Chem. Phys. (USA)}, Volume = {93}, Number = {6}, Pages = {4192 - 210}, Year = {15}, url = {http://dx.doi.org/10.1063/1.458752}, Keywords = {atomic structure;elastic scattering of atoms and molecules;molecular electronic states;}, Abstract = {A formalism is developed for relating dynamic observables of collision processes to the electronic structure of the colliding species. Expressions are derived for functional derivatives of dynamic observables with respect to the full electronic wavefunction for the case of indistinguishable collision partners as well as for nonidentical partners. For wavefunctions described by orbitals, the formalism is extended to relate dynamic observables to electronic orbitals and orbital coefficients. The formalism is illustrated with the simple example of H+D and H+H elastic scattering cross sections at energies between 0.5 and 5.0 eV. Regions of the wavefunction which have particularly strong influence on the cross sections are identified by the functional derivatives. The manner in which the dynamics enters into the sensitivity is discussed. Particle indistinguishability is seen to influence the sensitivity of the collision to electronic structure}, Key = {3747324} } @article{4787086, Author = {Lazarides, A.A. and Rabitz, H. and McCourt, F.R.W.}, Title = {A quantitative technique for revealing the usefulness of experimental data in refining a potential surface}, Journal = {J. Chem. Phys. (USA)}, Volume = {101}, Number = {6}, Pages = {4735 - 49}, Year = {15}, url = {http://dx.doi.org/10.1063/1.467396}, Keywords = {intermolecular mechanics;potential energy curves and surfaces of molecules;potential energy functions;}, Abstract = {A singular value decomposition is used to determine how much and what kind of information about a potential surface is obtainable from a given set of measurements. From the functional sensitivities which relate a set of observable cross sections to the potential, an orthogonal set of potential variations is produced which provides a basis set for describing errors in the potential model. Corresponding to each basis function is an image vector representing a linear combination of cross sections which is the observable response to that particular correlated potential variation. The inclusion of realistic models of measurement uncertainties and potential model uncertainties in the analysis makes possible the division of the potential variation space spanned by the potential variation basis into (i) a subspace of measurable model errors and (ii) a complementary subspace of model errors which the proposed measurements will be unable to estimate. The analysis procedure may be used to assess the value of proposed measurements for inversion, and the technique is compatible with an allied inversion method under development. The method is illustrated for the He-H, rigid rotor system using as observables a candidate set of generalized cross sections, which could be obtained from measurements of viscosity and thermal conductivity in the presence and absence of a magnetic field. The set of observables considered here is found to be capable of providing five distinguishable pieces of information, primarily about the repulsive potential wall and its anisotropy. Field effect measurements of the quality now available are thus shown to offer a means for refining existing models of the anisotropy of the rare-gas-diatom interaction}, Key = {4787086} } @article{6772212, Author = {Lazarides, A.A. and Lance Kelly and K. and Jensen, T.R. and Schatz, G.C.}, Title = {Optical properties of metal nanoparticles and nanoparticle aggregates important in biosensors}, Journal = {THEOCHEM (Netherlands)}, Volume = {529}, Pages = {59 - 63}, Address = {Vicksburg, MS, USA}, Year = {8}, url = {http://dx.doi.org/10.1016/S0166-1280(00)00532-7}, Keywords = {biosensors;finite element analysis;nanostructured materials;optical properties;}, Abstract = {This article describes recent advances in electrodynamics theory that are being used to describe the extinction spectra of noble metal nanoparticles and of aggregates of nanoparticles. In one application we have extended the finite element discrete dipole approximation theory to the description of nonspherical metal particles, including the substrate on which they are sitting. In another application, we have developed a new dynamic effective medium approximation for the description of aggregates of spherical gold nanoparticles that are linked using DNA}, Key = {6772212} } %% Setton, Lori A. @booklet{Upton06, Author = {M. L. Upton and A. Hennerbichler and B. Fermor and F. Guilak and J. B. Weinberg and L. A. Setton}, Title = {Biaxial strain effects on cells from the inner and outer regions of the meniscus}, Journal = {Connective Tissue Research}, Volume = {47}, Number = {4}, Pages = {207 -- 214}, Year = {2006}, ISSN = {0300-8207}, Abstract = {During knee joint loading, the fibrocartilaginous menisci experience significant spatial variations in mechanical stimuli. Meniscus cells also exhibit significant variations in biosynthesis and gene expression depending on their location within the tissue. These metabolic patterns are consistent with a more chondrocytic phenotype for cells located within the avascular inner two-thirds compared with a more fibroblastic phenotype for cells within the vascularized outer periphery. The spatial distribution of cell biosynthesis and gene expression patterns within the meniscus suggest that cells may exhibit intrinsically different responses to mechanical stimuli. The objective of our study was to test for intrinsic differences in the responsiveness of these meniscus cell populations to an equivalent mechanical stimulus. Cellular biosynthesis and gene expression for extracellular matrix proteins in isolated inner and outer meniscus cells in monolayer were quantified following cyclic biaxial stretch. The results demonstrate that inner and outer meniscus cells exhibit significant differences in matrix biosynthesis and gene expression regardless of stretching condition. Both inner and outer meniscus cells responded to stretch with increased nitric oxide production and total protein synthesis. The results suggest that inner and outer meniscus cells may respond similarly to biaxial stretch in vitro with measures of biosynthesis and gene expression.}, Key = {Upton06} } @article{7435933, Author = {Flahiff, C.M. and Narmoneva, D.A. and Huebner, J.L. and Kraus, V.B. and Guilak, F. and Setton, L.A.}, Title = {Osmotic loading to determine the intrinsic material properties of guinea pig knee cartilage}, Journal = {J. Biomech. (UK)}, Volume = {35}, Number = {9}, Pages = {1285 - 90}, url = {http://dx.doi.org/10.1016/S0021-9290(02)00079-9}, Keywords = {biochemistry;biological techniques;biological tissues;biomechanics;elastic moduli;fluorescence;optical microscopy;osmosis;swelling;}, Abstract = {Few methods exist to study cartilage mechanics in small animal joints due to the difficulties associated with handling small tissue samples. In this study, we apply an osmotic loading method to quantify the intrinsic material properties of articular cartilage in small animal joints. Cartilage samples were studied from the femoral condyle and tibial plateau of two-month old guinea pigs. Swelling strains were measured using confocal fluorescence scanning microscopy in samples subjected to osmotic loading. A histochemical staining method was developed and calibrated for quantification of negative fixed charge density in guinea pig cartilage. Site-matched swelling strain data and fixed charge density values were then used with a triphasic theoretical model for cartilage swelling to determine the uniaxial modulus of the cartilage solid matrix. Moduli obtained in this study (7.2 MPa femoral condyle; 10.8 MPa, tibial plateau) compare well with previously reported values for the tensile moduli of human and other animal cartilages determined from uniaxial tension experiments. This study provides the first available data for material properties and fixed charge density in cartilage from the guinea pig knee and suggests a promising method for tracking changes in cartilage mechanics in small animal models of degeneration}, Key = {7435933} } %% Therien, Michael J. @article{fds376278, Author = {Mastrocinque, F and Bullard, G and Alatis, JA and Albro, JA and Nayak, A and Williams, NX and Kumbhar, A and Meikle, H and Widel, ZXW and Bai, Y and Harvey, AK and Atkin, JM and Waldeck, DH and Franklin, AD and Therien, MJ}, Title = {Band gap opening of metallic single-walled carbon nanotubes via noncovalent symmetry breaking.}, Journal = {Proceedings of the National Academy of Sciences of the United States of America}, Volume = {121}, Number = {12}, Pages = {e2317078121}, Year = {2024}, Month = {March}, url = {http://dx.doi.org/10.1073/pnas.2317078121}, Abstract = {Covalent bonding interactions determine the energy-momentum (<i>E</i>-<i>k</i>) dispersion (band structure) of solid-state materials. Here, we show that noncovalent interactions can modulate the <i>E</i>-<i>k</i> dispersion near the Fermi level of a low-dimensional nanoscale conductor. We demonstrate that low energy band gaps may be opened in metallic carbon nanotubes through polymer wrapping of the nanotube surface at fixed helical periodicity. Electronic spectral, chiro-optic, potentiometric, electronic device, and work function data corroborate that the magnitude of band gap opening depends on the nature of the polymer electronic structure. Polymer dewrapping reverses the conducting-to-semiconducting phase transition, restoring the native metallic carbon nanotube electronic structure. These results address a long-standing challenge to develop carbon nanotube electronic structures that are not realized through disruption of π conjugation, and establish a roadmap for designing and tuning specialized semiconductors that feature band gaps on the order of a few hundred meV.}, Doi = {10.1073/pnas.2317078121}, Key = {fds376278} } @article{fds373968, Author = {Ko, C-H and Zhu, Q and Bullard, G and Tassinari, F and Morisue, M and Naaman, R and Therien, MJ}, Title = {Electron Spin Polarization and Rectification Driven by Chiral Perylene Diimide-Based Nanodonuts.}, Journal = {The journal of physical chemistry letters}, Volume = {14}, Number = {45}, Pages = {10271-10277}, Year = {2023}, Month = {November}, url = {http://dx.doi.org/10.1021/acs.jpclett.3c02722}, Abstract = {The chirality-induced spin selectivity (CISS) effect allows thin-film layers of chiral conjugated molecules to function as spin filters at ambient temperature. Through solvent-modulated dropcasting of chiral l- and d-perylene diimide (PDI) monomeric building blocks, two types of aggregate morphologies, nanofibers and nanodonuts, may be realized. Spin-diode behavior is evidenced in the nanodonut structures. Stacked PDI units, which form the conjugated core of these nanostructures, dominate the nanodonut-Au electrode contact; in contrast, the AFM tip contacts largely the high-resistance solubilizing alkyl chains of the chiral monomers that form these nanodonuts. Current-voltage responses of the nanodonuts, measured by magnetic conductive AFM (mC-AFM), demonstrate substantial spin polarizations as well as spin current rectification ratios (>10) that exceed the magnitudes of those determined to date for other chiral nanoscale systems. These results underscore the potential for chiral nanostructures, featuring asymmetric molecular junctions, to enable CISS-based nanoscale spin current rectifiers.}, Doi = {10.1021/acs.jpclett.3c02722}, Key = {fds373968} } @article{fds370709, Author = {Liu, R and Zhu, J and Rawson, J and Pederson, LR and Cinnater, VL and Mansergh, JP and Therien, MJ}, Title = {Synthesis and functionalization of electron-deficient perfluoroalkyl porphyrin building blocks for supermolecular systems}, Journal = {Journal of Porphyrins and Phthalocyanines}, Volume = {27}, Number = {5}, Pages = {741-756}, Year = {2023}, Month = {May}, url = {http://dx.doi.org/10.1142/S1088424623500451}, Abstract = {Synthetic strategies for electron-deficient meso-perfluoroalkylporphyrins bearing diverse functional groups are described. Scalable and efficient syntheses for 5-triisopropylsilylethynyl-10,15,20-tris(heptafluoropropyl)porphyrin and 5-triisopropylsilylethynyl-10,20-bis(heptafluoropropyl)porphyrin that equip meso-ethynyl functional groups via the bilane route have been established, along with a refined route to [5,15-bis(heptafluoropropyl)porphinato]zinc(II). meso-Position halogenation of [5,15-bis(heptafluoropropyl)porphinato]zinc(II) was achieved by selective meso-nitration and subsequent reduction, diazonium salt formation, and iodination reactions. Computational data describe the low energy excited states of these chromophores and the electronic structural factors that control reactivity of these meso-perfluoroalkyl substituted porphyrin complexes. meso-Functionalized [5-triisopropylsilylethynyl-10,20-bis(heptafluoropropyl)porphinato]zinc(II) and [5-iodo-10,20-bis(heptafluoropropyl)porphinato]zinc(II) building blocks lay the foundation for the construction of highly conjugated multiporphyrin arrays that feature electronic structural properties important for the development of n-type materials and high potential photooxidants.}, Doi = {10.1142/S1088424623500451}, Key = {fds370709} } @article{fds369835, Author = {Lu, S and Smith, BN and Meikle, H and Therien, MJ and Franklin, AD}, Title = {All-Carbon Thin-Film Transistors Using Water-Only Printing.}, Journal = {Nano letters}, Volume = {23}, Number = {6}, Pages = {2100-2106}, Year = {2023}, Month = {March}, url = {http://dx.doi.org/10.1021/acs.nanolett.2c04196}, Abstract = {Printing thin-film transistors (TFTs) using nanomaterials is a promising approach for future electronics. Yet, most inks rely on environmentally harmful solvents for solubilizing and postprint processing the nanomaterials. In this work, we demonstrate water-only TFTs printed from all-carbon inks of semiconducting carbon nanotubes (CNTs), conducting graphene, and insulating crystalline nanocellulose (CNC). While suspending these nanomaterials into aqueous inks is readily achieved, printing the inks into thin films of sufficient surface coverage and in multilayer stacks to form TFTs has proven elusive without high temperatures, hazardous chemicals, and/or lengthy postprocessing. Using aerosol jet printing, our approach involves a maximum temperature of 70 °C and no hazardous chemicals─all inks are aqueous and only water is used for processing. An intermittent rinsing technique was utilized to address the surface adhesion challenges that limit film density of printed aqueous CNTs. These findings provide promising steps toward an environmentally friendly realization of thin-film electronics.}, Doi = {10.1021/acs.nanolett.2c04196}, Key = {fds369835} } %% Truskey, George A. @article{6739753, Author = {Torgan, C.E. and Burge, S.S. and Collinsworth, A.M. and Truskey, G.A. and Kraus, W.E.}, Title = {Differentiation of mammalian skeletal muscle cells cultured on microcarrier beads in a rotating cell culture system}, Journal = {Med. Biol. Eng. Comput. (UK)}, Volume = {38}, Number = {5}, Pages = {583 - 90}, Keywords = {aerospace biophysics;biological techniques;biomechanics;cellular biophysics;muscle;}, Abstract = {The growth and repair of adult skeletal muscle are due in part to activation of muscle precursor cells, commonly known as satellite cells or myoblasts. These cells are responsive to a variety of environmental cues, including mechanical stimuli. The overall goal of the research is to examine the role of mechanical signalling mechanisms in muscle growth and plasticity through utilisation of cell culture systems where other potential signalling pathways (i.e. chemical and electrical stimuli) are controlled. To explore the effects of decreased mechanical loading on muscle differentiation, mammalian myoblasts are cultured in a bioreactor (rotating cell culture system), a model that has been utilised to simulate microgravity. C<sub>2</sub>C<sub>12</sub> murine myoblasts are cultured on microcarrier beads in a bioreactor and followed throughout differentiation as they form a network of multinucleated myotubes. In comparison with three-dimensional control cultures that consist of myoblasts cultured on microcarrier beads in teflon bags, myoblasts cultured in the bioreactor exhibit an attenuation in differentiation. This is demonstrated by reduced immunohistochemical staining for myogenin and α-actinin. Western analysis shows a decrease, in bioreactor cultures compared with control cultures, in levels of the contractile proteins myosin (47% decrease, p<0.01) and tropomyosin (63% decrease, p<0.01). Hydrodynamic measurements indicate that the decrease in differentiation may be due, at least in part, to fluid stresses acting on the myotubes. In addition, constraints on aggregate size imposed by the action of fluid forces in the bioreactor affect differentiation. These results may have implications for muscle growth and repair during spaceflight}, Key = {6739753} } %% Vo-Dinh, Tuan @article{fds376827, Author = {Canning, AJ and Vo-Dinh, T}, Title = {Caged gold nanostars: a novel plasmonic nanoplatform with potential theranostic applications.}, Journal = {Nanoscale}, Year = {2024}, Month = {April}, url = {http://dx.doi.org/10.1039/d3nr04130a}, Abstract = {Here, we first introduce caged gold nanostars (C-GNS), a novel hybrid nanoplatform combining the exceptional plasmonic properties of nanostars with the loading capability of hollow-shell structures. We present two synthetic routes used to produce C-GNS particles and highlight the benefits of the galvanic replacement-free approach. FEM simulations explore the enhanced plasmonic properties of this novel nanoparticle morphology. Finally, in a proof-of-concept study, we successfully demonstrate <i>in vivo</i> hyperspectral imaging and photothermal treatment of tumors in a mouse model with the C-GNS nanoplatform.}, Doi = {10.1039/d3nr04130a}, Key = {fds376827} } @article{fds376671, Author = {Naquin, TD and Canning, AJ and Gu, Y and Chen, J and Naquin, CM and Xia, J and Lu, B and Yang, S and Koroza, A and Lin, K and Wang, H-N and Jeck, WR and Lee, LP and Vo-Dinh, T and Huang, TJ}, Title = {Acoustic separation and concentration of exosomes for nucleotide detection: ASCENDx.}, Journal = {Sci Adv}, Volume = {10}, Number = {10}, Pages = {eadm8597}, Year = {2024}, Month = {March}, url = {http://dx.doi.org/10.1126/sciadv.adm8597}, Abstract = {Efficient isolation and analysis of exosomal biomarkers hold transformative potential in biomedical applications. However, current methods are prone to contamination and require costly consumables, expensive equipment, and skilled personnel. Here, we introduce an innovative spaceship-like disc that allows Acoustic Separation and Concentration of Exosomes and Nucleotide Detection: ASCENDx. We created ASCENDx to use acoustically driven disc rotation on a spinning droplet to generate swift separation and concentration of exosomes from patient plasma samples. Integrated plasmonic nanostars on the ASCENDx disc enable label-free detection of enriched exosomes via surface-enhanced Raman scattering. Direct detection of circulating exosomal microRNA biomarkers from patient plasma samples by the ASCENDx platform facilitated a diagnostic assay for colorectal cancer with 95.8% sensitivity and 100% specificity. ASCENDx overcomes existing limitations in exosome-based molecular diagnostics and holds a powerful position for future biomedical research, precision medicine, and point-of-care medical diagnostics.}, Doi = {10.1126/sciadv.adm8597}, Key = {fds376671} } @article{fds376236, Author = {Atta, S and Canning, AJ and Vo-Dinh, T}, Title = {A simple low-cost flexible plasmonic patch based on spiky gold nanostars for ultra-sensitive SERS sensing.}, Journal = {The Analyst}, Volume = {149}, Number = {7}, Pages = {2084-2096}, Year = {2024}, Month = {March}, url = {http://dx.doi.org/10.1039/d3an02246c}, Abstract = {Recently, transparent and flexible surface-enhanced Raman scattering (SERS) substrates have received great interest for direct point-of-care detection of analytes on irregular nonplanar surfaces. In this study, we proposed a simple cost-effective strategy to develop a flexible SERS patch utilizing multibranched sharp spiked gold nanostars (GNS) decorated on a commercially available adhesive Scotch Tape for achieving ultra-high SERS sensitivity. The experimental SERS measurements were correlated with theoretical finite element modeling (FEM), which indicates that the GNS having a 2.5 nm branch tip diameter (GNS-4) exhibits the strongest SERS enhancement. Using rhodamine 6G (R6G) as a model analyte, the SERS performance of the flexible SERS patch exhibited a minimum detection limit of R6G as low as 1 pM. The enhancement factor of the SERS patch with GNS-4 was calculated as 6.2 × 10<sup>8</sup>, which indicates that our flexible SERS substrate has the potential to achieve ultra-high sensitivity. The reproducibility was tested with 30 different spots showing a relative standard deviation (RSD) of SERS intensity of about 5.4%, indicating good reproducibility of the SERS platform. To illustrate the usefulness of the flexible SERS sensor patch, we investigated the detection of a carcinogenic compound crystal violet (CV) on fish scales, which is often used as an effective antifungal agent in the aquaculture industry. The results realized the trace detection of CV with the minimum detection limit as low as 1 pM. We believe that our transparent, and flexible SERS patch based on GNS-4 has potential as a versatile, low-cost platform for real-world SERS sensing applications on nonplanar surfaces.}, Doi = {10.1039/d3an02246c}, Key = {fds376236} } @article{fds376672, Author = {Atta, S and Zhao, Y and Li, JQ and Vo-Dinh, T}, Title = {Dual-Modal Colorimetric and Surface-Enhanced Raman Scattering (SERS)-Based Lateral Flow Immunoassay for Ultrasensitive Detection of SARS-CoV-2 Using a Plasmonic Gold Nanocrown.}, Journal = {Analytical chemistry}, Volume = {96}, Number = {12}, Pages = {4783-4790}, Year = {2024}, Month = {March}, url = {http://dx.doi.org/10.1021/acs.analchem.3c04361}, Abstract = {The 2019 coronavirus disease (COVID-19) outbreak created an unprecedented need for rapid, sensitive, and cost-effective point-of-care diagnostic tests to prevent and mitigate the spread of the SARS-CoV-2 virus. Herein, we demonstrated an advanced lateral flow immunoassay (LFIA) platform with dual-functional [colorimetric and surface-enhanced Raman scattering (SERS)] detection of the spike 1 (S1) protein of SARS-CoV-2. The nanosensor was integrated with a specially designed core-gap-shell morphology consisting of a gold shell decorated with external nanospheres, a structure referred to as gold nanocrown (GNC), labeled with a Raman reporter molecule 1,3,3,1',3',3'-hexamethyl-2,2'-indotricarbocyanine iodide (HITC) to produce a strong colorimetric signal as well as an enhanced SERS signal. Among the different plasmonics-active GNC nanostructures, the GNC-2 morphology, which has a shell decorated with an optimum number and size of nanospheres, produces an intense dark-blue colorimetric signal and ultrahigh SERS signal. The limit of detection (LOD) of the S1 protein via colorimetric detection LFIA was determined to be 91.24 pg/mL. On the other hand, the LOD for the SERS LFIA method was more than three orders of magnitude lower at 57.21 fg/mL. Furthermore, we analyzed the performance of the GNC-2 nanosensor for directly analyzing the S1 protein spiked in saliva samples without any sample pretreatment and achieving the LOD as low as 39.65 fg/mL using SERS-based plasmonics-enhanced LFIA, indicating ultrahigh detection sensitivity. Overall, our GNC nanosensor showed excellent sensitivity, reproducibility, and rapid detection of the SARS-CoV-2 S1 protein, demonstrating excellent potential as a promising point-of-care platform for the early detection of respiratory virus infections.}, Doi = {10.1021/acs.analchem.3c04361}, Key = {fds376672} } @article{fds373360, Author = {Vu, T and Klippel, P and Canning, AJ and Ma, C and Zhang, H and Kasatkina, LA and Tang, Y and Xia, J and Verkhusha, VV and Vo-Dinh, T and Jing, Y and Yao, J}, Title = {On the Importance of Low-Frequency Signals in Functional and Molecular Photoacoustic Computed Tomography.}, Journal = {IEEE transactions on medical imaging}, Volume = {43}, Number = {2}, Pages = {771-783}, Year = {2024}, Month = {February}, url = {http://dx.doi.org/10.1109/tmi.2023.3320668}, Abstract = {In photoacoustic computed tomography (PACT) with short-pulsed laser excitation, wideband acoustic signals are generated in biological tissues with frequencies related to the effective shapes and sizes of the optically absorbing targets. Low-frequency photoacoustic signal components correspond to slowly varying spatial features and are often omitted during imaging due to the limited detection bandwidth of the ultrasound transducer, or during image reconstruction as undesired background that degrades image contrast. Here we demonstrate that low-frequency photoacoustic signals, in fact, contain functional and molecular information, and can be used to enhance structural visibility, improve quantitative accuracy, and reduce spare-sampling artifacts. We provide an in-depth theoretical analysis of low-frequency signals in PACT, and experimentally evaluate their impact on several representative PACT applications, such as mapping temperature in photothermal treatment, measuring blood oxygenation in a hypoxia challenge, and detecting photoswitchable molecular probes in deep organs. Our results strongly suggest that low-frequency signals are important for functional and molecular PACT.}, Doi = {10.1109/tmi.2023.3320668}, Key = {fds373360} } @article{fds373887, Author = {Li, JQ and Neng-Wang, H and Canning, AJ and Gaona, A and Crawford, BM and Garman, KS and Vo-Dinh, T}, Title = {Surface-Enhanced Raman Spectroscopy-Based Detection of Micro-RNA Biomarkers for Biomedical Diagnosis Using a Comparative Study of Interpretable Machine Learning Algorithms.}, Journal = {Appl Spectrosc}, Volume = {78}, Number = {1}, Pages = {84-98}, Year = {2024}, Month = {January}, url = {http://dx.doi.org/10.1177/00037028231209053}, Abstract = {Surface-enhanced Raman spectroscopy (SERS) has wide diagnostic applications due to narrow spectral features that allow multiplex analysis. We have previously developed a multiplexed, SERS-based nanosensor for micro-RNA (miRNA) detection called the inverse molecular sentinel (iMS). Machine learning (ML) algorithms have been increasingly adopted for spectral analysis due to their ability to discover underlying patterns and relationships within large and complex data sets. However, the high dimensionality of SERS data poses a challenge for traditional ML techniques, which can be prone to overfitting and poor generalization. Non-negative matrix factorization (NMF) reduces the dimensionality of SERS data while preserving information content. In this paper, we compared the performance of ML methods including convolutional neural network (CNN), support vector regression, and extreme gradient boosting combined with and without NMF for spectral unmixing of four-way multiplexed SERS spectra from iMS assays used for miRNA detection. CNN achieved high accuracy in spectral unmixing. Incorporating NMF before CNN drastically decreased memory and training demands without sacrificing model performance on SERS spectral unmixing. Additionally, models were interpreted using gradient class activation maps and partial dependency plots to understand predictions. These models were used to analyze clinical SERS data from single-plexed iMS in RNA extracted from 17 endoscopic tissue biopsies. CNN and CNN-NMF, trained on multiplexed data, performed most accurately with RMSElabel = 0.101 and 9.68 × 10-2, respectively. We demonstrated that CNN-based ML shows great promise in spectral unmixing of multiplexed SERS spectra, and the effect of dimensionality reduction on performance and training speed.}, Doi = {10.1177/00037028231209053}, Key = {fds373887} } @article{fds375326, Author = {Atta, S and Canning, AJ and Vo-Dinh, T}, Title = {Rapid SERS assay for determination of the opioid fentanyl using silver-coated sharply branched gold nanostars.}, Journal = {Mikrochimica acta}, Volume = {191}, Number = {2}, Pages = {110}, Year = {2024}, Month = {January}, url = {http://dx.doi.org/10.1007/s00604-023-06172-5}, Abstract = {A high-throughput surface-enhanced Raman scattering (SERS)-sensing platform is presented for FNT detection in human urine without any sample preparation. The sensing platform is based on plasmonics-active silver-coated sharply branched gold nanostars (SGNS). The effect of silver thickness was investigated experimentally and theoretically, and the results indicated that SERS enhancement was maximum at an optimum silver thickness of 45 nm on the sharply spiked SGNS. The proposed high-throughput SERS platform exhibited ultrahigh sensitivity and excellent enhancement uniformity for a model analyte, i.e., crystal violet. Moreover, the SERS-sensing platform demonstrated good sensitivity of FNT spiked in human urine samples with two differential linear response ranges of 2 to 0.2 µg/mL and 0.1 µg/mL to 100 pg/mL, respectively, with a detection limit as low as 10.02 pg/mL. The spiked human urine samples show satisfactory recovery values from 92.5 to 102% with relative standard deviations (RSD) of less than 10%. In summary, the high-throughput performance of the proposed microplate-based SERS platform demonstrated great potential for rapid low-cost SERS-based sensing applications.}, Doi = {10.1007/s00604-023-06172-5}, Key = {fds375326} } @article{fds372689, Author = {Atta, S and Li, JQ and Vo-Dinh, T}, Title = {Multiplex SERS detection of polycyclic aromatic hydrocarbon (PAH) pollutants in water samples using gold nanostars and machine learning analysis.}, Journal = {The Analyst}, Volume = {148}, Number = {20}, Pages = {5105-5116}, Year = {2023}, Month = {October}, url = {http://dx.doi.org/10.1039/d3an00636k}, Abstract = {Polycyclic aromatic hydrocarbons (PAHs) have attracted a lot of environmental concern because of their carcinogenic and mutagenic properties, and the fact they can easily contaminate natural resources such as drinking water and river water. This study presents a simple and sensitive point-of-care SERS detection of PAHs combined with machine learning algorithms to predict the PAH content more precisely and accurately in real-life samples such as drinking water and river water. We first synthesized multibranched sharp-spiked surfactant-free gold nanostars (GNSs) that can generate strong surface-enhanced Raman scattering (SERS) signals, which were further coated with cetyltrimethylammonium bromide (CTAB) for long-term stability of the GNSs as well as to trap PAHs. We utilized CTAB-capped GNSs for solution-based 'mix and detect' SERS sensing of various PAHs including pyrene (PY), nitro-pyrene (NP), anthracene (ANT), benzo[a]pyrene (BAP), and triphenylene (TP) spiked in drinking water and river water using a portable Raman module. Very low limits of detection (LOD) were achieved in the nanomolar range for the PAHs investigated. More importantly, the detected SERS signal was reproducible for over 90 days after synthesis. Furthermore, we analyzed the SERS data using artificial intelligence (AI) with machine learning algorithms based on the convolutional neural network (CNN) model in order to discriminate the PAHs in samples more precisely and accurately. Using a CNN classification model, we achieved a high prediction accuracy of 90% in the nanomolar detection range and an f1 score (harmonic mean of precision and recall) of 94%, and using a CNN regression model, achieved an RMSE<sub>conc</sub> = 1.07 × 10<sup>-1</sup> μM. Overall, our SERS platform can be effectively and efficiently used for the accurate detection of PAHs in real-life samples, thus opening up a new, sensitive, selective, and practical approach for point-of-need SERS diagnosis of small molecules in complex practical environments.}, Doi = {10.1039/d3an00636k}, Key = {fds372689} } @article{fds372430, Author = {Srinivasan, ES and Liu, Y and Odion, RA and Chongsathidkiet, P and Wachsmuth, LP and Haskell-Mendoza, AP and Edwards, RM and Canning, AJ and Willoughby, G and Hinton, J and Norton, SJ and Lascola, CD and Maccarini, PF and Mariani, CL and Vo-Dinh, T and Fecci, PE}, Title = {Gold Nanostars Obviate Limitations to Laser Interstitial Thermal Therapy (LITT) for the Treatment of Intracranial Tumors.}, Journal = {Clin Cancer Res}, Volume = {29}, Number = {16}, Pages = {3214-3224}, Year = {2023}, Month = {August}, url = {http://dx.doi.org/10.1158/1078-0432.CCR-22-1871}, Abstract = {PURPOSE: Laser interstitial thermal therapy (LITT) is an effective minimally invasive treatment option for intracranial tumors. Our group produced plasmonics-active gold nanostars (GNS) designed to preferentially accumulate within intracranial tumors and amplify the ablative capacity of LITT. EXPERIMENTAL DESIGN: The impact of GNS on LITT coverage capacity was tested in ex vivo models using clinical LITT equipment and agarose gel-based phantoms of control and GNS-infused central "tumors." In vivo accumulation of GNS and amplification of ablation were tested in murine intracranial and extracranial tumor models followed by intravenous GNS injection, PET/CT, two-photon photoluminescence, inductively coupled plasma mass spectrometry (ICP-MS), histopathology, and laser ablation. RESULTS: Monte Carlo simulations demonstrated the potential of GNS to accelerate and specify thermal distributions. In ex vivo cuboid tumor phantoms, the GNS-infused phantom heated 5.5× faster than the control. In a split-cylinder tumor phantom, the GNS-infused border heated 2× faster and the surrounding area was exposed to 30% lower temperatures, with margin conformation observed in a model of irregular GNS distribution. In vivo, GNS preferentially accumulated within intracranial tumors on PET/CT, two-photon photoluminescence, and ICP-MS at 24 and 72 hours and significantly expedited and increased the maximal temperature achieved in laser ablation compared with control. CONCLUSIONS: Our results provide evidence for use of GNS to improve the efficiency and potentially safety of LITT. The in vivo data support selective accumulation within intracranial tumors and amplification of laser ablation, and the GNS-infused phantom experiments demonstrate increased rates of heating, heat contouring to tumor borders, and decreased heating of surrounding regions representing normal structures.}, Doi = {10.1158/1078-0432.CCR-22-1871}, Key = {fds372430} } @article{fds370600, Author = {Li, S and Anwar, IJ and Canning, AJ and Vo-Dinh, T and Kirk, AD and Xu, H}, Title = {Xenorecognition and costimulation of porcine endothelium-derived extracellular vesicles in initiating human porcine-specific T cell immune responses.}, Journal = {Am J Transplant}, Volume = {23}, Number = {7}, Pages = {904-919}, Year = {2023}, Month = {July}, url = {http://dx.doi.org/10.1016/j.ajt.2023.04.006}, Abstract = {Porcine vascular endothelial cells (PECs) form a mechanistic centerpiece of xenograft rejection. Here, we determined that resting PECs release swine leukocyte antigen class I (SLA-I) but not swine leukocyte antigen class-II DR (SLA-DR) expressing extracellular vesicles (EVs) and investigated whether these EVs proficiently initiate xenoreactive T cell responses via direct xenorecognition and costimulation. Human T cells acquired SLA-I+ EVs with or without direct contact to PECs, and these EVs colocalized with T cell receptors. Although interferon gamma-activated PECs released SLA-DR+ EVs, the binding of SLA-DR+ EVs to T cells was sparse. Human T cells demonstrated low levels of proliferation without direct contact to PECs, but marked T cell proliferation was induced following exposure to EVs. EV-induced proliferation proceeded independent of monocytes/macrophages, suggesting that EVs delivered both a T cell receptor signal and costimulation. Costimulation blockade targeting B7, CD40L, or CD11a significantly reduced T cell proliferation to PEC-derived EVs. These findings indicate that endothelial-derived EVs can directly initiate T cell-mediated immune responses, and suggest that inhibiting the release of SLA-I EVs from organ xenografts has the potential to modify the xenograft rejection. We propose a secondary-direct pathway for T cell activation via xenoantigen recognition/costimulation by endothelial-derived EVs.}, Doi = {10.1016/j.ajt.2023.04.006}, Key = {fds370600} } @article{fds372690, Author = {Wang, H-N and Vo-Dinh, T}, Title = {Cascade Amplified Plasmonics Molecular Biosensor for Sensitive Detection of Disease Biomarkers.}, Journal = {Biosensors}, Volume = {13}, Number = {8}, Pages = {774}, Year = {2023}, Month = {July}, url = {http://dx.doi.org/10.3390/bios13080774}, Abstract = {Recent advances in molecular technologies have provided various assay strategies for monitoring biomarkers, such as miRNAs for early detection of various diseases and cancers. However, there is still an urgent unmet need to develop practical and accurate miRNA analytical tools that could facilitate the incorporation of miRNA biomarkers into clinical practice and management. In this study, we demonstrate the feasibility of using a cascade amplification method, referred to as the "Cascade Amplification by Recycling Trigger Probe" (CARTP) strategy, to improve the detection sensitivity of the inverse Molecular Sentinel (iMS) nanobiosensor. The iMS nanobiosensor developed in our laboratory is a unique homogeneous multiplex bioassay technique based on surface-enhanced Raman scattering (SERS) detection, and was used to successfully detect miRNAs from clinical samples. The CARTP strategy based on the toehold-mediated strand displacement reaction is triggered by a linear DNA strand, called the "Recycling Trigger Probe" (RTP) strand, to amplify the iMS SERS signal. Herein, by using the CARTP strategy, we show a significantly improved detection sensitivity with the limit of detection (LOD) of 45 fM, which is 100-fold more sensitive than the non-amplified iMS assay used in our previous report. We envision that the further development and optimization of this strategy ultimately will allow multiplexed detection of miRNA biomarkers with ultra-high sensitivity for clinical translation and application.}, Doi = {10.3390/bios13080774}, Key = {fds372690} } @article{fds369676, Author = {Atta, S and Vo-Dinh, T}, Title = {Ultra-trace SERS detection of cocaine and heroin using bimetallic gold-silver nanostars (BGNS-Ag).}, Journal = {Analytica chimica acta}, Volume = {1251}, Pages = {340956}, Year = {2023}, Month = {April}, url = {http://dx.doi.org/10.1016/j.aca.2023.340956}, Abstract = {A rapid, in-field, and reliable method for the detection of illegal drugs of abuse in biological fluids without any sample pretreatment would potentially be helpful for law enforcement, drug control officials, and public healthcare. In this study, we presented a cost-effective and highly reproducible solution-based surface-enhanced Raman scattering (SERS) platform utilizing a portable Raman instrument for fast sensitive SERS detection of illegal drugs, such as cocaine, and heroin in human urine without any sample preprocessing. The SERS platform was constructed for the first time by combining the superior SERS enhancement properties of bimetallic silver-coated gold nanostars (BGNS-Ag) and the advantages of suitable alkaline metal salts such as NaI for SERS signal amplification. The effects of the silver thickness of BGNS-Ag and alkaline salts on the SERS performance were investigated in detail; we observed that the maximum SERS enhancement was obtained for BGNS-Ag with the maximum silver thickness (54 ± 5 nm) in presence of NaI salt. Our SERS platform shows ultra-high sensitivity of cocaine and heroin with a limit of detection (LOD) as low as 10 pg/mL for cocaine and 100 pg/mL for heroin, which was 100 times lower than that of the traditional silver nanoparticle-based illegal drug detection. As a demonstration, the platform was further applied to detect cocaine and heroin spiked in human urine without any sample preprocessing achieving a LOD of 100 pg/mL for cocaine and 1 ng/mL for heroin. Overall, our SERS detection platform shows potential for rapid, onsite, ultra-low-cost portable applications for trace detection of illegal drugs and biomarkers.}, Doi = {10.1016/j.aca.2023.340956}, Key = {fds369676} } @article{fds369935, Author = {Atta, S and Vo-Dinh, T}, Title = {A hybrid plasmonic nanoprobe using polyvinylpyrrolidone-capped bimetallic silver-gold nanostars for highly sensitive and reproducible solution-based SERS sensing.}, Journal = {The Analyst}, Volume = {148}, Number = {8}, Pages = {1786-1796}, Year = {2023}, Month = {April}, url = {http://dx.doi.org/10.1039/d2an01876d}, Abstract = {Practical solution-based assays using surface-enhanced Raman spectroscopy (SERS) with portable instrumentation are currently of particular interest for rapid, efficient, and low-cost detection of analytes. However, current assays still have limited applicability due to their poor sensitivity and reproducibility. Herein, we demonstrate highly stable polyvinylpyrrolidone (PVP)-capped bimetallic silver-coated gold nanostars (BGNS-Ag-PVP) as a solution-based SERS nanoprobe that is capable of producing a strong, uniform, and reproducible SERS signal using a portable Raman instrument. The developed hybrid BGNS-Ag-PVP nanostructure shows tunable optical properties with improved SERS sensitivity and reproducibility as compared to gold nanostars. We have synthesized bimetallic nanoprobes BGNS-Ag-PVP having three different silvers, referred to as BGNS-Ag-PVP-1, BGNS-Ag-PVP-2, and BGNS-Ag-PVP-3. The SERS performance of BGNS-Ag-PVP was studied using methylene blue (Meb) as a probe molecule, and we achieved a detection limit of up to 10 nM indicating the high sensitivity of the solution-based SERS platform. The application of such bimetallic nanoparticles is demonstrated <i>via</i> the sensitive detection of the antithyroid drug methimazole (Mz) used as a model analyte system. We have achieved a detection limit of 1 nM for Mz spiked with human urine indicating three orders of magnitude lower than previously reported solution-based SERS detection methods. Furthermore, the SERS performance was reproducible over 3 months indicating excellent stability and repeatability. The result illustrates the potential of this solution-based SERS detection platform as a promising sensing tool for analytes such as illicit drugs, and biomarkers that have affinity to bind on nanoprobes.}, Doi = {10.1039/d2an01876d}, Key = {fds369935} } @article{fds369834, Author = {Atta, S and Canning, AJ and Odion, R and Wang, HN and Hau, D and Devadhasan, JP and Summers, AJ and Gates-Hollingsworth, MA and Pflughoeft, KJ and Gu, J and Montgomery, DC and AuCoin, DP and Zenhausern, F and Vo-Dinh, T}, Title = {Sharp Branched Gold Nanostar-Based Lateral-Flow Immunoassay for Detection of Yersinia pestis}, Journal = {ACS Applied Nano Materials}, Volume = {6}, Number = {5}, Pages = {3884-3892}, Year = {2023}, Month = {March}, url = {http://dx.doi.org/10.1021/acsanm.2c05557}, Abstract = {Over the past few decades, colorimetric paper-based lateral flow immunoassay (LFIA) has emerged as a versatile analytical tool for rapid point-of-care detection of infectious diseases with high simplicity and flexibility. The LFIA sensitivity is based on color visualization of the antibody-labeled nanoparticles bound with the target analytes at the test line. Therefore, the nanoparticle design is crucial for LFIA sensitivity. The traditional LFIA is based on spherical gold nanoparticles, which usually suffer from poor sensitivity because of very low optical contrast at the test line. To improve the LFIA sensitivity, we have developed an LFIA based on gold nanostars (GNSs) with different branch lengths and sharpness (GNS-1, GNS-2, and GNS-3), which possess higher optical contrast than conventional gold nanospheres (GNSPs). We have selected the bacterium Yersinia pestis as a model analyte system. The effective affinity of GNSPs and GNSs with the Y. pestis fraction 1 (F1) protein was quantitively investigated by colorimetric and optical density measurements of the test line. The results show that GNS-3, which has maximum spike length and branch sharpness, exhibits the highest analytical sensitivity based on the limit of detection of the LFIA readout compared to other GNSs and GNSPs. The detection limit of the Y. pestis F1 antigen was achieved up to 0.1 ng/mL for GNS-3, which is 100 times lower than that for the GNSP at a 1 pmol/L concentration and 10 times lower than that for the reported procedure based on traditional gold nanoparticles. Overall, our prototype LFIA platform based on a highly spiked GNS (GNS-3) exhibits high analytical sensitivity, indicating it to be a promising candidate for routine LFIA application to detect infectious diseases.}, Doi = {10.1021/acsanm.2c05557}, Key = {fds369834} } @article{fds369936, Author = {Cupil-Garcia, V and Li, JQ and Norton, SJ and Odion, RA and Strobbia, P and Menozzi, L and Ma, C and Hu, J and Zentella, R and Boyanov, MI and Finfrock, YZ and Gursoy, D and Douglas, DS and Yao, J and Sun, T-P and Kemner, KM and Vo-Dinh, T}, Title = {Plasmonic nanorod probes' journey inside plant cells for in vivo SERS sensing and multimodal imaging.}, Journal = {Nanoscale}, Volume = {15}, Number = {13}, Pages = {6396-6407}, Year = {2023}, Month = {March}, url = {http://dx.doi.org/10.1039/d2nr06235f}, Abstract = {Nanoparticle-based platforms are gaining strong interest in plant biology and bioenergy research to monitor and control biological processes in whole plants. However, <i>in vivo</i> monitoring of biomolecules using nanoparticles inside plant cells remains challenging due to the impenetrability of the plant cell wall to nanoparticles beyond the exclusion limits (5-20 nm). To overcome this physical barrier, we have designed unique bimetallic silver-coated gold nanorods (AuNR@Ag) capable of entering plant cells, while conserving key plasmonic properties in the near-infrared (NIR). To demonstrate cellular internalization and tracking of the nanorods inside plant tissue, we used a comprehensive multimodal imaging approach that included transmission electron microscopy (TEM), confocal fluorescence microscopy, two-photon luminescence (TPL), X-ray fluorescence microscopy (XRF), and photoacoustics imaging (PAI). We successfully acquired SERS signals of nanorods <i>in vivo</i> inside plant cells of tobacco leaves. On the same leaf samples, we applied orthogonal imaging methods, TPL and PAI techniques for <i>in vivo</i> imaging of the nanorods. This study first demonstrates the intracellular internalization of AuNR@Ag inside whole plant systems for <i>in vivo</i> SERS analysis in tobacco cells. This work demonstrates the potential of this nanoplatform as a new nanotool for intracellular <i>in vivo</i> biosensing for plant biology.}, Doi = {10.1039/d2nr06235f}, Key = {fds369936} } @article{fds369321, Author = {Atta, S and Vo-Dinh, T}, Title = {Solution-Based Ultra-Sensitive Surface-Enhanced Raman Scattering Detection of the Toxin Bacterial Biomarker Pyocyanin in Biological Fluids Using Sharp-Branched Gold Nanostars.}, Journal = {Analytical chemistry}, Volume = {95}, Number = {5}, Pages = {2690-2697}, Year = {2023}, Month = {February}, url = {http://dx.doi.org/10.1021/acs.analchem.2c03210}, Abstract = {There is a critical need for sensitive rapid point-of-care detection of bacterial infection biomarkers in complex biological fluids with minimal sample preparation, which can improve early-stage diagnosis and prevent several bacterial infections and fatal diseases. A solution-based surface-enhanced Raman scattering (SERS) detection platform has long been sought after for low cost, rapid, and on-site detection of analyte molecules, but current methods still exhibit poor sensitivity. In this study, we have tuned the morphology of the surfactant-free gold nanostars (GNSs) to achieve sharp protruding spikes for maximum SERS enhancement. We have controlled the GNS spike morphologies and optimized SERS performance in the solution phase using para-mercaptobenzoic acid as an SERS probe. To illustrate the potential for point-of-care applications, we have utilized a portable Raman instrument for measurements. For pathogenic agent sensing applications, we demonstrated rapid and sensitive detection of the toxin biomarker pyocyanin (PYO) used as the bacterial biomarker model system. Pyocyanin is a toxic compound produced and secreted by the common water-borne Gram-negative bacterium <i>Pseudomonas aeruginosa</i>, a pathogen known for advanced antibiotic resistance and association with serious diseases such as ventilator-associated pneumonia and cystic fibrosis. The limit of detection (LOD) achieved for PYO was 0.05 nM using sharp branched GNSs. Furthermore, as a proof of strategy, this SERS detection of PYO was performed directly in drinking water, human saliva, and human urine without any sample treatment pre-purification, achieving an LOD of 0.05 nM for drinking water and 0.4 nM for human saliva and urine. This work provides a proof-of-principle demonstration for the high sensitivity detection of the bacterial toxin biomarker with minimal sample preparation: the "mix and detect" detection of the GNS platform is simple, robust, and rapid, taking only 1-2 min for each measurement. Overall, our SERS detection platform shows great potential for point-of-need sensing and point-of-care diagnostics in biological fluids.}, Doi = {10.1021/acs.analchem.2c03210}, Key = {fds369321} } @article{fds367636, Author = {Canning, AJ and Chen, X and Li, JQ and Jeck, WR and Wang, H-N and Vo-Dinh, T}, Title = {miRNA probe integrated biosensor platform using bimetallic nanostars for amplification-free multiplexed detection of circulating colorectal cancer biomarkers in clinical samples.}, Journal = {Biosens Bioelectron}, Volume = {220}, Pages = {114855}, Year = {2023}, Month = {January}, url = {http://dx.doi.org/10.1016/j.bios.2022.114855}, Abstract = {There is a critical need for sensitive and rapid detection technologies utilizing molecular biotargets such as microRNAs (miRNAs), which regulate gene expression and are a promising class of diagnostic biomarkers for disease detection. Here, we present the development and fabrication of a highly reproducible and robust plasmonic bimetallic nanostar biosensing platform to detect miRNA targets using surfaced-enhanced Raman scattering (SERS)-based gene probes called the inverse Molecular Sentinel (iMS). We investigated and optimized the integration of iMS gene probes onto this SERS substrate, achieving ultra-sensitive detection with limits of detection of 6.8 and 16.7 zmol within the sensing region for two miRNA sequences of interest. Finally, we demonstrated the biomedical usefulness of this nanobiosensor platform with the multiplexed detection of upregulated miRNA targets, miR21 and miR221, from colorectal cancer patient plasma. The resulting SERS data are in excellent agreement with PCR data obtained from patient samples and can distinguish between healthy and cancerous patient samples. These results underline the potential of the iMS-integrated substrate nanobiosensing platform for rapid and sensitive diagnostics of cancer biomarkers for point-of-care applications.}, Doi = {10.1016/j.bios.2022.114855}, Key = {fds367636} } @article{fds371687, Author = {Devadhasan, JP and Summers, AJ and Gu, J and Smith, S and Thomas, B and Fattahi, A and Helton, J and Pandit, SG and Gates-Hollingsworth, M and Hau, D and Pflughoeft, KJ and Montgomery, DC and Atta, S and Vo-Dinh, T and AuCoin, D and Zenhausern, F}, Title = {Point-of-care vertical flow immunoassay system for ultra-sensitive multiplex biothreat-agent detection in biological fluids.}, Journal = {Biosensors & bioelectronics}, Volume = {219}, Pages = {114796}, Year = {2023}, Month = {January}, url = {http://dx.doi.org/10.1016/j.bios.2022.114796}, Abstract = {This paper presents simple, fast, and sensitive detection of multiple biothreat agents by paper-based vertical flow colorimetric sandwich immunoassay for detection of Yersinia pestis (LcrV and F1) and Francisella tularensis (lipopolysaccharide; LPS) antigens using a vertical flow immunoassay (VFI) prototype with portable syringe pump and a new membrane holder. The capture antibody (cAb) printing onto nitrocellulose membrane and gold-labelled detection antibody (dAb) were optimized to enhance the assay sensitivity and specificity. Even though the paper pore size was relaxed from previous 0.1 μm to the current 0.45 μm for serum samples, detection limits as low as 0.050 ng/mL for LcrV and F1, and 0.100 ng/mL for FtLPS have been achieved in buffer and similarly in diluted serum (with LcrV and F1 LODs remained the same and LPS LOD reduced to 0.250 ng/mL). These were 40, 80, and 50X (20X for LPS in serum) better than those from lateral flow configuration. Furthermore, the comparison of multiplex format demonstrated low cross-reactivity and equal sensitivity to that of the singleplex assay. The optimized VFI platform thus provides a portable and rapid on-site monitoring system for multiplex biothreat detection with the potential for high sensitivity, specificity, reproducibility, and multiplexing capability, supporting its utility in remote and resource-limited settings.}, Doi = {10.1016/j.bios.2022.114796}, Key = {fds371687} } @booklet{Panjehpour08, Author = {M. Panjehpour and D. Coppola and B. F. Overholt and T. Vo-dinh and S. Overholt}, Title = {Photodynamic therapy of Barrett's esophagus: Ablation of Barrett's mucosa and reduction in p53 protein expression after treatment}, Journal = {Anticancer Research}, Volume = {28}, Number = {1B}, Pages = {485 -- 489}, Year = {2008}, ISSN = {0250-7005}, Abstract = {Background: The effectiveness of photodynamic therapy (PDT) for ablation of high grade dysplasia (HGD) in Barrett's esophagus (BE) is typically reported histologically. Following successful PDT, Barrett's mucosa is replaced with neosquamous mucosa. The objective of this study was to compare the expression of p53 protein in neosquamous mucosa as compared to that in HGD samples not treated with PDT. Patients and Methods: The patients were divided into two groups. Group I patients (n=12) had been treated with PDT for HGD and provided 23 biopsy samples of neosquamous mucosa. Group II patients (n = 10) had not received any ablative therapies for BE and provided 14 HGD samples. The immunohistochemical (IHC) staining for p53 protein was performed using mouse anti-human monoclonal antibody DO-1. The degree of p53 protein expression in the cell nuclei was scored using an established IHC scoring system (0 for negative samples and range of 2 to 8 for positive samples). Results: The HGD samples showed diffuse strong p53 staining. The median IHC score for HGD was 7.0. The median IHC score for neosquamous mucosa following PDT was 4.0, with positive scores indicating weak staining in the basal layer of the neosquamous samples. There was significantly lower p53 expression in the neosquamous samples compared to that in the HGD samples (p$<$0.001). Conclusion: Significantly lower p53 protein expression was detected in neosquamous mucosa of patients who had received PDT for HGD, suggesting a decreased risk for neoplastic progression after treatment.}, Key = {Panjehpour08} } @booklet{Vo-dinh08a, Author = {T. Vo-dinh}, Title = {Nanobiosensing using plasmonic nanoprobes}, Journal = {Ieee Journal Of Selected Topics In Quantum Electronics}, Volume = {14}, Number = {1}, Pages = {198 -- 205}, Year = {2008}, ISSN = {1077-260X}, Abstract = {This paper provides an overview of the development and applications of plasmonics-active nanoprobes in biomedical diagnostics. Specific examples of detection techniques using surface-enhanced Raman scattering are presented to illustrate the usefulness and potential of the plasmonics nanoprobes for gene detection and nanobiosensing. The detection of specific target deoxyribonucleic acids sequences using a novel "molecular sentinel" nanoprobe method is presented and discussed in detail.}, Key = {Vo-dinh08a} } %% Zauscher, Stefan @article{fds369714, Author = {Young, MN and Sindoni, MJ and Lewis, AH and Zauscher, S and Grandl, J}, Title = {The energetics of rapid cellular mechanotransduction.}, Journal = {Proc Natl Acad Sci U S A}, Volume = {120}, Number = {8}, Pages = {e2215747120}, Year = {2023}, Month = {February}, url = {http://dx.doi.org/10.1073/pnas.2215747120}, Abstract = {Cells throughout the human body detect mechanical forces. While it is known that the rapid (millisecond) detection of mechanical forces is mediated by force-gated ion channels, a detailed quantitative understanding of cells as sensors of mechanical energy is still lacking. Here, we combine atomic force microscopy with patch-clamp electrophysiology to determine the physical limits of cells expressing the force-gated ion channels (FGICs) Piezo1, Piezo2, TREK1, and TRAAK. We find that, depending on the ion channel expressed, cells can function either as proportional or nonlinear transducers of mechanical energy and detect mechanical energies as little as ~100 fJ, with a resolution of up to ~1 fJ. These specific energetic values depend on cell size, channel density, and cytoskeletal architecture. We also make the surprising discovery that cells can transduce forces either nearly instantaneously (<1 ms) or with a substantial time delay (~10 ms). Using a chimeric experimental approach and simulations, we show how such delays can emerge from channel-intrinsic properties and the slow diffusion of tension in the membrane. Overall, our experiments reveal the capabilities and limits of cellular mechanosensing and provide insights into molecular mechanisms that different cell types may employ to specialize for their distinct physiological roles.}, Doi = {10.1073/pnas.2215747120}, Key = {fds369714} } | |
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