Molecular Biosciences Scholarly Works
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Conversion of Polyethylenes into Fungal Secondary Metabolites
(Wiley, 2022-11-03)Waste plastics represent major environmental and economic burdens due to their ubiquity, slow breakdown rates, and inadequacy of current recycling routes. Polyethylenes are particularly problematic, because they lack robust ... -
The genetic basis of adaptation to copper pollution in Drosophila melanogaster
(Frontiers Media, 2023-04-04)Introduction: Heavy metal pollutants can have long lasting negative impacts on ecosystem health and can shape the evolution of species. The persistent and ubiquitous nature of heavy metal pollution provides an opportunity ... -
TOM-1/tomosyn acts with the UNC-6/netrin receptor UNC-5 to inhibit growth cone protrusion in Caenorhabditis elegans
(The Company of Biologists, 2023-04-04)In the polarity/protrusion model of growth cone repulsion from UNC-6/netrin, UNC-6 first polarizes the growth cone of the VD motor neuron axon via the UNC-5 receptor, and then regulates protrusion asymmetrically across the ... -
The reporting quality and transparency of orthopaedic studies using Bayesian analysis requires improvement: A systematic review
(Elsevier, 2023-04-07)Background Bayesian methods are being used more frequently in orthopaedics. To advance the use and transparent reporting of Bayesian studies, reporting guidelines have been recommended. There is currently little known ... -
Inhibitors of One or More Cellular Aurora Kinases Impair the Replication of Herpes Simplex Virus 1 and Other DNA and RNA Viruses with Diverse Genomes and Life Cycles
(American Society for Microbiology, 2022-12-20)We utilized a high-throughput cell-based assay to screen several chemical libraries for inhibitors of herpes simplex virus 1 (HSV-1) gene expression. From this screen, four aurora kinase inhibitors were identified that ... -
EWSR1 prevents the induction of aneuploidy through direct regulation of Aurora B
(Frontiers Media, 2023-02-15)EWSR1 (Ewing sarcoma breakpoint region 1) was originally identified as a part of an aberrant EWSR1/FLI1 fusion gene in Ewing sarcoma, the second most common pediatric bone cancer. Due to formation of the EWSR1/FLI1 fusion ... -
Sustainable Methodologies for Efficient Gel Electrophoresis and Streamlined Screening of Difficult Plasmids
(MDPI, 2023-03-06)We describe a workflow for efficient, environmentally attentive, and sustainable practices related to routine agarose gel electrophoresis. The methods reduce plastic waste and improve efficiency, especially for the exhaustive ... -
Sustainable and Cost-Effective Gel Documentation
(MDPI, 2023-02-21)A common laboratory method involves gel electrophoresis followed by photographic documentation of the results, a procedure which is performed worldwide by students and experienced scientists alike. Proprietary Gel Documentation ... -
Branched actin networks are assembled on microtubules by adenomatous polyposis coli for targeted membrane protrusion
(Rockefeller University Press, 2020-06-29)Cell migration is driven by pushing and pulling activities of the actin cytoskeleton, but migration directionality is largely controlled by microtubules. This function of microtubules is especially critical for neuron ... -
Editorial: Mechanisms, thermodynamics and kinetics of ligand binding revealed from molecular simulations and machine learning
(Frontiers Media, 2023-01-17) -
GLOW: A Workflow Integrating Gaussian-Accelerated Molecular Dynamics and Deep Learning for Free Energy Profiling
(American Chemical Society, 2022-02-24)We introduce a Gaussian-accelerated molecular dynamics (GaMD), deep learning (DL), and free energy profiling workflow (GLOW) to predict molecular determinants and map free energy landscapes of biomolecules. All-atom ... -
Induction and inhibition of Drosophila X chromosome gene expression are both impeded by the dosage compensation complex
(Oxford University Press, 2022-07-06)Sex chromosomes frequently differ from the autosomes in the frequencies of genes with sexually dimorphic or tissue-specific expression. Multiple hypotheses have been put forth to explain the unique gene content of the X ... -
Docking-based long timescale simulation of cell-size protein systems at atomic resolution
(National Academy of Sciences, 2022-10-03)Computational methodologies are increasingly addressing modeling of the whole cell at the molecular level. Proteins and their interactions are the key component of cellular processes. Techniques for modeling protein ... -
Septate junction proteins are required for cell shape changes, actomyosin reorganization and cell adhesion during dorsal closure in Drosophila
(Frontiers Media, 2022-09-27)Septate junctions (SJs) serve as occluding barriers in invertebrate epithelia. In Drosophila, at least 30 genes are required for the formation or maintenance of SJs. Interestingly, loss-of-function mutations in core SJ ... -
Analytical Approaches for Deriving Friction Coefficients for Selected α‑Helical Peptides Based Entirely on Molecular Dynamics Simulations
(American Chemical Society, 2022-10-27)In this paper we derive analytically from molecular dynamics (MD) simulations the friction coefficients related to conformational transitions within several model peptides with α-helical structures. We study a series of ... -
Size of the protein-protein energy funnel in crowded environment
(Frontiers Media, 2022-11-08)Association of proteins to a significant extent is determined by their geometric complementarity. Large-scale recognition factors, which directly relate to the funnel-like intermolecular energy landscape, provide important ... -
Discovery of malathion resistance QTL in Drosophila melanogaster using a bulked phenotyping approach
(Oxford University Press, 2022-10-17)Drosophila melanogaster has proved an effective system with which to understand the evolutionary genetics and molecular mechanisms of insecticide resistance. Insecticide use has left signatures of selection in the fly ... -
Genetic variation in P-element dysgenic sterility is associated with double-strand break repair and alternative splicing of TE transcripts
(Public Library of Science, 2022-12-07)The germline mobilization of transposable elements (TEs) by small RNA mediated silencing pathways is conserved across eukaryotes and critical for ensuring the integrity of gamete genomes. However, genomes are recurrently ... -
QAUST: Protein Function Prediction Using Structure Similarity, Protein Interaction, and Functional Motifs
(Elsevier, 2021-02-23)The number of available protein sequences in public databases is increasing exponentially. However, a significant percentage of these sequences lack functional annotation, which is essential for the understanding of how ... -
Linearized Siderophore Products Secreted via MacAB Efflux Pump Protect Salmonella enterica Serovar Typhimurium from Oxidative Stress
(American Society for Microbiology, 2020-05-05)Nontyphoidal salmonellae (NTS) are exposed to reactive oxygen species (ROS) during their residency in the gut. To survive oxidative stress encountered during infection, salmonellae employ several mechanisms. One of these ...
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