Episodes
Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.11.21.392266v1?rss=1 Authors: Phapale, P., Palmer, A., Gathungu, R. M., Kale, D., Brugger, B., Alexandrov, T. Abstract: Liquid chromatography-mass spectrometry(LC-MS)-based untargeted metabolomics studies require high-quality spectral libraries for reliable metabolite identification. We have constructed EMBL-MCF, an open LC-MS/MS spectral library that currently contains over 1600 fragmentation spectra from 435 authentic...
Published 11/22/20
Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.11.21.391326v1?rss=1 Authors: FUCHS, R. P., Isogawa, A., Paulo, J. A., Onizuka, K., Takahashi, T., Amunugama, R., Duxin, J. P., Fujii, S. Abstract: Temozolomide, a DNA methylating agent, is the primary chemotherapeutic drug used in glioblastoma treatment. TMZ induces mostly N-alkylation adducts (N7-methylguanine and N3-methyladenine) and some O6-methylguanine (O6mG). Current models propose that during DNA replication,...
Published 11/22/20
Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.11.21.392803v1?rss=1 Authors: Brilot, A. F., Lyon, A., Zelter, A., Viswanath, S., Maxwell, A., MacCoss, M. J., Muller, E. G., Sali, A., Davis, T. N., Agard, D. A. Abstract: Microtubule (MT) nucleation is regulated by the {gamma}-tubulin ring complex ({gamma}TuRC), conserved from yeast to humans. In Saccharomyces cerevisiae, {gamma}TuRC is composed of seven identical {gamma}-tubulin small complex ({gamma}TuSC) sub-assemblies...
Published 11/22/20
Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.11.20.390914v1?rss=1 Authors: Chacin, E., Bansal, P., Reusswig, K.-U., Diaz-Santin, L., Ortega, P., Vizjak, P., Gomez-Gonzalez, B., Mueller-Planitz, F., Aguilera, A., Pfander, B., Cheung, A., Kurat, C. Abstract: The replication of chromosomes during S phase is critical for cellular and organismal function. Replicative stress can result in genome instability, which is a major driver of cancer. Yet how chromatin is made...
Published 11/22/20
Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.11.21.392548v1?rss=1 Authors: de Lima, C. K. F., Sisnande, T., da Silva, R. V., da Silva, V. D., do Amaral, J. J., Ochs, S. M., Roedel dos Santos, B. L., Miranda, A. L. P., Lima, L. M. T. d. R. Abstract: Zinc (Zn) is an essential micronutrient involved in a large diversity of cellular metabolism, included in the physiology of nervous system and pain modulation. There is little evidence for the role of Zn nutritional...
Published 11/22/20
Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.11.20.392019v1?rss=1 Authors: Arnling Baath, J., Borch, K., Jensen, K., Brask, J., Westh, P. Abstract: The potential of bioprocessing in a circular plastic economy has strongly stimulated research in enzymatic degradation of different synthetic resins. Particular interest has been devoted to the commonly used polyester, poly(ethylene terephthalate) (PET), and a number of PET hydrolases have been described. However, a kinetic...
Published 11/21/20
Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.11.18.388355v1?rss=1 Authors: Rohden, F., Teixeira, L. V., Bernardi, L. P., Marques, N. P. F., Colombo, M., Teixeira, G. R., de Oliveira, F. d. S., Cirne Lima, E. O., Guma, F. C. R., Souza, D. O. Abstract: Ischemic stroke is a prominent cause of death and disability, demanding innovative therapeutic strategies. Accordingly, extracellular vesicles (EVs) released from mesenchymal stem cells are promising tools for stroke...
Published 11/19/20
Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.11.19.389403v1?rss=1 Authors: Jonathan, H. P., Temponeras, I., Kuiper, J., Cortes, A., Korczynska, J., Kitchen, S., Stratikos, E. Abstract: Objective: Polymorphic variation of immune system proteins can drive variability of individual immune responses. ER aminopeptidase 1 (ERAP1) generates antigenic peptides for presentation by MHC class I molecules. Coding single nucleotide polymorphisms (SNPs) in ERAP1 have been associated...
Published 11/19/20
Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.11.19.389429v1?rss=1 Authors: Lee, E., Kang, C., Purhonen, P., Hebert, H., Bouazoune, K., Hohng, S., Song, J.-J. Abstract: Chromodomain-Helicase DNA binding protein 7 (CHD7) is an ATP dependent chromatin remodeler involved in maintaining open chromatin structure. Mutations of CHD7 gene causes multiple developmental disorders, notably CHARGE syndrome. However, there is not much known about the molecular mechanism by which...
Published 11/19/20
Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.11.18.388868v1?rss=1 Authors: Mehalko, J., Drew, M., Snead, K., Denson, J.-P., Wall, V., Taylor, T., Sadtler, K., Messing, S., Gillette, W., Esposito, D. Abstract: The receptor-binding domain (RBD) of the SARS-CoV-2 spike protein is a commonly used antigen for serology assays critical to determining the extent of SARS-CoV-2 exposure in the population. Different versions of the RBD protein have been developed and utilized in...
Published 11/18/20
Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.11.18.388496v1?rss=1 Authors: Hallin, E. I., Markusson, S., Bottger, L., Torda, A. E., Bramham, C. R., Kursula, P. Abstract: Synaptic plasticity is vital for brain function and memory formation. One of the key proteins in long-term synaptic plasticity and memory is the activity-regulated cytoskeleton-associated protein (Arc). Mammalian Arc forms virus-like capsid-like structures in a process requiring the N-terminal domain...
Published 11/18/20
Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.11.18.389155v1?rss=1 Authors: Guo, S., Vance, T., Zahiri, H., Eves, R., Stevens, C., Hehemann, J.-H., Vidal-Melgosa, S., Davies, P. Abstract: Carbohydrate recognition by lectins governs critical host-microbe interactions. MpPA14 lectin is a domain of a 1.5-MDa adhesin responsible for a symbiotic bacterium-diatom interaction in Antarctica. Here we show MpPA14 binds various monosaccharides, with L-fucose and N-acetyl...
Published 11/18/20
Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.11.17.387910v1?rss=1 Authors: Okumura, M., Kanemura, S., Matsusaki, M., Kinoshita, M., Saio, T., Ito, D., Hirayama, C., Kumeta, H., Watabe, M., Amagai, Y., Lee, Y.-H., Akiyama, S., Inaba, K. Abstract: P5, also known as PDIA6, is a PDI-family member that plays an important role in the ER quality control. Herein, we revealed that P5 dimerizes via a unique adhesive motif contained in the N-terminal thioredoxin-like domain. This...
Published 11/18/20
Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.11.17.387829v1?rss=1 Authors: Huang, X., Kim, D. S., Huang, P., Vater, A. W., Siegel, J. B. Abstract: Computational protein design is growing in popularity as a means to engineer enzymes. Currently, protein design algorithms can predict the stability and function of the enzymes to only a limited degree. Thus, further experimental data is required for training software to more accurately characterize the structure-function...
Published 11/18/20
Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.11.18.388215v1?rss=1 Authors: Vandebroek, L., Noguchi, H., Kamata, K., Tame, J. R. H., Van Meervelt, L., Parac-Vogt, T. N., Voet, A. R. D. Abstract: The controlled formation of protein supramolecular assemblies is challenging but it could provide an important route for the development of hybrid biomaterials. In this work, we demonstrate formation of well-defined complexes formed between the 8-fold symmetrical designer...
Published 11/18/20
Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.11.16.385856v1?rss=1 Authors: Oliveira Bortot, L., Lopes Rangel, V., A. Pavlovici, F., El Omari, K., Wagner, A., Brandao-Neto, J., Talon, R., von Delft, F., G Reidenbach, A., M Vallabh, S., Vallabh Minikel, E., Schreiber, S., Cristina Nonato, M. Abstract: Prion disease is caused by the misfolding of the cellular prion protein, PrPC, into a self-templating conformer, PrPSc. Nuclear magnetic resonance (NMR) and X-ray...
Published 11/17/20
Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.11.17.386979v1?rss=1 Authors: Bantis, L. E., Parente, D. J., Fenton, A. W., Swint-Kruse, L. Abstract: Amino acid variation at "rheostat" positions provides opportunity to modulate various aspects of protein function - such as binding affinity or allosteric coupling - across a wide range. Previously a subclass of "multiplex" rheostat positions was identified at which substitutions simultaneously modulated more than one...
Published 11/17/20
Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.11.17.386177v1?rss=1 Authors: Cuevas-Navarro, A., Van, R., Cheng, A., Urisman, A., Castel, P., McCormick, F. Abstract: The spindle assembly checkpoint (SAC) is an evolutionarily conserved safety mechanism that maintains genomic stability. However, despite the understanding of the fundamental mechanisms that control the SAC, it remains unknown how signaling pathways directly interact with and regulate the mitotic checkpoint...
Published 11/17/20
Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.11.17.387241v1?rss=1 Authors: Alexander, L. E., Gilbertson, J. S., Xie, B., Song, Z., Nikolau, B. J. Abstract: The extensive collection of glossy (gl) and eceriferum (cer) mutants of maize and Arabidopsis have proven invaluable in dissecting the branched metabolic pathways that support cuticular lipid deposition. This branched pathway integrates the fatty acid elongation-decarbonylative branch and the fatty acid...
Published 11/17/20
Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.11.17.387142v1?rss=1 Authors: Zhang, W., Kim, C., Tam, C. P., Lelyveld, V., Bala, S., Chaput, J., Szostak, J. W. Abstract: The prebiotic synthesis of ribonucleotides is likely to have been accompanied by the synthesis of noncanonical nucleotides including the threo-nucleotide building blocks of TNA. Here we examine the ability of activated threo-nucleotides to participate in nonenzymatic template-directed polymerization. We...
Published 11/17/20
Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.11.16.379206v1?rss=1 Authors: Takahashi, M., Seino, R., Ezoe, T., Ishiyama, M., Ueno, Y. Abstract: The plasma membrane (PM) plays a critical role in many cellular processes, and PM dysfunction is a key biomarker related to the cell status and several diseases. Imaging techniques using small fluorescent probes have become increasingly important tools for visualizing living cells, and particularly, their PMs. Among the...
Published 11/17/20
Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.11.16.385187v1?rss=1 Authors: Oganesyan, I., Lento, C., Tandon, A., Wilson, D. J. Abstract: Both normal and pathological functions of -synuclein (SN), an abundant protein in the central and peripheral nervous system, have been linked to its interaction with membrane lipid bilayers. The ability to characterize structural transitions of SN upon membrane complexation will clarify molecular mechanisms associated with SN-linked...
Published 11/17/20
Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.11.16.384339v1?rss=1 Authors: Ngah, Y. E., Cho, F. N., Etagha, B. S., Fusi, N. G., Francisca, N., Ikomey, M. G., Ibrahim, N. Abstract: Introduction The incidence of hepatotoxicity is life-threatening and can result to an end-stage liver disease in long-term patients on combined antiretroviral therapy (cART). Our study sought to evaluate the incidence and predictors of cART-induced hepatotoxicity (CIH) among long term users...
Published 11/16/20
Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.11.16.384594v1?rss=1 Authors: Brun, J., Vasiljevic, S., Gangadharan, B., Hensen, M., Chandran, A. V., Hill, M. L., Kiappes, J. L., Dwek, R. A., Alonzi, D. S., Struwe, W. B., Zitzmann, N. Abstract: Severe acute respiratory syndrome coronavirus 2 is the causative pathogen of the COVID-19 pandemic which as of Nov 15, 2020 has claimed 1,319,946 lives worldwide. Vaccine development focuses on the viral trimeric spike glycoprotein...
Published 11/16/20