BBA Advances最新文献

{"title":"Water content, transition temperature and fragility influence protection and anhydrobiotic capacity","authors":"John F. Ramirez ,&nbsp;U.G.V.S.S. Kumara ,&nbsp;Navamoney Arulsamy ,&nbsp;Thomas C. Boothby","doi":"10.1016/j.bbadva.2024.100115","DOIUrl":"https://doi.org/10.1016/j.bbadva.2024.100115","url":null,"abstract":"<div><p>Water is essential for metabolism and all life processes. Despite this, many organisms distributed across the kingdoms of life survive near-complete desiccation or anhydrobiosis. Increased intracellular viscosity, leading to the formation of a vitrified state is necessary, but not sufficient, for survival while dry. What properties of a vitrified system make it desiccation-tolerant or -sensitive are unknown. We have analyzed 18 different <em>in vitro</em> vitrified systems, composed of one of three protective disaccharides (trehalose, sucrose, or maltose) and glycerol, quantifying their enzyme-protective capacity and their material properties in a dry state. Protection conferred by mixtures containing maltose correlates strongly with increased water content, increased glass-transition temperature, and reduced glass former fragility, while the protection of glasses formed with sucrose correlates with increased glass transition temperature and the protection conferred by trehalose glasses correlates with reduced glass former fragility. Thus, <em>in vitro</em> different vitrified sugars confer protection through distinct material properties. Next, we examined the material properties of a dry desiccation tolerant and intolerant life stage from three different organisms. The dried desiccation tolerant life stage of all organisms had an increased glass transition temperature and reduced glass former fragility relative to its dried desiccation intolerant life stage. These results suggest in nature organismal desiccation tolerance relies on a combination of various material properties. This study advances our understanding of how protective and non-protective glasses differ in terms of material properties that promote anhydrobiosis. This knowledge presents avenues to develop novel stabilization technologies for pharmaceuticals that currently rely on the cold-chain.</p></div><div><h3>Statement of significance</h3><p>For the past three decades the anhydrobiosis field has lived with a paradox, while vitrification is necessary for survival in the dry state, it is not sufficient. Understanding what property(s) distinguishes a desiccation tolerant from an intolerant vitrified system and how anhydrobiotic organisms survive drying is one of the enduring mysteries of organismal physiology. Here we show <em>in vitro</em> the enzyme-protective capacity of different vitrifying sugars can be correlated with distinct material properties. However, <em>in vivo,</em> diverse desiccation tolerant organisms appear to combine these material properties to promote their survival in a dry state.</p></div>","PeriodicalId":34672,"journal":{"name":"BBA Advances","volume":"5 ","pages":"Article 100115"},"PeriodicalIF":0.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2667160324000036/pdfft?md5=ed2e3390db18c48e022e768fae36c3db&pid=1-s2.0-S2667160324000036-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139652661","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Effect of halo-tolerance gene Hal5 on ethanol tolerance of Saccharomyces cerevisiae","authors":"L. Singh ,&nbsp;J. Rai ,&nbsp;S.C. Sharma","doi":"10.1016/j.bbadva.2024.100123","DOIUrl":"10.1016/j.bbadva.2024.100123","url":null,"abstract":"<div><div>Hal5 gene is involved in halo-tolerance of <em>Saccharomyces cerevisiae</em> during high salt stress. Ethanol stress and high salt stress have similarities, as both decrease the availability of water for cells and strain the osmotic homeostasis across the cell membrane. The Hal5 over-expression strain of yeast has more ethanol tolerance, but the Hal5 null mutant strain also has more ethanol tolerance than the wild-type strain. Hal5 over-expression in this yeast strain may help in adaptation to ethanol stress by way of directly stabilizing the proteins (trk1-trk2) that are responsible for maintaining osmotic homeostasis. Dysfunction of Hal5 in the null mutant may result in increased trehalose, which also stabilizes proteins and increases ethanol tolerance in comparison to wild type, although not as much as over-expression of Hal5. In biochemical assays and FTIR, we observed an increase in trehalose in Hal5 mutant in comparison to the wild-type, as well as a further increase in response to ethanol stress. The ethanol stress increases ROS, protein carbonylation, and lipid peroxidation in all strains, but the Hal5 over-expression and Hal5 null mutation mitigate these adverse effects of ethanol stress.</div></div>","PeriodicalId":34672,"journal":{"name":"BBA Advances","volume":"6 ","pages":"Article 100123"},"PeriodicalIF":0.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142434382","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Helping proteins come in from the cold: 5 burning questions about cold-active enzymes","authors":"Jan Stanislaw Nowak,&nbsp;Daniel E. Otzen","doi":"10.1016/j.bbadva.2023.100104","DOIUrl":"https://doi.org/10.1016/j.bbadva.2023.100104","url":null,"abstract":"<div><p>Enzymes from psychrophilic (cold-loving) organisms have attracted considerable interest over the past decades for their potential in various low-temperature industrial processes. However, we still lack large-scale commercialization of their activities. Here, we review their properties, limitations and potential. Our review is structured around answers to 5 central questions: 1. How do cold-active enzymes achieve high catalytic rates at low temperatures? 2. How is protein flexibility connected to cold-activity? 3. What are the sequence-based and structural determinants for cold-activity? 4. How does the thermodynamic stability of psychrophilic enzymes reflect their cold-active capabilities? 5. How do we effectively identify novel cold-active enzymes, and can we apply them in an industrial context? We conclude that emerging screening technologies combined with big-data handling and analysis make it reasonable to expect a bright future for our understanding and exploitation of cold-active enzymes.</p></div>","PeriodicalId":34672,"journal":{"name":"BBA Advances","volume":"5 ","pages":"Article 100104"},"PeriodicalIF":0.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2667160323000339/pdfft?md5=f27e6c998034f4927c2ff5aab4df7138&pid=1-s2.0-S2667160323000339-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138558725","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Exploiting the full potential of cryo-EM maps","authors":"Thomas Bick ,&nbsp;Paulina M. Dominiak ,&nbsp;Petra Wendler","doi":"10.1016/j.bbadva.2024.100113","DOIUrl":"https://doi.org/10.1016/j.bbadva.2024.100113","url":null,"abstract":"<div><p>The Coulomb potential maps generated by electron microscopy (EM) experiments contain not only information about the position but also about the charge state of the atom. This feature of EM maps allows the identification of specific ions and the protonation state of amino acid side chains in the sample. Here, we summarize qualitative observations of charges in EM maps, discuss the difficulties in interpreting the charge in Coulomb potential maps with respect to distinguishing it from radiation damage, and outline considerations to implement the correct charge in fitting algorithms.</p></div>","PeriodicalId":34672,"journal":{"name":"BBA Advances","volume":"5 ","pages":"Article 100113"},"PeriodicalIF":0.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2667160324000012/pdfft?md5=f261dfc8c5e72a92dd283540a845751f&pid=1-s2.0-S2667160324000012-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139436321","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Should scientists teach: Balancing research and teaching","authors":"Purusharth I Rajyaguru","doi":"10.1016/j.bbadva.2024.100122","DOIUrl":"10.1016/j.bbadva.2024.100122","url":null,"abstract":"<div><div>Every kid starts out as a natural-born scientist, and then we beat it out of them. A few trickle through the system with their wonder and enthusiasm for science intact - Carl Sagan. This statement, made decades ago, still rings true. The teaching philosophy and methodology adopted by teachers around the world, in general, are often blamed for such an outcome. Who better to fix this teaching problem than the scientists themselves? People actively experimenting with different aspects of science are best placed to explain the fundamentals of science to ignite and sustain enthusiasm towards science. Although active scientists (researchers in laboratories) may find it challenging to teach science to school kids regularly, it would be ideally in their domain to teach the bright students they encounter in the classrooms at their university/institute. This brings me to the topic of this essay's discussion about whether scientists should only focus on research or contribute to teaching as well.</div></div>","PeriodicalId":34672,"journal":{"name":"BBA Advances","volume":"6 ","pages":"Article 100122"},"PeriodicalIF":0.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142526234","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Emerging technologies for single-cell glycomics","authors":"Sunada Keisham ,&nbsp;Hiroaki Tateno","doi":"10.1016/j.bbadva.2024.100125","DOIUrl":"10.1016/j.bbadva.2024.100125","url":null,"abstract":"<div><div>Glycans are present on virtually all cellular surfaces and are important regulators of multicellular communications. Advances in single-cell omics technologies have revolutionized life science research by elucidating cellular heterogeneity through integrated multimodal analyses, providing a comprehensive view of cellular functions. However, dissecting the heterogeneity of glycans at the single-cell level has been challenging due to their structural complexity and unamplifiable nature. Recently, we developed a novel technology called single-cell glycan and RNA sequencing (scGR-seq), which converts glycan information into genetic information using DNA-barcoded lectins, amplifies it by PCR, and simultaneously measures the glycome and transcriptome in thousands of single cells on a next-generation sequencer. In this mini-review, we review the recent advances in single-cell glycomics, focusing on our scGR-seq technology.</div></div>","PeriodicalId":34672,"journal":{"name":"BBA Advances","volume":"6 ","pages":"Article 100125"},"PeriodicalIF":0.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142747968","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"4-Phenyl-thiazole-based dual inhibitors of fatty acid amide hydrolase and soluble epoxide hydrolase do not alleviate orofacial inflammatory pain in female rats","authors":"Daniel Carr ,&nbsp;Christopher Chin ,&nbsp;Tiffany Chacon ,&nbsp;Monijeh Khoja Herawi ,&nbsp;Michael Gonzalez ,&nbsp;Ryan West ,&nbsp;Christophe Morisseau ,&nbsp;Bruce D. Hammock ,&nbsp;Stevan Pecic ,&nbsp;Ram Kandasamy","doi":"10.1016/j.bbadva.2024.100119","DOIUrl":"10.1016/j.bbadva.2024.100119","url":null,"abstract":"<div><p>Pain arising from trigeminal systems such as headache is common, debilitating, and current treatments (e.g., sumatriptan) are limited. New treatments that target novel mechanisms of action may be required to innovate both short- and long-term pain therapy. Fatty acid amide hydrolase and soluble epoxide hydrolase are two pain-related enzymes that regulate pain and inflammation via independent pathways. We have previously demonstrated that simultaneous inhibition of these enzymes using a novel dual inhibitor alleviates acute inflammatory pain in the hindpaw and does not depress wheel running in rats. Here, we expanded on these findings and performed structure-activity relationships of our lead compound, the 4-phenyl-thiazole-based dual inhibitor SW-17, to generate 18 analogs and tested them for their inhibition at both enzymes. Conversion of the sulfonamide group to a tertiary amine led to a general decrease in the potency for the sEH enzyme, while this change was well-tolerated at the FAAH enzyme yielding several strong inhibitors. Six selected inhibitors were evaluated in mouse and rat sEH inhibition assays and results showed a species difference, i.e. 4-phenyl-thiazole-based analogs are significantly less or not active in mouse sEH compared to human and rat enzymes. The most potent inhibitor, SW-17, was evaluated in a plasma stability assay in human and rat plasma and showed moderate stability. However, SW-17 did not alleviate orofacial inflammatory pain in female rats compared to the traditional anti-migraine agent sumatriptan. Although modification of 4-phenyl-thiazole-based dual inhibitor SW-17 changes potencies at both FAAH and sEH, these approaches may not produce antinociception against trigeminal pain. Key Words: polypharmacology, formalin, inflammation, enzyme inhibition, structure-activity relationship studies</p></div>","PeriodicalId":34672,"journal":{"name":"BBA Advances","volume":"6 ","pages":"Article 100119"},"PeriodicalIF":0.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2667160324000073/pdfft?md5=6311e0c6c7b55d1415bc388b77c8a3ee&pid=1-s2.0-S2667160324000073-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141979924","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Five questions on the cell-to-cell movement of Orthotospoviruses","authors":"Pratibha Singh ,&nbsp;Rishi Raj ,&nbsp;H.S. Savithri","doi":"10.1016/j.bbadva.2024.100124","DOIUrl":"10.1016/j.bbadva.2024.100124","url":null,"abstract":"<div><div>Plant viruses employ Movement proteins (MP) for their cell to cell spread through plasmodesmata (PD). MP modifies the PD and increases its size exclusion limit (SEL). However, the mechanism by which MPs are targeted to the PD is still unresolved and there is a lack of consensus owing to limited studies on their biochemical and structural characters. The non structural protein m (NSm) functions as the MP in <em>Orthotospoviruses</em>. Tospoviral NSm associate with ER membrane. They also form tubules in protoplasts. Groundnut bud necrosis virus (GBNV), a tospovirus, infects several crop plants throughout India and is economically very important. GBNV NSm associates with the membrane strongly <em>via</em> the C-terminal coiled-coil domain, modifies the membrane and causes vesicle fusion <em>in vitro</em> and remodels the ER network into vesicles <em>in vivo</em>. These vesicles are in contrast to the tubules formed by other related tospovirus in cells lacking cell wall. In this review, five important questions on the cell-to-cell movement of tospoviruses have been addressed and based on the various reports, a plausible model on the cell-to-cell movement of Orthotospoviruses is presented.</div></div>","PeriodicalId":34672,"journal":{"name":"BBA Advances","volume":"6 ","pages":"Article 100124"},"PeriodicalIF":0.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142526115","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Five questions on improving diversity, equity and inclusion in UK bioscience research or “How can UK bioscience be changed so that those from marginalised groups can thrive?”","authors":"Anna L Cox ,&nbsp;Sara E Mole","doi":"10.1016/j.bbadva.2024.100114","DOIUrl":"10.1016/j.bbadva.2024.100114","url":null,"abstract":"<div><p>Diversity, equity, and inclusion play pivotal roles in advancing science and innovation by fostering a rich and supportive environment that benefits both individuals and society. UK bioscience research units are still on a journey towards being inclusive, and existing research on effecting changes in diversity, equity, and inclusion has yet to make an impact at the scale needed to transform the sector, leaving many to wonder <em>How can UK bioscience be changed so that those from marginalised groups can thrive?</em> This paper considers some of the questions that arise in addressing this, discusses what we already know and what we do not, and in doing so outlines a research agenda that aims to find out what works to effect diversity, equity and inclusion in UK bioscience.</p></div>","PeriodicalId":34672,"journal":{"name":"BBA Advances","volume":"5 ","pages":"Article 100114"},"PeriodicalIF":0.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2667160324000024/pdfft?md5=701687b2bfff001344d301629181344f&pid=1-s2.0-S2667160324000024-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139537790","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"N-glycosylation in Archaea – Expanding the process, components and roles of a universal post-translational modification","authors":"Zlata Vershinin,&nbsp;Marianna Zaretsky,&nbsp;Jerry Eichler","doi":"10.1016/j.bbadva.2024.100120","DOIUrl":"10.1016/j.bbadva.2024.100120","url":null,"abstract":"<div><p>While performed by all three domains of life, N-glycosylation in Archaea is less well described than are the parallel eukaryal and bacterial processes. Still, what is known of the archaeal version of this universal post-translational modification reveals numerous seemingly domain-specific traits. Specifically, the biosynthesis of archaeal N-linked glycans relies on distinct pathway steps and components, rare sugars and sugar modifications, as well as unique lipid carriers upon which N-linked glycans are assembled. At the same time, Archaea possess the apparently unique ability to simultaneously modify their glycoproteins with very different N-linked glycans. In addition to these biochemical aspects of archaeal N-glycosylation, such post-translational modification has been found to serve a wide range of roles possibly unique to Archaea, including allowing these microorganisms to not only cope with the harsh physical conditions of the niches they can inhabit but also providing the ability to adapt to transient changes in such environments.</p></div>","PeriodicalId":34672,"journal":{"name":"BBA Advances","volume":"6 ","pages":"Article 100120"},"PeriodicalIF":0.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2667160324000085/pdfft?md5=896bbdf1d425c728d4c5f08576262f7f&pid=1-s2.0-S2667160324000085-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142137229","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}