FEBS Open Bio最新文献

{"title":"Corrigendum to: Fibulin-4 as a potential extracellular vesicle marker of fibrosis in patients with cirrhosis https://doi.org/10.1002/2211-5463.13842","authors":"","doi":"10.1002/2211-5463.13885","DOIUrl":"10.1002/2211-5463.13885","url":null,"abstract":"<p>The author affiliations of the paper by Terai <i>et al</i>. [1] contains a typographical error:</p><p>2. Future Medical Research Center for Exosome and Designer Cells (F-DEC), Niigata University Japan</p><p>The correct affiliation acronym is shown below:</p><p>2. Future Medical Research Center for Exosome and Designer Cells (F-EDC), Niigata University Japan</p>","PeriodicalId":12187,"journal":{"name":"FEBS Open Bio","volume":"14 11","pages":"1927"},"PeriodicalIF":2.8,"publicationDate":"2024-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/2211-5463.13885","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142035562","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Corrigendum to: Identification and expression analysis of LEA gene family members in pepper (Capsicum annuum L.) https://doi.org/10.1002/2211-5463.13718","authors":"","doi":"10.1002/2211-5463.13875","DOIUrl":"10.1002/2211-5463.13875","url":null,"abstract":"<p>The Acknowledgements section of the paper by Zhao <i>et al</i>. [1] was incorrect. The correct Acknowledgements section is provided here.</p>","PeriodicalId":12187,"journal":{"name":"FEBS Open Bio","volume":"14 11","pages":"1926"},"PeriodicalIF":2.8,"publicationDate":"2024-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/2211-5463.13875","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142035563","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Development of nanobodies against the coat protein of maize chlorotic mottle virus","authors":"Faith Njeru,&nbsp;Olivier Zwaenepoel,&nbsp;Geert Haesaert,&nbsp;Gerald Misinzo,&nbsp;Kris De Jonghe,&nbsp;Jan Gettemans","doi":"10.1002/2211-5463.13882","DOIUrl":"10.1002/2211-5463.13882","url":null,"abstract":"<p>Maize lethal necrosis (MLN) is a maize disease caused by the maize chlorotic mottle virus (MCMV), a potyvirus which causes yield losses of 30–100%. The present study aimed to isolate nanobodies against the MCMV coat protein (CP) for the diagnosis of MLN. MCMV CP expressed in <i>Escherichia coli</i> was used for llama immunization. VHH (i.e. variable heavy domain of heavy chain) gene fragments were prepared from blood drawn from the immunized llama and used to generate a library in <i>E. coli</i> TG1 cells. MCMV specific nanobodies were selected by three rounds of phage display and panning against MCMV CP. The selected nanobodies were finally expressed in <i>E. coli</i> WK6 cells and purified. Eleven MCMV-specific nanobodies were identified and shown to detect MCMV in infected maize plants. Thus, our results show that nanobodies isolated from llama immunized with MCMV CP can distinguish infected and healthy maize plants, potentially enabling development of affordable MCMV detection protocols.</p>","PeriodicalId":12187,"journal":{"name":"FEBS Open Bio","volume":"14 10","pages":"1746-1757"},"PeriodicalIF":2.8,"publicationDate":"2024-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11452299/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142016826","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"An image processing pipeline for electron cryo-tomography in RELION-5","authors":"Alister Burt,&nbsp;Bogdan Toader,&nbsp;Rangana Warshamanage,&nbsp;Andriko von Kügelgen,&nbsp;Euan Pyle,&nbsp;Jasenko Zivanov,&nbsp;Dari Kimanius,&nbsp;Tanmay A. M. Bharat,&nbsp;Sjors H. W. Scheres","doi":"10.1002/2211-5463.13873","DOIUrl":"10.1002/2211-5463.13873","url":null,"abstract":"<p>Electron tomography of frozen, hydrated samples allows structure determination of macromolecular complexes that are embedded in complex environments. Provided that the target complexes may be localised in noisy, three-dimensional tomographic reconstructions, averaging images of multiple instances of these molecules can lead to structures with sufficient resolution for <i>de novo</i> atomic modelling. Although many research groups have contributed image processing tools for these tasks, a lack of standardisation and interoperability represents a barrier for newcomers to the field. Here, we present an image processing pipeline for electron tomography data in RELION-5, with functionality ranging from the import of unprocessed movies to the automated building of atomic models in the final maps. Our explicit definition of metadata items that describe the steps of our pipeline has been designed for interoperability with other software tools and provides a framework for further standardisation.</p>","PeriodicalId":12187,"journal":{"name":"FEBS Open Bio","volume":"14 11","pages":"1788-1804"},"PeriodicalIF":2.8,"publicationDate":"2024-08-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/2211-5463.13873","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141987749","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Cytotoxicity by endocrine disruptors through effects on ER Ca2+ transporters, aberrations in Ca2+ signalling pathways and ER stress","authors":"Francesco Michelangeli,&nbsp;Noor A. Mohammed,&nbsp;Brogan Jones,&nbsp;Monsurat Tairu,&nbsp;Fawaz Al-Mousa","doi":"10.1002/2211-5463.13880","DOIUrl":"10.1002/2211-5463.13880","url":null,"abstract":"<p>Concerns regarding man-made organic chemicals pervading our ecosystem and having adverse and detrimental effects upon organisms, including man, have now been studied for several decades. Since the 1970s, some environmental pollutants were identified as having endocrine disrupting affects. These endocrine disrupting chemicals (EDC) were initially shown to have estrogenic or anti-estrogenic properties and some were also shown to bind to a variety of hormone receptors. However, since the 1990s it has also been identified that many of these EDC additionally, have the ability of causing abnormal alterations in Ca²⁺ signalling pathways (also commonly involved in hormone signalling), leading to exaggerated elevations in cytosolic [Ca²⁺] levels, that is known to cause activation of a number of cell death pathways. The major emphasis of this review is to present a personal perspective of the evidence for some types of EDC, specifically alkylphenols and brominated flame retardants (BFRs), causing direct effects on Ca²⁺ transporters (mainly the SERCA Ca²⁺ ATPases), culminating in acute cytotoxicity and cell death. Evidence is also presented to indicate that this Ca²⁺ATPase inhibition, which leads to abnormally elevated cytosolic [Ca²⁺], as well as a decreased luminal ER [Ca²⁺], which triggers the ER stress response, are both involved in acute cytotoxicity.</p>","PeriodicalId":12187,"journal":{"name":"FEBS Open Bio","volume":"14 9","pages":"1384-1396"},"PeriodicalIF":2.8,"publicationDate":"2024-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/2211-5463.13880","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141975453","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Crystal structure of pectocin M1 reveals diverse conformations and interactions during its initial step via the ferredoxin uptake system","authors":"Nawee Jantarit,&nbsp;Hideaki Tanaka,&nbsp;Yuxi Lin,&nbsp;Young-Ho Lee,&nbsp;Genji Kurisu","doi":"10.1002/2211-5463.13874","DOIUrl":"10.1002/2211-5463.13874","url":null,"abstract":"<p>Pectocin M1 (PM1), the bacteriocin from phytopathogenic <i>Pectobacterium carotovorum</i> which causes soft rot disease, has a unique ferredoxin domain that allows it to use FusA of the plant ferredoxin uptake system. To probe the structure-based mechanism of PM1 uptake, we determined the X-ray structure of full-length PM1, containing an N-terminal ferredoxin and C-terminal catalytic domain connected by helical linker, at 2.04 Å resolution. Based on published FusA structure and NMR data for PM1 ferredoxin domain titrated with FusA, we modeled docking of the ferredoxin domain with FusA. Combining the docking models with the X-ray structures of PM1 and FusA enables us to propose the mechanism by which PM1 undergoes dynamic domain rearrangement to translocate across the target cell outer membrane.</p>","PeriodicalId":12187,"journal":{"name":"FEBS Open Bio","volume":"14 10","pages":"1731-1745"},"PeriodicalIF":2.8,"publicationDate":"2024-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11452297/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141912315","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Periplasmic binding proteins Bug69 and Bug27 from Bordetella pertussis are in vitro high-affinity quinolinate binders with a potential role in NAD biosynthesis","authors":"Leonardo Sorci,&nbsp;Gabriele Minazzato,&nbsp;Adolfo Amici,&nbsp;Francesca Mazzola,&nbsp;Nadia Raffaelli","doi":"10.1002/2211-5463.13876","DOIUrl":"10.1002/2211-5463.13876","url":null,"abstract":"<p><i>Bordetella</i>'s genome contains a large family of periplasmic binding proteins (PBPs) known as Bugs, whose functions are mainly unassigned. Two members, Bug27 and Bug69, have previously been considered potential candidates for the uptake of small pyridine precursors, possibly linked to NAD biosynthesis. Here, we show an <i>in vitro</i> affinity of Bug27 and Bug69 for quinolinate in the submicromolar range, with a marked preference over other NAD precursors. A combined sequence similarity network and genome context analysis identifies a cluster of Bug69/27 homologs that are genomically associated with the NAD transcriptional regulator NadQ and the enzyme quinolinate phosphoribosyltransferase (QaPRT, gene <i>nadC</i>), suggesting a functional linkage to NAD metabolism. Integrating molecular docking and structure-based multiple alignments confirms that quinolinate is the preferred ligand for Bug27 and Bug69.</p>","PeriodicalId":12187,"journal":{"name":"FEBS Open Bio","volume":"14 10","pages":"1718-1730"},"PeriodicalIF":2.8,"publicationDate":"2024-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11452294/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141906367","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Complete pipeline for Oxford Nanopore Technology amplicon sequencing (ONT-AmpSeq): from pre-processing to creating an operational taxonomic unit table","authors":"Patrick Skov Schacksen,&nbsp;Stine Karstenskov Østergaard,&nbsp;Mathias Helmer Eskildsen,&nbsp;Jeppe Lund Nielsen","doi":"10.1002/2211-5463.13868","DOIUrl":"10.1002/2211-5463.13868","url":null,"abstract":"<p>Amplicon sequencing has long served as a robust method for characterising microbial communities, and despite inherent resolution limitations, it remains a preferred technique, offering cost- and time-effective insights into bacterial compositions. Here, we introduce ONT-AmpSeq, a user-friendly pipeline designed for processing amplicon sequencing data generated from Oxford Nanopore Technology (ONT) devices. Our pipeline enables efficient creation of taxonomically annotated operational taxonomic unit (OTU) tables from ONT sequencing data, with the flexibility to multiplex amplicons on the same barcode. The pipeline encompasses six main steps—statistics, quality filtering, alignment, clustering, polishing, and taxonomic classification—integrating various state-of-the-art software tools. We provide a detailed description of each step, along with performance tests and robustness evaluations using both test data and a ZymoBIOMICS^® Microbial Community Standard mock community dataset. Our results demonstrate the ability of ONT-AmpSeq to effectively process ONT amplicon data, offering valuable insights into microbial community composition. Additionally, we discuss the influence of polishing tools on taxonomic insight and the impact of taxonomic annotation methods on the derived microbial composition. Overall, ONT-AmpSeq represents a comprehensive solution for analysing ONT amplicon sequencing data, facilitating streamlined and reliable microbial community analysis. The pipeline, along with test data, is freely available for public use.</p>","PeriodicalId":12187,"journal":{"name":"FEBS Open Bio","volume":"14 11","pages":"1779-1787"},"PeriodicalIF":2.8,"publicationDate":"2024-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/2211-5463.13868","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141897178","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Characterization of the gastrointestinal microbiome of the Syrian hamster (Mesocricetus auratus) and comparison to data from mice","authors":"Linda F. Böswald,&nbsp;Bastian Popper,&nbsp;Dana Matzek,&nbsp;Klaus Neuhaus,&nbsp;Jasmin Wenderlein","doi":"10.1002/2211-5463.13869","DOIUrl":"10.1002/2211-5463.13869","url":null,"abstract":"<p>Syrian hamsters (<i>Mesocricetus auratus</i>) have been increasingly used as rodent models in recent years, especially for SARS-CoV-2 since the pandemic. However, the physiology of this animal model is not yet well-understood, even less when considering the digestive tract. Generally, the gastrointestinal microbiome influences the immune system, drug metabolism, and vaccination efficacy. However, a detailed understanding of the gastrointestinal microbiome of hamsters is missing. Therefore, we analyzed 10 healthy 11-week-old RjHan:AURA hamsters fed a pelleted standard diet. Their gastrointestinal content was sampled (i.e., forestomach, glandular stomach, ileum, cecum, and colon) and analyzed using 16S rRNA gene amplicon sequencing. Results displayed a distinct difference in the bacterial community before and after the cecum, possibly due to the available nutrients and digestive functions. Next, we compared hamsters with the literature data of young-adult C57BL/6J mice, another important animal model. We sampled the same gastrointestinal regions and analyzed the differences in the microbiome between both rodents. Surprisingly, we found strong differences in their specific gastrointestinal bacterial communities. For instance, <i>Lactobacillaceae</i> were more abundant in hamsters' forestomach and ileum, while <i>Muribaculaceae</i> dominated in the mouse forestomach and ileum. Similarly, in mouse cecum and colon, <i>Muribaculaceae</i> were dominant, while in hamsters, <i>Lachnospiraceae</i> and <i>Erysipelotrichaceae</i> dominated the bacterial community. Molecular strains of <i>Muribaculaceae</i> in both rodent species displayed some species specificity. This comparison allows a better understanding of the suitability of the Syrian hamster as an animal model, especially regarding its comparability to other rodent models. Thereby, this work contributes to the characterization of the hamster model and allows better experimental planning.</p>","PeriodicalId":12187,"journal":{"name":"FEBS Open Bio","volume":"14 10","pages":"1701-1717"},"PeriodicalIF":2.8,"publicationDate":"2024-08-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11452302/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141888894","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A framework for decolonising and diversifying biomedical sciences curricula: rediscovery, representation and readiness","authors":"Tianqi Lu,&nbsp;Zafar I. Bashir,&nbsp;Alessia Dalceggio,&nbsp;Caroline M. McKinnon,&nbsp;Lydia Miles,&nbsp;Amy Mosley,&nbsp;Bronwen R. Burton,&nbsp;Alice Robson","doi":"10.1002/2211-5463.13867","DOIUrl":"10.1002/2211-5463.13867","url":null,"abstract":"<p>To date, most efforts to decolonise curricula have focussed on the arts and humanities, with many believing that science subjects are objective, unbiased, and unaffected by colonial legacies. However, science is shaped by both contemporary and historical culture. Science has been used to support imperialism, to extract and exploit knowledge and natural resources, and to justify racist and ableist ideologies. Colonial legacies continue to affect scientific knowledge generation and shape contemporary research priorities. In the biomedical sciences, research biases can feed into wider health inequalities. Reflection of these biases in our taught curricula risks perpetuating long-standing inequities to future generations of scientists. We examined attitudes and understanding towards decolonising and diversifying the curriculum among students and teaching staff in the biomedical sciences at the University of Bristol, UK, to discover whether our current teaching practice is perceived as inclusive. We used a mixed methods study including surveys of staff (<i>N</i> = 71) and students (<i>N</i> = 121) and focus groups. Quantitative data showed that staff and students think decolonising the curriculum is important, but this is more important to female respondents (<i>P</i> &lt; 0.001). Students are less aware than staff of current efforts to decolonise the curriculum, while students from minority ethnic groups feel less represented by the curriculum than white students. Thematic analysis of qualitative data revealed three themes that are important for a decolonised curriculum in our context: rediscovery, representation and readiness. We propose that this ‘3Rs framework’ could guide future efforts to decolonise and diversify the curriculum in the biomedical sciences and beyond.</p>","PeriodicalId":12187,"journal":{"name":"FEBS Open Bio","volume":"14 11","pages":"1762-1778"},"PeriodicalIF":2.8,"publicationDate":"2024-08-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/2211-5463.13867","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141878616","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}