Fly最新文献

{"title":"<i>Drosophila melanogaster</i>: a fruitful model for oncohistones.","authors":"Amel Chaouch,&nbsp;Paul Lasko","doi":"10.1080/19336934.2020.1863124","DOIUrl":"https://doi.org/10.1080/19336934.2020.1863124","url":null,"abstract":"<p><p><i>Drosophila melanogaster</i> has proven to be a powerful genetic model to study human disease. Approximately 75% of human disease-associated genes have homologs in the fruit fly and regulatory pathways are highly conserved in <i>Drosophila</i> compared to humans. <i>Drosophila</i> is an established model organism for the study of genetics and developmental biology related to human disease and has also made a great contribution to epigenetic research. Many key factors that regulate chromatin condensation through effects on histone post-translational modifications were first discovered in genetic screens in <i>Drosophila</i>. Recently, the importance of chromatin regulators in cancer progression has been uncovered, leading to a rapid expansion in the knowledge on how perturbations of chromatin can result in the pathogenesis of human cancer. In this review, we provide examples of how <i>Drosophila melanogaster</i> has contributed to better understanding the detrimental effects of mutant forms of histones, called 'oncohistones', that are found in different human tumours.</p>","PeriodicalId":12128,"journal":{"name":"Fly","volume":null,"pages":null},"PeriodicalIF":1.2,"publicationDate":"2021-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/19336934.2020.1863124","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39138005","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":"Drosophila as a useful model for understanding the evolutionary physiology of obesity resistance and metabolic thrift.","authors":"Lindsey J Gray,&nbsp;Marla B Sokolowski,&nbsp;Stephen J Simpson","doi":"10.1080/19336934.2021.1896960","DOIUrl":"https://doi.org/10.1080/19336934.2021.1896960","url":null,"abstract":"<p><p>Evolved metabolic thriftiness in humans is a proposed contributor to the obesity epidemic. Insect models have been shown to evolve both 'metabolic thrift' in response to rearing on high-protein diets that promote leanness, and 'obesity resistance' when reared on fattening high-carbohydrate, low-protein foods. Despite the hypothesis that human obesity is caused by evolved metabolic thrift, genetic contributions to this physiological trait remain elusive. Here we conducted a pilot study to determine whether thrift and obesity resistance can arise under laboratory based 'quasi-natural selection' in the genetic model organism <i>Drosophila melanogaster</i>. We found that both these traits can evolve within 16 generations. Contrary to predictions from the 'thrifty genotype/phenotype' hypothesis, we found that when animals from a metabolic thrift inducing high-protein environment are mismatched to fattening high-carbohydrate foods, they did not become 'obese'. Rather, they accumulate less triglyceride than control animals, not more. We speculate that this may arise through as yet un-quantified parental effects - potentially epigenetic. This study establishes that <i>D. melanogaster</i> could be a useful model for elucidating the role of the trans- and inter-generational effects of diet on the genetics of metabolic traits in higher animals.</p>","PeriodicalId":12128,"journal":{"name":"Fly","volume":null,"pages":null},"PeriodicalIF":1.2,"publicationDate":"2021-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/19336934.2021.1896960","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25475814","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":"Sperm viability varies with buffer and genotype in <i>Drosophila melanogaster</i>.","authors":"Ruijian Guo,&nbsp;Anna-Lena Henke,&nbsp;Klaus Reinhardt","doi":"10.1080/19336934.2020.1837592","DOIUrl":"https://doi.org/10.1080/19336934.2020.1837592","url":null,"abstract":"<p><p>Sperm quality, an important male fitness trait, is commonly compared between studies. However, few studies consider how genetic and environmental variation affect sperm quality, even in the genetic model <i>Drosophila melanogaster</i>. Here we show that sperm viability, the proportion of live sperm, differed across the genotypes Oregon-R, Dahomey, and Canton-S by more than 15%, and across buffers (phosphate-buffered saline (PBS), Grace's Medium and <i>Drosophila</i> Ringer solution) by more than 20%. In terms of genotype-buffer pair comparisons, nearly half of the comparisons would produce significant differences in sperm viability (15 in 36), or its temporal decrease in a stress medium (19 in 36). Grace's medium produced the longest-lived sperm <i>in vitro</i> and the smallest differences between genotypes, <i>Drosophila</i> Ringer Solution produced the shortest lifespan and the largest differences. Our results suggest that fly and other sperm researchers would benefit from a standardized protocol of measuring sperm viability.</p>","PeriodicalId":12128,"journal":{"name":"Fly","volume":null,"pages":null},"PeriodicalIF":1.2,"publicationDate":"2021-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/19336934.2020.1837592","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38583257","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":"PseudoBase: a genomic visualization and exploration resource for the <i>Drosophila pseudoobscura</i> subgroup.","authors":"Katharine L Korunes, Russell B Myers, Ryan Hardy, Mohamed A F Noor","doi":"10.1080/19336934.2020.1864201","DOIUrl":"10.1080/19336934.2020.1864201","url":null,"abstract":"<p><p><i>Drosophila pseudoobscura</i> is a classic model system for the study of evolutionary genetics and genomics. Given this long-standing interest, many genome sequences have accumulated for <i>D. pseudoobscura</i> and closely related species <i>D. persimilis, D. miranda</i>, and <i>D. lowei</i>. To facilitate the exploration of genetic variation within species and comparative genomics across species, we present PseudoBase, a database that couples extensive publicly available genomic data with simple visualization and query tools via an intuitive graphical interface, amenable for use in both research and educational settings. All genetic variation (SNPs and indels) within the database is derived from the same workflow, so variants are easily comparable across data sets. Features include an embedded JBrowse interface, ability to pull out alignments of individual genes/regions, and batch access for gene lists. Here, we introduce PseudoBase, and we demonstrate how this resource facilitates use of extensive genomic data from flies of the <i>Drosophila pseudoobscura</i> subgroup.</p>","PeriodicalId":12128,"journal":{"name":"Fly","volume":null,"pages":null},"PeriodicalIF":1.2,"publicationDate":"2021-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7808432/pdf/KFLY_15_1864201.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38714228","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":"Dawning of the open era.","authors":"Howy Jacobs","doi":"10.1080/19336934.2021.1943285","DOIUrl":"https://doi.org/10.1080/19336934.2021.1943285","url":null,"abstract":"","PeriodicalId":12128,"journal":{"name":"Fly","volume":null,"pages":null},"PeriodicalIF":1.2,"publicationDate":"2021-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/19336934.2021.1943285","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39161015","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":"<i>Drosophila</i> GFAT1 and GFAT2 enzymes encode obligate developmental functions.","authors":"Po Chen,&nbsp;Sarah Visokay,&nbsp;John M Abrams","doi":"10.1080/19336934.2020.1784674","DOIUrl":"https://doi.org/10.1080/19336934.2020.1784674","url":null,"abstract":"<p><p>Glutamine: fructose-6-phosphate amidotransferase (GFAT) enzymes catalyse the first committed step of the hexosamine biosynthesis pathway (HBP) using glutamine and fructose-6-phosphate to form glucosamine-6-phosphate (GlcN6P). Numerous species (e.g. mouse, rat, zebrafish, chicken) including humans and <i>Drosophila</i> encode two broadly expressed copies of this enzyme but whether these perform redundant, partially overlapping or distinct functions is not known. To address this question, we produced single gene null mutations in the fly counterparts of <i>gfat1</i> and <i>gfat2</i>. Deletions for either enzyme were fully lethal and homozygotes lacking either GFAT1 or GFAT2 died at or prior to the first instar larval stage. Therefore, when genetically eliminated, neither isoform was able to compensate for the other. Importantly, dietary supplementation with D-glucosamine-6-phosphate rescued GFAT2 deficiency and restored viability to <i>gfat2^-/-</i> mutants. In contrast, glucosamine-6-phosphate did not rescue <i>gfat1^-/-</i> animals.</p>","PeriodicalId":12128,"journal":{"name":"Fly","volume":null,"pages":null},"PeriodicalIF":1.2,"publicationDate":"2020-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/19336934.2020.1784674","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38117106","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":"The DNA polymerases of <i>Drosophila melanogaster</i>.","authors":"Steven J Marygold,&nbsp;Helen Attrill,&nbsp;Elena Speretta,&nbsp;Kate Warner,&nbsp;Michele Magrane,&nbsp;Maria Berloco,&nbsp;Sue Cotterill,&nbsp;Mitch McVey,&nbsp;Yikang Rong,&nbsp;Masamitsu Yamaguchi","doi":"10.1080/19336934.2019.1710076","DOIUrl":"https://doi.org/10.1080/19336934.2019.1710076","url":null,"abstract":"<p><p>DNA synthesis during replication or repair is a fundamental cellular process that is catalyzed by a set of evolutionary conserved polymerases. Despite a large body of research, the DNA polymerases of <i>Drosophila melanogaster</i> have not yet been systematically reviewed, leading to inconsistencies in their nomenclature, shortcomings in their functional (Gene Ontology, GO) annotations and an under-appreciation of the extent of their characterization. Here, we describe the complete set of DNA polymerases in <i>D. melanogaster</i>, applying nomenclature already in widespread use in other species, and improving their functional annotation. A total of 19 genes encode the proteins comprising three replicative polymerases (alpha-primase, delta, epsilon), five translesion/repair polymerases (zeta, eta, iota, Rev1, theta) and the mitochondrial polymerase (gamma). We also provide an overview of the biochemical and genetic characterization of these factors in <i>D. melanogaster</i>. This work, together with the incorporation of the improved nomenclature and GO annotation into key biological databases, including FlyBase and UniProtKB, will greatly facilitate access to information about these important proteins.</p>","PeriodicalId":12128,"journal":{"name":"Fly","volume":null,"pages":null},"PeriodicalIF":1.2,"publicationDate":"2020-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/19336934.2019.1710076","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37538629","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":"SUMO conjugation regulates immune signalling.","authors":"Sushmitha Hegde, Amarendranath Soory, Bhagyashree Kaduskar, Girish S Ratnaparkhi","doi":"10.1080/19336934.2020.1808402","DOIUrl":"10.1080/19336934.2020.1808402","url":null,"abstract":"<p><p>Post-translational modifications (PTMs) are critical drivers and attenuators for proteins that regulate immune signalling cascades in host defence. In this review, we explore functional roles for one such PTM, the small ubiquitin-like modifier (SUMO). Very few of the SUMO conjugation targets identified by proteomic studies have been validated in terms of their roles in host defence. Here, we compare and contrast potential SUMO substrate proteins in immune signalling for flies and mammals, with an emphasis on NFκB pathways. We discuss, using the few mechanistic studies that exist for validated targets, the effect of SUMO conjugation on signalling and also explore current molecular models that explain regulation by SUMO. We also discuss in detail roles of evolutionary conservation of mechanisms, SUMO interaction motifs, crosstalk of SUMO with other PTMs, emerging concepts such as group SUMOylation and finally, the potentially transforming roles for genome-editing technologies in studying the effect of PTMs.</p>","PeriodicalId":12128,"journal":{"name":"Fly","volume":null,"pages":null},"PeriodicalIF":1.2,"publicationDate":"2020-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7714519/pdf/KFLY_14_1808402.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38258296","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 pipeline for precise and efficient genome editing by sgRNA-Cas9 RNPs in <i>Drosophila</i>.","authors":"Kevin G Nyberg, Joseph Q Nguyen, Yong-Jae Kwon, Shelby Blythe, Greg J Beitel, Richard Carthew","doi":"10.1080/19336934.2020.1832416","DOIUrl":"10.1080/19336934.2020.1832416","url":null,"abstract":"<p><p>Genome editing via homology-directed repair (HDR) has made possible precise and deliberate modifications to gene sequences. CRISPR/Cas9-mediated HDR is the simplest means to carry this out. However, technical challenges remain to improve efficiency and broaden applicability to any genetic background of <i>Drosophila melanogaster</i> as well as to other <i>Drosophila</i> species. To address these issues, we developed a two-stage marker-assisted strategy in which embryos are injected with RNPs and pre-screened using T7EI. Using sgRNA in complex with recombinant Cas9 protein, we assayed each sgRNA for genome-cutting efficiency. We then conducted HDR using sgRNAs that efficiently cut target genes and the application of a transformation marker that generates RNAi against <i>eyes absent</i>. This allows for screening based on eye morphology rather than colour. These new tools can be used to make a single change or a series of allelic substitutions in a region of interest, or to create additional genetic tools such as balancer chromosomes.</p>","PeriodicalId":12128,"journal":{"name":"Fly","volume":null,"pages":null},"PeriodicalIF":1.2,"publicationDate":"2020-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/19336934.2020.1832416","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9278192","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":"Short is still sweet.","authors":"Howy Jacobs","doi":"10.1080/19336934.2020.1831879","DOIUrl":"https://doi.org/10.1080/19336934.2020.1831879","url":null,"abstract":"Shortly after taking over as Chief Editor of my former journal, EMBO Reports, I penned an editorial outlining the kind of research articles we were seeking as submissions [1]. The message was straightforward: we were looking for manuscripts reporting single key findings of note, which were backed up by multiple lines of evidence. Although EMBO Reports embodied the idea of short-format papers in its very name, I’m trying to bring the same philosophy to Fly. A common fault of many submitted ‘in-brief’ papers is that they present the results of just one experiment, often accompanied by exorbitant claims as to their significance. Reviewers, unconvinced that what was presented is a substantial advance, or even doubting its veracity entirely, then propose other experiments that they themselves dreamed up, which go off on a tangent, even if it’s an interesting tangent. The end result is that the paper becomes an unwieldy composite of two, three, or four disparate experiments, none of them backed up by independent evidence. When authors carry out an experiment demanded by a reviewer, which produces the anticipated result (‘the authors must demonstrate that ....’), the satisfied reviewer is often inclined to disregard the fact that the finding is of small magnitude, statistically questionable, or lacks independent repeats which the journal’s revision timetable made impossible. The published paper therefore ends up full of holes, is fundamentally unreliable, meanders all over the place and is rarely cited because nobody knows what it is really trying to say, even if the data are believable. At the opposite extreme, junior investigators often try to bend the parameters of a manuscript so that it includes every possibly relevant experiment they have ever done. The submitted draft thus resembles a ramble built from scraps demanded by reviewers, but from a much earlier stage. If the reviewers are awake, they will often seek removal of extraneous materials until, finally, little of substance is left, and it risks actually becoming the one-experiment paper that lacks evidentiary rigour; unless the editor is also awake. To me, the perfect short-format paper should have a laser focus on one simply formulated scientific question, that is then tested by different experimental approaches. Beyond that I would not seek to be prescriptive. The various streams of verification could be, for example, a bioinformatic prediction of an interaction, plus a biophysical test in vitro, plus a set of pulldown assays from a cell-line grown under different conditions and, finally, a phenotypic analysis of an in vivo model. Or any of hundreds of other possible combinations. The experiments should not simply be linked by a keyword, but should constitute parallel or sequential experimental tests of the specific hypothesis, where the outcome could be either ‘positive’ or ‘negative’, but should be coherent and statistically sound. Note that negative findings can provide at least as much ","PeriodicalId":12128,"journal":{"name":"Fly","volume":null,"pages":null},"PeriodicalIF":1.2,"publicationDate":"2020-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/19336934.2020.1831879","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38506343","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}