Briefings in Functional Genomics最新文献_第8页

Respiratory tract infection: an unfamiliar risk factor in high-altitude pulmonary edema. 呼吸道感染：高海拔肺水肿的一个陌生风险因素。

IF 4 3区生物学

Briefings in Functional Genomics Pub Date : 2024-01-18 DOI: 10.1093/bfgp/elac048

Raushni Choudhary, Swati Kumari, Manzoor Ali, Tashi Thinlas, Stanzen Rabyang, Aastha Mishra

{"title":"Respiratory tract infection: an unfamiliar risk factor in high-altitude pulmonary edema.","authors":"Raushni Choudhary, Swati Kumari, Manzoor Ali, Tashi Thinlas, Stanzen Rabyang, Aastha Mishra","doi":"10.1093/bfgp/elac048","DOIUrl":"10.1093/bfgp/elac048","url":null,"abstract":"The dramatic changes in physiology at high altitude (HA) as a result of the characteristic hypobaric hypoxia condition can modify innate and adaptive defense mechanisms of the body. As a consequence, few sojourners visiting HA with mild or asymptomatic infection may have an enhanced susceptibility to high-altitude pulmonary edema (HAPE), an acute but severe altitude sickness. It develops upon rapid ascent to altitudes above 2500 m, in otherwise healthy individuals. Though HAPE has been studied extensively, an elaborate exploration of the HA disease burden and the potential risk factors associated with its manifestation are poorly described. The present review discusses respiratory tract infection (RTI) as an unfamiliar but important risk factor in enhancing HAPE susceptibility in sojourners for two primary reasons. First, the symptoms of RTI s resemble those of HAPE. Secondly, the imbalanced pathways contributing to vascular dysfunction in HAPE also participate in the pathogenesis of the infectious processes. These pathways have a crucial role in shaping host response against viral and bacterial infections and may further worsen the clinical outcomes at HA. Respiratory tract pathogenic agents, if screened in HAPE patients, can help in ascertaining their role in disease risk and also point toward their association with the disease severity. The microbial screenings and identifications of pathogens with diseases are the foundation for describing potential molecular mechanisms underlying host response to the microbial challenge. The prior knowledge of such infections may predict the manifestation of disease etiology and provide better therapeutic options.","PeriodicalId":55323,"journal":{"name":"Briefings in Functional Genomics","volume":null,"pages":null},"PeriodicalIF":4.0,"publicationDate":"2024-01-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10364149","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Experimental and computational methods for studying the dynamics of RNA-RNA interactions in SARS-COV2 genomes. 研究 SARS-COV2 基因组中 RNA-RNA 相互作用动态的实验和计算方法。

IF 4 3区生物学

Briefings in Functional Genomics Pub Date : 2024-01-18 DOI: 10.1093/bfgp/elac050

Mansi Srivastava, Matthew R Dukeshire, Quoseena Mir, Okiemute Beatrice Omoru, Amirhossein Manzourolajdad, Sarath Chandra Janga

{"title":"Experimental and computational methods for studying the dynamics of RNA-RNA interactions in SARS-COV2 genomes.","authors":"Mansi Srivastava, Matthew R Dukeshire, Quoseena Mir, Okiemute Beatrice Omoru, Amirhossein Manzourolajdad, Sarath Chandra Janga","doi":"10.1093/bfgp/elac050","DOIUrl":"10.1093/bfgp/elac050","url":null,"abstract":"Long-range ribonucleic acid (RNA)-RNA interactions (RRI) are prevalent in positive-strand RNA viruses, including Beta-coronaviruses, and these take part in regulatory roles, including the regulation of sub-genomic RNA production rates. Crosslinking of interacting RNAs and short read-based deep sequencing of resulting RNA-RNA hybrids have shown that these long-range structures exist in severe acute respiratory syndrome coronavirus (SARS-CoV)-2 on both genomic and sub-genomic levels and in dynamic topologies. Furthermore, co-evolution of coronaviruses with their hosts is navigated by genetic variations made possible by its large genome, high recombination frequency and a high mutation rate. SARS-CoV-2's mutations are known to occur spontaneously during replication, and thousands of aggregate mutations have been reported since the emergence of the virus. Although many long-range RRIs have been experimentally identified using high-throughput methods for the wild-type SARS-CoV-2 strain, evolutionary trajectory of these RRIs across variants, impact of mutations on RRIs and interaction of SARS-CoV-2 RNAs with the host have been largely open questions in the field. In this review, we summarize recent computational tools and experimental methods that have been enabling the mapping of RRIs in viral genomes, with a specific focus on SARS-CoV-2. We also present available informatics resources to navigate the RRI maps and shed light on the impact of mutations on the RRI space in viral genomes. Investigating the evolution of long-range RNA interactions and that of virus-host interactions can contribute to the understanding of new and emerging variants as well as aid in developing improved RNA therapeutics critical for combating future outbreaks.","PeriodicalId":55323,"journal":{"name":"Briefings in Functional Genomics","volume":null,"pages":null},"PeriodicalIF":4.0,"publicationDate":"2024-01-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10799312/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10666297","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Multi-omics studies in interpreting the evolving standard model for immune functions. 解释不断演变的免疫功能标准模型的多组学研究。

IF 4 3区生物学

Briefings in Functional Genomics Pub Date : 2024-01-18 DOI: 10.1093/bfgp/elad003

Dipyaman Ganguly

{"title":"Multi-omics studies in interpreting the evolving standard model for immune functions.","authors":"Dipyaman Ganguly","doi":"10.1093/bfgp/elad003","DOIUrl":"10.1093/bfgp/elad003","url":null,"abstract":"A standard model that is able to generalize data on myriad involvement of the immune system in organismal physio-pathology and to provide a unified evolutionary teleology for immune functions in multicellular organisms remains elusive. A number of such 'general theories of immunity' have been proposed based on contemporaneously available data, starting with the usual description of self-nonself discrimination, followed by the 'danger model' and the more recent 'discontinuity theory.' More recent data deluge on involvement of immune mechanisms in a wide variety of clinical contexts, a number of which fail to get readily accommodated into the available teleologic standard models, makes deriving a standard model of immunity more challenging. But technological advances enabling multi-omics investigations into an ongoing immune response, covering genome, epigenome, coding and regulatory transcriptome, proteome, metabolome and tissue-resident microbiome, bring newer opportunities for developing a more integrative insight into immunocellular mechanisms within different clinical contexts. The new ability to map the heterogeneity of composition, trajectory and endpoints of immune responses, in both health and disease, also necessitates incorporation into the potential standard model of immune functions, which again can only be achieved through multi-omics probing of immune responses and integrated analyses of the multi-dimensional data.","PeriodicalId":55323,"journal":{"name":"Briefings in Functional Genomics","volume":null,"pages":null},"PeriodicalIF":4.0,"publicationDate":"2024-01-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9088073","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Systematic analysis of the transcriptional landscape of melanoma reveals drug-target expression plasticity. 对黑色素瘤转录景观的系统分析揭示了药物靶点表达的可塑性。

IF 4 3区生物学

Briefings in Functional Genomics Pub Date : 2024-01-05 DOI: 10.1093/bfgp/elad055

Brad Balderson, Mitchell Fane, Tracey J Harvey, Michael Piper, Aaron Smith, Mikael Bodén

{"title":"Systematic analysis of the transcriptional landscape of melanoma reveals drug-target expression plasticity.","authors":"Brad Balderson, Mitchell Fane, Tracey J Harvey, Michael Piper, Aaron Smith, Mikael Bodén","doi":"10.1093/bfgp/elad055","DOIUrl":"10.1093/bfgp/elad055","url":null,"abstract":"Metastatic melanoma originates from melanocytes of the skin. Melanoma metastasis results in poor treatment prognosis for patients and is associated with epigenetic and transcriptional changes that reflect the developmental program of melanocyte differentiation from neural crest stem cells. Several studies have explored melanoma transcriptional heterogeneity using microarray, bulk and single-cell RNA-sequencing technologies to derive data-driven models of the transcriptional-state change which occurs during melanoma progression. No study has systematically examined how different models of melanoma progression derived from different data types, technologies and biological conditions compare. Here, we perform a cross-sectional study to identify averaging effects of bulk-based studies that mask and distort apparent melanoma transcriptional heterogeneity; we describe new transcriptionally distinct melanoma cell states, identify differential co-expression of genes between studies and examine the effects of predicted drug susceptibilities of different cell states between studies. Importantly, we observe considerable variability in drug-target gene expression between studies, indicating potential transcriptional plasticity of melanoma to down-regulate these drug targets and thereby circumvent treatment. Overall, observed differences in gene co-expression and predicted drug susceptibility between studies suggest bulk-based transcriptional measurements do not reliably gauge heterogeneity and that melanoma transcriptional plasticity is greater than described when studies are considered in isolation.","PeriodicalId":55323,"journal":{"name":"Briefings in Functional Genomics","volume":null,"pages":null},"PeriodicalIF":4.0,"publicationDate":"2024-01-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139106948","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Computational drug repurposing for viral infectious diseases: a case study on monkeypox. 病毒性传染病的计算药物再利用：猴痘案例研究。

IF 4 3区生物学

Briefings in Functional Genomics Pub Date : 2024-01-05 DOI: 10.1093/bfgp/elad058

Sovan Saha, Piyali Chatterjee, Mita Nasipuri, Subhadip Basu, Tapabrata Chakraborti

引用次数: 0

Cell type and gene regulatory network approaches in the evolution of spiralian biomineralisation. 螺旋动物生物矿化进化中的细胞类型和基因调控网络方法。

IF 4 3区生物学

Briefings in Functional Genomics Pub Date : 2023-11-17 DOI: 10.1093/bfgp/elad033

Victoria A Sleight

引用次数: 0

High-level RNA editing diversifies the coleoid cephalopod brain proteome. 高水平的RNA编辑使coleoid头足类动物脑蛋白质组多样化

IF 4 3区生物学

Briefings in Functional Genomics Pub Date : 2023-11-17 DOI: 10.1093/bfgp/elad034

Gjendine Voss, Joshua J C Rosenthal

{"title":"High-level RNA editing diversifies the coleoid cephalopod brain proteome.","authors":"Gjendine Voss, Joshua J C Rosenthal","doi":"10.1093/bfgp/elad034","DOIUrl":"10.1093/bfgp/elad034","url":null,"abstract":"Coleoid cephalopods (octopus, squid and cuttlefish) have unusually complex nervous systems. The coleoid nervous system is also the only one currently known to recode the majority of expressed proteins through A-to-I RNA editing. The deamination of adenosine by adenosine deaminase acting on RNA (ADAR) enzymes produces inosine, which is interpreted as guanosine during translation. If this occurs in an open reading frame, which is the case for tens of thousands of editing sites in coleoids, it can recode the encoded protein. Here, we describe recent findings aimed at deciphering the mechanisms underlying high-level recoding and its adaptive potential. We describe the complement of ADAR enzymes in cephalopods, including a recently discovered novel domain in sqADAR1. We further summarize current evidence supporting an adaptive role of high-level RNA recoding in coleoids, and review recent studies showing that a large proportion of recoding sites is temperature-sensitive. Despite these new findings, the mechanisms governing the high level of RNA recoding in coleoid cephalopods remain poorly understood. Recent advances using genome editing in squid may provide useful tools to further study A-to-I RNA editing in these animals.","PeriodicalId":55323,"journal":{"name":"Briefings in Functional Genomics","volume":null,"pages":null},"PeriodicalIF":4.0,"publicationDate":"2023-11-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43557580","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Functional genomics in Spiralia. 螺旋藻的功能基因组学研究

IF 4 3区生物学

Briefings in Functional Genomics Pub Date : 2023-11-17 DOI: 10.1093/bfgp/elad036

Francisco M Martín-Zamora, Billie E Davies, Rory D Donnellan, Kero Guynes, José M Martín-Durán

{"title":"Functional genomics in Spiralia.","authors":"Francisco M Martín-Zamora, Billie E Davies, Rory D Donnellan, Kero Guynes, José M Martín-Durán","doi":"10.1093/bfgp/elad036","DOIUrl":"10.1093/bfgp/elad036","url":null,"abstract":"Our understanding of the mechanisms that modulate gene expression in animals is strongly biased by studying a handful of model species that mainly belong to three groups: Insecta, Nematoda and Vertebrata. However, over half of the animal phyla belong to Spiralia, a morphologically and ecologically diverse animal clade with many species of economic and biomedical importance. Therefore, investigating genome regulation in this group is central to uncovering ancestral and derived features in genome functioning in animals, which can also be of significant societal impact. Here, we focus on five aspects of gene expression regulation to review our current knowledge of functional genomics in Spiralia. Although some fields, such as single-cell transcriptomics, are becoming more common, the study of chromatin accessibility, DNA methylation, histone post-translational modifications and genome architecture are still in their infancy. Recent efforts to generate chromosome-scale reference genome assemblies for greater species diversity and optimise state-of-the-art approaches for emerging spiralian research systems will address the existing knowledge gaps in functional genomics in this animal group.","PeriodicalId":55323,"journal":{"name":"Briefings in Functional Genomics","volume":null,"pages":null},"PeriodicalIF":4.0,"publicationDate":"2023-11-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10658182/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41607119","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Spiralian genomics and the evolution of animal genome architecture. 螺旋体基因组学和动物基因组结构的进化。

IF 4 3区生物学

Briefings in Functional Genomics Pub Date : 2023-11-17 DOI: 10.1093/bfgp/elad029

Isabel Jiah-Yih Liao, Tsai-Ming Lu, Mu-En Chen, Yi-Jyun Luo

引用次数: 0

Emerging questions on the mechanisms and dynamics of 3D genome evolution in spiralians. 螺旋体三维基因组进化机制和动力学的新问题。

IF 4 3区生物学

Briefings in Functional Genomics Pub Date : 2023-11-17 DOI: 10.1093/bfgp/elad043

Thea F Rogers, Oleg Simakov

引用次数: 0