Briefings in Functional Genomics最新文献_第9页

Genomic islands and their role in fitness traits of two key sepsis-causing bacterial pathogens. 两种主要败血症致病细菌的基因组岛及其在适应性特征中的作用。

IF 4 3区生物学

Briefings in Functional Genomics Pub Date : 2024-01-18 DOI: 10.1093/bfgp/elac051

Mohd Ilyas, Dyuti Purkait, Krishnamohan Atmakuri

{"title":"Genomic islands and their role in fitness traits of two key sepsis-causing bacterial pathogens.","authors":"Mohd Ilyas, Dyuti Purkait, Krishnamohan Atmakuri","doi":"10.1093/bfgp/elac051","DOIUrl":"10.1093/bfgp/elac051","url":null,"abstract":"To survive and establish a niche for themselves, bacteria constantly evolve. Toward that, they not only insert point mutations and promote illegitimate recombinations within their genomes but also insert pieces of 'foreign' deoxyribonucleic acid, which are commonly referred to as 'genomic islands' (GEIs). The GEIs come in several forms, structures and types, often providing a fitness advantage to the harboring bacterium. In pathogenic bacteria, some GEIs may enhance virulence, thus altering disease burden, morbidity and mortality. Hence, delineating (i) the GEIs framework, (ii) their encoded functions, (iii) the triggers that help them move, (iv) the mechanisms they exploit to move among bacteria and (v) identification of their natural reservoirs will aid in superior tackling of several bacterial diseases, including sepsis. Given the vast array of comparative genomics data, in this short review, we provide an overview of the GEIs, their types and the compositions therein, especially highlighting GEIs harbored by two important pathogens, viz. Acinetobacter baumannii and Klebsiella pneumoniae, which prominently trigger sepsis in low- and middle-income countries. Our efforts help shed some light on the challenges these pathogens pose when equipped with GEIs. We hope that this review will provoke intense research into understanding GEIs, the cues that drive their mobility across bacteria and the ways and means to prevent their transfer, especially across pathogenic bacteria.","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":"10364958","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

Significance of understanding the genomics of host-pathogen interaction in limiting antibiotic resistance development: lessons from COVID-19 pandemic. 了解宿主与病原体相互作用的基因组学对限制抗生素耐药性发展的意义：从 COVID-19 大流行中汲取的教训。

IF 4 3区生物学

Briefings in Functional Genomics Pub Date : 2024-01-18 DOI: 10.1093/bfgp/elad001

Vikas Yadav, Srividhya Ravichandran

引用次数: 0

Role of gut-microbiota in disease severity and clinical outcomes. 肠道微生物群在疾病严重程度和临床结果中的作用。

IF 4 3区生物学

Briefings in Functional Genomics Pub Date : 2024-01-18 DOI: 10.1093/bfgp/elac037

Monika Yadav, Nar Singh Chauhan

引用次数: 0

Integrative genomics important to understand host-pathogen interactions. 整合基因组学对了解宿主与病原体之间的相互作用非常重要。

IF 4 3区生物学

Briefings in Functional Genomics Pub Date : 2024-01-18 DOI: 10.1093/bfgp/elac021

Priyanka Mehta, Aparna Swaminathan, Aanchal Yadav, Partha Chattopadhyay, Uzma Shamim, Rajesh Pandey

{"title":"Integrative genomics important to understand host-pathogen interactions.","authors":"Priyanka Mehta, Aparna Swaminathan, Aanchal Yadav, Partha Chattopadhyay, Uzma Shamim, Rajesh Pandey","doi":"10.1093/bfgp/elac021","DOIUrl":"10.1093/bfgp/elac021","url":null,"abstract":"Infectious diseases are the leading cause of morbidity and mortality worldwide. Causative pathogenic microbes readily mutate their genome and lead to outbreaks, challenging the healthcare and the medical support. Understanding how certain symptoms manifest clinically is integral for therapeutic decisions and vaccination efficacy/protection. Notably, the interaction between infecting pathogens, host response and co-presence of microbes influence the trajectories of disease progression and clinical outcome. The spectrum of observed symptomatic patients (mild, moderate and severe) and the asymptomatic infections highlight the challenges and the potential for understanding the factors driving protection/susceptibility. With the increasing repertoire of high-throughput tools, such as cutting-edge multi-omics profiling and next-generation sequencing, genetic drivers of factors linked to heterogeneous disease presentations can be investigated in tandem. However, such strategies are not without limits in terms of effectively integrating host-pathogen interactions. Nonetheless, an integrative genomics method (for example, RNA sequencing data) for exploring multiple layers of complexity in host-pathogen interactions could be another way to incorporate findings from high-throughput data. We further propose that a Holo-transcriptome-based technique to capture transcriptionally active microbial units can be used to elucidate functional microbiomes. Thus, we provide holistic perspective on investigative methodologies that can harness the same genomic data to investigate multiple seemingly independent but deeply interconnected functional domains of host-pathogen interaction that modulate disease severity and clinical outcomes.","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":"40659724","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

Recent insights into crosstalk between genetic parasites and their host genome. 关于遗传寄生虫与其宿主基因组之间串扰的最新见解。

IF 4 3区生物学

Briefings in Functional Genomics Pub Date : 2024-01-18 DOI: 10.1093/bfgp/elac032

Amit K Mandal

引用次数: 0

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

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