scholarly journals Application of Functional Genomics for Bovine Respiratory Disease Diagnostics

2015 ◽  
Vol 9s2 ◽  
pp. BBI.S30525 ◽  
Author(s):  
Aswathy N. Rai ◽  
William B. Epperson ◽  
Bindu Nanduri
Keyword(s):  
Functional Genomics ◽  
Respiratory Disease ◽  
High Throughput ◽  
Molecular Mechanisms ◽  
Bovine Respiratory Disease ◽  
Rna Seq ◽  
Complex Interactions ◽  
Disease Diagnostics ◽  
Genome Scale ◽  
Important Disease

Bovine respiratory disease (BRD) is the most common economically important disease affecting cattle. For developing accurate diagnostics that can predict disease susceptibility/resistance and stratification, it is necessary to identify the molecular mechanisms that underlie BRD. To study the complex interactions among the bovine host and the multitude of viral and bacterial pathogens, as well as the environmental factors associated with BRD etiology, genome-scale high-throughput functional genomics methods such as microarrays, RNA-seq, and proteomics are helpful. In this review, we summarize the progress made in our understanding of BRD using functional genomics approaches. We also discuss some of the available bioinformatics resources for analyzing high-throughput data, in the context of biological pathways and molecular interactions. Although resources for studying host response to infection are available, the corresponding information is lacking for majority of BRD pathogens, impeding progress in identifying diagnostic signatures for BRD using functional genomics approaches.

Pharmacological considerations of antibiotic failures in bovine respiratory disease cases

2020 ◽  
pp. 1-2
Author(s):  
Brian V. Lubbers
Keyword(s):  
Respiratory Disease ◽  
Treatment Success ◽  
Bovine Respiratory Disease ◽  
Individual Animal ◽  
Success Rates ◽  
Cattle Production ◽  
Animal Host ◽  
Antimicrobial Prescribing ◽  
Complex Interactions ◽  
Beef Cattle Production

Abstract Bovine respiratory disease (BRD) is one of the most common indications for antimicrobial therapy in beef cattle production and research trials demonstrate that antibiotic therapy greatly improves clinical outcome for BRD. These trials also show that BRD treatment success rates are less than 100% and that there are opportunities to optimize antimicrobial prescribing and improve clinical outcomes if the underlying cause(s) of BRD treatment failures can be identified and addressed. As the etiology of BRD in an individual animal is frequently multi-factorial in nature; it is likely that BRD treatment failures also result from complex interactions between the drug, drug administrator, animal host, pathogens, and the environment. This review will focus specifically on the pharmacological aspects, specifically the interactions between the host and the drug and the drug and the drug administrator, of BRD treatment failures and the actions that veterinary practitioners can take to investigate and mitigate therapeutic failures in future cases.

scholarly journals Functional genomics in the study of yeast cell polarity: moving in the right direction

2013 ◽  
Vol 368 (1629) ◽  
pp. 20130118 ◽  
Author(s):  
Erin Styles ◽  
Ji-Young Youn ◽  
Mojca Mattiazzi Usaj ◽  
Brenda Andrews
Keyword(s):  
Functional Genomics ◽  
Cell Polarity ◽  
High Throughput ◽  
Budding Yeast ◽  
Model Organism ◽  
Genetic Screens ◽  
High Conservation ◽  
The Right ◽  
Genome Scale ◽  
Integrate Data

The budding yeast Saccharomyces cerevisiae has been used extensively for the study of cell polarity, owing to both its experimental tractability and the high conservation of cell polarity and other basic biological processes among eukaryotes. The budding yeast has also served as a pioneer model organism for virtually all genome-scale approaches, including functional genomics, which aims to define gene function and biological pathways systematically through the analysis of high-throughput experimental data. Here, we outline the contributions of functional genomics and high-throughput methodologies to the study of cell polarity in the budding yeast. We integrate data from published genetic screens that use a variety of functional genomics approaches to query different aspects of polarity. Our integrated dataset is enriched for polarity processes, as well as some processes that are not intrinsically linked to cell polarity, and may provide new areas for future study.

scholarly journals Identification of conserved hepatic transcriptomic responses to 17β-estradiol using high-throughput sequencing in brown trout

2015 ◽  
Vol 47 (9) ◽  
pp. 420-431 ◽  
Author(s):  
Tamsyn M. Uren Webster ◽  
Janice A. Shears ◽  
Karen Moore ◽  
Eduarda M. Santos
Keyword(s):  
High Throughput ◽  
Brown Trout ◽  
Ribosome Biogenesis ◽  
Molecular Mechanisms ◽  
High Throughput Sequencing ◽  
Cellular Proliferation ◽  
Sequence Information ◽  
Rna Seq ◽  
Mechanisms Of Toxicity ◽  
17Β Estradiol

Estrogenic chemicals are major contaminants of surface waters and can threaten the sustainability of natural fish populations. Characterization of the global molecular mechanisms of toxicity of environmental contaminants has been conducted primarily in model species rather than species with limited existing transcriptomic or genomic sequence information. We aimed to investigate the global mechanisms of toxicity of an endocrine disrupting chemical of environmental concern [17β-estradiol (E2)] using high-throughput RNA sequencing (RNA-Seq) in an environmentally relevant species, brown trout ( Salmo trutta). We exposed mature males to measured concentrations of 1.94, 18.06, and 34.38 ng E2/l for 4 days and sequenced three individual liver samples per treatment using an Illumina HiSeq 2500 platform. Exposure to 34.4 ng E2/L resulted in 2,113 differentially regulated transcripts (FDR < 0.05). Functional analysis revealed upregulation of processes associated with vitellogenesis, including lipid metabolism, cellular proliferation, and ribosome biogenesis, together with a downregulation of carbohydrate metabolism. Using real-time quantitative PCR, we validated the expression of eight target genes and identified significant differences in the regulation of several known estrogen-responsive transcripts in fish exposed to the lower treatment concentrations (including esr1 and zp2.5). We successfully used RNA-Seq to identify highly conserved responses to estrogen and also identified some estrogen-responsive transcripts that have been less well characterized, including nots and tgm2l. These results demonstrate the potential application of RNA-Seq as a valuable tool for assessing mechanistic effects of pollutants in ecologically relevant species for which little genomic information is available.

scholarly journals RNA-Seq Based Transcriptional Map of Bovine Respiratory Disease Pathogen “Histophilus somni 2336”

PLoS ONE ◽  
2012 ◽  
Vol 7 (1) ◽  
pp. e29435 ◽  
Author(s):  
Ranjit Kumar ◽  
Mark L. Lawrence ◽  
James Watt ◽  
Amanda M. Cooksey ◽  
Shane C. Burgess ◽  
...  
Keyword(s):  
Respiratory Disease ◽  
Bovine Respiratory Disease ◽  
Rna Seq ◽  
Histophilus Somni

scholarly journals Establishment of a Reverse Genetics System for Influenza D Virus

2020 ◽  
Vol 94 (10) ◽  
Author(s):  
Hiroho Ishida ◽  
Shin Murakami ◽  
Haruhiko Kamiki ◽  
Hiromichi Matsugo ◽  
Akiko Takenaka-Uema ◽  
...  
Keyword(s):  
Respiratory Disease ◽  
Recombinant Virus ◽  
Reverse Genetics ◽  
Molecular Mechanisms ◽  
Bovine Respiratory Disease ◽  
Wild Type Virus ◽  
Type Virus ◽  
Genomic Rna ◽  
Wild Type ◽  
Bovine Respiratory Disease Complex

ABSTRACT Influenza D virus (IDV) was initially isolated in the United States in 2011. IDV is distributed worldwide and is one of the causative agents of the bovine respiratory disease complex (BRDC), which causes high morbidity and mortality in feedlot cattle. The molecular mechanisms of IDV pathogenicity are still unknown. Reverse genetics systems are vital tools not only for studying the biology of viruses, but also for use in applications such as recombinant vaccine viruses. Here, we report the establishment of a plasmid-based reverse genetics system for IDV. We first verified that the 3′-terminal nucleotide of each 7-segmented genomic RNA contained uracil (U), contrary to previous reports, and we were then able to successfully generate recombinant IDV by cotransfecting 7 plasmids containing these genomic RNAs along with 4 plasmids expressing polymerase proteins and nucleoprotein into human rectal tumor 18G (HRT-18G) cells. The recombinant virus had a growth deficit compared to the wild-type virus, and we determined the reason for this growth difference by examining the genomic RNA content of the viral particles. We found that the recombinant virus incorporated an unbalanced ratio of viral RNA segments into particles compared to that of the wild-type virus, and thus we adjusted the amount of each plasmid used in transfection to obtain a recombinant virus with the same replicative capacity as the wild-type virus. Our work here in establishing a reverse genetics system for IDV will have a broad range of applications, including uses in studies focused on better understanding IDV replication and pathogenicity, as well as in those contributing to the development of BRDC countermeasures. IMPORTANCE The bovine respiratory disease complex (BRDC) causes high mortality and morbidity in cattle, causing economic losses worldwide. Influenza D virus (IDV) is considered to be a causative agent of the BRDC. Here, we developed a reverse genetics system that allows for the generation of IDV from cloned cDNAs and the introduction of mutations into the IDV genome. This reverse genetics system will become a powerful tool for use in studies related to understanding the molecular mechanisms of viral replication and pathogenicity and will also lead to the development of new countermeasures against the BRDC.

scholarly journals Enhanced Pathogenesis Caused by Influenza D Virus and Mycoplasma bovis Coinfection in Calves: a Disease Severity Linked with Overexpression of IFN-γ as a Key Player of the Enhanced Innate Immune Response in Lungs

2021 ◽  
Vol 9 (3) ◽  
Author(s):  
Adrien Lion ◽  
Aurélie Secula ◽  
Camille Rançon ◽  
Olivier Boulesteix ◽  
Anne Pinard ◽  
...  
Keyword(s):  
Immune Response ◽  
Respiratory Disease ◽  
Disease Severity ◽  
Innate Immune Response ◽  
Bovine Respiratory Disease ◽  
Innate Immune ◽  
Mycoplasma Bovis ◽  
Complex Interactions ◽  
Young Cattle ◽  
Ifn Γ

Bovine respiratory disease (BRD) is among the most prevalent diseases in young cattle. BRD is due to complex interactions between viruses and/or bacteria, most of which have a moderate individual pathogenicity.

scholarly journals Establishment of a Reverse Genetics System for Influenza D Virus

2019 ◽  
Author(s):  
Hiroho Ishida ◽  
Shin Murakami ◽  
Haruhiko Kamiki ◽  
Hiromichi Matsugo ◽  
Akiko Takenaka-Uema ◽  
...  
Keyword(s):  
Respiratory Disease ◽  
Recombinant Virus ◽  
Reverse Genetics ◽  
Molecular Mechanisms ◽  
Bovine Respiratory Disease ◽  
Wild Type Virus ◽  
Type Virus ◽  
Genomic Rna ◽  
Wild Type ◽  
Bovine Respiratory Disease Complex

ABSTRACTInfluenza D virus (IDV) was initially isolated in the USA in 2011. IDV is distributed worldwide and is one of the causative agents of bovine respiratory disease complex (BRDC), which exhibits high morbidity and mortality in feedlot cattle. Molecular mechanisms of IDV pathogenicity are still unknown. Reverse genetics systems are vital tools not only for studying the biology of viruses, but also for use in applications such as recombinant vaccine viruses. Here, we report the establishment of a plasmid-based reverse genetics system for IDV. We first verified that the 3′-terminal nucleotide of each 7-segmented genomic RNA contained uracil in contrary to the previous report, and were then able to successfully generate recombinant IDV by co-transfecting 7 plasmids containing these genomic RNAs along with 4 plasmids expressing polymerase proteins and NP into HRT-18G cells. The recombinant virus had a growth deficit compared to the wild-type virus, and we determined the reason for this growth difference by examining the genomic RNA content of the viral particles. We found that recombinant virus incorporated an unbalanced ratio of viral RNA segments into particles as compared to the wild-type virus, and thus we adjusted the amount of each plasmid used in transfection to obtain recombinant virus with the same replicative capacity as wild-type virus. Our work here in establishing a reverse genetics system for IDV will have a broad range of applications, including uses in studies focused on better understanding IDV replication and pathogenicity as well as those contributing to the development of BRDC countermeasures.IMPORTANCEBovine respiratory disease complex (BRDC) exhibits high mortality and morbidity in cattle, causing economic losses worldwide. Influenza D virus (IDV) is considered to be a causative agent of BRDC. Here, we developed a reverse genetics system that allows for the generation of IDV from cloned cDNAs, and the introduction of mutations into the IDV genome. This reverse genetics system will become a powerful tool for use in studies related to understanding the molecular mechanisms of viral replication and pathogenicity, and will also lead to the development of new countermeasures against BRDC.

scholarly journals Integrated Network Analysis to Identify Key Modules and Potential Hub Genes Involved in Bovine Respiratory Disease: A Systems Biology Approach

2021 ◽  
Vol 12 ◽  
Author(s):  
Aliakbar Hasankhani ◽  
Abolfazl Bahrami ◽  
Negin Sheybani ◽  
Farhang Fatehi ◽  
Roxana Abadeh ◽  
...  
Keyword(s):  
Immune Response ◽  
Systems Biology ◽  
Respiratory Disease ◽  
Molecular Mechanisms ◽  
Bovine Respiratory Disease ◽  
Hub Genes ◽  
Ppi Networks ◽  
Gene Coexpression ◽  
Highly Correlated ◽  
Coexpression Networks

Background: Bovine respiratory disease (BRD) is the most common disease in the beef and dairy cattle industry. BRD is a multifactorial disease resulting from the interaction between environmental stressors and infectious agents. However, the molecular mechanisms underlying BRD are not fully understood yet. Therefore, this study aimed to use a systems biology approach to systematically evaluate this disorder to better understand the molecular mechanisms responsible for BRD.Methods: Previously published RNA-seq data from whole blood of 18 healthy and 25 BRD samples were downloaded from the Gene Expression Omnibus (GEO) and then analyzed. Next, two distinct methods of weighted gene coexpression network analysis (WGCNA), i.e., module–trait relationships (MTRs) and module preservation (MP) analysis were used to identify significant highly correlated modules with clinical traits of BRD and non-preserved modules between healthy and BRD samples, respectively. After identifying respective modules by the two mentioned methods of WGCNA, functional enrichment analysis was performed to extract the modules that are biologically related to BRD. Gene coexpression networks based on the hub genes from the candidate modules were then integrated with protein–protein interaction (PPI) networks to identify hub–hub genes and potential transcription factors (TFs).Results: Four significant highly correlated modules with clinical traits of BRD as well as 29 non-preserved modules were identified by MTRs and MP methods, respectively. Among them, two significant highly correlated modules (identified by MTRs) and six nonpreserved modules (identified by MP) were biologically associated with immune response, pulmonary inflammation, and pathogenesis of BRD. After aggregation of gene coexpression networks based on the hub genes with PPI networks, a total of 307 hub–hub genes were identified in the eight candidate modules. Interestingly, most of these hub–hub genes were reported to play an important role in the immune response and BRD pathogenesis. Among the eight candidate modules, the turquoise (identified by MTRs) and purple (identified by MP) modules were highly biologically enriched in BRD. Moreover, STAT1, STAT2, STAT3, IRF7, and IRF9 TFs were suggested to play an important role in the immune system during BRD by regulating the coexpressed genes of these modules. Additionally, a gene set containing several hub–hub genes was identified in the eight candidate modules, such as TLR2, TLR4, IL10, SOCS3, GZMB, ANXA1, ANXA5, PTEN, SGK1, IFI6, ISG15, MX1, MX2, OAS2, IFIH1, DDX58, DHX58, RSAD2, IFI44, IFI44L, EIF2AK2, ISG20, IFIT5, IFITM3, OAS1Y, HERC5, and PRF1, which are potentially critical during infection with agents of bovine respiratory disease complex (BRDC).Conclusion: This study not only helps us to better understand the molecular mechanisms responsible for BRD but also suggested eight candidate modules along with several promising hub–hub genes as diagnosis biomarkers and therapeutic targets for BRD.

scholarly journals RNA-Seq-based transcriptional map of the bovine respiratory disease pathogen Histophilus somni 2336

2011 ◽  
Vol 12 (Suppl 1) ◽  
pp. P40
Author(s):  
Ranjit Kumar ◽  
Mark L Lawrence ◽  
James Watt ◽  
Amanda Cooksey ◽  
Shane C Burgess ◽  
...  
Keyword(s):  
Respiratory Disease ◽  
Bovine Respiratory Disease ◽  
Rna Seq ◽  
Histophilus Somni

High throughput phenotype screening pipeline for functional genomics in Magnaporthe oryzae

2007 ◽  
Author(s):  
Sook-Young Park ◽  
Myoung-Hwan Chi ◽  
Junhyun Jeon ◽  
Yong-Hwan Lee
Keyword(s):  
Functional Genomics ◽  
High Throughput ◽  
Magnaporthe Oryzae ◽  
Phenotype Screening
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