Differential expression of NAT1 translational repressor during development of bovine intramuscular adipocytes

2002 ◽  
Vol 10 (2) ◽  
pp. 49-56 ◽  
Author(s):  
Kirby D. Childs ◽  
David W. Goad ◽  
Mark F. Allan ◽  
Daniel Pomp ◽  
Clinton Krehbiel ◽  
...  
Keyword(s):  
Differential Expression ◽  
High Energy ◽  
Homology Search ◽  
Treatment Groups ◽  
Translational Repressor ◽  
Feedlot Steers ◽  
Differential Gene ◽  
Pooled Samples ◽  
Adipocyte Development ◽  
Blast Homology Search

This study was undertaken to test for differential gene expression in intramuscular adipocytes during fat deposition of feedlot steers. Angus × Hereford steers ( n = 50) were fed a high-energy concentrate ration ad libitum for 20 ( n = 5), 86 ( n = 15), 121 ( n = 15), and 146 days ( n = 15) to obtain various degrees of intramuscular adipocyte development. Carcass traits were significantly different ( P < 0.05) between the groups. Intramuscular adipose tissue was excised from the longissimus dorsi and snap frozen in liquid nitrogen. Pooled samples of total RNA representing each group were analyzed by differential-display polymerase chain reaction using 200 primer combinations comprising 20 arbitrary (5′) and 10 anchor (3′) oligonucleotides. Bands ( n = 70) representing putative differences among treatment groups were excised, sequenced, and subjected to BLAST homology search. From these, 40 contained significant homology to known genes. One was of particular interest, the translational repressor NAT1 (novel APOBEC-1 target-1). NAT1 mRNA was quantified in individual animals to confirm differential expression among treatment groups. Results indicate that NAT1 message is more abundant ( P < 0.05) in intramuscular adipocytes of younger/leaner animals.

Identifying Breast Cancer-induced gene perturbations and its application in guiding drug repurposing

2020 ◽  
Vol 15 ◽  
Author(s):  
Jujuan Zhuang ◽  
Shuang Dai ◽  
Lijun Zhang ◽  
Pan Gao ◽  
Yingmin Han ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Differential Expression ◽  
Enrichment Analysis ◽  
Cancer Tissue ◽  
Connectivity Analysis ◽  
Cancer Drugs ◽  
Normal Tissues ◽  
Differential Gene ◽  
Differential Modules ◽  
Differential Connectivity

Background: Breast cancer is a complex disease with high prevalence in women, the molecular mechanisms of which are still unclear at present. Most transcriptomic studies on breast cancer focus on differential expression of each gene between tumor and the adjacent normal tissues, while the other perturbations induced by breast cancer including the gene regulation variations, the changes of gene modules and the pathways, which might be critical to the diagnosis, treatment and prognosis of breast cancer are more or less ignored. Objective: We presented a complete process to study breast cancer from multiple perspectives, including differential expression analysis, constructing gene co-expression networks, modular differential connectivity analysis, differential gene connectivity analysis, gene function enrichment analysis key driver analysis. In addition, we prioritized the related anti-cancer drugs based on enrichment analysis between differential expression genes and drug perturbation signatures. Methods: The RNA expression profiles of 1109 breast cancer tissue and 113 non-tumor tissues were downloaded from The Cancer Genome Atlas (TCGA) database. Differential expression of RNAs was identified using the “DESeq2” bioconductor package in R, and gene co-expression networks was constructed using the weighted gene co-expression network analysis (WGCNA). To compare the module changes and gene co-expression variations between tumor and the adjacent normal tissues, modular differential connectivity (MDC) analysis and differential gene connectivity analysis (DGCA) were performed. Results: Top differential genes like MMP11 and COL10A1 were known to be associated with breast cancer. And we found 23 modules in the tumor network had significantly different co-expression patterns. The top differential modules were enriched in Goterms related to breast cancer like MHC protein complex, leukocyte activation, regulation of defense response and so on. In addition, key genes like UBE2T driving the top differential modules were significantly correlated with the patients’ survival. Finally, we predicted some potential breast cancer drugs, such as Eribulin, Taxane, Cisplatin and Oxaliplatin. Conclusion: As an indication, this framework might be useful in understanding the molecular pathogenesis of diseases like breast cancer and inferring useful drugs for personalized medication

scholarly journals Best practices on the differential expression analysis of multi-species RNA-seq

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Matthew Chung ◽  
Vincent M. Bruno ◽  
David A. Rasko ◽  
Christina A. Cuomo ◽  
José F. Muñoz ◽  
...  
Keyword(s):  
Best Practices ◽  
Differential Expression ◽  
Expression Analysis ◽  
Differential Expression Analysis ◽  
Single Species ◽  
Rna Seq ◽  
Species Analysis ◽  
Differential Gene ◽  
Multiple Species ◽  
Downstream Analysis

AbstractAdvances in transcriptome sequencing allow for simultaneous interrogation of differentially expressed genes from multiple species originating from a single RNA sample, termed dual or multi-species transcriptomics. Compared to single-species differential expression analysis, the design of multi-species differential expression experiments must account for the relative abundances of each organism of interest within the sample, often requiring enrichment methods and yielding differences in total read counts across samples. The analysis of multi-species transcriptomics datasets requires modifications to the alignment, quantification, and downstream analysis steps compared to the single-species analysis pipelines. We describe best practices for multi-species transcriptomics and differential gene expression.

scholarly journals The Western Diet Regulates Hippocampal Microvascular Gene Expression: An Integrated Genomic Analyses in Female Mice

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Saivageethi Nuthikattu ◽  
Dragan Milenkovic ◽  
John Rutledge ◽  
Amparo Villablanca
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Differential Expression ◽  
Differential Gene Expression ◽  
Gene Networks ◽  
Molecular Mechanisms ◽  
Western Diet ◽  
Protein Coding ◽  
Female Mice ◽  
Differential Gene

AbstractHyperlipidemia is a risk factor for dementia, and chronic consumption of a Western Diet (WD) is associated with cognitive impairment. However, the molecular mechanisms underlying the development of microvascular disease in the memory centers of the brain are poorly understood. This pilot study investigated the nutrigenomic pathways by which the WD regulates gene expression in hippocampal brain microvessels of female mice. Five-week-old female low-density lipoprotein receptor deficient (LDL-R−/−) and C57BL/6J wild type (WT) mice were fed a chow or WD for 8 weeks. Metabolics for lipids, glucose and insulin were determined. Differential gene expression, gene networks and pathways, transcription factors, and non-protein coding RNAs were evaluated by genome-wide microarray and bioinformatics analysis of laser captured hippocampal microvessels. The WD resulted in differential expression of 2,412 genes. The majority of differential gene expression was attributable to differential regulation of cell signaling proteins and their transcription factors, approximately 7% was attributable to differential expression of miRNAs, and a lesser proportion was due to other non-protein coding RNAs, primarily long non-coding RNAs (lncRNAs) and small nucleolar RNAs (snoRNAs) not previously described to be modified by the WD in females. Our findings revealed that chronic consumption of the WD resulted in integrated multilevel molecular regulation of the hippocampal microvasculature of female mice and may provide one of the mechanisms underlying vascular dementia.

scholarly journals RankerGUI: A Computational Framework to Compare Differential Gene Expression Profiles Using Rank Based Statistics

2019 ◽  
Vol 20 (23) ◽  
pp. 6098 ◽  
Author(s):  
Amarinder Singh Thind ◽  
Kumar Parijat Tripathi ◽  
Mario Rosario Guarracino
Keyword(s):  
Gene Expression ◽  
Differential Expression ◽  
Differential Gene Expression ◽  
Web Application ◽  
Cellular Response ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Gene Expression Profiles ◽  
Experimental Conditions ◽  
Differential Gene

The comparison of high throughput gene expression datasets obtained from different experimental conditions is a challenging task. It provides an opportunity to explore the cellular response to various biological events such as disease, environmental conditions, and drugs. There is a need for tools that allow the integration and analysis of such data. We developed the “RankerGUI pipeline”, a user-friendly web application for the biological community. It allows users to use various rank based statistical approaches for the comparison of full differential gene expression profiles between the same or different biological states obtained from different sources. The pipeline modules are an integration of various open-source packages, a few of which are modified for extended functionality. The main modules include rank rank hypergeometric overlap, enriched rank rank hypergeometric overlap and distance calculations. Additionally, preprocessing steps such as merging differential expression profiles of multiple independent studies can be added before running the main modules. Output plots show the strength, pattern, and trends among complete differential expression profiles. In this paper, we describe the various modules and functionalities of the developed pipeline. We also present a case study that demonstrates how the pipeline can be used for the comparison of differential expression profiles obtained from multiple platforms’ data of the Gene Expression Omnibus. Using these comparisons, we investigate gene expression patterns in kidney and lung cancers.

scholarly journals Molecular evolution in immune genes across the avian tree of life

2019 ◽  
Vol 5 ◽  
Author(s):  
Diana C. Outlaw ◽  
V. Woody Walstrom ◽  
Haley N. Bodden ◽  
Chuan-yu Hsu ◽  
Mark Arick ◽  
...  
Keyword(s):  
Purifying Selection ◽  
Tree Of Life ◽  
Innate Immune ◽  
Phylogenetic Study ◽  
Significant Differential Expression ◽  
Immune Genes ◽  
Treatment Groups ◽  
Show Evidence ◽  
Differential Gene ◽  
Innate Immune Genes

Abstract All organisms encounter pathogens, and birds are especially susceptible to infection by malaria parasites and other haemosporidians. It is important to understand how immune genes, primarily innate immune genes which are the first line of host defense, have evolved across birds, a highly diverse group of tetrapods. Here, we find that innate immune genes are highly conserved across the avian tree of life and that although most show evidence of positive or diversifying selection within specific lineages or clades, the number of sites is often proportionally low in this broader context of putative constraint. Rather, evidence shows a much higher level of negative or purifying selection in these innate immune genes – rather than adaptive immune genes – which is consistent with birds' long coevolutionary history with pathogens and the need to maintain a rapid response to infection. We further explored avian responses to haemosporidians by comparing differential gene expression in wild birds (1) uninfected with haemosporidians, (2) infected with Plasmodium and (3) infected with Haemoproteus (Parahaemoproteus). We found patterns of significant differential expression with some genes unique to infection with each genus and a few shared between ‘treatment’ groups, but none that overlapped with the genes included in the phylogenetic study.

The influence of pre-weaning nutrition on biochemical and myofibre characteristics of bovine semitendinosus muscle

2001 ◽  
Vol 52 (9) ◽  
pp. 891 ◽  
Author(s):  
Peter G. Allingham ◽  
Gregory S. Harper ◽  
David W. Hennessy ◽  
V. Hutton Oddy
Keyword(s):  
Muscle Development ◽  
Late Pregnancy ◽  
High Energy ◽  
Eating Quality ◽  
Growth Path ◽  
Semitendinosus Muscle ◽  
Calf Growth ◽  
Treatment Groups ◽  
Sarcoplasmic Protein ◽  
Biophysical Attributes

This study investigates pre-weaning growth of cattle and its effect on biochemical and histochemical markers of muscle development and subsequent biophysical attributes of eating quality. Combinations of cow (late pregnancy to mid-lactation) and pre-weaning (varying duration of access to a high-energy ration) supplementation were used to vary calf growth to weaning in 6 treatment groups. After weaning, calves were grazed together on pasture (backgrounding) and then grown rapidly on a feedlot ration (finishing) until slaughter. Biochemical and myofibre characteristics were determined in semitendinosus muscle samples collected just prior to weaning (7 months), at the end of backgrounding (13 months), and at slaughter (17 months). The concentration of sarcoplasmic protein and the activity of lactate dehydrogenase in the muscle at weaning were associated with differences in pre-weaning growth and both variables correlated positively with liveweight at weaning. Isocitrate dehydrogenase activity varied with sex, not treatment, at weaning and at the end of backgrounding. The size of myofibres at weaning related to differences in growth path and correlated positively with liveweight. Pre-weaning growth effects on these characteristics were not evident at slaughter. Biophysical properties of the meat were not affected by earlier growth path treatment, and were not correlated with biochemical characteristics or myofibre type profile. Variation in both shear peak force and adhesion was related to sex. We conclude that the effects of divergent early life growth do not persist 10 months after weaning, at least in meat quality characteristics.

scholarly journals Differential Gene Expression in High- and Low-Active Inbred Mice

2014 ◽  
Vol 2014 ◽  
pp. 1-9 ◽  
Author(s):  
Michelle Dawes ◽  
Trudy Moore-Harrison ◽  
Alicia T. Hamilton ◽  
Tyrone Ceaser ◽  
Kelli J. Kochan ◽  
...  
Keyword(s):  
Gene Expression ◽  
Physical Activity ◽  
Differential Expression ◽  
Candidate Genes ◽  
Inbred Mice ◽  
Regulatory Sequences ◽  
Functional Roles ◽  
Genomic Structural Variation ◽  
Differential Gene ◽  
Or Gene

Numerous candidate genes have been suggested in the recent literature with proposed roles in regulation of voluntary physical activity, with little evidence of these genes’ functional roles. This study compared the haplotype structure and expression profile in skeletal muscle and brain of inherently high- (C57L/J) and low- (C3H/HeJ) active mice. Expression of nine candidate genes [Actn2,Actn3,Casq1,Drd2,Lepr,Mc4r,Mstn,Papss2, andGlut4(a.k.a.Slc2a4)] was evaluated via RT-qPCR. SNPs were observed in regions ofActn2,Casq1,Drd2,Lepr, andPapss2; however, no SNPs were located in coding sequences or associated with any known regulatory sequences. In mice exposed to a running wheel,Casq1(P=0.0003) andMstn(P=0.002) transcript levels in the soleus were higher in the low-active mice. However, when these genes were evaluated in naïve animals, differential expression was not observed, demonstrating a training effect. Among naïve mice, no genes in either tissue exhibited differential expression between strains. Considering that no obvious SNP mechanisms were determined or differential expression was observed, our results indicate that genomic structural variation or gene expression data alone is not adequate to establish any of these genes’ candidacy or causality in relation to regulation of physical activity.

scholarly journals Cloning and Expression Analysis of the pcbAB-pcbC β-Lactam Genes in the Marine Fungus Kallichroma tethys

2003 ◽  
Vol 69 (2) ◽  
pp. 1308-1314 ◽  
Author(s):  
Chi-fai Kim ◽  
Simon K. Y. Lee ◽  
Jackie Price ◽  
Ralph W. Jack ◽  
Geoffrey Turner ◽  
...  
Keyword(s):  
Expression Analysis ◽  
Marine Fungus ◽  
Cloning And Expression ◽  
Homology Search ◽  
High Sequence Identity ◽  
Dna Library ◽  
Homologous Genes ◽  
Close Relationship ◽  
Genomic Dna Library ◽  
Blast Homology Search

ABSTRACT Here we report the identification of the β-lactam biosynthesis genes pcbAB and pcbC from a cosmid genomic DNA library of the marine fungus Kallichroma tethys. A BLAST homology search showed that they share high sequence identity with the δ-(l-α-aminoadipyl)-l-cysteinyl-d-valine (ACV) synthetases and isopenicillin N synthases, respectively, of various fungal and bacterial β-lactam producers, while phylogenetic analysis indicated a close relationship with homologous genes of the cephalosporin-producing pyrenomycete Acremonium chrysogenum. Expression analysis by reverse transciption-PCR suggested that both genes are highly regulated and are expressed in the late growth phase of K. tethys cultures. Complementation of an Aspergillus nidulans strain deficient in ACV synthetase suggested that at least pcbAB is functional, although attempts to isolate active antibiotic from K. tethys were unsuccessful.

scholarly journals Defining cell identity beyond the premise of differential gene expression

2021 ◽  
Vol 10 (1) ◽  
Author(s):  
Hani Jieun Kim ◽  
Patrick P. L. Tam ◽  
Pengyi Yang
Keyword(s):  
Gene Expression ◽  
Differential Expression ◽  
Cell Fate ◽  
Differential Gene Expression ◽  
Cell Types ◽  
Cell Identity ◽  
Gene Transcripts ◽  
Differential Gene ◽  
Biological Attributes

AbstractIdentifying genes that define cell identity is a requisite step for characterising cell types and cell states and predicting cell fate choices. By far, the most widely used approach for this task is based on differential expression (DE) of genes, whereby the shift of mean expression are used as the primary statistics for identifying gene transcripts that are specific to cell types and states. While DE-based methods are useful for pinpointing genes that discriminate cell types, their reliance on measuring difference in mean expression may not reflect the biological attributes of cell identity genes. Here, we highlight the quest for non-DE methods and provide an overview of these methods and their applications to identify genes that define cell identity and functionality.

scholarly journals HIV-associated nephropathy: Protocol and rationale for an exploratory genotype-phenotype study in a sub-Saharan African population

PLoS ONE ◽  
2021 ◽  
Vol 16 (4) ◽  
pp. e0249567
Author(s):  
Aminu Abba Yusuf ◽  
Baba Maiyaki Musa ◽  
Najibah Aliyu Galadanci ◽  
Musa Babashani ◽  
Aminu Zakari Mohammed ◽  
...  
Keyword(s):  
Gene Expression ◽  
Kidney Disease ◽  
Differential Expression ◽  
Differential Gene Expression ◽  
Teaching Hospital ◽  
African Population ◽  
Hiv Positive ◽  
Differential Gene ◽  
Sub Saharan ◽  
Risk Categories

Background HIV-positive persons of African descent are disproportionately affected by chronic kidney disease (CKD). Deterioration to end-stage kidney disease (ESKD) also occurs in this population at a higher frequency. There remains a lot to learn about the genetic susceptibility to CKD in HIV positive patients, and the pathophysiology of progression to ESKD. Objectives We will conduct an exploratory genotype-phenotype study in HIV-positive persons with CKD in Aminu Kano Teaching Hospital, Nigeria, to determine blood-based differential gene expression biomarkers in different kidney risk groups according to the KDIGO 2012 criteria. Methods We will consecutively screen 150 HIV-positive adults (≥18 years of age) attending the HIV clinic of Aminu Kano Teaching Hospital, Kano, Nigeria, for CKD based on proteinuria and elevation of estimated glomerular filtration rate. Among these, two separate groups of 16 eligible participants each (n = 32) will be selected in the four (4) KDIGO 2012 kidney risk categories. The groups will be matched for age, sex, viral suppression level and antiretroviral (ARV) regimen. In the first group (n = 16), we will determine differential gene expression markers in peripheral blood mononuclear cells using mRNA-sequencing (RNA-Seq). We will validate the differential expression markers in the second group (n = 16) using reverse transcription quantitative polymerase chain reaction (RT-qPCR). Using a systems-based approach, we will construct, visualize and analyze gene-gene interaction networks to determine the potential biological roles of identified differential expression markers based on published literature and publicly available databases. Results Our exploratory study will provide valuable information on the potential roles of differential expression biomarkers in the pathophysiology of HIV-associated kidney disease by identifying novel biomarkers in different risk categories of CKD in a sub-Saharan African population. The results of this study will provide the basis for population-based genome-wide association studies to guide future personalized medicine approaches. Conclusion Validated biomarkers can be potential targets for the development of stage-specific therapeutic interventions, an essential paradigm in precision medicine.

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