Development of a metatranscriptomic analysis method for multiple intestinal sites and its application to the common marmoset intestine

Background: The intestinal microbiome is closely related to host health, and metatranscriptomic analysis can assess the functional activity of microbiomes by quantifying the bacterial gene expression level, which helps to elucidate the interaction between the microbiome and the environment. However, functional changes in the microbiome along the host intestinal tract remain unknown, and previous analytical methods have limitations, such as potentially overlooking unknown genes due to dependence on existing databases and being unable to take full advantage of metatranscriptome to reveal the functional change among multiple environments. Result: To close these gaps, we develop a novel method that integrates metagenome and metatranscriptome to analyze the functional activity of microbiomes between intestinal sites. This method reconstructs a reference metagenomic sequence across multiple intestinal sites, allowing the gene expression levels of microbiome including unknown bacterial genes to be compared between multiple sites. As a result of applying this method to metatranscriptomic analysis in the intestinal tract of common marmoset, the reconstructed metagenome covered most of the expressed genes and it revealed that the changes in bacterial gene expressions among the caecum, transverse colon, and faeces were more dynamic and sensitive to environmental shifts than its abundance. In typical, the coenzyme synthesis gene and antibacterial resistance gene were more highly expressed in the caecum and transverse colon than in faeces, while there was no significant change in abundance of these genes. Conclusion: Our findings demonstrate that an analytical method that integrates metagenome and metatranscriptome in multiple intestinal sites captures functional changes in the microbiomes at the gene resolution level.

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Faculty Opinions recommendation of Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1010338.169508 ◽

2002 ◽

Author(s):

Niles Lehman

Keyword(s):

Gene Expression ◽

Messenger Rnas ◽

Bacterial Gene ◽

Bacterial Gene Expression

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Faculty Opinions recommendation of Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1010338.156608 ◽

2002 ◽

Author(s):

Richard Gourse

Keyword(s):

Gene Expression ◽

Messenger Rnas ◽

Bacterial Gene ◽

Bacterial Gene Expression

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Chemoprotective Effects of Propolis on Aflatoxin B1-Induced Hepatotoxicity in Rats: Oxidative Damage and Hepatotoxicity by Modulating TP53, Oxidative Stress

Current Proteomics ◽

10.2174/1570164617666190925121720 ◽

2020 ◽

Vol 17 (3) ◽

pp. 191-199

Author(s):

Seval Yilmaz ◽

Fatih Mehmet Kandemir ◽

Emre Kaya ◽

Mustafa Ozkaraca

Keyword(s):

Oxidative Stress ◽

Gene Expression ◽

Oxidative Damage ◽

Aflatoxin B1 ◽

Tp53 Gene ◽

Control Group ◽

Glutathione S Transferase ◽

Gene Expressions ◽

Cat Gene ◽

Gst Activity

Objective: This study aimed to detect hepatic oxidative damage caused by aflatoxin B1 (AFB1), as well as to examine how propolis protects against hepatotoxic effects of AFB1. Method: Rats were split into four groups as control group, AFB1 group, propolis group, AFB1+ propolis group. Results: There was significant increase in malondialdehyde (MDA) level and tumor suppressor protein (TP53) gene expression, Glutathione (GSH) level, Catalase (CAT) activity, CAT gene expression decreased in AFB1 group in blood. MDA level and Glutathione-S-Transferase (GST) activity, GST and TP53 gene expressions increased in AFB1 group, whereas GSH level and CAT activity alongside CAT gene expression decreased in liver. AFB1+propolis group showed significant decrease in MDA level, GST activity, TP53 and GST gene expressions, GSH level and CAT activity and CAT gene expression increased in liver compared to AFB1 group. Conclusion: These results suggest that propolis may potentially be natural agent that prevents AFB1- induced oxidative stress and hepatotoxicity.

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SorTn-seq: a high-throughput functional genomics approach to discovering regulators of bacterial gene expression

Nature Protocols ◽

10.1038/s41596-021-00582-6 ◽

2021 ◽

Author(s):

Leah M. Smith ◽

Simon A. Jackson ◽

Paul P. Gardner ◽

Peter C. Fineran

Keyword(s):

Gene Expression ◽

Functional Genomics ◽

High Throughput ◽

Bacterial Gene ◽

Bacterial Gene Expression

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Mining The Cancer Genome Atlas gene expression data for lineage markers in distinguishing bladder urothelial carcinoma and prostate adenocarcinoma

Scientific Reports ◽

10.1038/s41598-021-85993-x ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Ewe Seng Ch’ng

Keyword(s):

Gene Expression ◽

Gene Expression Data ◽

The Cancer Genome Atlas ◽

Relative Importance ◽

Expression Data ◽

Gene Expressions ◽

Urothelial Carcinomas ◽

Cancer Genome Atlas ◽

Lineage Markers ◽

Genome Atlas

AbstractDistinguishing bladder urothelial carcinomas from prostate adenocarcinomas for poorly differentiated carcinomas derived from the bladder neck entails the use of a panel of lineage markers to help make this distinction. Publicly available The Cancer Genome Atlas (TCGA) gene expression data provides an avenue to examine utilities of these markers. This study aimed to verify expressions of urothelial and prostate lineage markers in the respective carcinomas and to seek the relative importance of these markers in making this distinction. Gene expressions of these markers were downloaded from TCGA Pan-Cancer database for bladder and prostate carcinomas. Differential gene expressions of these markers were analyzed. Standard linear discriminant analyses were applied to establish the relative importance of these markers in lineage determination and to construct the model best in making the distinction. This study shows that all urothelial lineage genes except for the gene for uroplakin III were significantly expressed in bladder urothelial carcinomas (p < 0.001). In descending order of importance to distinguish from prostate adenocarcinomas, genes for uroplakin II, S100P, GATA3 and thrombomodulin had high discriminant loadings (> 0.3). All prostate lineage genes were significantly expressed in prostate adenocarcinomas(p < 0.001). In descending order of importance to distinguish from bladder urothelial carcinomas, genes for NKX3.1, prostate specific antigen (PSA), prostate-specific acid phosphatase, prostein, and prostate-specific membrane antigen had high discriminant loadings (> 0.3). Combination of gene expressions for uroplakin II, S100P, NKX3.1 and PSA approached 100% accuracy in tumor classification both in the training and validation sets. Mining gene expression data, a combination of four lineage markers helps distinguish between bladder urothelial carcinomas and prostate adenocarcinomas.

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Histochemical Characterisation and Gene Expression Analysis of Skeletal Muscles from Maremmana and Aubrac Steers Reared on Grazing and Feedlot Systems

Animals ◽

10.3390/ani11030656 ◽

2021 ◽

Vol 11 (3) ◽

pp. 656

Author(s):

Giulia Foggi ◽

Francesca Ciucci ◽

Maria Conte ◽

Laura Casarosa ◽

Andrea Serra ◽

...

Keyword(s):

Gene Expression ◽

Physical Activity ◽

Muscle Fibre ◽

Skeletal Muscles ◽

Gene Expression Analysis ◽

Type I ◽

Triceps Brachii ◽

Gene Expressions ◽

Muscle Properties ◽

Voluntary Physical Activity

This study aimed to characterise the fibre composition of Triceps brachii (TB) and Semimembranosus (SM) muscles from 20 Maremmana (MA) and 20 Aubrac (AU) steers, and the effect of grazing activity in comparison with feedlot system. The histochemical method was performed with the m-ATPase method with an acid pre-incubation, thus allowing to distinguish type I, IIA, and IIB fibres. Additionally, on total RNA extracted from SM muscle, the expressions of atp1a1, mt-atp6, and capn1 genes were evaluated, in order to find potential associations with muscle fibre histochemical characteristics. In SM muscle, the MA steers had the greater frequency of oxidative fibres (type I and IIA) and the higher atp1a1 expression, in comparison to AU steers. Conversely, AU steers had a greater frequency of type IIB fibres, and the higher capn1 expression. A similar histochemical pattern was observed in TB muscle. The grazing activity was probably insufficient to determine differences both for fibre proportion and size, and gene expressions, except for mt-atp6 expression that was surprisingly highest in feedlot MA in comparison to other steers. These findings further the knowledge of muscle properties belonging to these breeds, and the effect of voluntary physical activity since few studies were available in this regard.

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Microarray analysis identification of key pathways and interaction network of differential gene expressions during osteogenic differentiation

Human Genomics ◽

10.1186/s40246-020-00293-1 ◽

2020 ◽

Vol 14 (1) ◽

Author(s):

Fatemeh Khodabandehloo ◽

Sara Taleahmad ◽

Reza Aflatoonian ◽

Farzad Rajaei ◽

Zahra Zandieh ◽

...

Keyword(s):

Gene Expression ◽

Stem Cells ◽

Signaling Pathway ◽

Expression Profiles ◽

Wnt Signaling Pathway ◽

Hub Genes ◽

Gene Expressions ◽

Cell Based Therapy ◽

Wnt Pathways ◽

Key Pathways

Abstract Background Adult bone marrow-derived mesenchymal stem cells (BM-MSCs) are multipotent stem cells that can differentiate into three lineages. They are suitable sources for cell-based therapy and regenerative medicine applications. This study aims to evaluate the hub genes and key pathways of differentially expressed genes (DEGs) related to osteogenesis by bioinformatics analysis in three different days. The DEGs were derived from the three different days compared with day 0. Results Gene expression profiles of GSE37558 were obtained from the Gene Expression Omnibus (GEO) database. A total of 4076 DEGs were acquired on days 8, 12, and 25. Gene ontology (GO) enrichment analysis showed that the non-canonical Wnt signaling pathway and lipopolysaccharide (LPS)-mediated signaling pathway were commonly upregulated DEGs for all 3 days. KEGG pathway analysis indicated that the PI3K-Akt and focal adhesion were also commonly upregulated DEGs for all 3 days. Ten hub genes were identified by CytoHubba on days 8, 12, and 25. Then, we focused on the association of these hub genes with the Wnt pathways that had been enriched from the protein-protein interaction (PPI) by the Cytoscape plugin MCODE. Conclusions These findings suggested further insights into the roles of the PI3K/AKT and Wnt pathways and their association with osteogenesis. In addition, the stem cell microenvironment via growth factors, extracellular matrix (ECM), IGF1, IGF2, LPS, and Wnt most likely affect osteogenesis by PI3K/AKT.

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Prenatal Arsenic Exposure and the Epigenome: Identifying Sites of 5-methylcytosine Alterations that Predict Functional Changes in Gene Expression in Newborn Cord Blood and Subsequent Birth Outcomes

Toxicological Sciences ◽

10.1093/toxsci/kfu210 ◽

2014 ◽

Vol 143 (1) ◽

pp. 97-106 ◽

Cited By ~ 103

Author(s):

Daniel Rojas ◽

Julia E. Rager ◽

Lisa Smeester ◽

Kathryn A. Bailey ◽

Zuzana Drobná ◽

...

Keyword(s):

Gene Expression ◽

Cord Blood ◽

Birth Outcomes ◽

Arsenic Exposure ◽

Functional Changes ◽

Subsequent Birth

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Effects of glutamine supplementation on oxidative stress-related gene expression and antioxidant properties in rats with streptozotocin-induced type 2 diabetes

British Journal Of Nutrition ◽

10.1017/s0007114511004168 ◽

2011 ◽

Vol 107 (8) ◽

pp. 1112-1118 ◽

Cited By ~ 26

Author(s):

Pei-Hsuan Tsai ◽

Jun-Jen Liu ◽

Chui-Li Yeh ◽

Wan-Chun Chiu ◽

Sung-Ling Yeh

Keyword(s):

Oxidative Stress ◽

Gene Expression ◽

Amino Acid ◽

Oxidative Damage ◽

Antioxidant Capacity ◽

Enzyme Activities ◽

Antioxidant Enzyme Activities ◽

Related Gene ◽

Gene Expressions ◽

Oxidative Stress Related Gene

There are close links among hyperglycaemia, oxidative stress and diabetic complications. Glutamine (GLN) is an amino acid with immunomodulatory properties. The present study investigated the effect of dietary GLN on oxidative stress-relative gene expressions and tissue oxidative damage in diabetes. There were one normal control (NC) and two diabetic groups in the present study. Diabetes was induced by an intraperitoneal injection of nicotinamide followed by streptozotocin (STZ). Rats in the NC group were fed a regular chow diet. In the two diabetic groups, one group (diabetes mellitus, DM) was fed a common semi-purified diet while the other group received a diet in which part of the casein was replaced by GLN (DM-GLN). GLN provided 25 % of total amino acid N. The experimental groups were fed the respective diets for 8 weeks, and then the rats were killed for further analysis. The results showed that blood thioredoxin-interacting protein (Txnip) mRNA expression in the diabetic groups was higher than that in the NC group. Compared with the DM group, the DM-GLN group had lower glutamine fructose-6-phosphate transaminase 1, a receptor of advanced glycation end products, and Txnip gene expressions in blood mononuclear cells. The total antioxidant capacity was lower and antioxidant enzyme activities were altered by the diabetic condition. GLN supplementation increased antioxidant capacity and normalised antioxidant enzyme activities. Also, the renal nitrotyrosine level and Txnip mRNA expression were lower when GLN was administered. These results suggest that dietary GLN supplementation decreases oxidative stress-related gene expression, increases the antioxidant potential and may consequently attenuate renal oxidative damage in rats with STZ-induced diabetes.

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