scholarly journals Physiological System Dysregulation in Gene Expression Correlates Negatively with Age

2020 ◽  
Author(s):  
Frédérik Dufour ◽  
Pierre-Étienne Jacques ◽  
Alan A. Cohen
Keyword(s):  
Gene Expression ◽  
Human Peripheral Blood ◽  
Expression Systems ◽  
Metabolic Functions ◽  
Clinical Biomarkers ◽  
Gene Expression Heterogeneity ◽  
Stress Functions ◽  
Response To Stress ◽  
Public Datasets ◽  
Identify Gene Expression

AbstractWe attempted to identify gene expression systems that dysregulate with age in human peripheral blood samples across five public datasets. Dysregulation of gene ontology (GO)-defined systems was measured using the Mahalanobis distance (DM), a measure of multivariant aberrance. We expected many weak positive DM-age correlations, indicating loss of homeostatic control. Out of the 5180 GO terms tested, we found 230 systems that replicated in at least three datasets. Surprisingly, all 230 systems showed negative DM-age correlations, in contrast to findings with clinical biomarkers. These systems were mostly metabolic functions related to small molecules and nitrogen compounds, transport functions, biosynthetic processes and response to stress functions. These results suggest a loss of responsiveness in these gene expression systems during the aging process, and contrast to some previous literature showing increased gene expression heterogeneity with age.

scholarly journals High-throughput transcriptomic analysis of human primary hepatocyte spheroids exposed to per- and polyfluoroalkyl substances (PFAS) as a platform for relative potency characterization

2021 ◽  
Author(s):  
A Rowan-Carroll ◽  
A Reardon ◽  
K Leingartner ◽  
R Gagné ◽  
A Williams ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cholesterol Biosynthesis ◽  
Health Hazard ◽  
Biological Responses ◽  
Similar Gene Expression Profile ◽  
Transcriptional Changes ◽  
Hazard And Risk ◽  
Hepatocyte Spheroids ◽  
Similar Gene ◽  
Identify Gene Expression

Abstract Per- and poly-fluoroalkyl substances (PFAS) are widely found in the environment because of their extensive use and persistence. Although several PFAS are well studied, most lack toxicity data to inform human health hazard and risk assessment. This study focussed on four model PFAS: perfluorooctanoic acid (PFOA; 8 carbon), perfluorobutane sulfonate (PFBS; 4 carbon), perfluorooctane sulfonate (PFOS; 8 carbon), and perfluorodecane sulfonate (PFDS; 10 carbon). Human primary liver cell spheroids (pooled from 10 donors) were exposed to 10 concentrations of each PFAS and analyzed at four time-points. The approach aimed to: (1) identify gene expression changes mediated by the PFAS; (2) identify similarities in biological responses; (3) compare PFAS potency through benchmark concentration analysis; and (4) derive bioactivity exposure ratios (ratio of the concentration at which biological responses occur, relative to daily human exposure). All PFAS induced transcriptional changes in cholesterol biosynthesis and lipid metabolism pathways, and predicted PPARα activation. PFOS exhibited the most transcriptional activity and had a highly similar gene expression profile to PFDS. PFBS induced the least transcriptional changes and the highest benchmark concentration (i.e., was the least potent). The data indicate that these PFAS may have common molecular targets and toxicities, but that PFOS and PFDS are the most similar. The transcriptomic bioactivity exposure ratios derived here for PFOA and PFOS were comparable to those derived using rodent apical endpoints in risk assessments. These data provide a baseline level of toxicity for comparison with other known PFAS using this testing strategy.

scholarly journals On the way toward regulatable expression systems in acetic acid bacteria: target gene expression and use cases

2021 ◽  
Author(s):  
Philipp Moritz Fricke ◽  
Angelika Klemm ◽  
Michael Bott ◽  
Tino Polen
Keyword(s):  
Gene Expression ◽  
Acetic Acid ◽  
Literature Search ◽  
Target Gene ◽  
Target Genes ◽  
Recombinant Dna ◽  
Acetic Acid Bacteria ◽  
Homoserine Lactone ◽  
Expression Systems ◽  
Target Gene Expression

Abstract Acetic acid bacteria (AAB) are valuable biocatalysts for which there is growing interest in understanding their basics including physiology and biochemistry. This is accompanied by growing demands for metabolic engineering of AAB to take advantage of their properties and to improve their biomanufacturing efficiencies. Controlled expression of target genes is key to fundamental and applied microbiological research. In order to get an overview of expression systems and their applications in AAB, we carried out a comprehensive literature search using the Web of Science Core Collection database. The Acetobacteraceae family currently comprises 49 genera. We found overall 6097 publications related to one or more AAB genera since 1973, when the first successful recombinant DNA experiments in Escherichia coli have been published. The use of plasmids in AAB began in 1985 and till today was reported for only nine out of the 49 AAB genera currently described. We found at least five major expression plasmid lineages and a multitude of further expression plasmids, almost all enabling only constitutive target gene expression. Only recently, two regulatable expression systems became available for AAB, an N-acyl homoserine lactone (AHL)-inducible system for Komagataeibacter rhaeticus and an l-arabinose-inducible system for Gluconobacter oxydans. Thus, after 35 years of constitutive target gene expression in AAB, we now have the first regulatable expression systems for AAB in hand and further regulatable expression systems for AAB can be expected. Key points • Literature search revealed developments and usage of expression systems in AAB. • Only recently 2 regulatable plasmid systems became available for only 2 AAB genera. • Further regulatable expression systems for AAB are in sight.

scholarly journals Effect of dithiocyano-methane on hexose monophosphate pathway in the respiratory metabolism of Escherichia coli

AMB Express ◽  
2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Yanfeng Chen ◽  
Wenjie Ke ◽  
Huabin Qin ◽  
Siwei Chen ◽  
Limei Qin ◽  
...  
Keyword(s):  
Gene Expression ◽  
Escherichia Coli ◽  
Control Group ◽  
Respiratory Metabolism ◽  
Hexose Monophosphate ◽  
Hexose Monophosphate Pathway ◽  
Response To Stress ◽  
Glucose Decomposition ◽  
Decomposition Pathway ◽  
Glucose 6 Phosphate Dehydrogenase

Abstract This paper studied the inhibitory effects of dithiocyano-methane (DM) on the glucose decomposition pathway in the respiratory metabolism of Escherichia coli. We investigated the effects of DM on the activities of key enzymes (ATPase and glucose-6-phosphate dehydrogenase, G6PDH), the levels of key product (nicotinamide adenosine denucleotide hydro-phosphoric acid, NADPH), and gene expression in the hexose monophosphate pathway (HMP). The results showed that the minimum inhibitory concentration (MIC) and the minimum bactericide concentration (MBC) of DM against the tested strains were 5.86 mg/L and 11.72 mg/L, respectively. Bacteria exposed to DM at MIC demonstrated an increase in bacterial ATPase and G6PDH activities, NADPH levels, and gene expression in the HMP pathway compared to bacteria in the control group, which could be interpreted as a behavioral response to stress introduced by DM. However, DM at a lethal concentration of 10 × MIC affected glucose decomposition by inhibiting mainly the HMP pathway in E. coli.

Construction of gene expression systems in insect cell lines using promoters from the silkworm, Bombyx mori

2008 ◽  
Vol 133 (1) ◽  
pp. 9-17 ◽  
Author(s):  
Jae Man Lee ◽  
Masateru Takahashi ◽  
Hiroaki Mon ◽  
Hitoshi Mitsunobu ◽  
Katsumi Koga ◽  
...  
Keyword(s):  
Gene Expression ◽  
Bombyx Mori ◽  
Cell Lines ◽  
Insect Cell ◽  
Expression Systems ◽  
Insect Cell Lines ◽  
Silkworm Bombyx Mori

Gene Expression Analysis in Human Peripheral Blood Cells after 900 MHz RF-EMF Short-Term Exposure

2018 ◽  
Vol 189 (5) ◽  
pp. 529-540 ◽  
Author(s):  
Andreas Lamkowski ◽  
Matthias Kreitlow ◽  
Jörg Radunz ◽  
Martin Willenbockel ◽  
Frank Sabath ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Analysis ◽  
Peripheral Blood ◽  
Blood Cells ◽  
Gene Expression Analysis ◽  
Human Peripheral Blood ◽  
Peripheral Blood Cells ◽  
Short Term ◽  
Short Term Exposure

Gerea: Prediction Of Gene Expression Regulators From Transcriptome Profiling Data To Transition Networks

2021 ◽  
Vol 16 ◽  
Author(s):  
Min Yao ◽  
Caiyun Jiang ◽  
Chenglong Li ◽  
Yongxia Li ◽  
Shan Jiang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Networks ◽  
Target Gene ◽  
Gene Expression Regulation ◽  
Transcriptome Profiling ◽  
Expression Regulation ◽  
Mouse Gene ◽  
Mouse Gene Expression ◽  
Causality Inference ◽  
Identify Gene Expression

Background: Mammalian genes are regulated at the transcriptional and post-transcriptional levels. These mechanisms may involve the direct promotion or inhibition of transcription via a regulator or post-transcriptional regulation through factors such as micro (mi)RNAs. Objective: This study aimed to construct gene regulation relationships modulated by causality inference-based miRNA-(transition factor)-(target gene) networks and analyze gene expression data to identify gene expression regulators. Methods: Mouse gene expression regulation relationships were manually curated from literature using a text mining method which was then employed to generate miRNA-(transition factor)-(target gene) networks. An algorithm was then introduced to identify gene expression regulators from transcriptome profiling data by applying enrichment analysis to these networks. Results: A total of 22,271 mouse gene expression regulation relationships were curated for 4,018 genes and 242 miRNAs. GEREA software was developed to perform the integrated analyses. We applied the algorithm to transcriptome data for synthetic miR-155 oligo-treated mouse CD4+ T-cells and confirmed that miR-155 is an important network regulator. The software was also tested on publicly available transcriptional profiling data for Salmonella infection, resulting in the identification of miR-125b as an important regulator. Conclusion: The causality inference-based miRNA-(transition factor)-(target gene) networks serve as a novel resource for gene expression regulation research, and GEREA is an effective and useful adjunct to the currently available methods. The regulatory networks and the algorithm implemented in the GEREA software package are available under a free academic license at website : http://www.thua45.cn/gerea.

scholarly journals UGA Read-Through Artifacts—When Popular Gene Expression Systems Need a pATCH

BioTechniques ◽  
1998 ◽  
Vol 24 (5) ◽  
pp. 789-794 ◽  
Author(s):  
Gavin MacBeath ◽  
Peter Kast
Keyword(s):  
Gene Expression ◽  
Expression Systems

Cytotoxic effect of doxycycline and its implications for tet-on gene expression systems

2003 ◽  
Vol 318 (1) ◽  
pp. 152-154 ◽  
Author(s):  
Gennady Ermak ◽  
Vincenzo J Cancasci ◽  
Kelvin J.A Davies
Keyword(s):  
Gene Expression ◽  
Cytotoxic Effect ◽  
Expression Systems
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