scholarly journals Full transcriptome analysis of gene expression in liver of mice in a comparative study of quercetin efficiency on two obesity models

2020 ◽  
Vol 66 (5) ◽  
pp. 31-47
Author(s):  
N. V. Trusov ◽  
S. A. Apryatin ◽  
V. A. Shipelin ◽  
I. V. Gmoshinski
Keyword(s):  
Gene Expression ◽  
Metabolic Syndrome ◽  
Metabolic Pathways ◽  
Dietary Treatment ◽  
Transcriptome Profiling ◽  
Biologically Active ◽  
Study Gene Expression ◽  
Preclinical Trials ◽  
Metabolic Correction ◽  
Genetically Determined

BACKGROUND: Quercetin (Q; 3,3',4',5,7 - pentahydroxyflavone) can help alleviate the pathological effects of nutritional obesity and metabolic syndrome when taken as part of products for special dietary needs and food supplements. The mechanisms of action of Q at the genetic level are not well understood.AIMS: To study gene expression in liver tissue of mice with alimentary and genetically determined obesity upon intake of Q with diet.MATERIALS AND METHODS: During 46 days of the experiment on 32 male C57Bl/6J mice fed a diet with an excess of fat and fructose and 24 male genetically obese db/db mice the effect of Q in dose of 25 or 100 mg/kg of body weight was studied on differential expression of 39430 genes in mice livers by full transcriptome profiling on microchip according to the Agilent One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling protocol (version 6.8). To identify metabolic pathways (KEGGs) that were targets of Q exposure, transcriptomic data were analyzed using bioinformatics methods in an “R” environment.RESULTS: Differences were revealed in the nature of Q supplementation action in animals with dietary induced and genetically determined obesity on a number of key metabolic pathways, including the metabolism of lipids and steroids (Saa3, Cidec, Scd1, Apoa4, Acss2, Fabp5, Car3, Acacb, Insig2 genes), amino acids and nitrogen bases (Ngef, Gls2), carbohydrates (G6pdx, Pdk4), regulation of cell growth, apoptosis and proliferation (Btg3, Cgref1, Fst, Nrep Tuba8), neurotransmission (Grin2d, Camk2b), immune system reactions (CD14i, Jchain, Ifi27l2b).CONCLUSIONS: The data obtained help to explain the ambiguous effectiveness of Q, like other polyphenols, in the dietary treatment of various forms of obesity in humans, as well as to form a set of sensitive biomarkers that allow us to elucidate the effectiveness of minor biologically active food substances in preclinical trials of new means of metabolic correction of obesity and metabolic syndrome.

Identification of Differentially Expressed Genes Using cDNA-AFLP During Six Days In Vitro Tuberization of Potato

Zuriat ◽  
2015 ◽  
Vol 14 (1) ◽  
Author(s):  
Nono Carsono ◽  
Christian Bachem
Keyword(s):  
Gene Expression ◽  
Developmental Process ◽  
Expression Patterns ◽  
Induction Medium ◽  
In Vitro Tuberization ◽  
Storage Organ ◽  
Developmentally Regulated ◽  
Study Gene Expression ◽  
Differential Pattern

Tuberization in potato is a complex developmental process resulting in the differentiation of stolon into the storage organ, tuber. During tuberization, change in gene expression has been known to occur. To study gene expression during tuberization over the time, in vitro tuberization system provides a suitable tool, due to its synchronous in tuber formation. An early six days axillary bud growing on tuber induction medium is a crucial development since a large number of genes change in their expression patterns during this period. In order to identify, isolate and sequencing the genes which displaying differential pattern between tuberizing and non-tuberizing potato explants during six days in vitro tuberization, cDNA-AFLP fingerprint, method for the visualization of gene expression using cDNA as template which is amplified to generate an RNA-fingerprinting, was used in this experiment. Seventeen primer combinations were chosen based on their expression profile from cDNA-AFLP fingerprint. Forty five TDFs (transcript derived fragment), which displayed differential expressions, were obtained. Tuberizing explants had much more TDFs, which developmentally regulated, than those from non tuberizing explants. Seven TDFs were isolated, cloned and then sequenced. One TDF did not find similarity in the current databases. The nucleotide sequence of TDF F showed best similarity to invertase ezymes from the databases. The homology of six TDFs with known sequences is discussed in this paper.

Edible Mushrooms: Novel Medicinal Agents to Combat Metabolic Syndrome and Associated Diseases

2020 ◽  
Vol 26 (39) ◽  
pp. 4970-4981
Author(s):  
Yu-Tang Tung ◽  
Chun-Hsu Pan ◽  
Yi-Wen Chien ◽  
Hui-Yu Huang
Keyword(s):  
Metabolic Syndrome ◽  
Unsaturated Fatty Acids ◽  
Edible Mushroom ◽  
Biologically Active ◽  
Edible Mushrooms ◽  
Beta Glucan ◽  
Medicinal Mushrooms ◽  
Associated Diseases ◽  
Increased Risk

Metabolic syndrome is an aggregation of conditions and associated with an increased risk of developing diabetes, obesity and cardiovascular diseases (CVD). Edible mushrooms are widely consumed in many countries and are valuable components of the diet because of their attractive taste, aroma, and nutritional value. Medicinal mushrooms are higher fungi with additional nutraceutical attributes having low-fat content and a transisomer of unsaturated fatty acids along with high fiber content, biologically active compounds such as polysaccharides or polysaccharide β-glucans, alkaloids, steroids, polyphenols and terpenoids. In vitro experiments, animal models, and even human studies have demonstrated not only fresh edible mushroom but also mushroom extract that has great therapeutic applications in human health as they possess many properties such as antiobesity, cardioprotective and anti-diabetic effect. They are considered as the unmatched source of healthy foods and drugs. The focus of this report was to provide a concise and complete review of the novel medicinal properties of fresh or dry mushroom and extracts, fruiting body or mycelium and its extracts, fiber, polysaccharides, beta-glucan, triterpenes, fucoidan, ergothioneine from edible mushrooms that may help to prevent or treat metabolic syndrome and associated diseases.

scholarly journals Gene Expression and Carcass Traits Are Different between Different Quality Grade Groups in Red-Faced Hereford Steers

Animals ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 1910
Author(s):  
Bailey Engle ◽  
Molly Masters ◽  
Jane Ann Boles ◽  
Jennifer Thomson
Keyword(s):  
Gene Expression ◽  
Transcriptome Profiling ◽  
Fat Deposition ◽  
Lower Shear ◽  
The Us ◽  
Quality Grade ◽  
Longissimus Lumborum ◽  
Muscle Biochemistry ◽  
Marbling Deposition ◽  
Insight Into

Fat deposition is important to carcass value and some palatability characteristics. Carcasses with higher USDA quality grades produce more value for producers and processors in the US system and are more likely to have greater eating satisfaction. Using genomics to identify genes impacting marbling deposition provides insight into muscle biochemistry that may lead to ways to better predict fat deposition, especially marbling and thus quality grade. Hereford steers (16) were managed the same from birth through harvest after 270 days on feed. Samples were obtained for tenderness and transcriptome profiling. As expected, steaks from Choice carcasses had a lower shear force value than steaks from Select carcasses; however, steaks from Standard carcasses were not different from steaks from Choice carcasses. A significant number of differentially expressed (DE) genes was observed in the longissimus lumborum between Choice and Standard carcass RNA pools (1257 genes, p < 0.05), but not many DE genes were observed between Choice and Select RNA pools. Exploratory analysis of global muscle tissue transcriptome from Standard and Choice carcasses provided insight into muscle biochemistry, specifically the upregulation of extracellular matrix development and focal adhesion pathways and the downregulation of RNA processing and metabolism in Choice versus Standard. Additional research is needed to explore the function and timing of gene expression changes.

Study of DYRK1B gene expression and its association with metabolic syndrome in a small cohort of Egyptians

2021 ◽  
Author(s):  
Yara Ahmed Mohamed ◽  
H. M. Hassaneen ◽  
Mohamed A. El-Dessouky ◽  
Gehan Safwat ◽  
Naglaa Abu-Mandil Hassan ◽  
...  
Keyword(s):  
Gene Expression ◽  
Metabolic Syndrome ◽  
Small Cohort

scholarly journals Evaluation of potential tumor markers that may predict neoadjuvant treatment efficiency in rectal cancer

2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Fatma Demet Arslan ◽  
Ayse Kocak ◽  
Cengiz Aydın ◽  
Emel Ebru Pala ◽  
Dilek Oncel ◽  
...  
Keyword(s):  
Gene Expression ◽  
Rectal Cancer ◽  
Tumor Markers ◽  
Locally Advanced ◽  
Neoadjuvant Treatment ◽  
Beclin 1 ◽  
Tumor Regression Grade ◽  
Protein Levels ◽  
Study Gene Expression ◽  
Regression Grade

AbstractObjectivesThe recurrence of rectal cancer or its resistance to neoadjuvant treatment develops due to the adaptation to hypoxia, apoptosis or autophagy. Survivin, one of the inhibitors of apoptosis; Beclin 1, which is a positive regulator in the autophagy pathway; and hypoxia-inducible factor-1α (HIF-1α) and carbonic anhydrase-9 (CA9), which are associated with tumor tissue hypoxia, may be related to resistance to treatment. Our aim was to evaluate the potential tumor markers that may help to monitor the response to neoadjuvant treatment in locally advanced rectal cancer (RC).MethodsTwenty-five patients with locally advanced RC were included in the study. Gene expression and protein levels of Beclin 1, Survivin, HIF-1α, and CA9 were analyzed in fresh tissue specimens and blood samples. The relationships of these markers to tumor staging and regression grade were evaluated.ResultsHigher blood CA9 gene expression levels and lower blood HIF-1α protein levels were found in the response group according to tumor regression grade. After neoadjuvant treatment, tissue Beclin 1 and blood Survivin gene expressions and tissue CA9, blood Beclin 1 and blood HIF-1α protein levels decreased significantly.ConclusionBeclin 1, Survivin, HIF-1α ve CA9 may help to predict the effects of the applied treatment approach.

scholarly journals Multilayer modelling of the human transcriptome and biological mechanisms of complex diseases and traits

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Tiago Azevedo ◽  
Giovanna Maria Dimitri ◽  
Pietro Lió ◽  
Eric R. Gamazon
Keyword(s):  
Gene Expression ◽  
The Cancer Genome Atlas ◽  
Human Transcriptome ◽  
Reactive Protein ◽  
Cancer Genome Atlas ◽  
New Gene ◽  
Improved Performance ◽  
Genomic Resource ◽  
The Uk ◽  
Genetically Determined

AbstractHere, we performed a comprehensive intra-tissue and inter-tissue multilayer network analysis of the human transcriptome. We generated an atlas of communities in gene co-expression networks in 49 tissues (GTEx v8), evaluated their tissue specificity, and investigated their methodological implications. UMAP embeddings of gene expression from the communities (representing nearly 18% of all genes) robustly identified biologically-meaningful clusters. Notably, new gene expression data can be embedded into our algorithmically derived models to accelerate discoveries in high-dimensional molecular datasets and downstream diagnostic or prognostic applications. We demonstrate the generalisability of our approach through systematic testing in external genomic and transcriptomic datasets. Methodologically, prioritisation of the communities in a transcriptome-wide association study of the biomarker C-reactive protein (CRP) in 361,194 individuals in the UK Biobank identified genetically-determined expression changes associated with CRP and led to considerably improved performance. Furthermore, a deep learning framework applied to the communities in nearly 11,000 tumors profiled by The Cancer Genome Atlas across 33 different cancer types learned biologically-meaningful latent spaces, representing metastasis (p < 2.2 × 10−16) and stemness (p < 2.2 × 10−16). Our study provides a rich genomic resource to catalyse research into inter-tissue regulatory mechanisms, and their downstream consequences on human disease.

scholarly journals Transcriptome profiling of immune tissues reveals habitat‐specific gene expression between lake and river sticklebacks

2016 ◽  
Vol 25 (4) ◽  
pp. 943-958 ◽  
Author(s):  
Yun Huang ◽  
Frédéric J. J. Chain ◽  
Mahesh Panchal ◽  
Christophe Eizaguirre ◽  
Martin Kalbe ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcriptome Profiling ◽  
Specific Gene ◽  
Specific Gene Expression ◽  
Immune Tissues

scholarly journals Pathophysiological, Genetic and Gene Expression Features of a Novel Rodent Model of the Cardio-Metabolic Syndrome

PLoS ONE ◽  
2008 ◽  
Vol 3 (8) ◽  
pp. e2962 ◽  
Author(s):  
Robert H. Wallis ◽  
Stephan C. Collins ◽  
Pamela J. Kaisaki ◽  
Karène Argoud ◽  
Steven P. Wilder ◽  
...  
Keyword(s):  
Gene Expression ◽  
Metabolic Syndrome ◽  
Rodent Model
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