scholarly journals Evidence of the Complexity of Gene Expression Analysis in Fish Wild Populations

2017 ◽  
Vol 2017 ◽  
pp. 1-14 ◽  
Author(s):  
Mbaye Tine
Keyword(s):  
Gene Expression ◽  
Differential Expression ◽  
Expression Analysis ◽  
Gene Expression Analysis ◽  
Expression Patterns ◽  
Cell Volume Regulation ◽  
Mitogen Activated Protein Kinase ◽  
Wild Populations ◽  
Natural Habitats ◽  
Evolutionary Forces

The present work examines the induction of theband 3 anion transport protein,mitogen-activated protein kinase, andlactate dehydrogenase, respectively related to osmolyte transport, cell volume regulation, and energy production in the gills of two tilapia strains exposed to either freshwater or hypersaline water. Overall, genes showed similar expression patterns between strains. However, a wild population survey across a range of natural habitats and salinities did not reveal the expected patterns. Although significant, the correlations between gene expression and salinity were slightly ambiguous and did not show any link with phenotypic differences in life history traits previously reported between the same populations. The differential expression was also not associated with the population genetic structure inferred from neutral markers. The results suggest that the differential expression observed is not the result of evolutionary forces such as genetic drift or adaptation by natural selection. Instead, it can be speculated that genes responded to various abiotic and biotic stressors, including factors intrinsic to animals. This study provides clear evidence of the complexity of gene expression analysis in wild populations and shows that more attention needs to be paid when selecting candidates as potential biomarkers for monitoring adaptive responses to a specific environmental perturbation.

Identification of candidate tumor related genes using comprehensive gene expression analysis of neuroblastic tumors

2006 ◽  
Vol 24 (18_suppl) ◽  
pp. 9051-9051
Author(s):  
J. Mora ◽  
C. Lavarino ◽  
G. Domenech ◽  
J. Rios ◽  
W. Gerald ◽  
...  
Keyword(s):  
Gene Expression ◽  
Differential Expression ◽  
Expression Analysis ◽  
Gene Expression Analysis ◽  
Protein Biosynthesis ◽  
Neuroblastoma Cell ◽  
Genetic Alterations ◽  
Altered Expression ◽  
Stage 4 ◽  
Neuroblastic Tumors

9051 Background: Neuroblastic tumors (NBTs) represent a heterogeneous and relatively well defined spectrum of neoplastic diseases. We performed gene expression analysis to molecularly characterize the distinct clinicobiological subtypes of NBTs. Methods: Gene expression analysis of 106 NBTs (10 ganglioneuromas, 10 stage 4s, 29 loco-regional (stages 1, 2, 3), and 57 stage 4) and 12 neuroblastoma cell lines was performed using Affymetrix Genechip Human Genome U95 Set Arrays. Differential expression between predefined groups of biological and clinical relevance was determined by differences >3 standard deviations between the means for groups, step-down permutation and false discovery rate methods. Results: Gene expression analysis of clinically defined groups including stage 4 infants versus children, metastatic versus non metastatic, and stroma poor loco-regional versus stage 4, revealed that many differentially expressed genes mapped to chromosomal regions with well described recurrent abnormalities in NBTs (chromosomes 1, 11, 17, 19 and X). Pairwise comparison analysis of biologically defined groups, including triploid versus diploid/tetraploid NBTs, identified significantly discriminating genes that map to the same chromosomal regions. Gene expression analysis of MYCN-amplified versus MYCN non amplified NBTs, confirmed a functional overrepresentation for genes involved in protein biosynthesis. Conclusions: Gene expression profile analysis of clinically and biologically relevant subgroups of NBTs revealed differential expression of genes at specific chromosomal regions known to have strong association between genetic alterations and NBT clinical features. The identification of altered expression helps to define critical chromosomal regions and identify tumor related candidate genes within each region. No significant financial relationships to disclose.

scholarly journals The Effect of Simulated Microgravity On The Antioxidant Capacity And Alkaloid Formation In The Hyoscyamus Niger

2021 ◽  
Author(s):  
Roghayeh Pourhabibian ◽  
Alireza Iranbakhsh ◽  
Mostafa Ebadi ◽  
Halimeh Hassanpour ◽  
Azadeh Hekmat
Keyword(s):  
Gene Expression ◽  
Antioxidant Activity ◽  
Antioxidant Capacity ◽  
Expression Analysis ◽  
Gene Expression Analysis ◽  
Simulated Microgravity ◽  
Tropane Alkaloids ◽  
Mitogen Activated Protein Kinase ◽  
Hyoscyamus Niger ◽  
Pal Activity

Abstract Microgravity is one of the most important abiotic stresses in space. In the case of plant exposure to short term microgravity, plants establish strategies to response to these stresses and promote growth and survival. We hypothesized that the simulated microgravity can promote the antioxidant capacity and the formation of secondary metabolites such as tropane alkaloids in the Hyoscyamus niger. Callus induction was conducted by putting hypocotyl segments of H. niger seedlings in solid MS medium supplemented with 1 mg L−1 2,4-D and 1 mg L−1 BAP growth regulators. Then, the sub-cultured calli were placed on a clinostat for 3, 7 and 10 days. We performed Atropine and Scopolamine determination through HPLC. PAL (Phenyle alanine amonalyase) and antioxidant activity were also determined. Gene expression analysis of jasmonic acid (JA), Hyoscyamine 6-beta Hydroxylase (H6H), Putrescine N-methyltransferase (PMT), mitogen-activated protein kinase (MAPK) and ethylene responsive element binding (EREB) was performed using quantitative real time PCR. Findings showed that microgravity had a positive effect on the antioxidant capacity, Atropine and Scopolamine production in the H. niger calli. However, microgravity had a negative effect on the PAL activity. Furthermore, gene expression analysis indicated that microgravity significantly induced gene expression of the H6H, PMT and JA. It was also revealed that callus growth, carbohydrate and protein content increased in response to microgravity treatment. We conclude that microgravity can be considered as a potent factor to induce plant antioxidant activity and tropane alkaloids formation to be applicable in the pharmaceutical and medicinal industries.

Comprehensive genomic analysis in metastatic pancreatic ductal adenocarcinoma (PDAC).

2016 ◽  
Vol 34 (4_suppl) ◽  
pp. 285-285
Author(s):  
Hui-Li Wong ◽  
Martin Jones ◽  
Peter Eirew ◽  
Joanna Karasinska ◽  
Kasmintan A Schrader ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Analysis ◽  
Gene Expression Analysis ◽  
De Novo ◽  
Expression Patterns ◽  
Genomic Analysis ◽  
Ductal Adenocarcinoma ◽  
Tumor Biopsy ◽  
Significant Difference ◽  
Gene Expression Signatures

285 Background: In the absence of defined tumor molecular subtypes and validated predictive markers, PDAC has been largely treated as a single disease. Recent studies of molecular subtyping in PDAC reveal a complex mutational landscape with data suggesting the presence of genomic and gene expression signatures that may have prognostic and therapeutic significance. These studies predominantly focused on resected PDAC and lack data on metastatic tumors. We aim to explore the clinical utility of whole genome sequencing (WGS) and transcriptome analysis from metastatic biopsy samples in patients (pts) with advanced PDAC. Methods: Pts with incurable advanced cancers undergo tumor biopsy for in-depth WGS and RNA sequencing (RNASeq) as part of an ongoing prospective study (NCT02155621). Comprehensive bioinformatics analysis is performed to identify somatic cancer aberrations, gene expression changes and cellular pathway abnormalities. Here we describe clinical and molecular data on the subset of pts with advanced PDAC. Results: Sixteen PDAC pts have been enrolled; median age 59 years, 8 males (50%), 10 with de novo metastases (63%). Full WGS and RNASeq were completed in 11 pts (1 failed biopsy, 4 had insufficient tumor). KRAS codon 12 and TP53 mutations were present in all but one pt. CDKN2A and SMAD4 were also frequently altered (7 and 4 pts respectively). Gene expression analysis for classical and basal subtypes similar to those recently described (PMID 26343385) identified 3 and 6 pts with classical and basal expression patterns respectively, and 2 pts with mixed expression. Overall survival (OS) was significantly worse for the basal subtype vs all others (median OS 7 vs. 13.9 months (ms), p = 0.017). When separated into 3 subtypes a significant difference was still noted (median OS 7 ms in basal, 19.2 ms in classical and 11.8 ms in mixed subtype, p = 0.032). Conclusions: WGS analysis demonstrated a similar mutation pattern to that described in resectable PDAC, with no novel actionable mutations identified. Gene expression analysis demonstrated the presence of distinct gene expression signatures significantly associated with outcome, despite small pt numbers. These results need to be validated prospectively in larger cohorts. Clinical trial information: NCT02155621.

scholarly journals Comparison of phenol-based and alternative RNA isolation methods for gene expression analyses

2010 ◽  
Vol 75 (8) ◽  
pp. 1053-1061 ◽  
Author(s):  
Ksenija Jakovljevic ◽  
Milena Spasic ◽  
Emina Malisic ◽  
Jelena Dobricic ◽  
Ana Krivokuca ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Analysis ◽  
Whole Blood ◽  
Gene Expression Analysis ◽  
Expression Patterns ◽  
Rna Extraction ◽  
Rna Isolation ◽  
Specific Gene ◽  
Isolation Methods ◽  
Gene Expression Analyses

The widespread use of gene expression analyses has been limited by the lack of a critical evaluation of the methods used to extract nucleic acids from human tissues. For evaluating gene expression patterns in whole blood or leukocytes, the method of RNA isolation needs to be considered as a critical variable in the design of the experiment. Quantitative real-time PCR (qPCR) is widely used for the quantification of gene expression in today?s clinical practice. Blood samples as a preferred RNA source for qPCR should be carefully handled and prepared to not inhibit gene expression analyses. The present study was designed to compare the frequently used guanidine thiocyanate-phenol-chloroformbased method (TRI Reagent?) with two alternative RNA isolation methods (6100 PrepStation and QIAamp?) from whole blood or leukocytes for the purpose of gene expression analysis in chronic myeloid leukemia (CML) patients. Based on the results of this study, for the best combination of yield and RNA extraction purity, taking into account the necessary amount of the clinical sample and performance time, the protocol using phenol-based TRI Reagent? for RNA extraction from leukocytes is suggested as the most suitable protocol for this specific gene expression analysis.

scholarly journals Comprehensive Gene Expression Analysis Detects Global Reduction of Proteasome Subunits in Schizophrenia

2020 ◽  
Author(s):  
Libi Hertzberg ◽  
Nicola Maggio ◽  
Inna Muler ◽  
Assif Yitzhaky ◽  
Michael Majer ◽  
...  
Keyword(s):  
Gene Expression ◽  
Differential Expression ◽  
Expression Analysis ◽  
Gene Expression Analysis ◽  
Enrichment Analysis ◽  
Pathway Enrichment Analysis ◽  
Down Regulation ◽  
Pathway Enrichment ◽  
Main Challenge ◽  
Proteasome Subunits

Abstract Background The main challenge in the study of schizophrenia is its high heterogeneity. While it is generally accepted that there exist several biological mechanisms that may define distinct schizophrenia subtypes, they have not been identified yet. We performed comprehensive gene expression analysis to search for molecular signals that differentiate schizophrenia patients from healthy controls and examined whether an identified signal was concentrated in a subgroup of the patients. Methods Transcriptome sequencing of 14 superior temporal gyrus (STG) samples of subjects with schizophrenia and 15 matched controls from the Stanley Medical Research Institute (SMRI) was performed. Differential expression and pathway enrichment analysis results were compared to an independent cohort. Replicability was tested on 6 additional independent datasets. Results The 2 STG cohorts showed high replicability. Pathway enrichment analysis of the down-regulated genes pointed to proteasome-related pathways. Meta-analysis of differential expression identified down-regulation of 12 of 39 proteasome subunit genes in schizophrenia. The signal of proteasome subunits down-regulation was replicated in 6 additional datasets (overall 8 cohorts with 267 schizophrenia and 266 control samples, from 5 brain regions). The signal was concentrated in a subgroup of patients with schizophrenia. Conclusions We detected global down-regulation of proteasome subunits in a subgroup of patients with schizophrenia. We hypothesize that the down-regulation of proteasome subunits leads to proteasome dysfunction that causes accumulation of ubiquitinated proteins, which has been recently detected in a subgroup of schizophrenia patients. Thus, down-regulation of proteasome subunits might define a biological subtype of schizophrenia.

scholarly journals Gene expression tomography

2002 ◽  
Vol 8 (2) ◽  
pp. 159-167 ◽  
Author(s):  
VANESSA M. BROWN ◽  
ALEX OSSADTCHI ◽  
ARSHAD H. KHAN ◽  
SANJIV S. GAMBHIR ◽  
SIMON R. CHERRY ◽  
...  
Keyword(s):  
Gene Expression ◽  
Image Reconstruction ◽  
Expression Analysis ◽  
Gene Expression Analysis ◽  
Expression Patterns ◽  
Brain Slices ◽  
Axial Rotation ◽  
Gene Expression Patterns ◽  
Rnase Protection ◽  
The Brain

Gene expression tomography, or GET, is a new method to increase the speed of three-dimensional (3-D) gene expression analysis in the brain. The name is evocative of the method’s dual foundations in high-throughput gene expression analysis and computerized tomographic image reconstruction, familiar from techniques such as positron emission tomography (PET) and X-ray computerized tomography (CT). In GET, brain slices are taken using a cryostat in conjunction with axial rotation about independent axes to create a series of “views” of the brain. Gene expression information obtained from the axially rotated views can then be used to recreate 3-D gene expression patterns. GET was used to successfully reconstruct images of tyrosine hydroxylase gene expression in the mouse brain, using both RNase protection and real-time quantitative reverse transcription PCR (QRT-PCR). A Monte-Carlo analysis confirmed the good quality of the GET image reconstruction. By speeding acquisition of gene expression patterns, GET may help improve our understanding of the genomics of the brain in both health and disease.

scholarly journals Gene Expression Analysis in Four Dogs With Canine Pemphigus Clinical Subtypes Reveals B Cell Signatures and Immune Activation Pathways Similar to Human Disease

2021 ◽  
Vol 8 ◽  
Author(s):  
Haya S. Raef ◽  
Cesar Piedra-Mora ◽  
Neil B. Wong ◽  
Diana Junyue Ma ◽  
Clement N. David ◽  
...  
Keyword(s):  
Gene Expression ◽  
B Cell ◽  
Expression Analysis ◽  
Clinical Characteristics ◽  
Gene Expression Analysis ◽  
Expression Patterns ◽  
Disease Prognosis ◽  
Examine Gene Expression ◽  
Perform Gene Expression ◽  
Activation Pathways

Pemphigus is a group of autoimmune-mediated mucocutaneous blistering diseases characterized by acantholysis. Pemphigus has also been recognized in dogs and shares similar clinical characteristics and variants with human pemphigus. While relationships between human and canine pemphigus have been reported, gene expression patterns across species have not been described in the literature. We sought to perform gene expression analysis of lesional skin tissue from four dogs with various forms of pemphigus to examine gene expression during spontaneous disease in dogs. We found increased T and B cell signatures in canine pemphigus lesions compared to controls, as well as significant upregulation of CCL3, CCL4, CXCL10, and CXCL8 (IL8), among other genes. Similar chemokine/cytokine expression patterns and immune infiltrates have been reported in humans, suggesting that these genes play a role in spontaneous disease. Direct comparison of our dataset to previously published human pemphigus datasets revealed five conserved differentially expressed genes: CD19, WIF1, CXCL10, CD86, and S100A12. Our data expands our understanding of pemphigus and facilitates identification of biomarkers for prediction of disease prognosis and treatment response, which may be useful for future veterinary and human clinical trials.

scholarly journals P015 Differential expression in colitis-associated cancer compared to Crohn′s disease and ulcerative colitis

2021 ◽  
Vol 15 (Supplement_1) ◽  
pp. S135-S136
Author(s):  
S Manna ◽  
M Sehn ◽  
D Cardoso da Silva ◽  
S Elezkurtaj ◽  
R Cineus ◽  
...  
Keyword(s):  
Gene Expression ◽  
Ulcerative Colitis ◽  
Data Analysis ◽  
Differential Expression ◽  
Expression Analysis ◽  
Gene Expression Analysis ◽  
Gene Panel ◽  
Heat Maps ◽  
Mesenchymal Transition ◽  
Mouse Colon

Abstract Background Crohn’s disease (CD) and ulcerative colitis (UC) are autoimmune-mediated conditions of chronic inflammation affecting the intestinal mucosa, that pose a lifelong risk to patients to develop a colitis-associated carcinoma (CAC). Much of current knowledge on mechanisms in CAC development result from murine CAC models, while studies on human CAC carcinogenesis are scarce. Thus, in our present study, we aimed to contribute to the understanding of colitis-associated carcinogenesis by comparative analysis of gene expression in human samples and further validation of these findings in colon organoids. Methods RNA isolation was done from microdissected surgical colon specimen from 60 patients that suffered from either UC, CD, UC-CAC, CD-CAC or inflammation-free healthy controls (10 patients per group). Nanostring nCounterTM technology with a gene panel comprising >630 genes was performed to examine genes focusing on mucosal immunology, epithelial barrier/polarity. nSolverTM data analysis software was used for primary data analysis and statistics. Patients were grouped using expression patterns (by heat maps), differential expression and pathway analysis. For organoid cultures, crypts were isolated from mouse colon and cultured using the R-Spondin method. Organoids were subjected to osteopontin treatment. Consecutively, RNA was isolated. This was followed by gene expression analysis of core EMT (epithelial to mesenchymal transition) transcription factors (TFs) focusing on Twist1, Snai1, Snai2 by RT-PCR. Results Heat maps generated from the expression data revealed close-to-optimal grouping recapitulating the clinical subgroups. Differential expression comparing CD with CD-CAC and UC with UC-CAC identified 203 and 271 differentially expressed genes, respectively. Genes most significantly upregulated included SPP1/Osteopontin (OPN), GRHL2 and EMT signature gene as fibronectin1 and ZEB1, generating the hypothesis of OPN driving EMT and thereby inducing inflammation-associated carcinogenesis. Furthermore, mouse colon organoids treated with OPN (50ng/µl) revealed an increased expression by 3fold of core the EMT TFs Twist1, Snai1, Snai2. Conclusion We provide a comprehensive quantitative gene expression analysis for CAC with comparison of gene expression in CAC to the respective underlying IBD, CD and UC. Identified upregulated or downregulated genes allow to allocate signal transduction pathways important for CAC carcinogenesis. OPN as the most upregulated gene in CAC in our gene panel might be crucial for regulating EMT in CAC carcinogenesis. Thus, our findings uncover the role of OPN in CAC carcinogenesis.

scholarly journals Genome-Wide Identification and Gene Expression Analysis of ABA Receptor Family Genes in Brassica juncea var. tumida

Genes ◽  
2019 ◽  
Vol 10 (6) ◽  
pp. 470 ◽  
Author(s):  
Cheng ◽  
Zhong ◽  
Cai ◽  
Su ◽  
Li
Keyword(s):  
Gene Expression ◽  
Brassica Juncea ◽  
Expression Analysis ◽  
Gene Expression Analysis ◽  
Expression Patterns ◽  
Plant Response ◽  
Specific Gene ◽  
Cis Elements ◽  
Physiological Processes ◽  
Aba Receptor

Abscisic acid (ABA) plays important roles in multiple physiological processes, such as plant response to stresses and plant development. The ABA receptors pyrabactin resistance (PYR)/ PYR1-like (PYL)/regulatory components of ABA receptor (RCAR) play a crucial role in ABA perception and signaling. However, little is known about the details regarding PYL family genes in Brassica juncea var. tumida. Here, 25 PYL family genes were identified in B. juncea var. tumida genome, including BjuPYL3, BjuPYL4s, BjuPYL5s, BjuPYL6s, BjuPYL7s, BjuPYL8s, BjuPYL10s, BjuPYL11s, and BjuPYL13. The results of phylogenic analysis and gene structure showed that the PYL family genes performed similar gene characteristics. By analyzing cis-elements in the promoters of those BjuPYLs, several hormone and stress related cis-elements were found. The results of gene expression analysis showed that the ABA receptor homologous genes were induced by abiotic and biotic stress. The tissue-specific gene expression patterns of BjuPYLs also suggested those genes might regulate the stem swelling during plant growth. These findings indicate that BjuPYLs are involved in plant response to stresses and organ development. This study provides valuable information for further functional investigations of PYL family genes in B. juncea var. tumida.

scholarly journals Comparative uterine gene expression analysis after dioxin and estradiol administration

2004 ◽  
Vol 33 (3) ◽  
pp. 763-771 ◽  
Author(s):  
H Watanabe ◽  
A Suzuki ◽  
M Goto ◽  
S Ohsako ◽  
C Tohyama ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Analysis ◽  
Gene Expression Analysis ◽  
Estrogenic Activity ◽  
Expression Patterns ◽  
Environmental Pollutant ◽  
Abnormal Development ◽  
Gene Expression Patterns ◽  
Endocrine Effects ◽  
Antiestrogenic Activity

The environmental pollutant 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) adversely affects many organisms. TCDD exposure is known to be associated with abnormal development, hepatotoxicity and endocrine effects. It has also been reported to have antiestrogenic activity in addition to estrogenic activity. In order to clarify the effects of TCDD in the uterus, we evaluated the patterns of gene expression after TCDD and estradiol administration. Of the 10 000 arrayed genes, only a few were affected by both estradiol and TCDD. Although the subset of genes that responded to estrogen was also activated by TCDD, the response to TCDD was more limited than that observed in response to estradiol. Therefore, according to our analysis of gene expression patterns, TCDD had partial and weak estrogenic activity in the uterus.

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