scholarly journals Transcriptional Characterizations of Differences between Eutopic and Ectopic Endometrium

Endocrinology ◽  
2006 ◽  
Vol 147 (1) ◽  
pp. 232-246 ◽  
Author(s):  
Yan Wu ◽  
André Kajdacsy-Balla ◽  
Estil Strawn ◽  
Zainab Basir ◽  
Gloria Halverson ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Patterns ◽  
Molecular Genetic ◽  
Uterine Cavity ◽  
Gene Clusters ◽  
Mapk Signaling ◽  
Menstrual Phase ◽  
Expression Analysis Systematic Explorer ◽  
Genetic Mechanisms ◽  
Gynecological Disease

Endometriosis, defined as the presence of endometrial glandular and stromal cells outside the uterine cavity, is a common gynecological disease with poorly understood pathogenesis. Using laser capture microdissection and a cDNA microarray with 9600 genes/expressed sequence tags (ESTs), we have conducted a comprehensive profiling of gene expression differences between the ectopic and eutopic endometrium taken from 12 women with endometriosis adjusted for menstrual phase and the location of the lesions. With dye-swapping and replicated arrays, we found 904 genes/ESTs that are differentially expressed. We validated the gene expression using real-time RT-PCR. We found that the expression patterns of these genes/ESTs correctly classified the 12 patients into ovarian and nonovarian endometriosis. We identified gene clusters that are location-specific. In addition, we identified several biological themes using Expression Analysis Systematic Explorer. Finally, we identified 79 pathways with over 100 genes with known functions, which include oxidative stress, focal adhesion, Wnt signaling, and MAPK signaling. The identification of these genes and their associated pathways provides new insight. Our findings will stimulate future investigations on molecular genetic mechanisms underlying the pathogenesis of endometriosis.

scholarly journals An Alternative Platform for Protein Expression Using an Innate Whole Expression Module from Metagenomic DNA

2019 ◽  
Vol 7 (1) ◽  
pp. 9 ◽  
Author(s):  
Dae-Eun Cheong ◽  
So-Youn Park ◽  
Ho-Dong Lim ◽  
Geun-Joong Kim
Keyword(s):  
Gene Expression ◽  
Regulatory Element ◽  
Expression System ◽  
Expression Patterns ◽  
Gene Clusters ◽  
Single Element ◽  
Reading Frame ◽  
Cis Acting ◽  
Dna Libraries ◽  
Expression Module

Many integrated gene clusters beyond a single genetic element are commonly trapped as the result of promoter traps in (meta)genomic DNA libraries. Generally, a single element, which is mainly the promoter, is deduced from the resulting gene clusters and employed to construct a new expression vector. However, expression patterns of target proteins under the incorporated promoter are often inconsistent with those shown in clones harboring plasmids with gene clusters. These results suggest that the integrated set of gene clusters with diverse cis- and trans-acting elements is evolutionarily tuned as a complete set for gene expression, and is an expression module with all the components for the expression of a nested open reading frame (ORF). This possibility is further supported by truncation and/or serial deletion analysis of this module in which the expression of the nested ORF is highly fluctuated or reduced frequently, despite being supported by plentiful cis-acting elements in the spanning regions around the ORF such as the promoter, ribosome binding site (RBS), terminator, and 3′-/5′-UTRs for gene expression. Here, we examined whether an innate module with a naturally overexpressed gene could be considered as a scaffold for an expression system. For a proof-of-principle study, we mined a complete expression module with an innately overexpressed ORF in E. coli from a metagenomics DNA library, and incorporated it into a vector that had no regulatory element for expressing the insert. We obtained successful expression of several inserts such as MBP, GFPuv, β-glucosidase, and esterase using this simple construct without tuning and codon optimization of the target insert.

scholarly journals A genomic analysis and transcriptomic atlas of gene expression inPsoroptes ovisreveals feeding- and stage-specific patterns of allergen expression

2019 ◽  
Author(s):  
Stewart TG Burgess ◽  
Edward J Marr ◽  
Kathryn Bartley ◽  
Francesca G Nunn ◽  
Rachel E Down ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Patterns ◽  
Draft Genome ◽  
Genomic Analysis ◽  
Gene Clusters ◽  
Specific Gene ◽  
Multigene Families ◽  
Psoroptes Ovis ◽  
Specific Expression ◽  
Development Of Resistance

ABSTRACTPsoroptic mange, caused by infestation with the ectoparasitic mite,Psoroptes ovis, is highly contagious, resulting in intense pruritus and represents a major welfare and economic concern for the livestock industry Worldwide. Control relies on injectable endectocides and organophosphate dips, but concerns over residues, environmental contamination, and the development of resistance threaten the sustainability of this approach, highlighting interest in alternative control methods. However, development of vaccines and identification of chemotherapeutic targets is hampered by the lack ofP. ovistranscriptomic and genomic resources. Building on the recent publication of theP. ovisdraft genome, here we present a genomic analysis and transcriptomic atlas of gene expression inP. ovisrevealing feeding- and stage-specific patterns of gene expression, including novel multigene families and allergens. Network-based clustering revealed 14 gene clusters demonstrating either single- or multi-stage specific gene expression patterns, with 3,075 female-specific, 890 male-specific and 112, 217 and 526 transcripts showing larval, protonymph and tritonymph specific-expression, respectively. Detailed analysis ofP. ovisallergens revealed stage-specific patterns of allergen gene expression, many of which were also enriched in “fed” mites and tritonymphs, highlighting an important feeding-related allergenicity in this developmental stage. Pair-wise analysis of differential expression between life-cycle stages identified patterns of sex-biased gene expression and also identified novelP. ovismultigene families including known allergens and novel genes with high levels of stage-specific expression. The genomic and transcriptomic atlas described here represents a unique resource for the acarid-research community, whilst the OrcAE platform makes this freely available, facilitating further community-led curation of the draftP. ovisgenome.

scholarly journals The Potential Role of Genetic Assimilation during Maize Domestication

2017 ◽  
Author(s):  
Anne Lorant ◽  
Sarah Pedersen ◽  
Irene Holst ◽  
Matthew B. Hufford ◽  
Klaus Winter ◽  
...  
Keyword(s):  
Gene Expression ◽  
Zea Mays ◽  
Potential Role ◽  
Expression Patterns ◽  
Genetic Assimilation ◽  
Genome Wide ◽  
A Genome ◽  
Genetic Mechanisms ◽  
Maize Domestication

ABSTRACTDomestication research has largely focused on identification of morphological and genetic differences between extant populations of crops and their wild relatives. Little attention has been paid to the potential effects of environment despite substantial known changes in climate from the time of domestication to modern day. Recent research, in which maize and teosinte (i.e., wild maize) were exposed to environments similar to the time of domestication, resulted in a plastic induction of domesticated phenotypes in teosinte and little response to environment in maize. These results suggest that early agriculturalists may have selected for genetic mechanisms that cemented domestication phenotypes initially induced by a plastic response of teosinte to environment, a process known as genetic assimilation. To better understand this phenomenon and the potential role of environment in maize domestication, we examined differential gene expression in maize (Zea mays ssp. mays) and teosinte (Zea mays ssp. parviglumis) between past and present conditions. We identified a gene set of over 2000 loci showing a change in expression across environmental conditions in teosinte and invariance in maize. In fact, overall we observed both greater plasticity in gene expression and more substantial re-wiring of expression networks in teosinte across environments when compared to maize. While these results suggest genetic assimilation played at least some role in domestication, genes showing expression patterns consistent with assimilation are not significantly enriched for previously identified domestication candidates, indicating assimilation did not have a genome-wide effect.

scholarly journals Gene expression and DNA methylation altering lead to the high oil content in wild allotetraploid peanut (A. monticola)

2022 ◽  
Author(s):  
Nian Liu ◽  
Manish Pandey ◽  
Bei Wu ◽  
Li Huang ◽  
Huaiyong Luo ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Transcription Factors ◽  
Arachis Hypogaea ◽  
Oil Content ◽  
Expression Patterns ◽  
Gene Clusters ◽  
Oil Accumulation ◽  
Species Specific ◽  
Wild Peanut

Abstract The wild allotetraploid peanut Arachis monticola contains higher oil content than cultivated allotetraploid Arachis hypogaea. To investigate its molecular mechanism controlling oil accumulation, we performed comparative transcriptomics from developing seeds between three Arachis monticola and five Arachis hypogaea varieties. The analysis not only showed species-specific grouping based on transcriptional profiles but also detected two gene clusters with divergent expression patterns enriched in lipid metabolism. Further, the differential expression gene analysis also indicated expression alteration in wild peanut leading to enhanced activity of oil biogenesis and limiting the rate of lipid degradation. We also constructed a regulatory network of lipid metabolic DEGs with co-expressed transcription factors. In addition, bisulfite sequencing was conducted to characterize the variation of DNA methylation between wild allotetraploid (245, WH 10025) and cultivated allotetraploid (Z16, Zhh 7720) genotypes. Genome-wide DNA methylation was found antagonistically correlated with gene expression during seed development. The results indicated that CG and CHG contexts methylation may negatively regulate specific lipid metabolic genes and transcription factors to subtly affect the difference of oil accumulation. Our work provided the first glimpse on the regulatory mechanism of gene expression altering for oil accumulation in wild peanut and gene resources for future breeding applications.

scholarly journals A Pathway-Based Genomic Approach to Identify Medications: Application to Alcohol Use Disorder

2019 ◽  
Vol 9 (12) ◽  
pp. 381
Author(s):  
Laura B. Ferguson ◽  
Shruti Patil ◽  
Bailey A. Moskowitz ◽  
Igor Ponomarev ◽  
Robert A. Harris ◽  
...  
Keyword(s):  
Gene Expression ◽  
Alcohol Use ◽  
Lupus Erythematosus ◽  
Alcohol Use Disorder ◽  
Expression Patterns ◽  
Mapk Signaling ◽  
Coagulation Cascade ◽  
Sufficient Evidence ◽  
Kegg Pathways ◽  
Novel Treatments

Chronic, excessive alcohol use alters brain gene expression patterns, which could be important for initiating, maintaining, or progressing the addicted state. It has been proposed that pharmaceuticals with opposing effects on gene expression could treat alcohol use disorder (AUD). Computational strategies comparing gene expression signatures of disease to those of pharmaceuticals show promise for nominating novel treatments. We reasoned that it may be sufficient for a treatment to target the biological pathway rather than lists of individual genes perturbed by AUD. We analyzed published and unpublished transcriptomic data using gene set enrichment of Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways to identify biological pathways disrupted in AUD brain and by compounds in the Library of Network-based Cellular Signatures (LINCS L1000) and Connectivity Map (CMap) databases. Several pathways were consistently disrupted in AUD brain, including an up-regulation of genes within the Complement and Coagulation Cascade, Focal Adhesion, Systemic Lupus Erythematosus, and MAPK signaling, and a down-regulation of genes within the Oxidative Phosphorylation pathway, strengthening evidence for their importance in AUD. Over 200 compounds targeted genes within those pathways in an opposing manner, more than twenty of which have already been shown to affect alcohol consumption, providing confidence in our approach. We created a user-friendly web-interface that researchers can use to identify drugs that target pathways of interest or nominate mechanism of action for drugs. This study demonstrates a unique systems pharmacology approach that can nominate pharmaceuticals that target pathways disrupted in disease states such as AUD and identify compounds that could be repurposed for AUD if sufficient evidence is attained in preclinical studies.

scholarly journals Global Transcriptome Analysis of Shewanella oneidensis MR-1 Exposed to Different Terminal Electron Acceptors

2005 ◽  
Vol 187 (20) ◽  
pp. 7138-7145 ◽  
Author(s):  
A. S. Beliaev ◽  
D. M. Klingeman ◽  
J. A. Klappenbach ◽  
L. Wu ◽  
M. F. Romine ◽  
...  
Keyword(s):  
Gene Expression ◽  
Metal Ion ◽  
Expression Patterns ◽  
Complex Structure ◽  
Shewanella Oneidensis ◽  
Gene Clusters ◽  
Electron Acceptors ◽  
Reducing Conditions ◽  
Wide Range ◽  
Metal Electron

ABSTRACT To gain insight into the complex structure of the energy-generating networks in the dissimilatory metal reducer Shewanella oneidensis MR-1, global mRNA patterns were examined in cells exposed to a wide range of metal and non-metal electron acceptors. Gene expression patterns were similar irrespective of which metal ion was used as electron acceptor, with 60% of the differentially expressed genes showing similar induction or repression relative to fumarate-respiring conditions. Several groups of genes exhibited elevated expression levels in the presence of metals, including those encoding putative multidrug efflux transporters, detoxification proteins, extracytoplasmic sigma factors and PAS-domain regulators. Only one of the 42 predicted c-type cytochromes in MR-1, SO3300, displayed significantly elevated transcript levels across all metal-reducing conditions. Genes encoding decaheme cytochromes MtrC and MtrA that were previously linked to the reduction of different forms of Fe(III) and Mn(IV), exhibited only slight decreases in relative mRNA abundances under metal-reducing conditions. In contrast, specific transcriptome responses were displayed to individual non-metal electron acceptors resulting in the identification of unique groups of nitrate-, thiosulfate- and TMAO-induced genes including previously uncharacterized multi-cytochrome gene clusters. Collectively, the gene expression results reflect the fundamental differences between metal and non-metal respiratory pathways of S. oneidensis MR-1, where the coordinate induction of detoxification and stress response genes play a key role in adaptation of this organism under metal-reducing conditions. Moreover, the relative paucity and/or the constitutive nature of genes involved in electron transfer to metals is likely due to the low-specificity and the opportunistic nature of the metal-reducing electron transport pathways.

Ischemic but not pharmacological preconditioning elicits a gene expression profile similar to unprotected myocardium

2004 ◽  
Vol 20 (1) ◽  
pp. 117-130 ◽  
Author(s):  
Rafaela da Silva ◽  
Eliana Lucchinetti ◽  
Thomas Pasch ◽  
Marcus C. Schaub ◽  
Michael Zaugg
Keyword(s):  
Gene Expression ◽  
Gene Expression Profile ◽  
Expression Profile ◽  
Ischemia Reperfusion ◽  
Expression Patterns ◽  
Principal Component ◽  
Gene Clusters ◽  
Stable Gene ◽  
Transcriptional Responses ◽  
Rat Hearts

Pharmacological (PPC) and ischemic preconditioning (IschPC) provide comparable protection against ischemia in the heart. However, the genomic phenotype may depend on the type of preconditioning. Isolated perfused rat hearts were used to evaluate transcriptional responses to PPC and IschPC in the presence (mediator/effector response) or absence (trigger response) of 40 min of test ischemia using oligonucleotide microarrays. IschPC was induced by 3 cycles of 5 min of ischemia, and PPC by 15 min of 2.1 vol% isoflurane. Unsupervised analysis methods were used to identify gene expression patterns. PPC and IschPC were accompanied by marked alterations in gene expression. PPC and IschPC shared only ∼25% of significantly up- and downregulated genes after triggering. The two types of preconditioning induced a more uniform genomic response after ischemia/reperfusion. Numerous genes separated preconditioned from unprotected ischemic hearts. Three stable gene clusters were identified in the trigger response to preconditioning, while eight stable clusters related to cytoprotection, inflammation, remodeling, and long interspersed nucleotide elements (LINEs) were delineated after prolonged ischemia. A single stable sample cluster emerged from cluster analysis for both IschPC and unprotected myocardium, indicating a close molecular relationship between these two treatments. Principal component analysis revealed differences between PPC vs. IschPC, and trigger vs. mediator/effector responses in transcripts predominantly related to biosynthesis and apoptosis. IschPC and PPC similarly but distinctly reprogram the genetic response to ischemic injury. IschPC elicits a postischemic gene expression profile closer to unprotected myocardium than PPC, which may be therefore more advantageous as therapeutic strategy in cardioprotection.

scholarly journals Uncovering the genetic blueprint of the C. elegans nervous system

2020 ◽  
Vol 117 (52) ◽  
pp. 33570-33577
Author(s):  
István A. Kovács ◽  
Dániel L. Barabási ◽  
Albert-László Barabási
Keyword(s):  
Gene Expression ◽  
Expression Profiling ◽  
Expression Patterns ◽  
Computational Framework ◽  
Computational Tools ◽  
C Elegans ◽  
Junction Formation ◽  
Cell Gene Expression ◽  
Genetic Mechanisms ◽  
Cell Gene

Despite rapid advances in connectome mapping and neuronal genetics, we lack theoretical and computational tools to unveil, in an experimentally testable fashion, the genetic mechanisms that govern neuronal wiring. Here we introduce a computational framework to link the adjacency matrix of a connectome to the expression patterns of its neurons, helping us uncover a set of genetic rules that govern the interactions between neurons in contact. The method incorporates the biological realities of the system, accounting for noise from data collection limitations, as well as spatial restrictions. The resulting methodology allows us to infer a network of 19 innexin interactions that govern the formation of gap junctions in Caenorhabditis elegans, five of which are already supported by experimental data. As advances in single-cell gene expression profiling increase the accuracy and the coverage of the data, the developed framework will allow researchers to systematically infer experimentally testable connection rules, offering mechanistic predictions for synapse and gap junction formation.

scholarly journals Antistress Action of Melanocortin Derivatives Associated with Correction of Gene Expression Patterns in the Hippocampus of Male Rats Following Acute Stress

2021 ◽  
Vol 22 (18) ◽  
pp. 10054
Author(s):  
Ivan B. Filippenkov ◽  
Vasily V. Stavchansky ◽  
Natalya Yu. Glazova ◽  
Elena A. Sebentsova ◽  
Julia A. Remizova ◽  
...  
Keyword(s):  
Gene Expression ◽  
Acute Stress ◽  
Expression Patterns ◽  
Molecular Genetic ◽  
Male Rats ◽  
Gene Expression Patterns ◽  
P Value ◽  
Behavioral Alterations ◽  
Expression Levels ◽  
Expression Of Genes

Natural melanocortins (MCs) have been used in the successful development of drugs with neuroprotective properties. Here, we studied the behavioral effects and molecular genetic mechanisms of two synthetic MC derivatives-ACTH(4–7)PGP (Semax) and ACTH(6–9)PGP under normal and acute restraint stress (ARS) conditions. Administration of Semax or ACTH(6–9)PGP (100 μg/kg) to rats 30 min before ARS attenuated ARS-induced behavioral alterations. Using high-throughput RNA sequencing (RNA-Seq), we identified 1359 differentially expressed genes (DEGs) in the hippocampus of vehicle-treated rats subjected to ARS, using a cutoff of >1.5 fold change and adjusted p-value (Padj) < 0.05, in samples collected 4.5 h after the ARS. Semax administration produced >1500 DEGs, whereas ACTH(6–9)PGP administration led to <400 DEGs at 4.5 h after ARS. Nevertheless, ~250 overlapping DEGs were identified, and expression of these DEGs was changed unidirectionally by both peptides under ARS conditions. Modulation of the expression of genes associated with biogenesis, translation of RNA, DNA replication, and immune and nervous system function was produced by both peptides. Furthermore, both peptides upregulated the expression levels of many genes that displayed decreased expression after ARS, and vice versa, the MC peptides downregulated the expression levels of genes that were upregulated by ARS. Consequently, the antistress action of MC peptides may be associated with a correction of gene expression patterns that are disrupted during ARS.

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