scholarly journals Differential gene expression in the mussel <i>Bathymodiolus azoricus</i> from the Menez Gwen and Lucky Strike deep-sea hydrothermal vent sites

2013 ◽  
Vol 10 (2) ◽  
pp. 2013-2038
Author(s):  
R. Bettencourt ◽  
M. I. Rodrigues ◽  
I. Barros ◽  
T. Cerqueira ◽  
C. Freitas ◽  
...  
Keyword(s):  
Gene Expression ◽  
Deep Sea ◽  
Hydrothermal Vent ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Lucky Strike ◽  
Immune Genes ◽  
Genes Encoding ◽  
Menez Gwen ◽  
Bacterial Genes

Abstract. The deep-sea hydrothermal vent mussel Bathymodiolus azoricus is a symbiont bearing bivalve that is found in great abundance at the Menez Gwen and Lucky Strike vent sites and in close vicinity off the Azores region near the Mid-Atlantic Ridge (MAR). The distinct relationships that vent mussels have developed with their physical and chemical environments are likely reflected in global gene expression profiles providing thus a means to distinguish geographically distinct vent mussels on the basis of gene expression studies, fluorescence in situ hybridization (FISH) experiments and 16S rRNA amplicon sequencing, to assess the natural expression of bacterial genes and vent mussel immune genes and the constitutive distribution and relative abundance of endosymbiotic bacteria within gill tissues. Our results confirmed the presence of methanotroph-related endosymbionts in Menez Gwen vent mussels whereas Lucky Strike specimens seem to harbor a different bacterial morphotype when a methane monooxygenase gene specific probe was used. No qualitative differences could be visualized between Menez Gwen and Lucky Strike individuals when tested with sulfur-oxidizing-related nucleic-acid probe. Quantitative PCR (qPCR) studies revealed varied gene expression profiles in both Menez Gwen and Lucky Strike mussel gill tissues for the immune genes selected. Genes encoding transcription factors presented noticeably low levels of fold expression whether in MG or LS animals whereas the genes encoding effector molecules appeared to have higher levels expression in MG gill tissues. The peptidoglycan recognition molecule, encoding gene, PGRP presented the highest level of transcriptional activity among the genes analyzed in MG gill tissues, seconded by carcinolectin and thus denoting the relevance of immune recognition molecules in early stage of the immune responses onset. Genes regarded as encoding molecules involved in signaling pathways were consistently expressed in both MG and LS gill tissues. Remarkably, the immunity-related GTPase encoding gene demonstrated in LS samples, the highest level of expression among the signaling molecule encoding genes tested when expressions levels were compared between MG and LG animals. A differential expression analysis of bacterial genes between MG and LS indicated a clear expression signature in LS gill tissues. The bacterial community structure ensued from the 16S rRNA sequencing analyses pointed at a unpredicted conservation of endosymbiont bacterial loads between MG and LS samples. Taken together, our results support the premise that Bathymodiolus azoricus exhibits different transcriptional statuses depending on which hydrothermal vent site it is collected from and within the same collection site while exhibiting differential levels of expression of genes corresponding to different immune functional categories. The present study represents a first attempt to characterize gene expression signatures in hydrothermal vent animals issued from distinct deep-sea environmental sites based on immune and bacterial genes expressions.

Site-related differences in gene expression and bacterial densities in the mussel Bathymodiolus azoricus from the Menez Gwen and Lucky Strike deep-sea hydrothermal vent sites

2014 ◽  
Vol 39 (2) ◽  
pp. 343-353 ◽  
Author(s):  
Raul Bettencourt ◽  
Mónica Rodrigues ◽  
Inês Barros ◽  
Teresa Cerqueira ◽  
Cátia Freitas ◽  
...  
Keyword(s):  
Gene Expression ◽  
Deep Sea ◽  
Hydrothermal Vent ◽  
Lucky Strike ◽  
Menez Gwen

scholarly journals Gene Expression Profiles for Recurrence of Lymph Node-positive Primary Breast Cancer in Women Over 40 Years of Age

2021 ◽  
Author(s):  
Sean Si Qian Ma ◽  
Luyi Ye ◽  
Fan Zhang ◽  
Tiansheng Xu ◽  
Zai-Si Ji ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Gene Expression ◽  
Lymph Node ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Olfactory Receptors ◽  
Specific Gene ◽  
Node Metastasis ◽  
Genes Encoding ◽  
Ffpe Samples

Abstract Background: Specific gene expression profiles correlate with recurrence of breast cancer in lymph node-negative patients. In contrast, insufficient knowledge is available regarding tumor-specific gene expression in patients with lymph node metastasis before surgery. Furthermore, such patients experience cumulative incidences of relapse greater than 50%. Methods: Sections of formalin-fixed paraffin embedded (FFPE) were prepared from breast tumors of 37 patients who were followed for at least 5 years. FFPE samples of patients with recurrent ductal breast cancer (n = 25) and 12 FFPE samples of such patients without recurrence were subjected to microarray analysis to identify gene expression profiles specifically associated with positive lymph nodes confirmed during surgery that were accompanied by lymphocytic invasion. Immunohistochemistry was employed to determine the estrogen receptor (ER) status of cancer tissues. All patients were administered tamoxifen after surgery, and this treatment continued for more than 5 years, or until cancer recurred. This strategy eliminated interactions between different therapeutics as potential confounding factors that influenced patients' outcomes.Results: Sixteen genes were expressed at significantly higher levels in patients with ER-positive (+) breast cancer with recurrence compared with those without recurrence. Gene Set Enrichment Analysis of The Kyoto Encyclopedia of Genes and Genomes (KEGG) identified 73 genes encoding olfactory receptors included in the “Olfactory transduction” pathway that were enriched in the ER+ recurrence group (FDR P < 0.05). The KEGG “Histidine metabolism” and “Retinol metabolism” pathways were enriched in patients with ER-negative (–) breast cancer with recurrence (FDR P < 0.05). Conclusions: The present study is the first, to our knowledge, to identify 16 genes encoding proteins with diverse functions as well as 73 genes encoding olfactory receptors. These genes may serve as presurgical biomarkers for the recurrence of ER+ breast cancers with lymph node metastasis before surgery. These findings identify potential therapeutic targets for preventing cancer relapse, particularly after lymph nodes metastasis.

scholarly journals Testosterone-induced permanent changes of hepatic gene expression in female mice sustained during Plasmodium chabaudi malaria infection

2010 ◽  
Vol 45 (6) ◽  
pp. 379-390 ◽  
Author(s):  
Denis Delić ◽  
Nicole Gailus ◽  
Hans-Werner Vohr ◽  
Mohamed Dkhil ◽  
Saleh Al-Quraishy ◽  
...  
Keyword(s):  
Gene Expression ◽  
Immune Response ◽  
Malaria Infection ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Liver Metabolism ◽  
Hepatic Gene Expression ◽  
Plasmodium Chabaudi ◽  
Female Mice ◽  
Genes Encoding

Testosterone has been previously shown to induce persistent susceptibility to Plasmodium chabaudi malaria in otherwise resistant female C57BL/6 mice. Here, we investigate as to whether this conversion coincides with permanent changes of hepatic gene expression profiles. Female mice aged 10–12 weeks were treated with testosterone for 3 weeks; then, testosterone treatment was discontinued for 12 weeks before challenging with 106 P. chabaudi-infected erythrocytes. Hepatic gene expression was examined after 12 weeks of testosterone withdrawal and after subsequent infection with P. chabaudi at peak parasitemia, using Affymetrix microarrays with 22 690 probe sets representing 14 000 genes. The expression of 54 genes was found to be permanently changed by testosterone, which remained changed during malaria infection. Most genes were involved in liver metabolism: the female-prevalent genes Cyp2b9, Cyp2b13, Cyp3a41, Cyp3a44, Fmo3, Sult2a2, Sult3a1, and BC014805 were repressed, while the male-prevalent genes Cyp2d9, Cyp7b1, Cyp4a10, Ugt2b1, Ugt2b38, Hsd3b5, and Slco1a1 were upregulated. Genes encoding different nuclear receptors were not persistently changed. Moreover, testosterone induced persistent upregulation of genes involved in hepatocellular carcinoma such as Lama3 and Nox4, whereas genes involved in immune response such as Ifnγ and Igk-C were significantly decreased. Our data provide evidence that testosterone is able to induce specific and robust long-term changes of gene expression profiles in the female mouse liver. In particular, those changes, which presumably indicate masculinized liver metabolism and impaired immune response, may be critical for the testosterone-induced persistent susceptibility of mice to P. chabaudi malaria.

scholarly journals Global Gene Expression Responses to Cadmium Toxicity in Escherichia coli

2005 ◽  
Vol 187 (9) ◽  
pp. 3259-3266 ◽  
Author(s):  
Anyou Wang ◽  
David E. Crowley
Keyword(s):  
Gene Expression ◽  
Escherichia Coli ◽  
Ribosomal Proteins ◽  
Molecular Mechanisms ◽  
Expression Profiles ◽  
Cadmium Toxicity ◽  
Gene Expression Profiles ◽  
Global Gene Expression ◽  
Temporal Gene Expression ◽  
Genes Encoding

ABSTRACT Genome-wide analysis of temporal gene expression profiles in Escherichia coli following exposure to cadmium revealed a shift to anaerobic metabolism and induction of several stress response systems. Disruption in the transcription of genes encoding ribosomal proteins and zinc-binding proteins may partially explain the molecular mechanisms of cadmium toxicity.

scholarly journals Finding immune gene expression differences induced by marine bacterial pathogens in the deep-sea hydrothermal vent mussel <i>Bathymodiolus azoricus</i>

2013 ◽  
Vol 10 (2) ◽  
pp. 2675-2703 ◽  
Author(s):  
E. Martins ◽  
A. Queiroz ◽  
R. Serrão Santos ◽  
R. Bettencourt
Keyword(s):  
Gene Expression ◽  
Deep Sea ◽  
Hydrothermal Vent ◽  
Post Infection ◽  
Defense Mechanisms ◽  
Bacterial Pathogens ◽  
Immune Gene ◽  
Immune Genes ◽  
Immune Gene Expression ◽  
Sds Page

Abstract. The deep-sea hydrothermal vent mussel Bathymodiolus azoricus lives in a natural environment characterized by extreme conditions of hydrostatic pressure, temperature, pH, high concentrations of heavy metals, methane and hydrogen sulphide. The deep-sea vent biological systems represent thus the opportunity to study and provide new insights into the basic physiological principles that govern the defense mechanisms in vent animals and to understand how they cope with microbial infections. Hence, the importance of understanding this animal's innate defense mechanisms, by examining its differential immune gene expressions toward different pathogenic agents. In the present study, B. azoricus mussels were infected with single suspensions of marine bacterial pathogens, consisting of Vibrio splendidus, Vibrio alginolyticus, or Vibrio anguillarum, and a pool of these Vibrio strains. Flavobacterium suspensions were also used as an irrelevant bacterium. Gene expression analyses were carried out using gill samples from animals dissected at 12 h and 24 h post-infection times by means of quantitative-Polymerase Chain Reaction aimed at targeting several immune genes. We also performed SDS-PAGE protein analyses from the same gill tissues. We concluded that there are different levels of immune gene expression between the 12 h and 24 h exposure times to various bacterial suspensions. Our results from qPCR demonstrated a general pattern of gene expression, decreasing from 12 h over 24 h post-infection. Among the bacteria tested, Flavobacterium is the microorganism species inducing the highest gene expression level in 12 h post-infections animals. The 24 h infected animals revealed, however, greater gene expression levels, using V. splendidus as the infectious agent. The SDS-PAGE analysis also pointed at protein profile differences between 12 h and 24 h, particularly around a protein area, of 18 KDa molecular mass, where most dissimilarities were found. Multivariate analyses demonstrated that immune genes, as well as experimental infections, clustered in discrete groups in accordance with the patterns observed in gene expression changes induced by bacterial pathogens.

scholarly journals Histone H3.3 G34 mutations promote aberrant PRC2 activity and drive tumor progression

2020 ◽  
Vol 117 (44) ◽  
pp. 27354-27364 ◽  
Author(s):  
Siddhant U. Jain ◽  
Sima Khazaei ◽  
Dylan M. Marchione ◽  
Stefan M. Lundgren ◽  
Xiaoshi Wang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Profiles ◽  
Tumor Development ◽  
Gene Expression Profiles ◽  
Osteoblastic Differentiation ◽  
Missense Mutations ◽  
Giant Cell Tumors ◽  
H3k36 Methylation ◽  
Genes Encoding

A high percentage of pediatric gliomas and bone tumors reportedly harbor missense mutations at glycine 34 in genes encoding histone variant H3.3. We find that these H3.3 G34 mutations directly alter the enhancer chromatin landscape of mesenchymal stem cells by impeding methylation at lysine 36 on histone H3 (H3K36) by SETD2, but not by the NSD1/2 enzymes. The reduction of H3K36 methylation by G34 mutations promotes an aberrant gain of PRC2-mediated H3K27me2/3 and loss of H3K27ac at active enhancers containing SETD2 activity. This altered histone modification profile promotes a unique gene expression profile that supports enhanced tumor development in vivo. Our findings are mirrored in G34W-containing giant cell tumors of bone where patient-derived stromal cells exhibit gene expression profiles associated with early osteoblastic differentiation. Overall, we demonstrate that H3.3 G34 oncohistones selectively promote PRC2 activity by interfering with SETD2-mediated H3K36 methylation. We propose that PRC2-mediated silencing of enhancers involved in cell differentiation represents a potential mechanism by which H3.3 G34 mutations drive these tumors.

scholarly journals Global Transcriptome Analysis of the Responses of a Fluoroquinolone-Resistant Streptococcus pneumoniae Mutant and Its Parent to Ciprofloxacin

2006 ◽  
Vol 50 (1) ◽  
pp. 269-278 ◽  
Author(s):  
Estelle Marrer ◽  
A. Tatsuo Satoh ◽  
Margaret M. Johnson ◽  
Laura J. V. Piddock ◽  
Malcolm G. P. Page
Keyword(s):  
Gene Expression ◽  
Streptococcus Pneumoniae ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Resistant Mutant ◽  
Multidrug Resistant ◽  
Altered Expression ◽  
Genes Encoding ◽  
High Concentrations ◽  
Branched Chain

ABSTRACT Streptococcus pneumoniae M22 is a multidrug-resistant mutant selected after exposure of capsulated wild-type S. pneumoniae NCTC 7465 (strain M4) to ciprofloxacin. DNA microarray analysis comparing the gene expression profiles of strain M22 with those of strain M4 showed that strain M22 constitutively expressed 22 genes at levels higher than those observed in strain M4 under all conditions studied. These included the genes encoding the enzymes involved in branched-chain amino acid biosynthesis and two genes (patA and patB) with sequences suggestive of ABC transporter proteins. Expression of the patA and patB genes was induced by ciprofloxacin in both strains, but in strain M4 it only reached the levels observed in strain M22 after long incubation with high concentrations of ciprofloxacin. The altered expression profile observed with strain M22 suggested that the mutation or mutations acquired during resistance selection bring the cell into a state in which the expression of critical genes is preemptively altered to correct for the potential effects of ciprofloxacin on gene expression in the parent strain.

scholarly journals Finding immune gene expression differences induced by marine bacterial pathogens in the Deep-sea hydrothermal vent mussel <i>Bathymodiolus azoricus</i>

2013 ◽  
Vol 10 (11) ◽  
pp. 7279-7291 ◽  
Author(s):  
E. Martins ◽  
A. Queiroz ◽  
R. Serrão Santos ◽  
R. Bettencourt
Keyword(s):  
Gene Expression ◽  
Deep Sea ◽  
Hydrothermal Vent ◽  
Defense Mechanisms ◽  
Bacterial Pathogens ◽  
Immune Gene ◽  
Immune Genes ◽  
Innate Defense ◽  
Immune Gene Expression ◽  
Sds Page

Abstract. The deep-sea hydrothermal vent mussel Bathymodiolus azoricus lives in a natural environment characterised by extreme conditions of hydrostatic pressure, temperature, pH, high concentrations of heavy metals, methane and hydrogen sulphide. The deep-sea vent biological systems represent thus the opportunity to study and provide new insights into the basic physiological principles that govern the defense mechanisms in vent animals and to understand how they cope with microbial infections. Hence, the importance of understanding this animal's innate defense mechanisms, by examining its differential immune gene expressions toward different pathogenic agents. In the present study, B. azoricus mussels were infected with single suspensions of marine bacterial pathogens, consisting of Vibrio splendidus, Vibrio alginolyticus, or Vibrio anguillarum, and a pool of these Vibrio bacteria. Flavobacterium suspensions were also used as a non-pathogenic bacterium. Gene expression analyses were carried out using gill samples from infected animals by means of quantitative-Polymerase Chain Reaction aimed at targeting several immune genes. We also performed SDS-PAGE protein analyses from the same gill tissues. We concluded that there are different levels of immune gene expression between the 12 h to 24 h exposure times to various bacterial suspensions. Our results from qPCR demonstrated a general pattern of gene expression, decreasing from 12 h over 24 h post-infection. Among the bacteria tested, Flavobacterium is the bacterium inducing the highest gene expression level in 12 h post-infections animals. The 24 h infected animals revealed, however, greater gene expression levels, using V. splendidus as the infectious agent. The SDS-PAGE analysis also pointed at protein profile differences between 12 h and 24 h, particularly evident for proteins of 18–20 KDa molecular mass, where most dissimilarity was found. Multivariate analyses demonstrated that immune genes, as well as experimental infections, clustered in discrete groups in accordance with the gene expression patterns induced by bacterial pathogens.

scholarly journals Gene expression profiles of Spo11−/− mouse testes with spermatocytes arrested in meiotic prophase I

Reproduction ◽  
2006 ◽  
Vol 132 (1) ◽  
pp. 67-77 ◽  
Author(s):  
Natalya A Smirnova ◽  
Peter J Romanienko ◽  
Pavel P Khil ◽  
R Daniel Camerini-Otero
Keyword(s):  
Gene Expression ◽  
Meiotic Recombination ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Specific Protein ◽  
Wild Type ◽  
Chromosomal Dna ◽  
Before And After ◽  
Genes Encoding ◽  
Protein Components

Spo11, a meiosis-specific protein, introduces double-strand breaks on chromosomal DNA and initiates meiotic recombination in a wide variety of organisms. Mouse null Spo11 spermatocytes fail to synapse chromosomes and progress beyond the zygotene stage of meiosis. We analyzed gene expression profiles in Spo11−/ −adult and juvenile wild-type testis to describe genes expressed before and after the meiotic arrest resulting from the knocking out of Spo11. These genes were characterized using the Gene Ontology data base. To focus on genes involved in meiosis, we performed comparative gene expression analysis of Spo11−/ −and wild-type testes from 15-day mice, when spermatocytes have just entered pachytene. We found that the knockout of Spo11 causes dramatic changes in the level of expression of genes that participate in meiotic recombination (Hop2, Brca2, Mnd1, FancG) and in the meiotic checkpoint (cyclin B2, Cks2), but does not affect genes encoding protein components of the synaptonemal complex. Finally, we discovered unknown genes that are affected by the disruption of the Spo11 gene and therefore may be specifically involved in meiosis and spermatogenesis.

scholarly journals Metatranscriptome Analysis of the Human Fecal Microbiota Reveals Subject-Specific Expression Profiles, with Genes Encoding Proteins Involved in Carbohydrate Metabolism Being Dominantly Expressed

2010 ◽  
Vol 76 (16) ◽  
pp. 5533-5540 ◽  
Author(s):  
Carien C. G. M. Booijink ◽  
Jos Boekhorst ◽  
Erwin G. Zoetendal ◽  
Hauke Smidt ◽  
Michiel Kleerebezem ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Fecal Microbiota ◽  
Aflp Analysis ◽  
Community Studies ◽  
Specific Expression ◽  
Functional Studies ◽  
Complex Microbial Community ◽  
Genes Encoding

ABSTRACT The human gastrointestinal (GI) tract provides home to a complex microbial community, collectively termed microbiota. Although major efforts have been made to describe the diversity and stability of the microbiota, functional studies have been largely restricted to intestinal isolates and include few community studies. The aim of this study was to explore the in situ gene expression of the fecal microbiota and to evaluate the RNA fingerprinting method cDNA-AFLP (cDNA amplified fragment length polymorphism) for this purpose. To this end, cDNA-AFLP analysis of enriched mRNA revealed that two healthy subjects showed highly divergent expression profiles with considerable fluctuations in time. Subsequent excision and sequence determination of bands from the mRNA-enriched profiles resulted in 122 identifiable sequences (transcripts and rRNAs). The classification of retrieved transcripts into functional clusters based on COG (cluster of orthologous genes) annotation showed that most assigned transcripts belonged to the metabolism cluster (26% of all sequences), underlining that even at the very end of the intestinal tract the microbiota is still very active. This study furthermore revealed that cDNA-AFLP is a useful tool to compare gene expression profiles in time in complex microbial communities.

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