scholarly journals Dynamics and Innovations within Oomycete Genomes: Insights into Biology, Pathology, and Evolution

2012 ◽  
Vol 11 (11) ◽  
pp. 1304-1312 ◽  
Author(s):  
Howard S. Judelson
Keyword(s):  
Protein Sequence ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Life Cycles ◽  
Aquatic Environments ◽  
Gene Fusions ◽  
Additional Species ◽  
Functional Studies ◽  
Eukaryotic Microbes ◽  
Genome Projects

ABSTRACT The eukaryotic microbes known as oomycetes are common inhabitants of terrestrial and aquatic environments and include saprophytes and pathogens. Lifestyles of the pathogens extend from biotrophy to necrotrophy, obligate to facultative pathogenesis, and narrow to broad host ranges on plants or animals. Sequencing of several pathogens has revealed striking variation in genome size and content, a plastic set of genes related to pathogenesis, and adaptations associated with obligate biotrophy. Features of genome evolution include repeat-driven expansions, deletions, gene fusions, and horizontal gene transfer in a landscape organized into gene-dense and gene-sparse sectors and influenced by transposable elements. Gene expression profiles are also highly dynamic throughout oomycete life cycles, with transcriptional polymorphisms as well as differences in protein sequence contributing to variation. The genome projects have set the foundation for functional studies and should spur the sequencing of additional species, including more diverse pathogens and nonpathogens.

scholarly journals De novo characterization of the Lycium ruthenicum transcriptome and analysis of its digital gene expression profiles during fruit development and ripening

2017 ◽  
Vol 69 (1) ◽  
pp. 181-190 ◽  
Author(s):  
Yong Peng ◽  
Huiqin Ma ◽  
Shangwu Chen
Keyword(s):  
Gene Expression ◽  
Developmental Stages ◽  
De Novo ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Gene Expression Profiles ◽  
Digital Gene Expression ◽  
Orthologous Group ◽  
Functional Studies ◽  
Lycium Ruthenicum

Lycium ruthenicum Murr., which belongs to the family Solanaceae, is a resource plant for Chinese traditional medicine and nutraceutical foods. In this study, RNA sequencing was applied to obtain raw reads of L. ruthenicum fruit at different stages of ripening, and a de novo assembly of its sequence was performed. Approximately 52.45 million 100-bp paired-end raw reads were generated from the samples by deep RNA-seq analysis. These short reads were assembled to obtain 164814 contigs, and the contigs were assembled into 84968 non-redundant unigenes using the Trinity method. Assembled sequences were annotated with gene descriptions, gene ontology, clusters of orthologous group and KEGG (Kyoto Encyclopedia of Genes and Genomes)pathway terms. Digital gene expression analysis was applied to compare gene-expression patterns at different fruit developmental stages. These results contribute to existing sequence resources for Lycium spp. during the fruit-ripening stages, which is valuable for further functional studies of genes involved in L. ruthenicum fruit nutraceutical quality.

scholarly journals Ashwin Gene Expression Profiles in Oocytes, Preimplantation Embryos, and Fetal and Adult Bovine Tissues

Animals ◽  
2020 ◽  
Vol 10 (2) ◽  
pp. 276
Author(s):  
Verónica Moreno-Brito ◽  
Daniel Morales-Adame ◽  
Elier Soto-Orduño ◽  
Susana Aideé González-Chávez ◽  
César Pacheco-Tena ◽  
...  
Keyword(s):  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Follicular Development ◽  
Immunohistochemical Localization ◽  
Preimplantation Embryos ◽  
Chain Reaction ◽  
Anteroposterior Patterning ◽  
Functional Studies ◽  
Spatiotemporal Expression ◽  
Polymerase Chain

The ashwin gene, originally identified in Xenopus laevis, was found to be expressed first in the neural plate and later in the embryonic brain, eyes, and spinal cord. Functional studies of ashwin suggest that it participates in cell survival and anteroposterior patterning. Furthermore, ashwin is expressed zygotically in this species, which suggests that it participates in embryonic development. Nevertheless, the expression of this gene has not been studied in mammals. Thus, the aim of this study was to analyze the ashwin expression pattern in bovine fetal and adult tissues, as well as in three independent samples of immature and mature oocytes, and in two- to four-, and eight-cell embryos, morula, and blastocysts. Spatiotemporal expression was analyzed using real-time polymerase chain reaction (PCR); ashwin mRNA was detected in all tissues analyzed, immature and mature oocytes, and two- to eight-cell embryos. It was down-regulated in morula and blastocysts, suggesting that this expression profile is similar to that of maternal genes. Immunohistochemical localization of the ashwin protein in fetal and adult ovaries and testes reveals that this protein is consistently present during all stages of follicular development and during bovine spermatogenesis. These observations lead us to propose ashwin as an important gene involved in mammalian reproduction.

scholarly journals The Role of miR-4256/HOXC8 Signaling Axis in the Gastric Cancer Progression: Evidence From lncRNA-miRNA-mRNA Network Analysis

2022 ◽  
Vol 11 ◽  
Author(s):  
Haijuan Gu ◽  
Yuejiao Zhong ◽  
Jibin Liu ◽  
Qian Shen ◽  
Rong Wei ◽  
...  
Keyword(s):  
Gastric Cancer ◽  
Cancer Progression ◽  
Molecular Mechanisms ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Differentially Expressed ◽  
Gastric Cancer Cells ◽  
Functional Studies ◽  
Cancer Tissues ◽  
Gastric Cancer Progression

Gastric cancer is a deadly human malignancy and the molecular mechanisms underlying gastric cancer pathophysiology are very complicated. Thus, further investigations are warranted to decipher the underlying molecular mechanisms. With the development of high-throughput screening and bioinformatics, gene expression profiles with large scale have been performed in gastric cancer. In the present study, we mined The Cancer Genome Atlas (TCGA) database and analyzed the gene expression profiles between gastric cancer tissues and normal gastric tissues. A series of differentially expressed lncRNAs, miRNAs and mRNAs between gastric cancer tissues and normal gastric tissues were identified. Based on the differentially expressed genes, we constructed miRNA-mRNA network, lncRNA-mRNA network and transcriptional factors-mRNA-miRNA-lncRNA network. Furthermore, the Kaplan survival analysis showed that high expression levels of EVX1, GBX2, GCM1, HOXC8, HOXC9, HOXC10, HOXC11, HOXC12 and HOXC13 were all significantly correlated with shorter overall survival of the patients with gastric cancer. On the other hand, low expression level of HOXA13 was associated with shorter overall survival of patients with gastric cancer. Among these hub genes, we performed the in vitro functional studies of HOXC8 in the gastric cancer cells. Knockdown of HOXC8 and overexpression of miR-4256 both significantly repressed the gastric cancer cell proliferation and migration, and miR-4256 repressed the expression of HOXC8 via targeting its 3’ untranslated region in gastric cancer cells. Collectively, our results revealed that a complex interaction networks of differentially expressed genes in gastric cancer, and further functional studies indicated that miR-4256/HOXC8 may be an important axis in regulating gastric cancer progression.

scholarly journals Transcriptome atlas of Phalaenopsis equestris

2020 ◽  
Author(s):  
Anna V. Klepikova ◽  
Artem S. Kasianov ◽  
Margarita A. Ezhova ◽  
Aleksey A. Penin ◽  
Maria D. Logacheva
Keyword(s):  
Gene Expression ◽  
Apical Meristem ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Rna Seq ◽  
Orphan Genes ◽  
Functional Studies ◽  
Transcriptome Variation ◽  
Predominant Expression

AbstractThe vast diversity of Orchidaceae together with sophisticated adaptations to pollinators and other unique features make this family an attractive model for evolutionary and functional studies. The sequenced genome of Phalaenopsis equestris facilitates Orchidaceae research. Here we present an RNA-seq based transcriptome map of P. equestris which covers 19 organs of the plant including leaves, roots, floral organs and shoot apical meristem. We demonstrated the high quality of the data and showed the similarity of P. equestris transcriptome map with gene expression atlases of other plants. The transcriptome map can be easily accessed through our database Transcriptome Variation Analysis (TraVA) visualizing gene expression profiles. As an example of the application we analyzed the expression of Phalaenopsis “orphan” genes – the ones that do not have recognizable similarity with genes of other plants. We found that about a half of them are not expressed; the ones that are expressed have a predominant expression pattern in reproductive structures.

scholarly journals Transcriptome atlas of Phalaenopsis equestris

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12600
Author(s):  
Anna V. Klepikova ◽  
Artem S. Kasianov ◽  
Margarita A. Ezhova ◽  
Aleksey A. Penin ◽  
Maria D. Logacheva
Keyword(s):  
Gene Expression ◽  
Apical Meristem ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Rna Seq ◽  
Orphan Genes ◽  
Functional Studies ◽  
Reproductive Structures ◽  
Transcriptome Variation

The vast diversity of Orchidaceae together with sophisticated adaptations to pollinators and other unique features make this family an attractive model for evolutionary and functional studies. The sequenced genome of Phalaenopsis equestris facilitates Orchidaceae research. Here, we present an RNA-seq-based transcriptome map of P. equestris that covers 19 organs of the plant, including leaves, roots, floral organs and the shoot apical meristem. We demonstrated the high quality of the data and showed the similarity of the P. equestris transcriptome map with the gene expression atlases of other plants. The transcriptome map can be easily accessed through our database Transcriptome Variation Analysis (TraVA) for visualizing gene expression profiles. As an example of the application, we analyzed the expression of Phalaenopsis “orphan” genes–those that do not have recognizable similarity with the genes of other plants. We found that approximately half of these genes were not expressed; the ones that were expressed were predominantly expressed in reproductive structures.

scholarly journals Effect of long-term corticosteroid treatment on microRNA and gene-expression profiles in COPD

2019 ◽  
Vol 53 (4) ◽  
pp. 1801202 ◽  
Author(s):  
Alen Faiz ◽  
Katrina Steiling ◽  
Mirjam P. Roffel ◽  
Dirkje S. Postma ◽  
Avrum Spira ◽  
...  
Keyword(s):  
Mirna Expression ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Corticosteroid Treatment ◽  
Nuclear Factor Κb ◽  
Airway Epithelial Cells ◽  
Chronic Obstructive ◽  
Functional Studies ◽  
Copd Patients ◽  
Epithelial Cultures

The aim was to investigate whether microRNA (miRNA) expression is modulated by inhaled corticosteroid (ICS) treatmentWe performed genome-wide miRNA analysis on bronchial biopsies of 69 moderate/severe chronic obstructive pulmonary disease (COPD) patients at baseline and after 6- and 30-month treatment with the ICS fluticasone propionate or placebo. The effect of ICS on miRNA expression was validated in differentiated primary bronchial epithelial cultures, and functional studies were conducted in BEAS-2B cells. MiRNAs affected by ICS and their predicted targets were compared to an independent miRNA dataset of bronchial brushings from COPD patients and healthy controls.Treatment with ICS for both 6 and 30 months significantly altered the expression of four miRNAs, including miR-320d, which was increased during ICS treatment compared with placebo. The ICS-induced increase of miR-320d was confirmed in primary airway epithelial cells. MiR-320d negatively correlated targets were enriched for pro-inflammatory genes and were increased in the bronchial brushes of patients with lower lung function in the independent dataset. Overexpression of miR-320d in BEAS-2B cells dampened cigarette smoke extract-induced pro-inflammatory activity via inhibition of nuclear factor-κB.Collectively, we identified miR-320d as a novel mediator of ICS, regulating the pro-inflammatory response of the airway epithelium.

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.

The characterization of distinct populations of murine skeletal cells that have different roles in B lymphopoiesis

Blood ◽  
2021 ◽  
Author(s):  
Alanna Claire Green ◽  
Gavin Tjin ◽  
Samuel C Lee ◽  
Alistair M Chalk ◽  
Lenny Straszkowski ◽  
...  
Keyword(s):  
Bone Marrow ◽  
Leptin Receptor ◽  
B Lymphocyte ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Surface Expression ◽  
Cell Surface Expression ◽  
B Lymphopoiesis ◽  
Functional Studies

Hematopoiesis is extrinsically controlled by cells of the bone marrow microenvironment, including skeletal lineage cells. The identification and subsequent studies of distinct subpopulations of maturing skeletal cells is currently limited due to a lack of methods to isolate these cells. We found that murine Lineage-CD31-Sca-1-CD51+ cells can be divided into four subpopulations using flow cytometry, based on their expression of the platelet derived growth factor receptors ⍺ and β (PDGFR⍺ and PDGFRβ). The use of different skeletal lineage reporters confirmed the skeletal origin of the four populations. Multiplex immunohistochemistry studies revealed that all four populations were localized near the growth plate and trabecular bone and were rarely found near cortical bone regions or in central bone marrow. Functional studies revealed differences in their abundance, colony-forming unit-fibroblast capacity and potential to differentiate into mineralized osteoblasts or adipocytes in vitro. Furthermore, the four populations had distinct gene expression profiles and differential cell surface expression of leptin receptor (LEPR) and vascular cell adhesion molecule 1 (VCAM-1). Interestingly, we discovered that one of these four different skeletal populations showed the highest expression of genes involved in the extrinsic regulation of B lymphopoiesis. This cell population varied in abundance between distinct hematopoietically active skeletal sites, and significant differences in the proportions of B lymphocyte precursors were also observed in these distinct skeletal sites. It also supported pre-B lymphopoiesis in culture. Our method to isolate four distinct maturing skeletal populations will assist in elucidating the roles of distinct skeletal niche cells in regulating hematopoiesis and bone.

scholarly journals Tuscan Varieties of Sweet Cherry Are Rich Sources of Ursolic and Oleanolic Acid: Protein Modeling Coupled to Targeted Gene Expression and Metabolite Analyses

Molecules ◽  
2019 ◽  
Vol 24 (8) ◽  
pp. 1590 ◽  
Author(s):  
Roberto Berni ◽  
Mubasher Zahir Hoque ◽  
Sylvain Legay ◽  
Giampiero Cai ◽  
Khawar Sohail Siddiqui ◽  
...  
Keyword(s):  
Gene Expression ◽  
Structure Prediction ◽  
Sweet Cherry ◽  
Prunus Avium ◽  
Expression Profiles ◽  
3D Structure ◽  
Gene Expression Profiles ◽  
Reaction Products ◽  
Functional Studies ◽  
Targeted Gene Expression

The potential of six ancient Tuscan sweet cherry (Prunus avium L.) varieties as a source of health-promoting pentacyclic triterpenes is here evaluated by means of a targeted gene expression and metabolite analysis. By using a sequence homology criterion, we identify five oxidosqualene cyclase genes (OSCs) and three cytochrome P450s (CYP85s) that are putatively involved in the triterpene production pathway in sweet cherries. We performed 3D structure prediction and induced-fit docking using cation intermediates and reaction products for some OSCs to predict their function. We show that the Tuscan varieties have different amounts of ursolic and oleanolic acids and that these variations are related to different gene expression profiles. This study stresses the interest of valorizing ancient fruits as alternative sources of functional molecules with nutraceutical value. It also provides information on sweet cherry triterpene biosynthetic genes, which could be the object of follow-up functional studies.

1327: Gene Expression Profiles in Benign Prostatic Hyperplasia

2004 ◽  
Vol 171 (4S) ◽  
pp. 349-350
Author(s):  
Gaelle Fromont ◽  
Michel Vidaud ◽  
Alain Latil ◽  
Guy Vallancien ◽  
Pierre Validire ◽  
...  
Keyword(s):  
Gene Expression ◽  
Benign Prostatic Hyperplasia ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Prostatic Hyperplasia
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