Transcriptome based identification and tissue expression profiles of chemosensory genes in Blattella germanica (Blattaria: Blattidae)

2016 ◽  
Vol 18 ◽  
pp. 30-43 ◽  
Author(s):  
Dong-Juan Niu ◽  
Yan Liu ◽  
Xiao-Tong Dong ◽  
Shuang-Lin Dong
Keyword(s):  
Expression Profiles ◽  
Blattella Germanica ◽  
Tissue Expression ◽  
Chemosensory Genes

scholarly journals Identification and Expression Profile of Chemosensory Genes in the Small Hive Beetle Aethina tumida

Insects ◽  
2021 ◽  
Vol 12 (8) ◽  
pp. 661
Author(s):  
Lixian Wu ◽  
Xin Zhai ◽  
Liangbin Li ◽  
Qiang Li ◽  
Fang Liu ◽  
...  
Keyword(s):  
Pest Control ◽  
Expression Profiles ◽  
Environmentally Friendly ◽  
Insect Behavior ◽  
Tissue Expression ◽  
Control Measures ◽  
Aethina Tumida ◽  
Chemosensory Genes ◽  
Genes Encoding ◽  
Odorant Binding

Aethina tumida is a parasite and predator of honeybee causing severe loss to the bee industry. No effective and environmentally friendly methods are available to control this pest at present. Chemosensory genes play key roles in insect behavior which can potentially be used as targets for developing environmentally friendly pest control agents. In this study, the putative chemosensory genes in antennae and forelegs of A. tumida involved in olfaction or contact chemical communication of adults were investigated using RNA transcriptome sequencing and PCR methods. Based on transcriptomic data, unigenes encoding 38 odorant receptors (ORs), 24 ionotropic receptors (IRs), 14 gustatory receptors (GRs), 3 sensory neuron membrane proteins (SNMPs), 29 odorant binding proteins (OBPs), and 22 chemosensory proteins (CSPs) were identified. The analyses of tissue expression profiles revealed that genes encoding 38 ORs, 13 antennal IRs, 11 GRs, 1 SNMP, 24 OBPs, and 12 CSPs were predominately expressed in antennae. No significant differences in expression levels of these genes were found between males and females. Genes encoding 5 non-NMDA iGluRs, 3 GRs, 2 SNMPs, 5 OBPs, and 12 CSPs were predominately expressed in forelegs. RT-PCR assays for SNMPs, OBPs and CSPs further revealed that 3 OBPs (AtumOBP3, 26 and 28) and 3 CSPs (AtumCSP7, 8 and 21) were highly expressed in antennae. Our results enrich the gene inventory of A. tumida and facilitate the discovery of potential novel targets for developing new pest control measures.

scholarly journals Identification of Chemosensory Genes Based on the Antennal Transcriptomic Analysis of Plagiodera versicolora

Insects ◽  
2021 ◽  
Vol 13 (1) ◽  
pp. 36
Author(s):  
Xiaolong Liu ◽  
Na Tong ◽  
Zheran Wu ◽  
Yang Li ◽  
Meiqi Ma ◽  
...  
Keyword(s):  
Expression Profiles ◽  
Gene Families ◽  
Tissue Expression ◽  
Vital Role ◽  
Plagiodera Versicolora ◽  
Male And Female ◽  
Functional Studies ◽  
Chemosensory Genes ◽  
Almost All ◽  
Chemosensory Systems

Insects can sense surrounding chemical signals by their accurate chemosensory systems. This system plays a vital role in the life history of insects. Several gene families participate in chemosensory processes, including odorant receptors (ORs), ionotropic receptors (IRs), gustatory receptors (GRs), chemosensory proteins (CSPs), odorant binding proteins (OBPs), and sensory neuron membrane proteins (SNMPs). Plagiodera versicolora (Coleoptera: Chrysomelidae), is a leaf-eating forest pest found in salicaceous trees worldwide. In this study, a transcriptome analysis of male and female adult antennae in P. versicolora individuals was conducted, which identified a total of 98 candidate chemosensory genes including 40 ORs, 7 IRs, 13 GRs, 10 CSPs, 24 OBPs, and 4 SNMPs. Subsequently, the tissue expression profiles of 15 P. versicolora OBPs (PverOBPs) and 39 ORs (PverORs) were conducted by quantitative real-time PCR. The data showed that almost all PverOBPs and PverORs were highly expressed in the male and female antennae. In addition, several OBPs and ORs (PverOBP10, PverOBP12, PverOBP18, PverOR24, and PverOR35) had higher expression levels in female antennae than those in the male antennae, indicating that these genes may be taking part in some female-specific behaviors, such as find mates, oviposition site, etc. This study deeply promotes further understanding of the chemosensory system and functional studies of the chemoreception genes in P. versicolora.

scholarly journals Development and Validation of a Prognostic Nomogram Based on DNA Methylation-Driven Genes for Patients With Ovarian Cancer

2021 ◽  
Vol 12 ◽  
Author(s):  
Min Zhou ◽  
Shasha Hong ◽  
Bingshu Li ◽  
Cheng Liu ◽  
Ming Hu ◽  
...  
Keyword(s):  
Ovarian Cancer ◽  
Dna Methylation ◽  
Mrna Expression ◽  
Risk Score ◽  
Cox Regression ◽  
Expression Profiles ◽  
Figo Stage ◽  
Prognostic Indicator ◽  
Tissue Expression ◽  
The Cancer Genome Atlas

Background: DNA methylation affects the development, progression, and prognosis of various cancers. This study aimed to identify DNA methylated-differentially expressed genes (DEGs) and develop a methylation-driven gene model to evaluate the prognosis of ovarian cancer (OC).Methods: DNA methylation and mRNA expression profiles of OC patients were downloaded from The Cancer Genome Atlas, Genotype-Tissue Expression, and Gene Expression Omnibus databases. We used the R package MethylMix to identify DNA methylation-regulated DEGs and built a prognostic signature using LASSO Cox regression. A quantitative nomogram was then drawn based on the risk score and clinicopathological features.Results: We identified 56 methylation-related DEGs and constructed a prognostic risk signature with four genes according to the LASSO Cox regression algorithm. A higher risk score not only predicted poor prognosis, but also was an independent poor prognostic indicator, which was validated by receiver operating characteristic (ROC) curves and the validation cohort. A nomogram consisting of the risk score, age, FIGO stage, and tumor status was generated to predict 3- and 5-year overall survival (OS) in the training cohort. The joint survival analysis of DNA methylation and mRNA expression demonstrated that the two genes may serve as independent prognostic biomarkers for OS in OC.Conclusion: The established qualitative risk score model was found to be robust for evaluating individualized prognosis of OC and in guiding therapy.

scholarly journals Breakdown of multiple sclerosis genetics to identify an integrated disease network and potential variant mechanisms

2019 ◽  
Vol 51 (11) ◽  
pp. 562-577
Author(s):  
C. Joy Shepard ◽  
Sara G. Cline ◽  
David Hinds ◽  
Seyedehameneh Jahanbakhsh ◽  
Jeremy W. Prokop
Keyword(s):  
Multiple Sclerosis ◽  
Immune Cell ◽  
Expression Profiles ◽  
Missense Variant ◽  
Cell Types ◽  
Tissue Expression ◽  
Specific Expression ◽  
Genomic Databases ◽  
Genetic Traits ◽  
Immune System Dysfunction

Genetics of multiple sclerosis (MS) are highly polygenic with few insights into mechanistic associations with pathology. In this study, we assessed MS genetics through linkage disequilibrium and missense variant interpretation to yield a MS gene network. This network of 96 genes was taken through pathway analysis, tissue expression profiles, single cell expression segregation, expression quantitative trait loci (eQTLs), genome annotations, transcription factor (TF) binding profiles, structural genome looping, and overlap with additional associated genetic traits. This work revealed immune system dysfunction, nerve cell myelination, energetic control, transcriptional regulation, and variants that overlap multiple autoimmune disorders. Tissue-specific expression and eQTLs of MS genes implicate multiple immune cell types including macrophages, neutrophils, and T cells, while the genes in neural cell types enrich for oligodendrocyte and myelin sheath biology. There are eQTLs in linkage with lead MS variants in 25 genes including the multitissue eQTL, rs9271640, for HLA-DRB1/ DRB5. Using multiple functional genomic databases, we identified noncoding variants that disrupt TF binding for GABPA, CTCF, EGR1, YY1, SPI1, CLOCK, ARNTL, BACH1, and GFI1. Overall, this paper suggests multiple genetic mechanisms for MS associated variants while highlighting the importance of a systems biology and network approach when elucidating intersections of the immune and nervous system.

scholarly journals Overlapping protein-coding genes in human genome and their coincidental expression in tissues

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Chao-Hsin Chen ◽  
Chao-Yu Pan ◽  
Wen-chang Lin
Keyword(s):  
Human Genome ◽  
Expression Profiles ◽  
Tissue Expression ◽  
Human Protein ◽  
Clear Understanding ◽  
Overlapping Genes ◽  
Genome Sequences ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Overlapping Gene

Abstract The completion of human genome sequences and the advancement of next-generation sequencing technologies have engendered a clear understanding of all human genes. Overlapping genes are usually observed in compact genomes, such as those of bacteria and viruses. Notably, overlapping protein-coding genes do exist in human genome sequences. Accordingly, we used the current Ensembl gene annotations to identify overlapping human protein-coding genes. We analysed 19,200 well-annotated protein-coding genes and determined that 4,951 protein-coding genes overlapped with their adjacent genes. Approximately a quarter of all human protein-coding genes were overlapping genes. We observed different clusters of overlapping protein-coding genes, ranging from two genes (paired overlapping genes) to 22 genes. We also divided the paired overlapping protein-coding gene groups into four subtypes. We found that the divergent overlapping gene subtype had a stronger expression association than did the subtypes of 5ʹ-tandem overlapping and 3ʹ-tandem overlapping genes. The majority of paired overlapping genes exhibited comparable coincidental tissue expression profiles; however, a few overlapping gene pairs displayed distinctive tissue expression association patterns. In summary, we have carefully examined the genomic features and distributions about human overlapping protein-coding genes and found coincidental expression in tissues for most overlapping protein-coding genes.

The SLC9A-C Mammalian Na+/H+Exchanger Family: Molecules, Mechanisms, and Physiology

2019 ◽  
Vol 99 (4) ◽  
pp. 2015-2113 ◽  
Author(s):  
S. F. Pedersen ◽  
L. Counillon
Keyword(s):  
State Of The Art ◽  
Expression Profiles ◽  
Tissue Expression ◽  
Gene Organization ◽  
Core Knowledge ◽  
Current State ◽  
Organ Systems ◽  
Evolutionarily Conserved ◽  
Solute Carrier ◽  
Art Research

Na+/H+exchangers play pivotal roles in the control of cell and tissue pH by mediating the electroneutral exchange of Na+and H+across cellular membranes. They belong to an ancient family of highly evolutionarily conserved proteins, and they play essential physiological roles in all phyla. In this review, we focus on the mammalian Na+/H+exchangers (NHEs), the solute carrier (SLC) 9 family. This family of electroneutral transporters constitutes three branches: SLC9A, -B, and -C. Within these, each isoform exhibits distinct tissue expression profiles, regulation, and physiological roles. Some of these transporters are highly studied, with hundreds of original articles, and some are still only rudimentarily understood. In this review, we present and discuss the pioneering original work as well as the current state-of-the-art research on mammalian NHEs. We aim to provide the reader with a comprehensive view of core knowledge and recent insights into each family member, from gene organization over protein structure and regulation to physiological and pathophysiological roles. Particular attention is given to the integrated physiology of NHEs in the main organ systems. We provide several novel analyses and useful overviews, and we pinpoint main remaining enigmas, which we hope will inspire novel research on these highly versatile proteins.

Identification of a β1 integrin isoform with restricted tissue expression in a teleost fish

2011 ◽  
Vol 23 (5) ◽  
pp. 654 ◽  
Author(s):  
Patricia Castillo-Briceño ◽  
Isabel Cabas ◽  
Marta Arizcun ◽  
Jose Meseguer ◽  
Victoriano Mulero ◽  
...  
Keyword(s):  
Teleost Fish ◽  
Sparus Aurata ◽  
Expression Profiles ◽  
Specific Inhibitor ◽  
Serum Levels ◽  
Tissue Expression ◽  
Gilthead Seabream ◽  
Β1 Integrin ◽  
Dependent Manner ◽  
Tissue Remodelling

The composition and organisation of extracellular matrix (ECM)-related molecules change during development. These components interact with different cell surface receptors to modulate the transduction of signals for cell growth, differentiation, migration, proliferation and apoptosis. Previous findings in the teleost fish gilthead seabream (Sparus aurata L., Teleostei), a marine protandrous hermaphrodite fish, showed that endocrine and immune stimuli are able to modulate the expression of ECM-related molecules, as well as specific correlations between them. In the present study, quantitative reverse transcription–polymerase chain reaction was used to examine the gene expression profile of β1 integrin isoform b (ITGB1b) and its possible role in reproductive physiology, especially in relation to spermatogenesis. Expression profiles were analysed in the context of the reproductive cycle (RC) and in relation with other ECM-related molecules, including matrix metalloproteinase (MMP)-2, MMP-9, MMP-13, tissue-specific inhibitor of metalloproteinase (TIMP)-2a, TIMP-2b, collagen (COL1A1) and ITGB1a. Expression of ITGB1b was found in the testis and brain and, to some extent, in endothelial cells. In contrast, ITGB1a was expressed ubiquitously. In the testis, the ITGB1b expression peaked during spermatogenesis, whereas the expression of the other ECM-related molecules is induced mainly during the post-spawning stage, both stages of marked tissue remodelling during the first and second RC in males. In addition, in fish exposed to the endocrine disruptor 17α-ethynyloestradiol (at 5 and 50 μg g–1 food during 7, 14 and 21 days), ITGB1b expression in the testis was inhibited in a dose- and time-dependent manner and was related to reduced serum levels of testosterone. Together, these results suggest a different functionality for the two ITGB1 isoforms in the gilthead seabream, where ITGB1b is more specifically involved in reproduction. This is the first report of an ITGB1 gene isoform whose expression is restricted to endocrine-related tissues in vertebrates.

scholarly journals Identification, characterization, and quantitative expression analysis of rainbow trout myostatin-1a and myostatin-1b genes

2006 ◽  
Vol 190 (3) ◽  
pp. 879-888 ◽  
Author(s):  
Dilip K Garikipati ◽  
Scott A Gahr ◽  
Buel D Rodgers
Keyword(s):  
Rainbow Trout ◽  
Genomic Organization ◽  
Expression Profiles ◽  
Muscle Growth ◽  
Fish Tissue ◽  
Tissue Expression ◽  
Negative Regulator ◽  
Cdna Clones ◽  
Mrna Levels ◽  
Quantitative Expression

Myostatin is a potent negative regulator of skeletal muscle growth. Although several cDNA clones have been characterized in different vertebrates, the genomic organization and bioactivity of non-mammalian homologs have not. The intron/exon organization and promoter subsequence analysis of two rainbow trout myostatin genes, rtMSTN-1a and rtMSTN-1b (formerly 1 and 2 respectively), as well as a quantitative assessment of their embryonic, larval, and adult tissue expression profiles are reported herein. Each gene was similarly organized into three exons of 490, 368, and 1600 bp for MSTN-1a and 486, 386, and 1419 bp for MSTN-1b. Comparative mapping of coding regions from several vertebrate myostatin genes revealed a common organization between species, including conserved pre-mRNA splice sites; the first among the fishes and the second across all vertebrate species. In silico subsequence analysis of the promoter regions identified E-boxes and other putative myogenic response elements. However, the number and diversity of elements were considerably less than those found in mammalian promoters or in the recently characterized zebrafish MSTN-2 gene. A quantitative analysis of the embryonic expression profile for both genes indicates that rtMSTN-1a expression is consistently greater than that of rtMSTN-1b and neither gene is significantly expressed throughout gastrulation. Expression of both steadily increases fourfold during somitogenesis and subsides as this period ends. After eyeing, however, rtMSTN-1a mRNA levels ultimately rise 20-fold by day 49 and peak before hatching and yolk sac absorption (YSA). Levels of rtMSTN-1b rise similarly, but do not peak before YSA. An analysis of adult (2-year-old fish) tissue expression indicates that both transcripts are present in most tissues although levels are highest in brain, testes, eyes, muscle, and surprisingly spleen. These studies suggest that strong selective pressures have preserved the genomic organization of myostatin genes throughout evolution. However, the different expression profiles and putative promoter elements in fishes versus mammals suggests that limitations in myostatin function may have evolved recently.

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