scholarly journals The whole body transcriptome of Coleophora obducta reveals important olfactory proteins

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8902
Author(s):  
Dongbai Wang ◽  
Jing Tao ◽  
Pengfei Lu ◽  
Youqing Luo ◽  
Ping Hu
Keyword(s):  
Phylogenetic Analysis ◽  
Binding Proteins ◽  
Expression Profiles ◽  
Whole Body ◽  
Gustatory Receptors ◽  
Specific Expression ◽  
Ionotropic Receptors ◽  
Olfactory Recognition ◽  
Lack Of Information ◽  
Olfactory Proteins

Background The tiny casebearer moth Coleophora obducta, an important defoliator of Larix spp., is a major threat to ecological security in north China. Studies have shown that C. obducta is strongly specific to host plants; it is unable complete its life cycle without Larix spp. The sex pheromones of C. obducta Z5-10:OH have been elucidated; and eight types of antennae sensilla, have been detected, indicating that an exploration of its olfactory proteins is necessary, due to the general lack of information on this topic. Methods We investigated the whole body transcriptome of C. obducta, performed a phylogenetic analysis of its olfactory proteins and produced expression profiles of three pheromone-binding proteins (CobdPBPs) by qRT–PCR. Results We identified 16 odorant binding proteins, 14 chemosensory proteins, three sensory neuron membrane proteins, six odorant degrading enzymes, five antennal esterases, 13 odorant receptors, seven ionotropic receptors and 10 gustatory receptors, including three PBPs and one odorant co-receptor. Additionally, three putative pheromone receptors, two bitter gustatory receptors and five functional ionotropic receptors were found by phylogenetic analysis. The expression profiles of three PBPs in males and females showed that all of them exhibited male-specific expression and two were expressed at significantly higher levels in males. These data provide a molecular foundation from which to explore the olfactory recognition process and may be useful in the development of a new integrated pest management strategy targeting olfactory recognition of C. obducta.

scholarly journals Lantern: an integrative repository of functional annotations for lncRNAs in the human genome

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Swapna Vidhur Daulatabad ◽  
Rajneesh Srivastava ◽  
Sarath Chandra Janga
Keyword(s):  
Human Genome ◽  
Cellular Localization ◽  
Expression Profiles ◽  
Free Text ◽  
Dynamic Visualization ◽  
Specific Expression ◽  
Web Resource ◽  
Functional Dynamics ◽  
Non Coding Rnas ◽  
Retrieval Engine

Abstract Background With advancements in omics technologies, the range of biological processes where long non-coding RNAs (lncRNAs) are involved, is expanding extensively, thereby generating the need to develop lncRNA annotation resources. Although, there are a plethora of resources for annotating genes, despite the extensive corpus of lncRNA literature, the available resources with lncRNA ontology annotations are rare. Results We present a lncRNA annotation extractor and repository (Lantern), developed using PubMed’s abstract retrieval engine and NCBO’s recommender annotation system. Lantern’s annotations were benchmarked against lncRNAdb’s manually curated free text. Benchmarking analysis suggested that Lantern has a recall of 0.62 against lncRNAdb for 182 lncRNAs and precision of 0.8. Additionally, we also annotated lncRNAs with multiple omics annotations, including predicted cis-regulatory TFs, interactions with RBPs, tissue-specific expression profiles, protein co-expression networks, coding potential, sub-cellular localization, and SNPs for ~ 11,000 lncRNAs in the human genome, providing a one-stop dynamic visualization platform. Conclusions Lantern integrates a novel, accurate semi-automatic ontology annotation engine derived annotations combined with a variety of multi-omics annotations for lncRNAs, to provide a central web resource for dissecting the functional dynamics of long non-coding RNAs and to facilitate future hypothesis-driven experiments. The annotation pipeline and a web resource with current annotations for human lncRNAs are freely available on sysbio.lab.iupui.edu/lantern.

Identification and expression analysis of Dazl homologue in Cynops cyanurus

Zygote ◽  
2021 ◽  
pp. 1-6
Author(s):  
Yinjiao Zhao ◽  
Ya Du ◽  
Qinglan Ge ◽  
Fang Yan ◽  
Shu Wei
Keyword(s):  
Phylogenetic Analysis ◽  
Comparative Studies ◽  
Rna Binding ◽  
Rna Binding Protein ◽  
Rna Recognition Motif ◽  
Rna Recognition ◽  
Specific Expression ◽  
Recognition Motif ◽  
Deleted In Azoospermia ◽  
Specific Expression Pattern

Summary The Dazl (deleted in azoospermia-like) gene encodes an RNA-binding protein containing an RNA recognition motif (RRM) and a DAZ motif. Dazl is essential for gametogenesis in vertebrates. In this study, we report the cloning of Dazl cDNA from Cynops cyanurus. Ccdazl mRNA showed a germline-specific expression pattern as expected. Ccdazl expression gradually decreased during oogenesis, suggesting that it may be involved in oocyte development. Phylogenetic analysis revealed that the Ccdazl protein shares conserved motifs/domains with Dazl proteins from other species. Cloning of Ccdazl provides a new tool to carry out comparative studies of germ cell development in amphibians.

Identification and expression profiles analysis of odorant‐binding proteins in soybean aphid, Aphis glycines (Hemiptera: Aphididae)

2019 ◽  
Vol 27 (5) ◽  
pp. 1019-1030 ◽  
Author(s):  
Ling Wang ◽  
Ying‐Dong Bi ◽  
Ming Liu ◽  
Wei Li ◽  
Miao Liu ◽  
...  
Keyword(s):  
Binding Proteins ◽  
Expression Profiles ◽  
Soybean Aphid ◽  
Aphis Glycines ◽  
Odorant Binding Proteins ◽  
Odorant Binding

scholarly journals Effects of Essential Oils-Based Supplement and Salmonella Infection on Gene Expression, Blood Parameters, Cecal Microbiome, and Egg Production in Laying Hens

Animals ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 360
Author(s):  
Georgi Yu. Laptev ◽  
Elena A. Yildirim ◽  
Larisa A. Ilina ◽  
Valentina A. Filippova ◽  
Ivan I. Kochish ◽  
...  
Keyword(s):  
Egg Production ◽  
Salmonella Enteritidis ◽  
Laying Hens ◽  
Expression Profiles ◽  
Blood Parameters ◽  
Post Inoculation ◽  
Production Traits ◽  
Immunological Parameters ◽  
Specific Expression ◽  
Blood Biochemical

One of the main roles in poultry resistance to infections caused by Salmonella is attributed to host immunity and intestinal microbiota. We conducted an experiment that involved challenging Lohmann White laying hens with Salmonella Enteritidis (SE), feeding them a diet supplemented with an EOs-based phytobiotic Intebio®. At 1 and 7 days post-inoculation, the expression profiles of eight genes related to immunity, transport of nutrients in the intestine, and metabolism were examined. Cecal microbiome composition and blood biochemical/immunological indices were also explored and egg production traits recorded. As a result, the SE challenge of laying hens and Intebio® administration had either a suppressive or activating effect on the expression level of the studied genes (e.g., IL6 and BPIFB3), the latter echoing mammalian/human tissue-specific expression. There were also effects of the pathogen challenge and phytobiotic intake on the cecal microbiome profiles and blood biochemical/immunological parameters, including those reflecting the activity of the birds’ immune systems (e.g., serum bactericidal activity, β-lysine content, and immunoglobulin levels). Significant differences between control and experimental subgroups in egg performance traits (i.e., egg weight/number/mass) were also found. The phytobiotic administration suggested a positive effect on the welfare and productivity of poultry.

scholarly journals Single-Cell Expression Landscape of SARS-CoV-2 Receptor ACE2 and Host Proteases in Normal and Malignant Lung Tissues from Pulmonary Adenocarcinoma Patients

Cancers ◽  
2021 ◽  
Vol 13 (6) ◽  
pp. 1250
Author(s):  
Guangchun Han ◽  
Ansam Sinjab ◽  
Kieko Hara ◽  
Warapen Treekitkarnmongkol ◽  
Patrick Brennan ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Single Cell ◽  
Cancer Patients ◽  
Expression Profiles ◽  
Lung Cells ◽  
Alveolar Type ◽  
Specific Expression ◽  
Lung Cancer Patients ◽  
Normal Tissues ◽  
Cell Expression

The novel coronavirus SARS-CoV-2 is the causative agent of the COVID-19 pandemic. Severely symptomatic COVID-19 is associated with lung inflammation, pneumonia, and respiratory failure, thereby raising concerns of elevated risk of COVID-19-associated mortality among lung cancer patients. Angiotensin-converting enzyme 2 (ACE2) is the major receptor for SARS-CoV-2 entry into lung cells. The single-cell expression landscape of ACE2 and other SARS-CoV-2-related genes in pulmonary tissues of lung cancer patients remains unknown. We sought to delineate single-cell expression profiles of ACE2 and other SARS-CoV-2-related genes in pulmonary tissues of lung adenocarcinoma (LUAD) patients. We examined the expression levels and cellular distribution of ACE2 and SARS-CoV-2-priming proteases TMPRSS2 and TMPRSS4 in 5 LUADs and 14 matched normal tissues by single-cell RNA-sequencing (scRNA-seq) analysis. scRNA-seq of 186,916 cells revealed epithelial-specific expression of ACE2, TMPRSS2, and TMPRSS4. Analysis of 70,030 LUAD- and normal-derived epithelial cells showed that ACE2 levels were highest in normal alveolar type 2 (AT2) cells and that TMPRSS2 was expressed in 65% of normal AT2 cells. Conversely, the expression of TMPRSS4 was highest and most frequently detected (75%) in lung cells with malignant features. ACE2-positive cells co-expressed genes implicated in lung pathobiology, including COPD-associated HHIP, and the scavengers CD36 and DMBT1. Notably, the viral scavenger DMBT1 was significantly positively correlated with ACE2 expression in AT2 cells. We describe normal and tumor lung epithelial populations that express SARS-CoV-2 receptor and proteases, as well as major host defense genes, thus comprising potential treatment targets for COVID-19 particularly among lung cancer patients.

scholarly journals Genome-Wide Identification, Characterization, and Expression Analysis of DDE_Tnp_4 Family Genes in Eriocheir sinensis

Antibiotics ◽  
2021 ◽  
Vol 10 (12) ◽  
pp. 1430
Author(s):  
Yuanfeng Xu ◽  
Jinbin Zheng ◽  
Yanan Yang ◽  
Zhaoxia Cui
Keyword(s):  
Phylogenetic Analysis ◽  
Environmental Stress ◽  
Tandem Duplication ◽  
High Salinity ◽  
Expression Profiles ◽  
Eriocheir Sinensis ◽  
Biological Processes ◽  
Synteny Analysis ◽  
Air Exposure ◽  
Genome Wide

DDE transposase 4 (DDE_Tnp_4) family is a large endonuclease family involved in a wide variety of biological processes. However, little information is available about this family in crustaceans. In this study, we used HMMER to identify 39 DDE_Tnp_4 family genes in Eriocheir sinensis genome, and the genes were classified into four subfamilies according to phylogenetic analysis. Gene expansions occurred among E. sinensis genome, and synteny analysis revealed that some DDE_Tnp_4 family genes were caused by tandem duplication. In addition, the expression profiles of DDE_Tnp_4 family genes in E. sinensis indicated that subfamily I and II genes were up-regulated in response to acute high salinity and air exposure stress. E. sinensis is a kind of economical crustacean with strong tolerance to environmental stress. We confirmed the expansion of DDE_Tnp_4 family genes in E. sinensis and speculated that this expansion is associated with strong tolerance of E. sinensis. This study sheds light on characterizations and expression profiles of DDE_Tnp_4 family genes in E. sinensis and provides an integrated framework for further investigation on environmental adaptive functions of DDE_Tnp_4 family in crustaceans.

Sign in / Sign up

Export Citation Format

Share Document