GO Annotation Analysis Research Articles

Wheat root transcriptional responses against Gaeumannomyces graminis var. tritici

Wheat root rot caused by Gaeumannomyces graminis var. tritici (Ggt) results in severe yield losses in wheat production worldwide. However, little is known about the molecular mechanism that regulates systemic symptom development in infected wheat. Fluorescent microscopy observation of the stained wheat roots infected by Ggt showed that lesions were visible when the fungus could be detected in the endodermis, pericycle and phloem at 5 days post inoculation (dpi), and rust symptoms were visible when there was extensive fungal colonization in the root cortex at 6 dpi. Transcriptome sequencing of Ggt-inoculated wheat roots and healthy control root samples was performed at 5 dpi to identify Ggt-induced gene expression changes in wheat roots at the time of lesion formation. A total of 3973 differentially expressed genes (DEGs) were identified, of which 1004 (25.27%) were up-regulated and 2969 (74.73%) were down-regulated in Ggt-inoculated wheat roots compared with those in control roots. GO annotation and KEGG pathway analysis of these DEGs revealed that many of them were associated with pathogen resistance, such as those involved in oxidation-reduction process, tryptophan biosynthesis process, and phenylpropanoid biosynthesis process. Analysis of DEGs revealed that 15 DEGs were involved in cellular regulation, 57 DEGs in signal transduction pathways, and 75 DEGs in cell wall reorganization, and 23 DEGs are pathogenesis-related proteins. Reverse transcription quantitative PCR (RT-qPCR) of 13 of those DEGs showed that these genes may play roles in wheat resistance against Ggt. Overall, this study represents the first transcriptional profiling of wheat roots in response to Ggt infection and further characterization of DEGs identified in this study may lead to better understanding of resistance against take-all in wheat.

Transcriptomics Study to Determine the Molecular Mechanism by which sIL-13Rα2-Fc Inhibits Caudal Intervertebral Disc Degeneration in Rats.

Background Intervertebral disc degeneration is related to tissue fibrosis. ADAMTS can degrade the important components of the ECM during the process of intervertebral disc degeneration, ultimately resulting in the loss of intervertebral disc function. sIL-13Rα2-Fc can inhibit fibrosis and slow down the degeneration process, but the mechanism involved remains unclear. Objective To determine the mechanism by which sIL-13Rα2-Fc inhibits ECM degradation and reduces intervertebral disc tissue fibrosis using a transcriptomics analysis. Methods A rat model of caudal intervertebral disc degeneration was established, and Sirius red staining was used to observe the pathological changes in the caudal intervertebral disc. Transcriptome sequencing was employed to assess the gene expression profiles of the intervertebral disc tissues in the model group and the sIL-13Rα2-Fc-treated group. Differentially expressed genes were identified and analyzed using GO annotation and KEGG pathway analyses. Real-time fluorescence quantitative PCR was used to verify the expression levels of candidate genes. The levels of GAG and HA were quantitatively assessed by ELISA, and the levels of collagen I and collagen II were analyzed by western blotting. Results Sirius red staining showed that in the model group, the annulus fibrosus was disordered, the number of breaks increased, and the type I collagen protein levels increased, whereas in the sIL-13Rα2-Fc group, the annulus fibrosus was ordered, the number of breaks decreased, and the type II collagen protein levels increased. In comparison with the model group, we identified 58 differentially expressed genes in the sIL-13Rα2-Fc group, and these were involved in 35 signaling pathways. Compared with those in the model group, the mRNA expression levels of Rnux1, Sod2, and Tnfaip6 in the IL-13Rα2-Fc group were upregulated, and the mRNA expression levels of Aldh3a1, Galnt3, Fgf1, Celsr1, and Adamts8 were downregulated; these results were verified by real-time fluorescence quantitative PCR. TIMP-1 (an ADAMTS inhibitor) and TIMP-1 combined with the sIL-13Rα2-Fc intervention increased the levels of GAG and HA, inhibited the expression of type I collagen, and promoted the expression of type II collagen. Conclusion Adamts8 may participate in the degradation of ECM components such as GAG and HA and lead to an imbalance in the ECM of the intervertebral disc, resulting in intervertebral disc degeneration. sIL-13Rα2-Fc promoted anabolism of the ECM and increased the levels of ECM components by inhibiting the expression of Adamts8, thus maintaining the dynamic equilibrium of the ECM and ultimately delaying intervertebral disc degeneration.

LncRNA TRPC7-AS1 regulates nucleus pulposus cellular senescence and ECM synthesis via competing with HPN for miR-4769-5p binding

Intervertebral disc (IVD) degeneration (IDD) is identified as an abnormal, cell-mediated, age-dependent and genetics-dependent molecular degeneration process in which NPCs (nucleus pulposus cells) senesce and the balance of ECM (extracellular matrix) synthesis and catabolism is disrupted. Increasing evidence reveals that IDD can be modulated by genetic factors, including non-coding RNAs. In the present study, we downloaded non-coding RNA profiling (GSE56081 and GSE63492) and performed GO annotation and enrichment analysis and association analyses on differentially-expressed genes. LncRNA TRPC7-AS1, miR-4769−5p, and Hepsin (HPN) may form a lncRNA-miRNA-mRNA network that can regulate NPC proliferation, senescence and ECM in IDD. LncRNA TRPC7-AS1 directly targets miR-4769−5p while miR-4769−5p directly targets HPN 3′UTR. miR-4769−5p overexpression inhibited HPN expression, suppressed NPC senescence, promoted NPC viability, and promoted ECM synthesis. The effect of TRPC7-AS1 silence on NPCs was similar as miR-4769−5p overexpression while the effect of HPN overexpression was opposite to miR-4769−5p overexpression. miR-4769−5p suppression or HPN overexpression could significantly attenuate the effect of TRPC7-AS1 silence. LncRNA TRPC7-AS1 relieves miR-4769−5p-induced inhibition on HPN via acting as a ceRNA, thus regulating NPC viability, senescence, and ECM synthesis. In summary, we regard lncRNA-miRNA-mRNA modulation as a new potent target for IDD treatment.

Systematic analysis of SmWD40s, and responding of SmWD40-170 to drought stress by regulation of ABA- and H2O2-induced stomal movement in Salvia miltiorrhiza bunge

WD40 proteins play crucial roles in response to abiotic stress. By screening the genome sequences of Salvia miltiorrhiza Bunge, 225 SmWD40 genes were identified and divided into 9 subfamilies (I-IX). Physiological, biochemical, gene structure, conserved protein motif and GO annotation analyses were performed on SmWD40 family members. The SmWD40-170 was found in 110 SmWD40 genes that contain drought response elements, SmWD40-170 was one of these genes whose response in terms of expression under drought was significant. The expression of SmWD40-170 was also up-regulated by ABA and H2O2. Through observed the stomatal phenotype of SmWD40-170 transgenic lines, the stomatal closure was abolished under dehydration, ABA and H2O2 treatment in SmWD40-170 knockdown lines. Abscisic acid (ABA), as the key phytohormone, elevates reactive oxygen species (ROS) levels under drought stress. The ABA-ROS interaction mediated the generation of H2O2 and the activation of anion channel in guard cells. The osmolality alteration of guard cells further accelerated the stomatal closure. As a second messenger, nitric oxide (NO) regulated ABA signaling, the NO stimulated protein kinase activity inhibited the K+ influx which result in stomatal closure. These NO-relevant events were essential for ABA-induced stomatal closure. The reduction of NO production was also observed in the guard cells of SmWD40-170 knockdown lines. The abolished of stomatal closure attributed to the SmWD40-170 deficiency induced the reduction of NO content. In general, the SmWD40-170 is a critical drought response gene in SmWD40 gene family and regulates ABA- and H2O2-induced stomatal movement by affecting the synthesis of NO.

Identification of the Hub Genes Related to Nerve Injury-Induced Neuropathic Pain

BackgroundThe reactivity enhancement of pain sensitive neurons in the nervous system is a feature of the pathogenesis for neuropathic pain (NP), yet the underlying mechanisms need to be fully understood. In this study, we made an attempt to clarify the NP-related hub genes and signaling pathways so as to provide effective diagnostic and therapeutic methods toward NP.MethodsMicroarray expression profile GSE30691 including the mRNA-seq data of the spared nerve injury (SNI)-induced NP rats was accessed from the GEO database. Then, genes associated with NP development were screened using differential analysis along with random walk with restart (RWR). GO annotation and KEGG pathway analyses were performed to explore the biological functions and signaling pathways where the genes were activated. Afterward, protein-protein interaction (PPI) analysis and GO analysis were conducted to further identify the hub genes which showed an intimate correlation with NP development.ResultsTotally 94 genes associated with NP development were screened by differential analysis and RWR analysis, and they were observed to be predominantly enriched in hormone secretion and transport, cAMP signaling pathway and other NP occurrence associated functions and pathways. Thereafter, the 94 genes were subjected to PPI analysis to find the genes much more associated with NP and a functional module composed of 48 genes were obtained. 8 hub genes including C3, C1qb, Ccl2, Cxcl13, Timp1, Fcgr2b, Gal, and Lyz2 were eventually identified after further association and functional enrichment analyses, and the expression of these 8 genes were all higher in SNI rats by comparison with those in Sham rats.ConclusionBased on the data collected from GEO database, this study discovered 8 hub genes that were closely related to NP occurrence and development, which help to provide potent theoretical basis for NP treatment.

Comparative analysis of excretory–secretory products of muscle larvae of three isolates of Trichinella pseudospiralis by the iTRAQ method

Trichinella pseudospiralis is a non-encapsulated intracellular parasitic nematode that can possess a strong ability to modulate the host immune response. Here, we compared the differentially expressed proteins of excretory-secretory (ES) products in three isolates of T. pseudospiralis muscle larvae (ML) [from Russia (RUS), United States of America (USA) and Australia (AUS)] using isobaric tags for relative and absolute quantification (iTRAQ)-based technology. A total of 2591 nonredundant proteins were identified, of which 65 (146), 72 (98) and 43 (103) significantly upregulated (downregulated) differentially expressed proteins were detected among pairwise comparisons (T4RUS vs T4USA, T4AUS vs T4USA and T4RUS vs T4AUS). In addition, GO annotation, KEGG and STRING analyses were carried out on the screened differentially altered proteins. The main biological processes involved included carbohydrate metabolic processes, DNA metabolic processes, cellular protein modification processes and homeostatic processes. The majority of KEGG pathways were found to be related to the metabolic pathways, lysosome pathway and protein processing in endoplasmic reticulum. Moreover, all ES protein expression levels involved in the lysosome pathway were significantly higher in the T4USA isolate than in the other two isolates. We also found differences in the expression of some important immunoregulatory proteins, such as protein disulfide-isomerase, thioredoxin protein and deoxyribonuclease-2-alpha, between different isolates of T. pseudospiralis ML. Flow cytometry was used to detect the increase in the CD4+/CD8 + T-cell ratio in pig peripheral blood and to verify the effect of T. pseudospiralis on the Th1/Th2 polarization of the host. Quantitative real-time PCR analysis also confirmed that the changes in the transcriptional level of genes were consistent with those at the proteomic level. These findings reveal the possible role of significantly differentially expressed proteins in ES products of the different isolates of T. pseudospiralis in antagonizing and participating in the regulation of the host immune response and maintaining a stable growth environment.

Study on hepatoprotective mechanisms of Veratrilla baillonii based on network pharmacology

The purpose of this study was to predict the active components, targets and signaling pathways of Veratrilla baillonii for the prevention and treatment of non-alcoholic liver diseases, preliminarily verify the active components and related targets through cell experiments, and elucidate the mechanism of V. baillonii on liver protection. The candidate active components of V. baillonii were screened by searching Chinese medicine ingredients and Chinese medicine pharmacology database and analysis platform, combined with the pharmacokinetic parameters(oral availability and drug-like principle); the target of candidate active ingredients were predicted by protein database, and the target of disease related to non-alcoholic liver disease was predicted. Cytoscape software was used to construct the network of "active component-target-disease", and the protein interaction network was constructed through the STRING database to infer the core target. GO annotation analysis, KEGG pathway analysis and enrichment analysis were conducted through DAVID bioinformatics annotation database. Finally, the core target and pathway of V. baillonii were preliminarily verified by the experimental model of H_2O_2-induced liver cell damage intervened by V. baillonii water extract(WVBF). The cell viability was detected by MTT assay and real-time unlabeled assay, and the expression of related genes was analyzed by Real-time quantitative polymerase chain reaction(PCR). Firstly, 14 active components were obtained from V. baillonii through network pharmacology. There were 287 potential targets corresponding to the components, 587 targets related to non-alcoholic liver disease, and 13 core targets after the interaction between active ingredient targets and disease targets. Secondly, GO enrichment analysis showed that these genes mainly affected 26 biological processes such as nuclear receptor activity, transcription factor activity, steroid hormone receptor activity, ubi-quitin-like protein ligase binding, protein heterodimerization activity, and transcription cofactor binding. KEGG enrichment analysis showed that PI3 K-AKT signaling pathway, HIF-1 signaling pathway, MAPK signaling pathway, insulin signaling pathway, TNF signaling pathway and some cancer-related pathways were more enriched. Finally, TNF-α and MAPK8 were successfully verified as important targets by hepatocytes in vitro, which suggested that V. baillonii could significantly improve liver damage. TNF-α and MAPK8 were one of the targets. Based on the above results, we systematically predicted the material basis and biological mechanism of V. baillonii through multi-component, multi-target and multi-pathway regulation of nonalcoholic liver disease, and the core targets were successfully verified by cells, providing data basis and scientific basis for the in-depth development of V. baillonii.

Genome\u2011wide integrated analysis demonstrates widespread functions of lncRNAs in mammary gland development and lactation in dairy goats

BackgroundThe mammary gland is a unique organ for milk synthesis, secretion and storage, and it undergoes cyclical processes of development, differentiation, lactation and degeneration. At different developmental periods, the biological processes governing mammary gland physiology and internal environmental homeostasis depend on a complex network of genes and regulatory factors. Emerging evidence indicates that lncRNAs have arbitrarily critical functions in regulating gene expression in many organisms; however, the systematic characteristics, expression, and regulatory roles of lncRNAs in the mammary gland tissues of dairy goats have not been determined.ResultIn the present study, we profiled long noncoding RNA (lncRNA) expression in the mammary gland tissues of Laoshan dairy goats (Capra hircus) from different lactation periods at the whole-genome level, to identify, characterize and explore the regulatory functions of lncRNAs. A total of 37,249 transcripts were obtained, of which 2381 lncRNAs and 37,249 mRNAs were identified, 22,488 transcripts, including 800 noncoding transcripts and 21,688 coding transcripts, differed significantly (p ≤ 0.01) among the different lactation stages. The results of lncRNA-RNA interaction analysis showed that six known lncRNAs belonging to four families were identified as the precursors of 67 known microRNAs; 1478 and 573 mRNAs were predicted as hypothetical cis-regulation elements and antisense mRNAs, respectively. GO annotation and KEGG analysis indicated that the coexpressed mRNAs were largely enriched in biological processes related to such activities as metabolism, immune activation, and stress,., and most genes were involved in pathways related to such phenomena as inflammation, cancer, signal transduction, and metabolism.ConclusionsOur results clearly indicated that lncRNAs involved in responses to stimuli, multiorganism processes, development, reproductive processes and growth, are closely related to mammary gland development and lactation.

Analysis of Long Non-Coding RNAs and mRNAs Associated with Lactation in the Crop of Pigeons (Columba livia).

Pigeons have the ability to produce milk and feed their squabs. The genetic mechanisms underlying milk production in the crops of ’lactating’ pigeons are not fully understood. In this study, RNA sequencing was employed to profile the transcriptome of lncRNA and mRNA in lactating and non-‘lactating’ pigeon crops. We identified 7066 known and 17,085 novel lncRNAs. Of these lncRNAs, 6166 were differentially expressed. Among the 15,138 mRNAs detected, 6483 were differentially expressed, including many predominant genes with known functions in the milk production of mammals. A GO annotation analysis revealed that these genes were significantly enriched in 55, 65, and 30 pathways of biological processes, cellular components, and molecular functions, respectively. A KEGG pathway enrichment analysis revealed that 12 pathways (involving 544 genes), including the biosynthesis of amino acids, the propanoate metabolism, the carbon metabolism and the cell cycle, were significantly enriched. The results provide fundamental evidence for the better understanding of lncRNAs’ and differentially expressed genes’ (DEGs) regulatory role in the molecular pathways governing milk production in pigeon crops. To our knowledge, this is the first genome-wide investigation of the lncRNAs in pigeon crop associated with milk production. This study provided valuable resources for differentially expressed lncRNAs and mRNAs, improving our understanding of the molecular mechanism of pigeon milk production.

Bioinformatics analysis for hepatocellular carcinoma genes based on the data of expression profile chip.

Hepatocellular carcinoma (HCC) is one of the most common malignant tumors worldwide, especially in Asia and Africa. However, the underlying mechanism is still unclear. Consequently, it is important to explore its key genes and prognosis-related genes via bioinformatics. This study aimed to explore the molecular mechanism of HCC by using bioinformatics analysis for HCC gene chip data. Microarray data of HCC genes were downloaded from public GEO database and screened for differentially expressed genes (DEGs) by GEO2R analysis. Then DAVID online tool was used for GO annotation and KEGG pathway enrichment analysis. STRING-DB online database and Cytoscape software were used for protein interaction network analysis.GEPIA and Ualcan were applied to evaluate prognosis and promoter methylation level. A total of 87 DEGs of HCC were screened, of which 15 genes were up-regulated and 72 genes were down-regulated. GO annotation indicated that most of the genes were involved in oxidation reduction,cellular amino acid derivative metabolic process, carboxylic acid catabolic process, and response to wounding. KEGG pathways were enriched in linoleic acid metabolism, retinol metabolism, complement and coagulation cascades,steroid hormone biosynthesis, drug metabolism, and other pathways. Two key modules and key genes AURKA and SPP2 were obtained by protein interaction network analysis. Prognostic analysis showed that the 2 genes were significantly correlated with the total survival time of patients with HCC. There was no significant difference in the methylation level of AURKA promoter between the primary tumor group and the normal group (P=0.296) and the methylation level of SPP2 promoter was significantly lower in the primary tumor group than that in the normal group (P<0.001). HCC-relevant AURKA and SPP2 are obtained via bioinformatics analysis, which are closely related to the prognosis of patients with HCC. Gene promoter methylation is not the main factor for AURKA and SPP2 expression levels.

An Integrated Analysis of mRNAs and miRNAs Microarray Profiles to Screen miRNA Signatures Involved in Nasopharyngeal Carcinoma.

Objective:We aim to identify several microRNAs (miRNAs/miRs)-messenger RNAs (mRNAs) biomarkers correlated to nasopharyngeal carcinoma (NPC) based on an integrated analysis of miRNA and mRNAs microarray expression profiles.Methods:The available mRNA and miRNA microarray datasets were retrieved from Gene Expression Omnibus (GEO) database according to pre-determined screening criteria. Differentially expressed miRNA and mRNAs (DEmiRNAs and DEmRNAs) were extracted between NPC and noncancerous nasopharyngeal tissues. The target genes of DEmiRNAs were predicted with miRTarBase followed by the construction of DEmiRNAs-target DEmRNAs network, and functional analyses were performed. The DEmiRNAs expressions were validated and the performance of these DEmiRNAs was assessed by the area under the curve (AUC) values. Finally, the correlations between DEmiRNAs and specific clinical factors were analyzed.Results:There were 1140 interaction pairs (including let-7d/f-MYC/HMGA2 and miR-452-ITGA9) in DEmiRNAs-target DEmRNAs network. The GO annotation analysis showed that several genes such as MYC, HMGA2 and ITGA9 primarily participated in cellular process. KEGG analysis showed that these targets were associated with cell cycle and cancer-related pathways. Down-regulated let-7(-d and –f) and up-regulated miR-452 were verified in datasets. The AUC values of these 3 DEmiRNAs (let-7d, let-7-f and miR-452) was 0.803, 0.835 and 0.735, respectively. Besides, miR-452 was significantly related to survival rate of NPC patients.Conclusion:The findings implied let-7d/f-MYC/HMGA2 and miR-452-ITGA9 might be promising targets for the detection and treatment of NPC.

Transcriptomic responses to yam ( Dioscorea oppositifolia L .) extract dietary supplementation in rainbow trout ( Oncorhynchus mykiss ) liver

Infectious diseases in rainbow trout (Oncorhynchus mykiss) have been seen in rainbow trout farming industry. Yam (Dioscorea oppositifolia L.) has a functional impact upon anti-disease and strengthens immunity. Understanding the molecular mechanisms which occur in rainbow trout in response to yam will be useful to decrease disease-related morbidity and mortality. In the present study, we conducted transcriptome analysis of liver in rainbow trout fed diets including yam extract (0, 0.2% and 0.4%), to identify yam extract-induced genes and pathways. Over 451 million clean reads were obtained from nine liver libraries. Two comparisons were separately implemented between yam extract groups and control group. Using |log2Fold-change|>1 and p-value < .05 as the threshold, a total of 2,693 differentially expressed unigenes (DEGs) were identified, including 1599 up-regulated and 1,094 down-regulated unigenes. The RNA-Seq results were verified by RT-qPCR. DEGs were classified into three categories by GO annotation and functional enrichment analysis: biological process (23 subclasses), cellular component (16 subclasses) and molecular function (16 subclasses). KEGG annotation and classifications of DEGs indicated endocrine system, immune system, lipid metabolism, carbohydrate metabolism and signal transduction pathways include a large number of DEGs. In addition, 526 overlap DEGs in two comparisons were annotated to 174 pathways in KEGG analysis, 7 top significantly enriched pathway terms include chemokine signalling pathway, platelet activation, progesterone-mediated oocyte maturation, insulin signalling pathway, FoxO signalling pathway, cGMP-PKG signalling pathway and sphingolipid signalling pathway. These findings provide valuable information for further analysis of the disease resistance mechanisms of rainbow trout fed yam.

Comprehensive analysis of long non-coding RNAs expression pattern in the pathogenesis of pulmonary tuberculosis

BackgroundLong non-coding RNAs (lncRNAs) play crucial roles in the progression and pathogenesis of cancer. Right now, less is known about the association between the expression of lncRNAs and the pathogenesis of pulmonary tuberculosis (PTB). MethodsIn present study, the expression profiles of lncRNAs were investigated by transcriptome sequencing from PTB patients vs. healthy individuals. ResultsA total of 449 differentially expressed (DE) (fold change ≥2, false discovery rate ≤ 0.05) lncRNAs were screened out from the PTB patients. Lnc-HNRNPU-1:7 and lnc-FAM76B-4:1 was found the most upregulated lncRNAs and downregulated lncRNAs in PTB patients, respectively. GO annotation and KEGG analysis were used to explore the potential roles of these DE lncRNAs. The JAK/STAT and TGF-β signaling pathways related to PTB pathogenesis were enriched in PTB patients. The co-expressed of a few lncRNAs and mRNAs on chromosome were shown by cis-regulatory gene analysis. Trans analysis indicated that STAT1, STAT2 and TAF7 transcription factors regulated the expression of lncRNA and mRNA. The constructed lncRNA ceRNA network suggested that lncRNAs regulating mRNAs expression may mediate by sponged miRNAs. ConclusionWe comprehensively analyzed the expression profiles of lncRNAs in PTB patients, thus providing new clues for exploring the regulatory mechanisms of dysregulated lncRNAs in the pathogenesis of PTB.

Identification and characterization of novel type of RNAs, circRNAs in crucian carp Carassius auratus gibelio

Circular RNAs (circRNAs) with regulatory potency activity was identified from varieties of species. Crucian carp (Carassius auratus gibelio) is one of the most freshwater aquaculture species in China. Every year, huge economic damage to the farming was caused by the virus and bacterial infection. Until now, there is any information about circRNA reported from the Crucian carp. In this study, the expression pattern of circRNA in Crucian carp was investigated with transcriptomic analysis. The results showed that only 37 circRNAs were identified from the Crucian carp, and these circRNAs biogenesis was formed with canonical GU-AG splicing mechanism with unevenly distributed on the chromosomes. Wherein, most of the circRNAs were derived from the sense overlapping strategy. Reverse transcript PCR and Sanger sequencing data indicated that these circRNAs were existed authenticity in Crucian carp. The bioinformatics analysis indicated that circRNAs identified from the Crucian carp with potential miRNA sponge regulate the expression level of mRNAs. GO annotation and KEGG pathway analysis of these circRNAs showed that more than 20% circRNAs were related with catalytic activity and binding in the category of molecular function, and these circRNAs were enriched in 9 signaling pathways, such as, Wnt signaling pathway, MAPK signaling pathway, Ubiquitin mediated proteolysis et al. 220 mRNAs would be regulated by the circRNAs via miRNAs mediation. These target mRNAs were further analyzed with functional annotation and KEGG analysis. GO annotation analysis showed that several genes were related with function of nucleotide binding, transcription regulatory activity. KEGG pathway analysis showed that 5 genes were enriched in the pathway of Endocytosis. The circRNA-miRNA-mRNA regulation network indicated that one miRNA can link one or more circRNA and one or more mRNA. Overall, these results will not only help us to further understand the novel RNA transcripts in Crucian carp, but also provide the novel clue to investigate the interaction between host and pathogens from this novel circRNA molecule.

Autoantibody-targeted TAAs in pancreatic cancer: A comprehensive analysis

BackgroundPancreatic cancer is one of the leading causes of cancer mortality and lacks efficient biomarkers for early diagnosis. In the early stages of pancreatic cancer, humoral immunity can respond to a certain amount of tumor-associated antigens (TAAs) with the production of corresponding autoantibodies. Such autoantibody-targeted TAAs (autoTAAs) are highly likely to indicate early events during pancreatic carcinogenesis. Herein, we performed a comprehensive analysis of these autoTAAs to explore their physiological function and their involvement and prognostic value in pancreatic cancer. MethodsWe first searched the literature to identify the autoTAAs. A PPI network of these autoTAAs was constructed, and core network modules were extracted by Cytoscape software. GO annotation and KEGG pathway analysis were performed to analyze the main physiological functions of these autoTAAs. The prognostic value of autoTAAs in pancreatic cancer was analyzed by using RNA-seq data generated by TCGA. ResultsThe PPI network including 98 autoTAAs was constructed, and 2 subgroups were extracted as core modules. GO and KEGG analysis revealed that key functions and pathways of these autoTAAs were significantly enriched in nucleotide repair, protein synthesis, and cancer-associated events. MSH2, EZR, PGK1, VCL and ANXA2 have prognostic value in pancreatic cancer, and high mRNA expression of these 5 proteins is associated with unfavorable prognosis in pancreatic cancer. ConclusionsAutoTAAs may be associated with early events in the carcinogenesis of pancreatic cancer. MSH2, EZR, PGK1, VCL and ANXA2 predict poor prognosis in pancreatic cancer. Some autoTAAs also have prognostic value in other cancers.

Transcriptomic analysis of small intestinal mucosa from porcine epidemic diarrhea virus infected piglets

Caused by porcine epidemic diarrhea virus (PEDV), porcine epidemic diarrhea (PED) is an acute infectious disease which causes damage to the intestine including intestinal villus atrophy and shedding, leading to serious economic losses to the pig industry worldwide. In order to obtain detailed information about the pathogenesis and host immune response in a PEDV-infected host for first In vivo study we used high-throughput sequencing to analyze the gene expression differences of the small intestinal mucosa after infection with PEDV. Transcripts obtained were over 65,525,000 clean reads after reassembly were 22,605 genes detected, of which 22,248 were known genes and 371 new genes were predicted. Moreover, 3168 genes expression was up-regulated and 3876 genes down-regulated. (Gene Ontology) GO annotation and functional enrichment analysis indicated that all of the DEGs (differentially expressed genes) were annotated into biological process, cellular component and molecular function. Most of these unigenes are annotated in cellular processes, the cell and binding. KEGG analysis of the DEGs showed that a total of 7044 DEGs unigenes were annotated into 323 pathways classified into 6 main categories. Most of these unigenes are annotated were related to immune system response to the infectious diseases pathways. In addition, 20 DEGs were verified by quantitative real-time PCR. As the first, in vivo, RNAseq analysis of piglets and PEDV infection, our study provides knowledge about the transcriptomics of intestinal mucosa in PEDV-infected piglets, from which a complex molecular pathways and pathogenesis-related biological processes are involved in PEDV interaction with piglet intestinal mucosa.

MusatransSSRDB (a transcriptome derived SSR database) – An advanced tool for banana improvement

Availability of transcriptome datasets for use in accelerated molecular-based breeding in Musa species is limited. Illumina Hiseq technology was employed to determine differential gene expression between the contrasting cultivars for three different stresses (Eumusae leaf spot -Mycosphaerella eumusae, root lesion nematode - Pratylenchus coffeae and moisture deficit stress) under challenged and unchallenged conditions. An average of 34.72 million of reads was assembled into ~47629 contigs, and ~5,466 simple sequence repeats (SSR) from each library were identified. GO annotation and KEGG pathway analysis were carried for all the transcripts and the SSR, SNPs were also detected. Based on this information, a MusatransSSRDB has been developed. Currently, the database consists of 32,800 SSRs with the unique information like putative function of the SSR-containing genes and their metabolic pathway and expression profiling under various stress conditions. This database provides information on in silico polymorphic SSRs (2830 SSRs) between the contrasting cultivars for each stress and within stress. Information on in silico polymorphic SSRs specific to differentially expressed genes under challenged condition for each stress can also be accessed. This database facilitates the retrieval of results by navigating the tabs for cultivars, stress and polymorphism. This database was developed using HTML, Java and PHP; datasets are stored in MySQL database and accessible in the public domain (http://bioinfnrcb.byethost7.com/nrcbbio/). This unique information facilitates the banana breeder to select the SSR primers based on specific objectives. MusatransSSRDB along with other genomics databases will facilitate the genetic dissection and breeding for complex traits in banana. Thus, this database is a step forward in economizing cost, time, manpower and other resources. Keywords.

Liver transcriptome analysis and de novo annotation of the orange-spotted groupers (Epinephelus coioides) under cold stress

Cold stress has caused great economic loss in fish culture worldwide. Orange-spotted grouper (Epinephelus coioides) is one of the most serious lost aquatic animals in 2016 cold fronts in South China. However, the molecular mechanism of grouper's cold resistance has remained largely unknown. In the present study, HiSeq™2000 (Illumina) was used to analyze the transcriptomic profiles of the liver from grouper under control temperature (CT, 28 °C) and low temperature (LT, 13 °C). Two normalized liver cDNA libraries of CT and LT groups were created. We obtained 51,944,970 and 51,905,036 clean reads from CT and LT groups, respectively. Comparing the LT group to the CT group, a total of 5905 significantly differentially expressed genes (DEGs) were identified, including 2093 up-regulated unigenes and 3812 down-regulated unigenes. GO annotation and functional enrichment analysis indicated that all of the DEGs were classified into three categories: biological process (23 subclasses), cellular component (18 subclasses) and molecular function (13 subclasses). KEGG analysis of the DEGs showed that 2732 DEGs were annotated to 253 signaling pathways. The most highly enriched pathways were cell adhesion molecules, Staphylococcus aureus infection, PPAR signaling pathway, Vibrio cholerae infection, primary immunodeficiency, fatty acid elongation, and we found cold stress mainly affects immunity, metabolic and signal transduction. Thirteen of the DEGs were further validated by qRT-PCR. Our results provide valuable information for further analysis of the mechanisms of groupers response under cold stress.

Lactobacillus gasseri LA39 Activates the Oxidative Phosphorylation Pathway in Porcine Intestinal Epithelial Cells.

Intestinal microbial interactions with the host epithelium have important roles in host health. Our previous data have suggested that Lactobacillus gasseri LA39 is the predominant intestinal Lactobacillus in weaned piglets. However, the regulatory role of L. gasseri LA39 in the intestinal epithelial protein expression in piglets remains unclear. In the present study, we conducted comparative proteomics approach to investigate the intestinal epithelial protein profile alteration caused by L. gasseri LA39 in piglets. The expressions of 15 proteins significantly increased, whereas the expressions of 13 proteins significantly decreased in the IPEC-J2 cells upon L. gasseri LA39 treatment. Bioinformatics analyses, including COG function annotation, GO annotation, and KEGG pathway analysis for the differentially expressed proteins revealed that the oxidative phosphorylation (OXPHOS) pathway in IPEC-J2 cells was significantly activated by L. gasseri LA39 treatment. Further data indicated that two differentially expressed proteins UQCRC2 and TCIRG1, associated with the OXPHOS pathway, and cellular ATP levels in IPEC-J2 cells were significantly up-regulated by L. gasseri LA39 treatment. Importantly, the in vivo data indicated that oral gavage of L. gasseri LA39 significantly increased the expression of UQCRC2 and TCIRG1 and the cellular ATP levels in the intestinal epithelial cells of weaned piglets. Our results, both in vitro and in vivo, reveal that L. gasseri LA39 activates the OXPHOS pathway and increases the energy production in porcine intestinal epithelial cells. These findings suggest that L. gasseri LA39 may be a potential probiotics candidate for intestinal energy production promotion and confers health-promoting functions in mammals.

Circular RNA alterations in the Bombyx mori midgut following B. mori nucleopolyhedrovirus infection

Thus far, no systematic studies have examined circRNA expression profiles in the silkworm following B.mori nucleopolyhedrovirus (BmNPV) infection. To explore the expression patterns of circRNAs in the silkworm midgut following BmNPV infection, circRNAs in normal midguts and BmNPV-infected midguts were analyzed by high-throughput sequencing. A total of 353 circRNAs were significantly differentially expressed, of which 241 were upregulated and 112 were downregulated following infection. GO annotation and KEGG pathways analyses of these circRNAs showed that many key immunity pathways and metabolism pathways were enriched in the BmNPV-infected midguts. The potential roles of the predicted targets of the miRNAs that interacted with the circRNAs showed that ubiquitin, apoptosis, and endocytosis signaling pathways were enriched significantly by BmNPV infection.