Molecular Function Terms Research Articles

ITRAQ proteome analysis of the antifungal mechanism of citral on mycelial growth and OTA production in Aspergillus ochraceus.

Aspergillus ochraceus causes food spoilage and produces mycotoxin ochratoxin A (OTA) during storage of agricultural commodities. In this study, citral was used to inhibit A. ochraceus growth and OTA accumulation, proteomic analysis was employed to verify the mechanism of citral. Citral was found to significantly inhibit fungal growth and mycotoxin production in A. ochraceus. Specifically, 75, 125, 150 and 200 μL L-1 citral suppressed mycelial growth by 33%, 46%, 50% and 100%, respectively. Additionally, 75 μL L-1 citral inhibited OTA accumulation by 25%. Proteomic analysis was performed to elucidate the inhibitory mechanism of citral on mycelial growth and OTA production at subinhibitory concentrations (75 μL L-1 ). Proteomics analysis identified 2646 proteins in A. ochraceus fc-1, of which 218 were differentially expressed between control and 75 μL L-1 citral treatment samples. Differentially expressed proteins were identified by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses of biological process, cellular component and molecular function terms. Potential factors affecting mycelial growth and OTA production were analysed, and OTA production was revealed to be a complex process involving many associated factors related to various processes including nutrient intake, sterol biosynthesis, ribosome biogenesis, energy metabolism, oxidative stress and amino acid metabolism. In addition, citral at 75 μL L-1 down-regulated OTA biosynthetic genes including pks and nrps, but slightly up-regulated the global regulatory factors veA, velB and laeA. The findings further demonstrate the potential of citral for the preservation of grains and other agricultural products, and provide new insight into its antifungal mechanisms at subinhibitory concentrations. © 2021 Society of Chemical Industry.

The analysis on the human protein domain targets and host-like interacting motifs for the MERS-CoV and SARS-CoV/CoV-2 infers the molecular mimicry of coronavirus.

The MERS-CoV, SARS-CoV, and SARS-CoV-2 are highly pathogenic viruses that can cause severe pneumonic diseases in humans. Unfortunately, there is a non-available effective treatment to combat these viruses. Domain-motif interactions (DMIs) are an essential means by which viruses mimic and hijack the biological processes of host cells. To disentangle how viruses achieve this process can help to develop new rational therapies. Data mining was performed to obtain DMIs stored as regular expressions (regexp) in 3DID and ELM databases. The mined regexp information was mapped on the coronaviruses’ proteomes. Most motifs on viral protein that could interact with human proteins are shared across the coronavirus species, indicating that molecular mimicry is a common strategy for coronavirus infection. Enrichment ontology analysis for protein domains showed a shared biological process and molecular function terms related to carbon source utilization and potassium channel regulation. Some of the mapped motifs were nested on B, and T cell epitopes, suggesting that it could be as an alternative way for reverse vaccinology. The information obtained in this study could be used for further theoretic and experimental explorations on coronavirus infection mechanism and development of medicines for treatment.

Mechanism of Danggui Sini Decoction in treatment of primary dysmenorrhea based on network pharmacology and molecular docking

Network pharmacology, molecular docking and in vivo experiments were used to explore the pharmacodynamic basis and potential mechanism of Danggui Sini Decoction in the treatment of primary dysmenorrhea(PD). The chemical constituents of Danggui(Angelicae Sinensis Radix), Guizhi(Cinnamomi Ramulus), Tongcao(Tetrapanacis Medulla), Baishao(Paeoniae Radix Alba), Xixin(Asari Radix et Rhizoma), Gancao(Glycyrrhizae Radix et Rhizoma), and Dazao(Jujubae Fructus) from Danggui Sini Decoction were retrieved through TCMSP(Traditional Chinese Medicine Systems Pharmacology Database), and the action targets of Danggui Sini Decoction were collected through DrugBank. "Primary dysmenorrhea" and "dysmenorrhea" were used as the key words to search the corresponding targets in the GeneCards, OMIM and TTD databases, and then the intersection targets of Danggui Sini Decoction and the primary dysmenorrhea targets were taken for reverse screening to obtain the corresponding active ingredients. Cytoscape 3.6.1 software was used to construct a traditional Chinese medicine-compound-target-disease network; STRING database was used to build a protein-protein interaction(PPI) network; Gene ontology(GO) function enrichment analysis and Kyoto encyclopedia of genes and genomes(KEGG) pathway enrichment analysis were conducted by using DAVID database. The action mechanism of the intersection targets were then predicted, and a histogram chart and bubble chart were drawn for visualization. Then the top five targets in the PPI network were used for docking with the most compounds. In animal experiments, Sprague Dawley(SD) female rats were used to establish a primary dysmenorrhea model by intraperitoneal injection of diethylstilbestrol once a day. A total of 60 SD female rats were randomly divided into 6 groups, namely control group, model group, Danggui Sini Decoction low(1.5 g·kg~(-1)), medium(3.0 g·kg~(-1)), high(6.0 g·kg~(-1)) dose groups, and ibuprofen(20 mg·kg~(-1)) positive control group, with 10 rats in each group. From day 4, except for the control group, rats in the other groups were given intragastric administration of corresponding drugs, and the control group received intragastric administration of normal saline for 7 consecutive days. The number of writhing before and after the administration, the ute-rine contraction inhibition rate and the uterine index after administration were observed, and ELISA assay was used to detect the levels of prostaglandin-endoperoxide synthase 2(PTGS2) and vascular endothelial growth factor A(VEGFA) in the tissues of each group as well as the levels of serum inflammatory factors interleukin 1(IL-1), interleukin 6(IL-6), and tumor necrosis factor-alpha(TNF-α). According to network analysis, 7 Chinese medicines contained 114 active ingredients, 149 targets, and 30 common target genes with PD were obtained. The key targets included VEGFA, IL6, PTGS2, TNF, etc.; GO function enrichment analysis showed a total of 399 terms(P<0.05) were obtained, 353 of which were biological process(BP) terms, 21 were cell composition(CC) terms, and 25 were molecular function(MF) terms. In KEGG pathway enrichment analysis, 14 signaling pathways were obtained, 3 of which were related to inflammation, namely arachidonic acid metabolism, MAPK signaling pathway and NOD-like receptor signaling pathway. The compounds in Danggui Sini Decoction can play a therapeutic role in the treatment of PD by acting on VEGFA, IL-6, PTGS2, TNF and other targets to regulate arachidonic acid and inflammatory signaling pathways.

Network pharmacology assessment of Qingkailing injection treatment of cholestatic hepatitis.

To investigate the targets and mechanisms of action of Qingkailing injection (，QKL) in the treatment of cholestatic hepatitis. A network pharmacology method was implemented using drug and disease databases to target QKL and cholestasis hepatitis, respectively. The functional protein association network STRING database was used to construct a protein-protein interaction network using R language and the Bioconductor toolkit. The org.Hs.eg.db and clusterProfiler packages were used for gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis, which explored biological functions and pathways of potential targets. Targets were then visualized using Cytoscape 3.6.0 software. We screened 121 compounds in QKL and identified 112 targets for the treatment of cholestatic hepatitis. QKL played a role in the treatment of cholestatic hepatitis through 305 biology process terms, 15 cellular component and 29 molecular function terms. The mechanism of QKL action was mainly related to tumor necrosis factor, mitogen-activated protein kinase, and PI3K-Akt signaling pathways. The treatment of cholestatic hepatitis by QKL involved multiple targets, biological functions, and signaling pathways that are closely associated with the disease.

Mechanism of Xuefu Zhuyu Decoction in treatment of myocardial infarction based on network pharmacology and molecular docking

To explore the action mechanism of Xuefu Zhuyu Decoction in treating myocardial infarction based on network pharmaco-logy and molecular docking. Active components and corresponding targets of Xuefu Zhuyu Decoction were obtained through Traditional Chinese Medicine Systems Pharmacology Database(TCMSP), and related targets of myocardial infarction were obtained through GeneCards, DisGeNET, and OMIM databases. Then the intersection targets were obtained by integrating the drug targets and disease targets. The "active component-target" network was constructed by Cytoscape software, and protein-protein interaction(PPI) network was drawn using STRING platform. Protein cluster analysis was carried out using MCODE. GO enrichment analysis and KEGG pathway analysis were carried out using DAVID database and ClueGO, and molecular docking was carried out using Autodock Vina and Pymol. Finally, 226 active components of Xuefu Zhuyu Decoction were obtained, 257 corresponding targets, 1 340 targets of myocardial infarction, and 109 drug and disease intersection targets were obtained. From GO enrichment analysis, 208 biological process terms, 38 molecular function terms, and 33 cellular component terms were obtained. From KEGG pathway analysis, NF-κB signaling pathway, IL-17 signaling pathway, HIF-1 signaling pathway, and other related pathways were obtained. The molecular docking results showed that the main active components(quercetin, kaempferol, β-sitosterol, luteolin, stigmasterol and baicalein) of Xuefu Zhuyu Decoction in the treatment of myocardial infarction had good binding properties with the core proteins IL6, ALB, VEGFA, TNF, MAPK3 and CASP3. The results suggested that Xuefu Zhuyu Decoction may play a role in the treatment of myocardial infarction by reducing the inflammatory response, reducing oxidative stress, inhibiting cell apoptosis, and promoting angiogenesis.

Quantitative Proteomic Profiling of Fungal Growth, Development, and Ochratoxin A Production in Aspergillus ochraceus on High- and Low-NaCl Cultures.

Dry-cured meat products are worldwide food with high-salt content, and filamentous fungi are beneficial to the maturation process. However, some salt-tolerant strains of Aspergillus and Penicillium produce ochratoxin A (OTA) on these products and thus threaten food safety. In our study, proteomic analysis was performed to reveal the mechanism of adaptability to high-salt environment by Aspergillus ochraceus. Twenty g/L and 70 g/L NaCl substrates were used to provide medium- and high-NaCl content environments, respectively. The NaCl addition could induce fungal growth, but only 20 g/L NaCl addition could induce spore production while 70 g/L repressed it. Proteomics analysis identified 2646 proteins in A. ochraceus fc-1, of which 237 and 251 were differentially expressed with 20 g/L and 70 g/L NaCl addition, respectively. Potential factors affecting fungal growth and development were identified by GO and KEGG analyses of biological process, cellular component, and molecular function terms. The results revealed that ergosterol synthesis pathway was significantly upregulated with 20 g/L and 70 g/L NaCl addition. However, fungal growth and development including OTA production were complex processes associated with many factors including nutrient uptake, cell membrane integrity, cell cycle, energy metabolism, intracellular redox homeostasis, protein synthesis and processing, autophagy, and secondary metabolism. Reactive oxygen species may be an important window to understand the mechanism that medium-salt content was conducive to intracellular signal transduction while high-salt content caused oxidative stress. The findings would help to improve the processes and storage conditions of dry-cured meat products.

Vitamin E can promote spermatogenesis by regulating the expression of proteins associated with the plasma membranes and protamine biosynthesis.

Vitamin E is generally believed to promote the production of ovine sperm mainly through its antioxidant effect. Our previous studies have shown that some non-antioxidant genes may also be key in mediating this process. The objective of this study was to identify key candidate proteins that were differentially expressed in response to a treatment with Vitamin E. Prepubertal ovine testicular cells were isolated and divided into two groups. They were either treated with 800μM Vitamin E (based on our previous results) or used as a non-treated control. After 24h, all the cells were harvested for proteomic analysis. We found 115 differentially expressed proteins, 4 of which were up-regulated and 111 were down-regulated. A GO term enrichment analysis identified 127 Biological Process, 63 Cell Component and 26 Molecular Function terms that were enriched. Within those terms, 13, 11 and 26 terms were significantly enriched, respectively. Terms related to membrane and enzyme activity including the inner acrosomal membrane, signal peptidase complex, cysteine-type endopeptidase activity, etc., were also markedly enriched, while none of the KEGG pathways were enriched. We found that many of the differentially expressed proteins, such as CD46 (membrane cofactor protein), FLNA (Filamin A), DYSF (Dysferlin), IFT20 (Intraflagellar transport 20), SPCS1 (Signal peptidase complex subunit 1) and SPCS3 (Signal peptidase complex subunit 3) were related to the acrosomal and plasma membranes. A parallel reaction monitoring (PRM) analysis verified that Vitamin E improved spermatogenesis by regulating the expression of FLNA, SPCS3, YBX3 and RARS, proteins that are associated with the plasma membranes and protamine biosynthesis of the spermatozoa.

Genetic Pathways Involved in the Pathogenesis of Parkinson's Disease.

Parkinson's disease (PD) is the second most common neurodegenerative disease. PD pathogenesis includes both genetic and environmental factors. Previous studies have linked the disease with several genes such as Parkin, SNCA, PINK1 and HTRA2. BiNGO software utilizes GO annotations in order to detect over-represented genes in terms of biological processes, cellular components and molecular functions. Three databases were utilized for this study (Ensembl, DisGeNET and UniProt). Data processing provided 110 genes associated with PD for further analysis. The aim of this study was to identify genes associated with PD and perform a functional enrichment analysis. Cytoscape and BiNGO software analysis presented several new genes that could play a potential role in pathogenesis of the disease. Future steps include additional research in order to establish the exact mechanism of action of these genes and pathways on PD.

Relationship between hepatocellular carcinoma and depression via online database analysis

ABSTRACT There may be a mutually reinforcing relationship between hepatocellular carcinoma (HCC) and depression, but the mechanism is unknown. This study used bioinformatics to evaluate the relationship between HCC and depression at the genetic level. Genes associated with HCC and depression were obtained from pubmed2ensemble. Overlapping genes were annotated by gene ontology (GO) function and enriched by Kyoto Encyclopedia of Genes and Genomes (KEGG) signal pathway. The cluster-1 genes obtained by Cytoscape were analyzed by GEPIA for expression and overall survival in HCC and, finally, introduced target genes to DGIdb to get associated drugs. A total of 199 genes were found to be in common between HCC and depression. GO term enrichment analysis on DAVID found the top-6 biological processes to be mainly associated with cell death and apoptosis. The top-6 cellular component terms are extracellular. The top-6 of molecular function terms are mainly associated with receptor binding. The top-6 pathways enriched by KEGG are mainly related to inflammatory response. IGF1, VEGFA, and SERPINE1 had statistical differences in expression and 10-year survival rate. There are total 45 drugs that act on VEGFA and SERPINE1. Based on our findings, we hypothesize that the mechanism of the interaction between HCC and depression may be related to cell death or apoptosis. Further studies are needed to verify this hypothesis.

Bioinformatics Study of Plasma Differentially Expressed Proteins in H-Type Hypertension with or without Acute Cerebral Infarction

Objective: To investigate the bioinformatics of differentially expressed proteins in plasma in patients with acute cerebral infarction associated with H-type hypertension. Methods: Gene chip public database (gene expression omnibus, GEO) GDS4521 chip data, in the chip in 30 cases of H patients with acute cerebral infarction with high blood pressure and age, gender, matching the 20 H hypertension patients as the research object, collects the mononuclear cells (PBMCs) is used to detect the gene chip, using the GO (gene Ontology, GO), protein function analysis tools such as KEGG, screening and analysis of enrichment of differentially expressed genes function and related signaling pathway. Results: 31 genes in PBMCs were significantly changed in h-type hypertension and H-type hypertension with acute cerebral infarction, 32 of which were increased and 2 of which were decreased. GO analysis showed that in terms of biological processes, the genes related to inflammatory response and neutrophil chemotaxis were the most. In terms of molecular function, chemokine activity-related genes are the most. KEGG signaling pathway analysis showed that the most differentially expressed genes were located in the TNF signaling pathway. Conclusion: H-type hypertension with acute cerebral infarction has a variety of functional proteins and signaling pathways changes, suggesting that inflammatory response in H-type hypertension with acute cerebral infarction recovery period may still play a role in the prognosis and reactivation of the disease.

PhyloGenes: An online phylogenetics and functional genomics resource for plant gene function inference.

We aim to enable the accurate and efficient transfer of knowledge about gene function gained from Arabidopsis thaliana and other model organisms to other plant species. This knowledge transfer is frequently challenging in plants due to duplications of individual genes and whole genomes in plant lineages. Such duplications result in complex evolutionary relationships between related genes, which may have similar sequences but highly divergent functions. In such cases, functional inference requires more than a simple sequence similarity calculation. We have developed an online resource, PhyloGenes (phylogenes.org), that displays precomputed phylogenetic trees for plant gene families along with experimentally validated function information for individual genes within the families. A total of 40 plant genomes and 10 non‐plant model organisms are represented in over 8,000 gene families. Evolutionary events such as speciation and duplication are clearly labeled on gene trees to distinguish orthologs from paralogs. Nearly 6,000 families have at least one member with an experimentally supported annotation to a Gene Ontology (GO) molecular function or biological process term. By displaying experimentally validated gene functions associated to individual genes within a tree, PhyloGenes enables functional inference for genes of uncharacterized function, based on their evolutionary relationships to experimentally studied genes, in a visually traceable manner. For the many families containing genes that have evolved to perform different functions, PhyloGenes facilitates the use of evolutionary history to determine the most likely function of genes that have not been experimentally characterized. Future work will enrich the resource by incorporating additional gene function datasets such as plant gene expression atlas data.

Bioinformatics analysis identifies potential diagnostic signatures for coronary artery disease.

BackgroundCoronary artery disease (CAD) is the leading cause of mortality worldwide. We aimed to screen out potential gene signatures and construct a diagnostic model for CAD.MethodWe downloaded two mRNA profiles, GSE66360 and GSE60993, and performed analyses of differential expression, gene ontology terms, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. The STRING database was used to identify protein–protein interactions (PPI). PPI network visualization and screening out of key genes were performed using Cytoscape software. Finally, a diagnostic model was constructed.ResultsA total of 2127 differentially expressed genes (DEGs) were identified in GSE66360, and 527 DEGs in GSE60993. Of the 153 DEGs from both datasets that showed differential expression between CAD patients and controls, 471 biological process terms, 35 cellular component terms, 17 molecular function terms, and 49 KEGG pathways were significantly enriched. The top 20 key genes in the PPI network were identified, and a diagnostic model constructed from five optimal genes that could efficiently separate CAD patients from controls.ConclusionWe identified several potential biomarkers for CAD and built a logistic regression model that will provide a valuable reference for future clinical diagnoses and guide therapeutic strategies.

Identifying MMP14 and COL12A1 as a potential combination of prognostic biomarkers in pancreatic ductal adenocarcinoma using integrated bioinformatics analysis.

BackgroundPancreatic ductal adenocarcinoma (PDAC) is a fatal malignant neoplasm. It is necessary to improve the understanding of the underlying molecular mechanisms and identify the key genes and signaling pathways involved in PDAC.MethodsThe microarray datasets GSE28735, GSE62165, and GSE91035 were downloaded from the Gene Expression Omnibus. Differentially expressed genes (DEGs) were identified by integrated bioinformatics analysis, including protein–protein interaction (PPI) network, Gene Ontology (GO) enrichment, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses. The PPI network was established using the Search Tool for the Retrieval of Interacting Genes (STRING) and Cytoscape software. GO functional annotation and KEGG pathway analyses were performed using the Database for Annotation, Visualization, and Integrated Discovery. Hub genes were validated via the Gene Expression Profiling Interactive Analysis tool (GEPIA) and the Human Protein Atlas (HPA) website.ResultsA total of 263 DEGs (167 upregulated and 96 downregulated) were common to the three datasets. We used STRING and Cytoscape software to establish the PPI network and then identified key modules. From the PPI network, 225 nodes and 803 edges were selected. The most significant module, which comprised 11 DEGs, was identified using the Molecular Complex Detection plugin. The top 20 hub genes, which were filtered by the CytoHubba plugin, comprised FN1, COL1A1, COL3A1, BGN, POSTN, FBN1, COL5A2, COL12A1, THBS2, COL6A3, VCAN, CDH11, MMP14, LTBP1, IGFBP5, ALB, CXCL12, FAP, MATN3, and COL8A1. These genes were validated using The Cancer Genome Atlas (TCGA) and Genotype–Tissue Expression (GTEx) databases, and the encoded proteins were subsequently validated using the HPA website. The GO analysis results showed that the most significantly enriched biological process, cellular component, and molecular function terms among the 20 hub genes were cell adhesion, proteinaceous extracellular matrix, and calcium ion binding, respectively. The KEGG pathway analysis showed that the 20 hub genes were mainly enriched in ECM–receptor interaction, focal adhesion, PI3K-Akt signaling pathway, and protein digestion and absorption. These findings indicated that FBN1 and COL8A1 appear to be involved in the progression of PDAC. Moreover, patient survival analysis performed via the GEPIA using TCGA and GTEx databases demonstrated that the expression levels of COL12A1 and MMP14 were correlated with a poor prognosis in PDAC patients (p < 0.05).ConclusionsThe results demonstrated that upregulation of MMP14 and COL12A1 is associated with poor overall survival, and these might be a combination of prognostic biomarkers in PDAC.

Bioinformatic Prediction of Gene Ontology Terms of Uncharacterized Proteins from Chromosome 11

In chromosome 11, 71 out of its 1254 proteins remain functionally uncharacterized on the basis of their existence evidence (uPE1s) following the latest version of neXtProt (release 2020-01-17). Because in vivo and in vitro experimental strategies are often time-consuming and labor-intensive, there is a need for a bioinformatics tool to predict the function annotation. Here, we used I-TASSER/COFACTOR provided on the neXtProt web site, which predicts gene ontology (GO) terms based on the 3D structure of the protein. I-TASSER/COFACTOR predicted 2413 GO terms with a benchmark dataset of the 22 proteins belonging to PE1 of chromosome 11. In this study, we developed a filtering algorithm in order to select specific GO terms using the GO map generated by I-TASSER/COFACTOR. As a result, 187 specific GO terms showed a higher average precision-recall score at the least cellular component term compared to 2413 predicted GO terms. Next, we applied 65 proteins belonging to uPE1s of chromosome 11, and then 409 out of 6684 GO terms survived, where 103 and 142 GO terms of molecular function and biological process, respectively, were included. Representatively, the cellular component GO terms of CCDC90B, C11orf52, and the SMAP were predicted and validated using the overexpression system into 293T cells and immunofluorescence staining. We will further study their biological and molecular functions toward the goal of the neXt-CP50 project as a part of C-HPP. We shared all results and programs in Github (https://github.com/heeyounh/I-TASSER-COFACTOR-filtering.git).

Salt tolerance involved candidate genes in rice: an integrative meta-analysis approach

BackgroundSalinity, as one of the main abiotic stresses, critically threatens growth and fertility of main food crops including rice in the world. To get insight into the molecular mechanisms by which tolerant genotypes responds to the salinity stress, we propose an integrative meta-analysis approach to find the key genes involved in salinity tolerance. Herein, a genome-wide meta-analysis, using microarray and RNA-seq data was conducted which resulted in the identification of differentially expressed genes (DEGs) under salinity stress at tolerant rice genotypes. DEGs were then confirmed by meta-QTL analysis and literature review.ResultsA total of 3449 DEGs were detected in 46 meta-QTL positions, among which 1286, 86, 1729 and 348 DEGs were observed in root, shoot, seedling, and leaves tissues, respectively. Moreover, functional annotation of DEGs located in the meta-QTLs suggested some involved biological processes (e.g., ion transport, regulation of transcription, cell wall organization and modification as well as response to stress) and molecular function terms (e.g., transporter activity, transcription factor activity and oxidoreductase activity). Remarkably, 23 potential candidate genes were detected in Saltol and hotspot-regions overlying original QTLs for both yield components and ion homeostasis traits; among which, there were many unreported salinity-responsive genes. Some promising candidate genes were detected such as pectinesterase, peroxidase, transcription regulator, high-affinity potassium transporter, cell wall organization, protein serine/threonine phosphatase, and CBS domain cotaining protein.ConclusionsThe obtained results indicated that, the salt tolerant genotypes use qualified mechanisms particularly in sensing and signalling of the salt stress, regulation of transcription, ionic homeostasis, and Reactive Oxygen Species (ROS) scavenging in response to the salt stress.

De novo assembly and discovery of genes related to blood digestion in the transcriptome of Dermanyssus gallinae (Acari: Dermanyssidae)

Dermanyssus gallinae is an economically important blood-feeding ectoparasite affecting layer chicken farms in many countries. Similar to other blood-feeding arthropods, the blood-meal digestion plays a key role in the survival and reproduction of D. gallinae. The knowledge of the genes involved in blood digestion processes may provide new targets for drug and vaccine against the red mites. In the present study, we sequenced and de novo assembled the transcriptomes of unfed and fed adult red mites using Illumina RNA sequencing (RNA-seq) technology. Up to 40,506 unigenes were assembled, and 13,018 unigenes were identified and annotated. GO analysis of the annotated unigenes clustered into three main GO terms. The dominant GO terms of biological processes were cellular process and metabolic process, the prevailing GO terms of the cellular component were cell part and membrane part, and the dominant GO terms of molecular functions were catalytic and binding activities. Up to 6,443 annotated sequences were assigned to 246 active pathways by KEGG analysis. Differentially expressed genes (DEGs) analysis identified 2,877 unigenes with upregulated 2,094 and downregulated 783 in fed female mites compared with unfed female mites. The biological function of these DEGs was further investigated using the KEGG and GO databases. The upregulated DEGs were potentially involved in nutrient metabolism, highlighting their importance in red mite biology. Quantitative reverse transcription real-time PCR (qRT-PCR) validated that the expression levels of the selected six upregulated DEGs were consistent with those in RNA-seq, indicating that the transcriptomic data are reliable. The present study provides valuable and fundamental knowledge that improves our understanding of the physiology of D. gallinae digestion at a molecular level. Moreover, these transcriptomic data will facilitate the identification of novel function genes and candidate antigens for the development of effective vaccines or drug targets to control D. gallinae.

Effect of Micromelalopha sieversi (Staudinger) Oviposition Behavior on the Transcriptome of Two Populus Section Aigeiros Clones

Research Highlights: The molecular mechanisms underlying woody plant resistance upon oviposition by herbivores remain unclear, as studies have focused on herbaceous plants. The effect of oviposition on gene expression in neighboring plants has also not been reported. Elucidating these molecular responses can help cultivate insect-resistant trees. Background and Objectives: Oviposition by herbivorous insects acts as an early warning signal, inducing plant resistance responses. Here, we employed poplar as a model woody plant to elucidate gene expression and the molecular mechanisms underlying plant resistance after oviposition by Micromelalopha sieversi (Staudinger) (Lepidoptera: Notodontidae). Materials and Methods: The differences in gene expression of two Populus section Aigeiros clones (‘108’ (Populus × euramericana ‘Guariento’) and ‘111’ (Populus × euramericana ‘Bellotto’)) were analyzed via high-throughput sequencing of oviposited, neighboring, and control plants. Results: We obtained 304,526,107 reads, with an average length of 300 bp and a total size of 40.77 Gb. Differentially expressed genes (DEGs) in gene ontology terms of biological process, cellular component, and molecular function were mainly enriched in the “cell part”, “catalytic”, and “metabolic process” functions. Moreover, DEGs were mainly enriched in the following pathways: plant-pathogen interaction, linoleic acid metabolism, and cyanoamino acid metabolism (108-O vs. 108-C); metabolic pathways, photosynthesis, photosynthesis-antenna proteins, nitrogen metabolism, and linoleic acid metabolism (111-O vs. 111-C); metabolic pathways and biosynthesis of secondary metabolites (111-N vs. 111-C); no pathways were significantly enriched in 108-N vs. 108-C. Up-regulated defense genes were associated with pathogenesis-related protein function, innate immune regulation, and biological stress response, with differences in specific genes. All genes related to photosynthetic activity were significantly down-regulated in oviposited and neighboring leaves of the two clones. Conclusions: Oviposited and neighboring ‘108’ and ‘111’ plants exhibited varying degrees of resistance upon oviposition, involving the up-regulation of various defense genes, decreased photosynthesis and nutrient accumulation, and increased secondary metabolic synthesis.

Transcriptomic Analysis of Short-Term Salt Stress Response in Watermelon Seedlings.

Watermelon (Citrullus lanatus L.) is a widely popular vegetable fruit crop for human consumption. Soil salinity is among the most critical problems for agricultural production, food security, and sustainability. The transcriptomic and the primary molecular mechanisms that underlie the salt-induced responses in watermelon plants remain uncertain. In this study, the photosynthetic efficiency of photosystem II, free amino acids, and transcriptome profiles of watermelon seedlings exposed to short-term salt stress (300 mM NaCl) were analyzed to identify the genes and pathways associated with response to salt stress. We observed that the maximal photochemical efficiency of photosystem II decreased in salt-stressed plants. Most free amino acids in the leaves of salt-stressed plants increased many folds, while the percent distribution of glutamate and glutamine relative to the amino acid pool decreased. Transcriptome analysis revealed 7622 differentially expressed genes (DEGs) under salt stress, of which 4055 were up-regulated. The GO analysis showed that the molecular function term “transcription factor (TF) activity” was enriched. The assembled transcriptome demonstrated up-regulation of 240 and down-regulation of 194 differentially expressed TFs, of which the members of ERF, WRKY, NAC bHLH, and MYB-related families were over-represented. The functional significance of DEGs associated with endocytosis, amino acid metabolism, nitrogen metabolism, photosynthesis, and hormonal pathways in response to salt stress are discussed. The findings from this study provide novel insights into the salt tolerance mechanism in watermelon.

TRANSCRIPTOME ANALASYS OF ADULT GULL-TAPEWORM DIBOTHRIOCHEPHALLUS DENDRITICUS (CESTODA)

In certain regions of Siberia and Baikal area, the main causative agent of diphyllobothriasis of human and animals is gull-tipeworm Dibothriochephallus dendriticus. In last decade, there was heightened interest to the study of molecules secreted by helminth which can modulate the immune response of their mammal hosts, particularly human. Bioinformatic analysis of transcriptomes gives opportunity to obtain data on proteins synthetized in certain time point and find among them ones the most significant for immunological functions. The aim of our study was to carry out transcriptome analysis of adult D. dendriticus. Adult D. dendriticus were pulled from the gut of herring gull. Total RNA was extracted with TRIzol reagent. Bar-coding transcriptome libraries were created. Sequencing obtained libraries was carried out using high-performance sequencer Illumina NextSeq550. De-novo assembly of transcriptome was performed. Annotation of obtained transcripts was done with Blast2Go software. Annotation allowed to describe their classification in terms of biological processes, molecular functions, and cellular components. At the next step, we plan to use D. dendriticus, assembled and annotated with transcriptome of plerocercoids, to search genes, potentially coding proteins that have an immunomodulatory effect on their hosts and also for identification of the proteins in secretome of parasites.

Comparative proteomic analysis of two wheat genotypes with contrasting grain softness index

Wheat is the crop most widely grown in the world and provides the daily protein and 20% food calories for 4.5 billion people. It is crucial to understand the genetic basis of grain hardness for improving wheat quality. In order to explore the molecular basis of the formation of wheat grain hardness, two wheat cultivars Chuanmai 66 and Shumai 969 with significant hardness difference in southwest wheat region were selected to analyze the proteins differential expression by TMT quantitative proteomics (tandem mass tags) and bioinformatic methods of function and pathway enrichment analysis. A total of 6020 effective proteins were identified and quantified, including 113 differentially expressed proteins (DEPs), of which 69 were up-regulated and 44 were down-regulated in soft wheat Chuanmai 66. These DEPs were enriched into 65 GO terms, including a biological process term, a cellular component term and six molecular function terms at extremely significant level. Based on the enrichment analysis, we suggested that nutrient reservoir activity proteins, enzyme inhibitor proteins and glutathione metabolism proteins might participate in the formation of wheat grain hardness, and grain hardness related proteins might mainly distribute in the extracellular region of cells and had defensive function. According to the phylogenetic analysis, it was inferred that puroindolines and its homologous proteins might be as not only wheat grain storage proteins, but also enzyme inhibitors regulating grain development. This study provides a basis for further exploring the genetic mechanism of wheat grain hardness.