scholarly journals Bioinformatic Analysis of Gene Variants from Gastroschisis Recurrence Identifies Multiple Novel Pathogenetic Pathways: Implication for the Closure of the Ventral Body Wall

2019 ◽  
Vol 20 (9) ◽  
pp. 2295 ◽  
Author(s):  
Víctor M. Salinas-Torres ◽  
Hugo L. Gallardo-Blanco ◽  
Rafael A. Salinas-Torres ◽  
Ricardo M. Cerda-Flores ◽  
José J. Lugo-Trampe ◽  
...  
Keyword(s):  
Biological Networks ◽  
Body Wall ◽  
Molecular Mechanisms ◽  
De Novo ◽  
Developmental Process ◽  
Interaction Analysis ◽  
Regulation Of Gene Expression ◽  
Bioinformatic Analysis ◽  
Recessive Model ◽  
Functional Enrichment

We investigated whether likely pathogenic variants co-segregating with gastroschisis through a family-based approach using bioinformatic analyses were implicated in body wall closure. Gene Ontology (GO)/Panther functional enrichment and protein-protein interaction analysis by String identified several biological networks of highly connected genes in UGT1A3, UGT1A4, UGT1A5, UGT1A6, UGT1A7, UGT1A8, UGT1A9, UGT1A10, AOX1, NOTCH1, HIST1H2BB, RPS3, THBS1, ADCY9, and FGFR4. SVS–PhoRank identified a dominant model in OR10G4 (also as heterozygous de novo), ITIH3, PLEKHG4B, SLC9A3, ITGA2, AOX1, and ALPP, including a recessive model in UGT1A7, UGT1A6, PER2, PTPRD, and UGT1A3. A heterozygous compound model was observed in CDYL, KDM5A, RASGRP1, MYBPC2, PDE4DIP, F5, OBSCN, and UGT1A. These genes were implicated in pathogenetic pathways involving the following GO related categories: xenobiotic, regulation of metabolic process, regulation of cell adhesion, regulation of gene expression, inflammatory response, regulation of vascular development, keratinization, left-right symmetry, epigenetic, ubiquitination, and regulation of protein synthesis. Multiple background modifiers interacting with disease-relevant pathways may regulate gastroschisis susceptibility. Based in our findings and considering the plausibility of the biological pattern of mechanisms and gene network modeling, we suggest that the gastroschisis developmental process may be the consequence of several well-orchestrated biological and molecular mechanisms which could be interacting with gastroschisis predispositions within the first ten weeks of development.

scholarly journals Dynamics of DNA Methylation and Its Functions in Plant Growth and Development

2021 ◽  
Vol 12 ◽  
Author(s):  
Suresh Kumar ◽  
Trilochan Mohapatra
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Genome Stability ◽  
De Novo ◽  
Developmental Process ◽  
Global Climate ◽  
Regulation Of Gene Expression ◽  
Biotic Stresses ◽  
Epigenome Editing ◽  
Dna Base

Epigenetic modifications in DNA bases and histone proteins play important roles in the regulation of gene expression and genome stability. Chemical modification of DNA base (e.g., addition of a methyl group at the fifth carbon of cytosine residue) switches on/off the gene expression during developmental process and environmental stresses. The dynamics of DNA base methylation depends mainly on the activities of the writer/eraser guided by non-coding RNA (ncRNA) and regulated by the developmental/environmental cues. De novo DNA methylation and active demethylation activities control the methylation level and regulate the gene expression. Identification of ncRNA involved in de novo DNA methylation, increased DNA methylation proteins guiding DNA demethylase, and methylation monitoring sequence that helps maintaining a balance between DNA methylation and demethylation is the recent developments that may resolve some of the enigmas. Such discoveries provide a better understanding of the dynamics/functions of DNA base methylation and epigenetic regulation of growth, development, and stress tolerance in crop plants. Identification of epigenetic pathways in animals, their existence/orthologs in plants, and functional validation might improve future strategies for epigenome editing toward climate-resilient, sustainable agriculture in this era of global climate change. The present review discusses the dynamics of DNA methylation (cytosine/adenine) in plants, its functions in regulating gene expression under abiotic/biotic stresses, developmental processes, and genome stability.

scholarly journals Network Protein Interaction in Parkinson's Disease and Periodontitis Interplay: A Bioinformatic Analysis

2020 ◽  
Author(s):  
João Botelho ◽  
Paulo Mascarenhas ◽  
José João Mendes ◽  
Vanessa Machado
Keyword(s):  
Protein Interaction ◽  
Protein Interactions ◽  
Molecular Mechanisms ◽  
Interaction Analysis ◽  
Bioinformatic Analysis ◽  
Comprehensive Analysis ◽  
Protein Network ◽  
Protein Protein Interactions ◽  
Network Interaction ◽  
Genes Encoding

Recent studies supported a clinical association between Parkinson’s Disease (PD) and periodontitis. Hence, investigating possible protein interactions between these two conditions is of interest. In this study, we conducted a protein-protein network interaction analysis with recognized genes encoding proteins for PD and periodontitis. Genes of interest were collected via GWAS database. Then, we conducted a protein interaction analysis using STRING database, with a highest confidence cut-off of 0.9. Our protein network casted a comprehensive analysis of potential protein-protein interactions between PD and periodontitis. This analysis may underpin valuable information for new candidate molecular mechanisms between PD and periodontitis and may serve new potential targets for research purposes. These results should be carefully interpreted giving the limitations of this approach.

scholarly journals Full-Length Transcriptome Analysis Reveals Candidate Genes Involved in Terpenoid Biosynthesis in Artemisia argyi

2021 ◽  
Vol 12 ◽  
Author(s):  
Yupeng Cui ◽  
Xinqiang Gao ◽  
Jianshe Wang ◽  
Zengzhen Shang ◽  
Zhibin Zhang ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Single Molecule ◽  
Molecular Mechanisms ◽  
De Novo ◽  
Enrichment Analysis ◽  
Full Length ◽  
Functional Enrichment ◽  
Terpenoid Biosynthesis ◽  
Sequencing Data ◽  
Artemisia Argyi

Artemisia argyi is an important medicinal plant widely utilized for moxibustion heat therapy in China. The terpenoid biosynthesis process in A. argyi is speculated to play a key role in conferring its medicinal value. However, the molecular mechanism underlying terpenoid biosynthesis remains unclear, in part because the reference genome of A. argyi is unavailable. Moreover, the full-length transcriptome of A. argyi has not yet been sequenced. Therefore, in this study, de novo transcriptome sequencing of A. argyi's root, stem, and leaf tissues was performed to obtain those candidate genes related to terpenoid biosynthesis, by combining the PacBio single-molecule real-time (SMRT) and Illumina sequencing NGS platforms. And more than 55.4 Gb of sequencing data and 108,846 full-length reads (non-chimeric) were generated by the Illumina and PacBio platform, respectively. Then, 53,043 consensus isoforms were clustered and used to represent 36,820 non-redundant transcripts, of which 34,839 (94.62%) were annotated in public databases. In the comparison sets of leaves vs roots, and leaves vs stems, 13,850 (7,566 up-regulated, 6,284 down-regulated) and 9,502 (5,284 up-regulated, 4,218 down-regulated) differentially expressed transcripts (DETs) were obtained, respectively. Specifically, the expression profile and KEGG functional enrichment analysis of these DETs indicated that they were significantly enriched in the biosynthesis of amino acids, carotenoids, diterpenoids and flavonoids, as well as the metabolism processes of glycine, serine and threonine. Moreover, multiple genes encoding significant enzymes or transcription factors related to diterpenoid biosynthesis were highly expressed in the A. argyi leaves. Additionally, several transcription factor families, such as RLK-Pelle_LRR-L-1 and RLK-Pelle_DLSV, were also identified. In conclusion, this study offers a valuable resource for transcriptome information, and provides a functional genomic foundation for further research on molecular mechanisms underlying the medicinal use of A. argyi leaves.

scholarly journals Integrating transcriptome and metabolome reveals molecular networks involved in genetic and environmental variation in tobacco

DNA Research ◽  
2020 ◽  
Vol 27 (2) ◽  
Author(s):  
Pingping Liu ◽  
Jie Luo ◽  
Qingxia Zheng ◽  
Qiansi Chen ◽  
Niu Zhai ◽  
...  
Keyword(s):  
Regulatory Networks ◽  
Molecular Mechanisms ◽  
Developmental Stages ◽  
De Novo ◽  
Developmental Process ◽  
Pearson Correlation ◽  
Molecular Networks ◽  
Environmental Perturbations ◽  
Carotenoid Metabolism ◽  
Gene Modules

Abstract Tobacco (Nicotiana tabacum) is one of the most widely cultivated commercial non-food crops with significant social and economic impacts. Here we profiled transcriptome and metabolome from 54 tobacco samples (2–3 replicates; n = 151 in total) collected from three varieties (i.e. genetic factor), three locations (i.e. environmental factor), and six developmental stages (i.e. developmental process). We identified 3,405 differentially expressed (DE) genes (DEGs) and 371 DE metabolites, respectively. We used quantitative real-time PCR to validate 20 DEGs, and confirmed 18/20 (90%) DEGs between three locations and 16/20 (80%) with the same trend across developmental stages. We then constructed nine co-expression gene modules and four co-expression metabolite modules , and defined seven de novo regulatory networks, including nicotine- and carotenoid-related regulatory networks. A novel two-way Pearson correlation approach was further proposed to integrate co-expression gene and metabolite modules to identify joint gene–metabolite relations. Finally, we further integrated DE and network results to prioritize genes by its functional importance and identified a top-ranked novel gene, LOC107773232, as a potential regulator involved in the carotenoid metabolism pathway. Thus, the results and systems-biology approaches provide a new avenue to understand the molecular mechanisms underlying complex genetic and environmental perturbations in tobacco.

scholarly journals Identification and Interaction Analysis of Significant Genes and MicroRNAs in Pterygium

2019 ◽  
Vol 2019 ◽  
pp. 1-12 ◽  
Author(s):  
Siying He ◽  
Hui Sun ◽  
Yifang Huang ◽  
Shiqi Dong ◽  
Chen Qiao ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Molecular Mechanisms ◽  
Interaction Analysis ◽  
Interaction Network ◽  
Enrichment Analysis ◽  
Functional Enrichment Analysis ◽  
Gene Expression Omnibus ◽  
Functional Enrichment ◽  
Differentially Expressed ◽  
Differentially Expressed Mirnas

Purpose. MiRNAs have been widely analyzed in the occurrence and development of many diseases, including pterygium. This study aimed to identify the key genes and miRNAs in pterygium and to explore the underlying molecular mechanisms. Methods. MiRNA expression was initially extracted and pooled by published literature. Microarray data about differentially expressed genes was downloaded from Gene Expression Omnibus (GEO) database and analyzed with the R programming language. Functional and pathway enrichment analyses were performed using the database for Annotation, Visualization and Integrated Discovery (DAVID). The protein-protein interaction network was constructed with the STRING database. The associations between chemicals, differentially expressed miRNAs, and differentially expressed genes were predicted using the online resource. All the networks were constructed using Cytoscape. Results. We found that 35 miRNAs and 301 genes were significantly differentially expressed. Functional enrichment analysis showed that upregulated genes were significantly enriched in extracellular matrix (ECM) organization, while downregulated genes were mainly involved in cell death and apoptotic process. Finally, we concluded the chemical-gene affected network, miRNA-mRNA interacted networks, and significant pathway network. Conclusion. We identified lists of differentially expressed miRNAs and genes and their possible interaction in pterygium. The networks indicated that ECM breakdown and EMT might be two major pathophysiological mechanisms and showed the potential significance of PI3K-Akt signalling pathway. MiR-29b-3p and collagen family (COL4A1 and COL3A1) might be new treatment target in pterygium.

scholarly journals Bioinformatic analysis deciphers the molecular toolbox in the endophytic/pathogenic behaviour in F. oxysporum f. sp. vanillae - V. planifolia Jacks interaction

2021 ◽  
Author(s):  
Marco Tulio Solano De la Cruz ◽  
Esteban Elías Escobar Hernández ◽  
Jorge Arturo Arciniega González ◽  
Rocío Del Pilar Rueda Zozaya ◽  
Mauricio Luna Rodríguez ◽  
...  
Keyword(s):  
Metabolic Pathways ◽  
Molecular Mechanisms ◽  
De Novo ◽  
Behavioral Genetics ◽  
Fusaric Acid ◽  
Bioinformatic Analysis ◽  
Rna Seq ◽  
Independent Manner ◽  
Underlying Mechanisms ◽  
Genomic Regions

Background: F. oxysporum as a species complex (FOSC) possess the capacity, to specialize into host-specific pathogens deriving into formae speciales. This with the help of horizontal gene transfer (HGT) between pathogenic and endophytic individuals of FOSC. From these pathogenic forma speciales, F. oxysporum f. sp. vanillae (Fov) is the causal agent of fusarium wilt producing root and stem rot (RSR) positions itself was the main phytosanitary problem in vanilla plantations worldwide. Nonetheless, the origin of this forma specialis and the behavioral genetics dictating the endophytic/pathogenic Fusarium lifestyles are still unknown. To elucidate the underlying molecular mechanisms that establish these behaviors we analyzed the RNA-seq libraries of two-times frames of vanilla-fov interactions. Results: Our analyses identified the sets of transcripts corresponding to Fov pathogenic strain JAGH3 during the two-times frames of the infection as the sets of the transcripts belonging to endophytic Fox in vanilla. Functional predictions of de novo annotated transcripts as the enriched GO terms with the overrepresented metabolic pathways associated to them allowed us to identify the molecular processes that establish the pathogenic lifestyle in Fov being virulence, hypervirulence, sporulation, conidiation, necrosis and fusaric acid related genes with the carbohydrates, amino acids and proteins, glycerophospholipids and autophagy metabolic pathways that are key regulators of spores germination and pathogenicity establishment as the underlying mechanisms behind this behavior. As the absence of these were found in the vanilla endophytic Fox. Conclusions: This work reveals the main players of the behavioral genetics in pathogenic Fov/endophytic Fox in V. planifolia Jacks. Its pathogenic strategy allows Fov to infect in a SIX genes-independent manner. As the other pathogenic elements found in this study could be explained by the presence of pathogenicity islands and genomic regions associated with supernumerary chromosomes in Fov. These play a central role as carriers of genes involved with pathogenic activity and can be obtained through HGT.

scholarly journals De novo profiling of long non-coding RNAs involved in MC-LR–induced liver injury in whitefish: discovery and perspectives

2020 ◽  
Author(s):  
Maciej Florczyk ◽  
Paweł Brzuzan ◽  
Maciej Woźny
Keyword(s):  
Liver Injury ◽  
Molecular Mechanisms ◽  
Liver Toxicity ◽  
De Novo ◽  
Sequence Data ◽  
Regulation Of Gene Expression ◽  
Model Organisms ◽  
Coregonus Lavaretus ◽  
Digital Repository ◽  
Non Coding Rnas

Abstract BackgroundMicrocystin-LR (MC-LR) is a potent hepatotoxin for which a substantial gap in knowledge persists regarding the underlying molecular mechanisms of liver toxicity and injury. Although long non-coding RNAs (lncRNAs) have been extensively studied in model organisms, and their roles have been identified in various cellular processes including participation in regulation of gene expression together with microRNAs, our knowledge concerning the role of lncRNAs in liver injury is limited even in mammals. Given that lncRNAs show low levels of sequence conservation, their role becomes even more unclear in non-model organisms without an annotated genome, like whitefish (Coregonus lavaretus). The objective of this study was to discover and profile aberrantly expressed polyadenylated lncRNAs that are involved in MC-LR–induced liver injury in whitefish.ResultsUsing polyA-enriched RNA-Seq data, we de novo assembled a high quality whitefish liver transcriptome. This enabled us to find 94 differentially expressed (DE) putative evolutionary-conserved lncRNAs (orthologous to known lncRNAs in other species), such as MALAT1, HOTTIP, HOTAIR or HULC and 4,429 DE putative novel whitefish lncRNAs, which differed from annotated protein-coding transcripts (PCTs) in terms of minimum free energy, GC base-pair content and length. Additionally, we identified DE non-coding transcripts that might be 3’ autonomous untranslated regions of mRNAs (3’UTRs). We found that, in response to MC-LR treatment, these potential 3’UTRs could either be coexpressed with PCTs from the same mRNA, or the 3’UTRs were upregulated while the corresponding PCTs were downregulated, suggesting 3’UTR-dependent gene regulation.ConclusionsTo our knowledge this is the first report on aberrantly expressed lncRNAs in MC-LR–induced liver injury in whitefish. We found both evolutionary conserved lncRNAs as well as novel whitefish lncRNAs that could serve as biomarkers of severe and chronic liver injury. The lncRNA sequence data files and raw sequence files are available in the Dryad Digital Repository and the NCBI Sequence Read Archive, respectively.

scholarly journals Bioinformatic Analysis of Transcriptomic Data Reveals Novel Key Genes Regulating Osteogenic Differentiation of Human Adipose Stem Cells

2019 ◽  
Vol 2019 ◽  
pp. 1-10
Author(s):  
Jinluo Cheng ◽  
Xinyuan Zhao ◽  
Juan Liu ◽  
Li Cui ◽  
Yanfeng Zhu ◽  
...  
Keyword(s):  
Stem Cells ◽  
Osteogenic Differentiation ◽  
Molecular Mechanisms ◽  
Interaction Analysis ◽  
Bioinformatic Analysis ◽  
Mapk Signaling ◽  
Adipose Stem Cells ◽  
Nodule Formation ◽  
Cell Cycle Protein ◽  
Osteoporosis Therapy

Adipose stem cells (ASCs) are an attractive cell source for treating many human diseases including osteoporosis. However, the molecular mechanisms accounting for ASC osteogenesis are poorly known. In this study, ASCs were first isolated from the fat tissues from the patients with osteoporosis. The global transcriptome profile between osteogenic differentiated ASCs and undifferentiated ASCs was compared using RNA sequencing (RNA-seq). Then, bioinformatic analysis was performed to reveal the central genes and pathways that regulated the osteogenic differentiation of ASCs. One of the interested genes C5AR1 was chosen for further investigation. A total of 1521 upregulated and 3020 downregulated genes were identified between the ASCs with osteogenic induction and controls. Functional gene ontology analysis revealed that these significantly differentially expressed genes (DEGs) were associated with cell cycle, protein binding, and nucleotide binding. Pathway analysis showed that many canonical pathways, such as the MAPK signaling pathway and the PI3K-AKT pathway, might actively be involved in regulating osteogenic differentiation of ASCs. A total of three subnetworks and 20 central nodes were identified by the protein-protein interaction analysis. In addition, the expression level of C5AR1 was significantly increased during osteogenic differentiation of ASCs. The downregulation of C5AR1 dramatically reduced the expression levels of osteogenic differentiation biomarkers and calcium nodule formation capacity. Collectively, we have provided a number of novel genes and pathways that might be indispensable for ASC osteogenic differentiation. Manipulating the levels of this candidate gene might contribute to the osteoporosis therapy.

scholarly journals Detoxification- and Immune-Related Transcriptomic Analysis of Gills from Bay Scallops (Argopecten irradians) in Response to Algal Toxin Okadaic Acid

Toxins ◽  
2018 ◽  
Vol 10 (8) ◽  
pp. 308 ◽  
Author(s):  
Cheng Chi ◽  
Sib Giri ◽  
Jin Jun ◽  
Sang Kim ◽  
Hyoun Kim ◽  
...  
Keyword(s):  
Immune System ◽  
Okadaic Acid ◽  
Molecular Mechanisms ◽  
De Novo ◽  
Biological Process ◽  
Quinone Reductase ◽  
Functional Enrichment ◽  
Related Factor ◽  
Illumina Hiseq ◽  
Bay Scallops

To reveal the molecular mechanisms triggered by okadaic acid (OA)-exposure in the detoxification and immune system of bay scallops, we studied differentially-expressed genes (DEGs) and the transcriptomic profile in bay scallop gill tissue after 48 h exposure to 500 nM of OA using the Illumina HiSeq 4000 deep-sequencing platform. De novo assembly of paired-end reads yielded 55,876 unigenes, of which 3204 and 2620 genes were found to be significantly up- or down-regulated, respectively. Gene ontology classification and enrichment analysis of the DEGs detected in bay scallops exposed to OA revealed four ontologies with particularly high functional enrichment, which were ‘cellular process’ (cellular component), ‘metabolic process’ (biological process), ‘immune system process’ (biological process), and ‘catalytic process’ (molecular function). The DEGs revealed that cyclic AMP-responsive element-binding proteins, acid phosphatase, toll-like receptors, nuclear erythroid 2-related factor, and the NADPH2 quinone reductase-related gene were upregulated. In contrast, the expression of some genes related to glutathione S-transferase 1, C-type lectin, complement C1q tumor necrosis factor-related protein, Superoxide dismutase 2 and fibrinogen C domain-containing protein, decreased. The outcomes of this study will be a valuable resource for the study of gene expression induced by marine toxins, and will help understanding of the molecular mechanisms underlying the scallops’ response to OA exposure.

scholarly journals Bioinformatic Analysis Reveals Novel Hub Genes pathways associated with IgA nephropathy

2020 ◽  
Author(s):  
xue Jiang ◽  
Zhijie Xu ◽  
Yuanyuan Du ◽  
Hongyu Chen
Keyword(s):  
Inflammatory Response ◽  
Molecular Mechanism ◽  
Biological Networks ◽  
Tissue Sample ◽  
Bioinformatic Analysis ◽  
Functional Enrichment ◽  
Control Group ◽  
Ppi Network ◽  
Hub Genes ◽  
Ppi Networks

Abstract Background Immunoglobulin A nephropathy (IgAN) is the most common primary glomerulopathy worldwide. However, the molecular events underlying IgAN remain to be fully elucidated. The aim of the study is to identify novel biomarkers of IgAN through bioinformatics analysis and elucidate the possible molecular mechanism. Methods Based on the microarray data GSE93798 and GSE37460 were downloaded from the Gene Expression Omnibus database, the differentially expressed genes (DEGs) between IgAN samples and normal controls were identified. With DEGs, we further performed a series of functional enrichment analyses. Protein-protein interaction (PPI) networks of the DEGs were built with the STRING online search tool and visualized by using Cytoscape, then further identified the hub gene and most important module in DEGs, Biological Networks Gene Oncology tool (BiNGO) were then performed to elucidate the molecular mechanism of IgAN. Results A total of 148 DEGs were recognized, consisting of 53 upregulated genes and 95 downregulated genes. GO analysis indicates that DEGs for IgAN were mainly enriched in extracellular exosome, region and space, fibroblast growth factor stimulus, inflammatory response, and innate immunity. The modules analysis showed that genes in the top 1 significant modules of PPI network were mainly associated with innate immune response, integrin-mediated signaling pathway and inflammatory response respectively. The top 10 hub genes were constructed in PPI network, which could well distinguish the IgAN and control group in monocytes sample and tissue sample. We finally identified ITGB2 and FCER1G gene may have important roles in the development of IgAN. Conclusions We identified a series of key genes along with the pathways that were most closely related with IgAN initiation and progression. Our results provide a more detailed molecular mechanism for the development of IgAN and novel candidate genes targets of IgAN.

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