scholarly journals Exploring the genes involved in biosynthesis of dihydroquercetin and dihydromyricetin in Ampelopsis grossedentata

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Zheng-Wen Yu ◽  
Ni Zhang ◽  
Chun-Yan Jiang ◽  
Shao-Xiong Wu ◽  
Xia-Yu Feng ◽  
...  
Keyword(s):  
Expression Profiles ◽  
Differentially Expressed Gene ◽  
Rna Seq ◽  
Illumina Hiseq ◽  
Genetic Studies ◽  
Sequencing Platform ◽  
Protein Databases ◽  
Helix Loop Helix ◽  
Wd40 Domain ◽  
Ampelopsis Grossedentata

AbstractDihydroquercetin (DHQ), an extremely low content compound (less than 3%) in plants, is an important component of dietary supplements and used as functional food for its antioxidant activity. Moreover, as downstream metabolites of DHQ, an extremely high content of dihydromyricetin (DHM) is up to 38.5% in Ampelopsis grossedentata. However, the mechanisms involved in the biosynthesis and regulation from DHQ to DHM in A. grossedentata remain unclear. In this study, a comparative transcriptome analysis of A. grossedentata containing extreme amounts of DHM was performed on the Illumina HiSeq 2000 sequencing platform. A total of 167,415,597 high-quality clean reads were obtained and assembled into 100,584 unigenes having an N50 value of 1489. Among these contigs, 57,016 (56.68%) were successfully annotated in seven public protein databases. From the differentially expressed gene (DEG) analysis, 926 DEGs were identified between the B group (low DHM: 210.31 mg/g) and D group (high DHM: 359.12 mg/g) libraries, including 446 up-regulated genes and 480 down-regulated genes (B vs. D). Flavonoids (DHQ, DHM)-related DEGs of ten structural enzyme genes, three myeloblastosis transcription factors (MYB TFs), one basic helix–loop–helix (bHLH) TF, and one WD40 domain-containing protein were obtained. The enzyme genes comprised three PALs, two CLs, two CHSs, one F3’H, one F3’5’H (directly converts DHQ to DHM), and one ANS. The expression profiles of randomly selected genes were consistent with the RNA-seq results. Our findings thus provide comprehensive gene expression resources for revealing the molecular mechanism from DHQ to DHM in A. grossedentata. Importantly, this work will spur further genetic studies about A. grossedentata and may eventually lead to genetic improvements of the DHQ content in this plant.

scholarly journals RNAseq Studies Reveal Distinct Transcriptional Response to Vitamin a (VA) Deficiency in Small Intestine (SI) versus Colon, Discovering Novel VA-regulated Genes (P15-002-19)

2019 ◽  
Vol 3 (Supplement_1) ◽  
Author(s):  
Zhi Chai ◽  
Yafei Lyu ◽  
Qiuyan Chen ◽  
Cheng-Hsin Wei ◽  
Lindsay Snyder ◽  
...  
Keyword(s):  
Gene Expression ◽  
Small Intestine ◽  
Vitamin A ◽  
Target Genes ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Differentially Expressed Gene ◽  
Gene Expression Profiles ◽  
Illumina Hiseq ◽  
The Impact

Abstract Objectives To characterize and compare the impact of vitamin A (VA) deficiency on gene expression patterns in the small intestine (SI) and the colon, and to discover novel target genes in VA-related biological pathways. Methods vitamin A deficient (VAD) mice were generated by feeding VAD diet to pregnant C57/BL6 dams and their post-weaning offspring. Total mRNA extracted from SI and colon were sequenced using Illumina HiSeq 2500 platform. Differentially Expressed Gene (DEG), Gene Ontology (GO) enrichment, and Weighted Gene Co-expression Network Analysis (WGCNA) were performed to characterize expression patterns and co-expression patterns. Results The comparison between vitamin A sufficient (VAS) and VAD groups detected 49 and 94 DEGs in SI and colon, respectively. According to GO information, DEGs in the SI demonstrated significant enrichment in categories relevant to retinoid metabolic process, molecule binding, and immune function. Immunity related pathways, such as “humoral immune response” and “complement activation,” were positively associated with VA in SI. On the contrary, in colon, “cell division” was the only enriched category and was negatively associated with VA. WGCNA identified modules significantly correlated with VA status in SI and in colon. One of those modules contained five known retinoic acid targets. Therefore we have prioritized the other module members (e.g., Mbl2, Mmp9, Mmp13, Cxcl14 and Pkd1l2) to be investigated as candidate genes regulated by VA. Comparison of co-expression modules between SI and colon indicated distinct VA effects on these two organs. Conclusions The results show that VA deficiency alters the gene expression profiles in SI and colon quite differently. Some immune-related genes (Mbl2, Mmp9, Mmp13, Cxcl14 and Pkd1l2) may be novel targets under the control of VA in SI. Funding Sources NIH training grant and NIH research grant. Supporting Tables, Images and/or Graphs

CNCTDISCRIMINATOR: CODING AND NONCODING TRANSCRIPT DISCRIMINATOR — AN EXCURSION THROUGH HYPOTHESIS LEARNING AND ENSEMBLE LEARNING APPROACHES

2013 ◽  
Vol 11 (05) ◽  
pp. 1342002 ◽  
Author(s):  
ASHIS KUMER BISWAS ◽  
BAOJU ZHANG ◽  
XIAOYONG WU ◽  
JEAN X. GAO
Keyword(s):  
Ensemble Learning ◽  
Expression Profiles ◽  
Open Reading Frames ◽  
Learning Approaches ◽  
Rna Seq ◽  
Sequencing Platform ◽  
Noncoding Transcript ◽  
Comparable Performance ◽  
Generation Sequencing ◽  
Reading Frames

The statistics about the open reading frames, the base compositions and the properties of the predicted secondary structures have potential to address the problem of discriminating coding and noncoding transcripts. Again, the Next Generation Sequencing platform, RNA-seq, provides us bounty of data from which expression profiles of the transcripts can be extracted which urged us adding a new set of dimension in this classification task. In this paper, we proposed CNCTDiscriminator — a coding and noncoding transcript discriminating system where we applied the integration of these four categories of features about the transcripts. The feature integration was done using both hypothesis learning and feature specific ensemble learning approaches. The CNCTDiscriminator model which was trained with composition and ORF features outperforms (precision 83.86%, recall 82.01%) other three popular methods — CPC (precision 98.31%, recall 25.95%), CPAT (precision 97.74%, recall 52.50%) and PORTRAIT (precision 84.37%, recall 73.2%) when applied to an independent benchmark dataset. However, the CNCTDiscriminator model that was trained using the ensemble approach shows comparable performance (precision 89.85%, recall 71.08%).

scholarly journals Shedding the Light on Litopenaeus vannamei Differential Muscle and Hepatopancreas Immune Responses in White Spot Syndrome Virus (WSSV) Exposure

Genes ◽  
2020 ◽  
Vol 11 (7) ◽  
pp. 805 ◽  
Author(s):  
Camilla A. Santos ◽  
Sónia C. S. Andrade ◽  
Jorge M. O. Fernandes ◽  
Patrícia D. Freitas
Keyword(s):  
Immune Responses ◽  
Litopenaeus Vannamei ◽  
White Spot Syndrome Virus ◽  
Reference Genome ◽  
Differentially Expressed Gene ◽  
White Spot ◽  
Rna Seq ◽  
Genetic Studies ◽  
Imd Pathway ◽  
White Spot Syndrome

White Spot Syndrome Virus (WSSV) is one of the main threats to farming Litopenaeus vannamei, the most important crustacean commercialized in aquaculture worldwide. Here, we performed RNA-seq analyses in hepatopancreas and muscle from WSSV-negative (healthy) and WSSV-positive (unhealthy) L. vannamei, previously exposed to the virus, to obtain new insights about the molecular basis of resistance to WSSV. We detected 71% of our reads mapped against the recently described L. vannamei genome. This is the first report mapping RNA-seq transcripts from shrimps exposed to WSSV against the species reference genome. Differentially expressed gene (DEG) analyses were performed for four independent comparisons, and 13,338 DEGs were identified. When the redundancies and isoforms were disregarded, we observed 8351 and 6514 DEGs, respectively. Interestingly, after crossing the data, we detected a common set of DEGs for hepatopancreas and healthy shrimps, as well as another one for muscle and unhealthy shrimps. Our findings indicate that genes related to apoptosis, melanization, and the Imd pathway are likely to be involved in response to WSSV, offering knowledge about WSSV defense in shrimps exposed to the virus but not infected. These data present potential to be applied in further genetic studies in penaeids and other farmed shrimp species.

scholarly journals Early “Rootprints” of Plant Terrestrialization: Selaginella Root Development Sheds Light on Root Evolution in Vascular Plants

2021 ◽  
Vol 12 ◽  
Author(s):  
Tao Fang ◽  
Hans Motte ◽  
Boris Parizot ◽  
Tom Beeckman
Keyword(s):  
Root Development ◽  
Current Knowledge ◽  
Expression Profiles ◽  
Economic Value ◽  
Sister Group ◽  
Rna Seq ◽  
Terrestrial Environment ◽  
Future Directions ◽  
Genetic Studies ◽  
Selaginella Moellendorffii

Roots provide multiple key functions for plants, including anchorage and capturing of water and nutrients. Evolutionarily, roots represent a crucial innovation that enabled plants to migrate from aquatic to terrestrial environment and to grow in height. Based on fossil evidence, roots evolved at least twice independently, once in the lycophyte clade and once in the euphyllophyte (ferns and seed plants) clade. In lycophytes, roots originated in a stepwise manner. Despite their pivotal position in root evolution, it remains unclear how root development is controlled in lycophytes. Getting more insight into lycophyte root development might shed light on how genetic players controlling the root meristem and root developmental processes have evolved. Unfortunately, genetic studies in lycophytes are lagging behind, lacking advanced biotechnological tools, partially caused by the limited economic value of this clade. The technology of RNA sequencing (RNA-seq) at least enabled transcriptome studies, which could enhance the understanding or discovery of genes involved in the root development of this sister group of euphyllophytes. Here, we provide an overview of the current knowledge on root evolution followed by a survey of root developmental events and how these are genetically and hormonally controlled, starting from insights obtained in the model seed plant Arabidopsis and where possible making a comparison with lycophyte root development. Second, we suggest possible key genetic regulators in root development of lycophytes mainly based on their expression profiles in Selaginella moellendorffii and phylogenetics. Finally, we point out challenges and possible future directions for research on root evolution.

scholarly journals Transcriptomic analysis of bovine monocytes in response to non-cytopathic bovine viral diarrhea virus infection

2020 ◽  
Author(s):  
Yanhua HE ◽  
Jinke HE ◽  
Yajun YANG ◽  
Xin HUANG ◽  
Yunfen ZHANG ◽  
...  
Keyword(s):  
Immune Response ◽  
Bovine Viral Diarrhea Virus ◽  
Expression Profiles ◽  
Differentially Expressed Gene ◽  
Bovine Viral Diarrhea ◽  
Type I ◽  
Rna Seq ◽  
Diarrhea Virus ◽  
Viral Diarrhea ◽  
Viral Diarrhea Virus

Abstract Background: Monocytes are significant players in the detection of invading pathogens, particularly in pathogen defense. Bovine Viral Diarrhea Virus (BVDV) can cause a persistent infection and immune suppression if animals are infected with an non-cytopathic (ncp) biotype. However, its exact role in ncp BVDV1-infected bovine monocytes remains poorly understood. Results: RNA sequencing (RNA-seq) was used to investigate the effect of ncp BVDV1 infection on the transcriptional profile of bovine monocytes. Compared with the non-infected cells, 9959 and 7977 differentially expressed gene (DEGs) were identified at 2 and 24 h hpi, respectively. These DEGs were associated with signal transduction, immune response, apoptotic process, cellular process , binding and cellular component. The differential expression profiles of select the type I interferon signaling pathway , interferon (IFN)-stimulated genes (ISGs), and genes involved in the innate immune response, including IRF7, DDX3X, TLR13, DDX58(RIG-I), MVAS, TLR9, TRAF6, IRF1, IFIT1, STAT1, ISG20, TRIM25, MX1,NLRX1, CYLD, SIKE1 and ZAP70 were confirmed by real-time quantitative PCR and consistent with the RNA-seq data. Conclusion: Our transciptome anslysis provides useful initial data towards better understanding of the infection mechanisms used by ncp BVDV1, while highlighting the potential molecular relationships occurring between the virus and the host’s immune response.

scholarly journals Comparative Transcriptomic and Expression Profiles Between the Foot Muscle and Mantle Tissues in the Giant Triton Snail Charonia tritonis

2021 ◽  
Vol 12 ◽  
Author(s):  
Gege Zhang ◽  
Meng Xu ◽  
Chenglong Zhang ◽  
Huixia Jia ◽  
Hua Zhang ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Dermatan Sulfate ◽  
Expression Profiles ◽  
Sulfur Metabolism ◽  
Illumina Hiseq ◽  
Sequencing Platform ◽  
Illumina Hiseq Sequencing ◽  
Coral Reef Ecosystems ◽  
Significant Divergence ◽  
Cellular Components

The giant triton snail (Charonia tritonis), an endangered gastropod species of ecological and economic importance, is widely distributed in coral reef ecosystems of the Indo-West Pacific region and the tropical waters of the South China Sea. Limited research on molecular mechanisms can be conducted because the complete genomic information on this species is unavailable. Hence, we performed transcriptome sequencing of the C. tritonis foot muscle and mantle using the Illumina HiSeq sequencing platform. In 109,722 unigenes, we detected 7,994 (3,196 up-regulated and 4,798 down-regulated) differentially expressed genes (DEGs) from the C. tritonis foot muscle and mantle transcriptomes. These DEGs will provide valuable resources to improve the understanding of molecular mechanisms involved in biomineralization of C. tritonis. In the Gene Ontology (GO) database, DEGs were clustered into three main categories (biological processes, molecular functions, and cellular components) and were involved in 50 functional subcategories. The top 20 GO terms in the molecular function category included sulfotransferase activity, transferring sulfur-containing groups, and calcium ion binding, which are terms considered to be related to biomineralization. In KEGG classifications, transcriptomic DEGs were mainly enriched in glycosaminoglycan biosynthesis-chondroitin sulfate/dermatan sulfate, and sulfur metabolism pathway, which may be related to biomineralization. The results of qPCR showed that three of the eight genes examined were significantly up-regulated in the mantle. The phylogenetic tree of BMP1 suggested a significant divergence between homologous genes in C. tritonis. Our results improve the understanding of biomineralization in C. tritonis and provide fundamental transcriptome information to study other molecular mechanisms such as reproduction.

scholarly journals MO049FUNCTIONAL IMPORTANCE OF MAPKBP1 PROTEIN DOMAINS IN NEPHRONOPHTHISIS

2021 ◽  
Vol 36 (Supplement_1) ◽  
Author(s):  
Christin Hartig ◽  
Ria Schönauer ◽  
Sebastian Sewerin ◽  
Anastasia Ertel ◽  
Wenjun Jin ◽  
...  
Keyword(s):  
Kidney Disease ◽  
Expression Profiles ◽  
Intracellular Localization ◽  
Significant Proportion ◽  
Protein Domains ◽  
Binding Domain ◽  
Protein Domain ◽  
Rna Seq ◽  
Wild Type ◽  
Wd40 Domain

Abstract Background and Aims Nephronophthisis is an autosomal-recessive kidney disease that accounts for a significant proportion of end-stage renal disease (ESRD) in childhood, adolescence and early adulthood. Biallelic pathogenic variants in MAPKBP1, encoding the c-Jun N-terminale kinase (JNK)-binding protein 1, are associated with development of Nephronophthisis and subsequent chronic kidney disease (CKD) (Macia et al, AJHG, 2017). We recently characterized MAPKBP1 as microtubule-associated protein that is able to localize to centrioles and the base of primary cilia depending on dimerization via its C-terminal coiled-coil domain (Schönauer et al, Kidney Int, 2020). However, the physiological function of its N-terminal WD40 and intermediate JNK-binding domain is still poorly understood. By in vitro comparison of artificial domain deletions with known and novel patient variants, we aim at pinpointing functional consequences of pathogenic MAPKBP1 in cilia and cell cycle control. Method N-terminally GFP-tagged MAPKBP1 constructs with either full-domain deletions or patient-derived variants were expressed in non-ciliated HeLa and ciliated H69 cells for fluorescence microscopy studies. Furthermore, RNA-seq analysis using primary patient cells was conducted to investigate differentially regulated molecular pathways compared to healthy control individuals. Results Immunofluorescence microscopy revealed inappropriate intracellular localization upon single or combined deletion of any MAPKBP1 protein domain. Compared to wild type, all deletion variants showed reduced intensity at the centrosome and ciliary base. Despite preserved dimerization ability, loss of the intermediate JNK-binding domain (JBD) most effectively abolished centrosomal or ciliary targeting, whereas loss of the N-terminal WD40-domain induced strongest mitotic aberrations. Unlike wild type, both, artificial and patient-derived truncating variants were able to enter the nucleus. RNA-seq analysis using primary patient fibroblasts with varying C-terminal truncations will allow important insights into common gene expression profiles unveiling consequences of aberrant intracellular trafficking. Conclusion In the present work, we demonstrate that all protein domains are indispensable for appropriate MAPKBP1 intracellular localization and function. Most of clinically reported patient variants exhibiting C-terminal truncation of varying lengths resulted in comparable intracellular behavior in presence of an intact N-terminal WD40 domain. Surprisingly, deletion of the JNK-binding domain alone aggravated functional disturbances hinting at a prominent regulatory role of this protein part interdepending with dimerization. Further insights into domain-specific functions will explain molecular disease mechanisms of MAPKBP1.

scholarly journals Transcriptome Profiling Provides Insights Into Potential Antagonistic Mechanisms Involved in Chaetomium globosum Against Bipolaris sorokiniana

2020 ◽  
Vol 11 ◽  
Author(s):  
K. Darshan ◽  
Rashmi Aggarwal ◽  
Bishnu Maya Bashyal ◽  
Jagmohan Singh ◽  
V. Shanmugam ◽  
...  
Keyword(s):  
De Novo ◽  
Gene Annotation ◽  
Expression Profiles ◽  
Glycosyl Hydrolase ◽  
Draft Genome ◽  
Transcriptome Profiling ◽  
Bipolaris Sorokiniana ◽  
Chaetomium Globosum ◽  
Rna Seq ◽  
Illumina Hiseq

Chaetomium globosum Kunze is recognized as a potential biocontrol fungus against spot blotch of wheat caused by Bipolaris sorokiniana. Its molecular mechanism of biocontrol activity and the biosynthetic pathways involved have not been yet elucidated. Here, global transcriptome profiling of C. globosum strain Cg2 during interaction with B. sorokiniana isolate BS112 using RNA-seq was performed in order to gain insights into the potential mechanisms of antagonism. The Illumina HiSeq platform (2 × 150 bp) yielded an average of 20–22 million reads with 50–58% GC. De novo assembly generated 45,582 transcripts with 27,957 unigenes. Transcriptome analysis displayed distinct expression profiles in the interaction (Cg2–BS112), out of which 6,109 unique differentially expressed genes were present. The predominant transcripts classified as genes involved in “catalytic activity” constituted 45.06%, of which 10.02% were associated with “hydrolytic activity” (GO:0008152), and similarly, in the biological process, 29.18% of transcripts were involved in “metabolic activity” (GO:0004096 and GO:0006979). Heat map and cluster categorization suggested an increase in the expression levels of genes encoding secondary metabolites like polyketide synthase (GO:0009058), S-hydroxymethyl glutathione dehydrogenase (GO:0006069), terpene cyclase (EC 4.2.3.-), aminotran_1_2 domain-containing protein (GO:0009058), and other hydrolytic CAZYmes such as the glycosyl hydrolase (GH) family (GH 13, GH 2, GH 31, and GH 81; GO:0005975), cellulase domain-containing protein, chitinases, β-1, 3-glucanases (GO:0004565), glucan endo-1,3-beta-glucanase (GO:0052861), and proteases (GO:0004177). The obtained RNA-seq data were validated by RT-qPCR using 20 randomly chosen genes, showing consistency with the RNA-seq results. The present work is worldwide the first effort to unravel the biocontrol mechanism of C. globosum against B. sorokiniana. It generated a novel dataset for further studies and facilitated improvement of the gene annotation models in the C. globosum draft genome.

scholarly journals Gene expression profiles and pathway enrichment analysis to identification of differentially expressed gene and signaling pathways in epithelial ovarian cancer based on high-throughput RNA-seq data

2019 ◽  
Author(s):  
A Siavoshi ◽  
M Taghizadeh ◽  
E Dookhe ◽  
M Piran
Keyword(s):  
Gene Expression ◽  
Ovarian Cancer ◽  
Epithelial Ovarian Cancer ◽  
Leucine Zipper ◽  
Expression Profiles ◽  
Differentially Expressed Gene ◽  
Differentially Expressed ◽  
Pathway Enrichment Analysis ◽  
Statistical Interpretation ◽  
Rna Seq

ABSTRACTEpithelial ovarian cancer (EOC) can be considered as a stressful and challenging disease among all women in the world, which has been associated with a poor prognosis and its molecular pathogenesis has remained unclear. In recent years, RNA Sequencing (RNA-seq) has become a functional and amazing technology for profiling gene expression. In the present study, RNA-seq raw data from Sequence Read Archive (SRA) of six tumor and normal ovarian sample was extracted, and then analysis and statistical interpretation was done with Linux and R Packages from the open-source Bioconductor. Gene Ontology (GO) term enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were applied for the identification of key genes and pathways involved in EOC. We identified 1091 Differential Expression Genes (DEGs) which have been reported in various studies of ovarian cancer as well as other types of cancer. Among them, 333 genes were up-regulated and 273 genes were down-regulated. In addition, Differentially Expressed Genes (DEGs) including RPL41, ALDH3A2, ERBB2, MIEN1, RBM25, ATF4, UPF2, DDIT3, HOXB8 and IL17D as well as Ribosome and Glycolysis/Gluconeogenesis pathway have had the potentiality to be used as targets for EOC diagnosis and treatment. In this study, unlike that of any other studies on various cancers, ALDH3A2 was most down-regulated gene in most KEGG pathways, and ATF4 was most up-regulated gene in leucine zipper domain binding term. In the other hand, RPL41 as a regulatory of cellular ATF4 level was up-regulated in many term and pathways and augmentation of ATF4 could justify the increase of RPL41 in the EOC. Pivotal pathways and significant genes, which were identified in the present study, can be used for adaptation of different EOC study. However, further molecular biological experiments and computational processes are required to confirm the function of the identified genes associated with EOC.

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