scholarly journals Mapping-based all-RNA-information sequencing analysis (ARIseq) pipeline simultaneously revealed taxonomic composition, gene expression, and their correlation in an acidic stream ecosystem

2017 ◽  
Author(s):  
Arisa Tsuboi ◽  
Misao Itoga ◽  
Yuichi Hongoh ◽  
Shigeharu Moriya
Keyword(s):  
Gene Expression ◽  
Expression Patterns ◽  
Taxonomic Composition ◽  
Rrna Genes ◽  
Reference Database ◽  
Similar Distribution ◽  
Sequencing Analysis ◽  
Protein Coding ◽  
Microbial Ecosystems ◽  
Sulfur Oxidizing

AbstractWe developed a new pipeline for simultaneous analyses of both rRNA profile as a taxonomic marker and mRNA profile as a functional marker, to understand microbial ecosystems in natural environments. Our pipeline, named All-RNA-Information sequencing (ARIseq), comprises a high-throughput sequencing of reverse transcribed total RNA and several widely used computational tools, and generates quantitatively reliable information on both community structures and gene expression patterns, which were verified by quantitative PCR analyses in this study. Particularly, correlation network analysis in the pipeline can reveal microbial taxa and expressed genes that share patterns of dynamics among different time and/or geographical points. The pipeline is primarily mapping-based, using a public database for small subunit rRNA genes and obtained contigs as the reference database for protein-coding genes. We applied this pipeline to biofilm samples, as examples, collected from an acidic spring water stream in the Chyatsubomi-goke Park in Gunma prefecture, Japan. Our analyses revealed the predominance of iron and sulfur-oxidizing bacteria and Pinnularia diatoms, and also indicated that the distributions of the iron-sulfur-oxidizing bacterial consortium and the Pinnularia diatoms largely overlapped but showed distinct patterns. In addition, our analyses showed that the iron-oxidizing bacterial genus Acidithiobacillus and co-occurring Acidiphilium shared similar distribution pattern whereas another iron-oxidizing genus Leptospirillum exhibited a distinct pattern. Our pipeline enables researchers to more easily capture the outline of microbial ecosystems based on the taxonomic composition, protein-coding gene expression, and their correlations.

Abstract W P73: Feasibility and Preliminary Results of Whole Blood RNA-Sequencing Analysis in Patients With Intracranial Aneurysms

Stroke ◽  
2014 ◽  
Vol 45 (suppl_1) ◽  
Author(s):  
Blake Haas ◽  
Nestor R Gonzalez ◽  
Elina Nikkola ◽  
Mark Connolly ◽  
William Hsu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Network Analysis ◽  
Rna Sequencing ◽  
Whole Blood ◽  
Intracranial Aneurysms ◽  
Small Sample Size ◽  
Expression Patterns ◽  
Small Sample ◽  
Cellular Respiration ◽  
Sequencing Analysis

Introduction: Intracranial aneurysms (IA) growth and rupture have been associated with chronic remodeling of the arterial wall. However, the pathobiology of this process remains poorly understood. The objective of the present study was to evaluate the feasibility of analyzing gene expression patterns in peripheral blood of patients with ruptured and unruptured saccular IAs. Materials and Methods: We analyzed human whole blood transcriptomes by performing paired-end, 100 bp RNA-sequencing (RNAseq) using the Illumina platform. We used STAR to align reads to the genome, HTSeq to count reads, and DESeq to normalize counts across samples. Self-reported patient information was used to correct expression values for ancestry, age, and sex. We utilized weighted gene co-expression network analysis (WGCNA) to identify gene expression network modules associated with IA size and rupture. The DAVID tool was employed to search for Gene Ontology enrichment in relevant modules. Results: Samples from 12 patients (9 females, age 57.6 +/-12) with IAs were analyzed. Four had ruptured aneurysms. RNA isolation and application of the methodology described above was successful in all samples. Although the small sample size prevents us from drawing definite conclusions, we observed promising novel co-expression networks for IAs: WCGNA analysis showed down-regulation of two transcript modules associated with ruptured IA status (r=-0.78, p=0.008 and r=-0.77, p=0.009), and up-regulation of two modules associated with aneurysm size (r=0.86, p=0.002 and r=0.9, p=4e-04), respectively. DAVID analyses showed that genes upregulated in an IA size-associated module were enriched with genes involved in cellular respiration and translation, while genes involved in transcription were down-regulated in a module associated with ruptured IAs. Conclusions: Whole blood RNAseq analysis is a feasible tool to capture transcriptome dynamics and achieve a better understanding of the pathophysiology of IAs. Further longitudinal studies of patients with IAs using network analysis are justified.

Abstract 18584: Decoding the Regulatory LncRNAs in Neonatal Heart During Perinatal Circulatory Transition

Circulation ◽  
2015 ◽  
Vol 132 (suppl_3) ◽  
Author(s):  
Marlin Touma ◽  
Ashley Cass ◽  
Xuedong Kang ◽  
Yan Zhao ◽  
Reshma Biniwale ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Cycle ◽  
Rna Sequencing ◽  
Expression Patterns ◽  
Regulatory Function ◽  
Newborn Mouse ◽  
Protein Coding ◽  
Congenital Diseases ◽  
Gene Pairs ◽  
Neonatal Heart

Background: Fetal to neonatal transition of heart is an elaborate process, during which, neonatal cardiomyocytes undergo functional maturation and terminal exit from the cell cycle. However, transcriptome programming in neonatal cardiac chambers during perinatal stages is understudied. In particular, the changes in long non-coding RNAs (lncRNAs) in neonatal heart have not been explored. Objective: To achieve transcriptome-wide analysis of lncRNAs in neonatal left ventricle (LV) and right ventricle (RV) during maturation stages using deep RNA-Sequencing Methods: Deep RNA-sequencing was performed on male newborn mouse (C57 BL) LV and RV at 3 time points of perinatal circulatory transition: P0, P3 and P7. Reads were mapped to mouse genome (mm10). The lncRNAs annotated in NONCODE database were identified. Differentially expressed lncRNAs were defined as those with coefficient of variation ≥0.2, at a false discovery rate ≤0.05, and expressed at ≥3 RPKM in at least one sample. Correlated lncRNAs/ gene pairs were identified using Pearson’s (r2≥0.8, P≤0.05). A subset of LncRNAs/gene expression was validated using qRT-PCR. Results: Out of the 70, 983 observed unique lncRNAs, approximately 7000 were identified exhibiting significant variation during maturation windows with highly spatial-temporal dependent expression patterns, including approximately 5000 known and 2000 novel lncRNAs. Notably, 20% of these lncRNAs were located within 50 KB of a protein coding gene. Out of a total of 2400 lncRNAs/gene pairs, 10 % exhibited significantly concordant (lncRNA/gene) expression patterns. These correlated genes were significantly enriched in metabolism, cell cycle and contractility functional ontology. Interestingly, some of these lncRNAs exhibited concordance with their neighboring gene in human tissues with congenital heart defects, suggesting conserved, potentially significant, regulatory function. Conclusions: Transcriptome programming during neonatal heart maturation involves global changes in lncRNAs. Their expression concordance with neighboring protein coding genes implicates potential important regulatory role of lncRNAs in neonatal heart chamber specification and congenital diseases.

scholarly journals A mini-atlas of gene expression for the domestic goat (Capra hircus) reveals transcriptional differences in immune signatures between sheep and goats

2019 ◽  
Author(s):  
Charity Muriuki ◽  
Stephen J. Bush ◽  
Mazdak Salavati ◽  
Mary E.B. McCulloch ◽  
Zofia M. Lisowski ◽  
...  
Keyword(s):  
Gene Expression ◽  
Reference Genome ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Small Ruminants ◽  
Capra Hircus ◽  
Specific Cell ◽  
Domestic Goat ◽  
Protein Coding ◽  
Genomic Resources

AbstractGoats (Capra hircus) are an economically important livestock species providing meat and milk across the globe. They are of particular importance in tropical agri-systems contributing to sustainable agriculture, alleviation of poverty, social cohesion and utilisation of marginal grazing. There are excellent genetic and genomic resources available for goats, including a highly contiguous reference genome (ARS1). However, gene expression information is limited in comparison to other ruminants. To support functional annotation of the genome and comparative transcriptomics we created a mini-atlas of gene expression for the domestic goat. RNA-Seq analysis of 22 transcriptionally rich tissues and cell-types detected the majority (90%) of predicted protein-coding transcripts and assigned informative gene names to more than 1000 previously unannotated protein-coding genes in the current reference genome for goat (ARS1). Using network-based cluster analysis we grouped genes according to their expression patterns and assigned those groups of co-expressed genes to specific cell populations or pathways. We describe clusters of genes expressed in the gastro-intestinal tract and provide the expression profiles across tissues of a subset of genes associated with functional traits. Comparative analysis of the goat atlas with the larger sheep gene expression atlas dataset revealed transcriptional differences between the two species in macrophage-associated signatures. The goat transcriptomic resource complements the large gene expression dataset we have generated for sheep and contributes to the available genomic resources for interpretation of the relationship between genotype and phenotype in small ruminants.

Next-generation sequencing analysis reveals segmental patterns of microRNA expression in yak epididymis

2020 ◽  
Vol 32 (12) ◽  
pp. 1067
Author(s):  
Wangsheng Zhao ◽  
Eugene Quansah ◽  
Meng Yuan ◽  
Pengcheng Li ◽  
Chuanping Yi ◽  
...  
Keyword(s):  
Gene Expression ◽  
Mirna Expression ◽  
Expression Patterns ◽  
Differentially Expressed ◽  
Sequencing Analysis ◽  
Differentially Expressed Mirnas ◽  
Next Generation Sequencing Analysis ◽  
Cauda Epididymidis ◽  
Caput Epididymidis

MicroRNAs (miRNAs) have emerged as potent regulators of gene expression and are widely expressed in biological systems. In reproduction, they have been shown to have a significant role in the acquisition and maintenance of male fertility, whereby deletion of Dicer in mouse germ cells leads to infertility. Evidence indicates that this role of miRNAs extends from the testis into the epididymis, controlling gene expression and contributing to regional variations in gene expression. In this study, RNA sequencing technology was used to investigate miRNA expression patterns in the yak epididymis. Region-specific miRNA expression was found in the yak epididymis. In all, 683 differentially expressed known miRNAs were obtained; 190, 186 and 307 differentially expressed miRNAs were identified for caput versus corpus, corpus versus cauda and caput versus cauda region pairs respectively. Kyoto Encyclopedia of Genes and Genomes results showed endocytosis as the most enriched pathway across region pairs, followed by protein processing in the endoplasmic reticulum, phagosome, spliceosome and biosynthesis of amino acids in region pair-specific hierarchical order. Gene ontology results showed varied enrichment in terms including cell, biogenesis, localisation, binding and locomotion across region pairs. In addition, significantly higher miR-34c expression was seen in the yak caput epididymidis relative to the corpus and cauda epididymidis.

scholarly journals Penicillium simile sp. nov. revealed by morphological and phylogenetic analysis

2012 ◽  
Vol 62 (2) ◽  
pp. 451-458 ◽  
Author(s):  
Domenico Davolos ◽  
Biancamaria Pietrangeli ◽  
Anna Maria Persiani ◽  
Oriana Maggi
Keyword(s):  
Sequence Data ◽  
Taxonomic Status ◽  
Distinct Species ◽  
Rrna Genes ◽  
Chain Gene ◽  
Sequencing Analysis ◽  
Internal Transcribed Spacer Region ◽  
Protein Coding ◽  
Nuclear Loci ◽  
Dna Sequencing Analysis

The morphology of three phenetically identical Penicillium isolates, collected from the bioaerosol in a restoration laboratory in Italy, displayed macro- and microscopic characteristics that were similar though not completely ascribable to Penicillium raistrickii. For this reason, a phylogenetic approach based on DNA sequencing analysis was performed to establish both the taxonomic status and the evolutionary relationships of these three peculiar isolates in relation to previously described species of the genus Penicillium. We used four nuclear loci (both rRNA and protein coding genes) that have previously proved useful for the molecular investigation of taxa belonging to the genus Penicillium at various evolutionary levels. The internal transcribed spacer region (ITS1–5.8S–ITS2), domains D1 and D2 of the 28S rDNA, a region of the tubulin beta chain gene (benA) and part of the calmodulin gene (cmd) were amplified by PCR and sequenced. Analysis of the rRNA genes and of the benA and cmd sequence data indicates the presence of three isogenic isolates belonging to a genetically distinct species of the genus Penicillium, here described and named Penicillium simile sp. nov. (ATCC MYA-4591T  = CBS 129191T). This novel species is phylogenetically different from P. raistrickii and other related species of the genus Penicillium (e.g. Penicillium scabrosum), from which it can be distinguished on the basis of morphological trait analysis.

scholarly journals Comparative genomics of muskmelon reveals a potential role for retrotransposons in the modification of gene expression

2020 ◽  
Vol 3 (1) ◽  
Author(s):  
Ryoichi Yano ◽  
Tohru Ariizumi ◽  
Satoko Nonaka ◽  
Yoichi Kawazu ◽  
Silin Zhong ◽  
...  
Keyword(s):  
Gene Expression ◽  
Fruit Ripening ◽  
Expression Patterns ◽  
Rna Seq ◽  
Protein Coding ◽  
Genome Wide ◽  
Oxford Nanopore ◽  
Melon Genome ◽  
Number Variation ◽  
Genome Assemblies

AbstractMelon exhibits substantial natural variation especially in fruit ripening physiology, including both climacteric (ethylene-producing) and non-climacteric types. However, genomic mechanisms underlying such variation are not yet fully understood. Here, we report an Oxford Nanopore-based high-grade genome reference in the semi-climacteric cultivar Harukei-3 (378 Mb + 33,829 protein-coding genes), with an update of tissue-wide RNA-seq atlas in the Melonet-DB database. Comparison between Harukei-3 and DHL92, the first published melon genome, enabled identification of 24,758 one-to-one orthologue gene pairs, whereas others were candidates of copy number variation or presence/absence polymorphisms (PAPs). Further comparison based on 10 melon genome assemblies identified genome-wide PAPs of 415 retrotransposon Gag-like sequences. Of these, 160 showed fruit ripening-inducible expression, with 59.4% of the neighboring genes showing similar expression patterns (r > 0.8). Our results suggest that retrotransposons contributed to the modification of gene expression during diversification of melon genomes, and may affect fruit ripening-inducible gene expression.

scholarly journals Upregulation of cancer-associated gene expression in activated fibroblasts in a mouse model of non-alcoholic steatohepatitis

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Masahiro Asakawa ◽  
Michiko Itoh ◽  
Takayoshi Suganami ◽  
Takeru Sakai ◽  
Sayaka Kanai ◽  
...  
Keyword(s):  
Gene Expression ◽  
Molecular Mechanisms ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Xenograft Model ◽  
Gene Expression Profiles ◽  
Sequencing Analysis ◽  
Alcoholic Steatohepatitis ◽  
Activated Fibroblasts

AbstractNon-alcoholic steatohepatitis (NASH), characterized by chronic inflammation and fibrosis, is predicted to be the leading cause of cirrhosis and hepatocellular carcinoma (HCC) in the next decade. Although recent evidence suggests the importance of fibrosis as the strongest determinant of HCC development, the molecular mechanisms underlying NASH-induced carcinogenesis still remain unclear. Here we performed RNA sequencing analysis to compare gene expression profiles of activated fibroblasts prepared from two distinct liver fibrosis models: carbon tetrachloride–induced fibrosis as a model without obesity and HCC and genetically obese melanocortin 4 receptor–deficient (MC4R-KO) mice fed Western diet, which develop steatosis, NASH, and eventually HCC. Our data showed that activated fibroblasts exhibited distinct gene expression patterns in each etiology, and that the ‘pathways in cancer’ were selectively upregulated in the activated fibroblasts from MC4R-KO mice. The most upregulated gene in these pathways was fibroblast growth factor 9 (FGF9), which was induced by metabolic stress such as palmitate. FGF9 exerted anti-apoptotic and pro-migratory effects in fibroblasts and hepatoma cells in vitro and accelerated tumor growth in a subcutaneous xenograft model. This study reveals upregulation of cancer-associated gene expression in activated fibroblasts in NASH, which would contribute to the progression from NASH to HCC.

scholarly journals Identification and Validation of Gene Expression Patterns in Cystitis Glandularis Patients and Controls

2017 ◽  
Vol 22 (6) ◽  
pp. 743-750 ◽  
Author(s):  
Chen-long Chu ◽  
Chen-hui Zhao ◽  
Zhi-wei Zhang ◽  
Ming-wei Wang ◽  
Zhao-hui Zhang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Urinary Bladder ◽  
Signaling Pathways ◽  
Expression Patterns ◽  
Gene Set Enrichment Analysis ◽  
Enzyme Linked Immunosorbent Assay ◽  
Sequencing Analysis ◽  
Healthy Controls ◽  
Expression Levels ◽  
Cystitis Glandularis

Our aim was to investigate differences in gene expression in bladder tissues between cystitis glandularis (CG) patients and healthy controls. Subsequent RNA was isolated from urinary bladder samples from CG patients and healthy controls, followed by RNA sequencing analysis. There were 4263 differentially expressed genes in urinary bladder between CG patients and controls, and 8 genes were verified with real-time PCR, Western blot, and enzyme-linked immunosorbent assay (ELISA) analysis. Gene set enrichment analysis (GSEA) revealed that 25 signaling pathways were upregulated in CG patients, and 17 signaling pathways were found upregulated in healthy controls. The mRNA expression levels of the indicated genes, including CCND1, CCNA1, EGFR, AR, CX3CL1, CXCL6, and CXCL1, were significantly increased in urinary bladder from CG and bladder cancer (BC) patients compared with healthy controls, while TP53 was decreased. CX3CL1, CXCL6, and CXCL1 concentrations in peripheral blood from CG and BC patients were significantly increased compared with healthy controls. The protein expression levels of CCND1, EGFR, and AR were significantly increased in urinary bladder from CG and BC patients compared with healthy controls. In conclusion, the gene expression profile of CG patients has established a foundation to study the gene mechanism of CG and BC progression.

scholarly journals Exposure to hypoxia causes stress erythropoiesis and downregulates immune response genes in spleen of mice

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Haijing Wang ◽  
Daoxin Liu ◽  
Pengfei Song ◽  
Feng Jiang ◽  
Xiangwen Chi ◽  
...  
Keyword(s):  
Gene Expression ◽  
Immune Response ◽  
Expression Patterns ◽  
Differentially Expressed ◽  
Hypoxic Exposure ◽  
Control Group ◽  
Sequencing Analysis ◽  
Erythroid Progenitors ◽  
Stress Erythropoiesis ◽  
Expression Of Genes

Abstract Background The spleen is the largest secondary lymphoid organ and the main site where stress erythropoiesis occurs. It is known that hypoxia triggers the expansion of erythroid progenitors; however, its effects on splenic gene expression are still unclear. Here, we examined splenic global gene expression patterns by time-series RNA-seq after exposing mice to hypoxia for 0, 1, 3, 5, 7 and 13 days. Results Morphological analysis showed that on the 3rd day there was a significant increase in the spleen index and in the proliferation of erythroid progenitors. RNA-sequencing analysis revealed that the overall expression of genes decreased with increased hypoxic exposure. Compared with the control group, 1380, 3430, 4396, 3026, and 1636 genes were differentially expressed on days 1, 3, 5, 7 and 13, respectively. Clustering analysis of the intersection of differentially expressed genes pointed to 739 genes, 628 of which were upregulated, and GO analysis revealed a significant enrichment for cell proliferation. Enriched GO terms of downregulated genes were associated with immune cell activation. Expression of Gata1, Tal1 and Klf1 was significantly altered during stress erythropoiesis. Furthermore, expression of genes involved in the immune response was inhibited, and NK cells decreased. Conclusions The spleen of mice conquer hypoxia exposure in two ways. Stress erythropoiesis regulated by three transcription factors and genes in immune response were downregulated. These findings expand our knowledge of splenic transcriptional changes during hypoxia.

scholarly journals Transcriptome change in Staphylococcus aureus in infecting mice

2021 ◽  
Author(s):  
Hiroshi Hamamoto ◽  
Suresh Panthee ◽  
Atmika Paudel ◽  
Ohgi Suguru ◽  
Yutaka Suzuki ◽  
...  
Keyword(s):  
Gene Expression ◽  
Staphylococcus Aureus ◽  
Serine Proteases ◽  
Mouse Liver ◽  
Expression Patterns ◽  
Anaerobic Respiration ◽  
Sequencing Analysis ◽  
Metal Transporters ◽  
Oxygenation Status

Abstract We performed in vivo RNA-sequencing analysis of Staphylococcus aureus in infected mouse liver using the 2-step cell-crush method. We compared the transcriptome of S. aureus at 6, 24, and 48 h post-infection (h.p.i) in mice and in culture medium. Genes related to anaerobic respiration were highly upregulated at 24 and 48 h.p.i. The gene expression patterns of virulence factors differed depending on the type of toxin. For example, hemolysins, but not leukotoxins and serine proteases, were highly upregulated at 6 h.p.i. Gene expression of metal transporters, such as iron transporters, gradually increased at 24 and 48 h.p.i. We also analyzed the transcriptome of mouse liver infected with S. aureus. Hypoxia response genes were upregulated at 24 and 48 h.p.i., and immune response genes were upregulated from 6 h.p.i. These findings suggest that gene expression of S. aureus in the host changes in response to changes in the host environment, such as oxygenation status or immune system attacks during infection.

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