A meta-analysis on genetic associations between Transcription Factor 7 Like 2 polymorphisms and type 2 diabetes mellitus.
CONCLUSIONS: Our findings supported that these TCF7L2 polymorphisms could be used to identify individuals at high risk of developing T2DM. PMID: 31288068 [PubMed - as supplied by publisher] (Source: Genomics)
Source: Genomics - July 6, 2019 Category: Genetics & Stem Cells Authors: Xi X, Ma J Tags: Genomics Source Type: research

Population structure and pangenome analysis of Enterobacter bugandensis uncover the presence of blaCTX-M-55, blaNDM-5 and blaIMI-1, along with sophisticated iron acquisition strategies.
We report the genome of a non-clinical E. bugandensis strain, which was integrated with publicly available genomes to study the pangenome and general population structure of E. bugandensis. Core- and whole-genome multilocus sequence typing allowed the detection of five E. bugandensis phylogroups (PG-A to E), which contain important antimicrobial resistance and virulence determinants. We uncovered several extended-spectrum β-lactamases, including blaCTX-M-55 and blaNDM-5, present in an IncX replicon type plasmid, described here for the first time in E. bugandensis. Genetic context analysis of blaNDM-5 revealed the rese...
Source: Genomics - July 4, 2019 Category: Genetics & Stem Cells Authors: Matteoli FP, Passarelli-Araujo H, Pedrosa-Silva F, Olivares FL, Venancio TM Tags: Genomics Source Type: research

Inactivation of Lgi1 in murine neuronal precursor cells leads to dysregulation of axon guidance pathways.
Abstract LGI1 mutations predispose to a rare epilepsy syndrome and when inactivated in mice leads to early onset seizures and premature death. Histopathology of the mature brain soon after birth shows cortical dysplasia in Lgi1 null mice with hypercellularity in the outer cortical layers. Here we show extensive gene expression changes in neuronal precursor cells from Lgi1 null mice compared with wild type mice. The most significantly dysregulated pathway involves canonical axon guidance signaling with multiple networks involved in cell movement, adhesion and invasion related to actin cytoskeleton reorganization. T...
Source: Genomics - July 2, 2019 Category: Genetics & Stem Cells Authors: Silva J, Hawthorn L, Cowell JK Tags: Genomics Source Type: research

Heuristic filter feature selection methods for medical datasets.
Abstract Gene selection is the process of selecting the optimal feature subset in an arbitrary dataset. The significance of gene selection is in high dimensional datasets in which the number of samples and features are low and high respectively. The major goals of gene selection are increasing the accuracy, finding the minimal effective feature subset, and increasing the performance of evaluations. This paper proposed two heuristic methods for gene selection, namely, Xvariance against Mutual Congestion. Xvariance tries to classify labels using internal attributes of features however Mutual Congestion is frequency ...
Source: Genomics - July 2, 2019 Category: Genetics & Stem Cells Authors: Alirezanejad M, Enayatifar R, Motameni H, Nematzadeh H Tags: Genomics Source Type: research

A 17-marker panel for global genomic instability in breast cancer.
, Helou K Abstract Genomic instability is a hallmark of cancer that plays a pivotal role in breast cancer development and evolution. A number of existing prognostic gene expression signatures for breast cancer are based on proliferation-related genes. Here, we identified a 17-marker panel associated with genome stability. A total of 136 primary breast carcinomas were stratified by genome stability. Matched gene expression profiles showed an innate segregation based on genome stability. We identified a 17-marker panel stratifying the training and validation cohorts into high- and low-risk patients. The 17 genes ass...
Source: Genomics - June 28, 2019 Category: Genetics & Stem Cells Authors: Biermann J, Nemes S, Parris TZ, Engqvist H, Rönnerman EW, Kovács A, Karlsson P, Helou K Tags: Genomics Source Type: research

Neural circular transcriptomes across mammalian species.
Abstract Circular RNAs (circRNAs) have recently attracted significant interest in the realm of science and the evolution of species. Given the lack of information available on circRNAs due to various barriers related to sequencing techniques and bioinformatics tools, little regarding their function is known. It has been predicted that circRNAs contribute to gene expression regulation, but aside from a few specific cases, this contention has yet to be proven. Although the role of circRNAs in evolution remains elusive, from the few studies that have shown circRNA conservation in mammalian species, tissue specificity...
Source: Genomics - June 27, 2019 Category: Genetics & Stem Cells Authors: Curry-Hyde A, Ueberham U, Arendt T, Janitz M Tags: Genomics Source Type: research

Transcriptome analysis of the distal small intestine of Cftr null mice.
Abstract Cystic fibrosis (CF) is caused by mutations in the gene encoding the CFTR anion channel. Loss of CFTR function in pancreatic, biliary and intestinal epithelia, severely affects gastrointestinal function. Transcriptome analysis indicated the activation of an innate and adaptive immune response in the distal small intestine of Cftr null mice. Inflammation was associated with differential regulation of numerous genes involved in the transport and metabolism of nutrients and, particularly, lipids, that are targeted by ligand-dependent nuclear receptors and/or HNF4α. Among the most strongly down-regulate...
Source: Genomics - June 25, 2019 Category: Genetics & Stem Cells Authors: Ikpa PT, Meijsen KF, Nieuwenhuijze NDA, Dulla K, de Jonge HR, Bijvelds MJC Tags: Genomics Source Type: research

Effects of early cold stress on gene expression in Chlamydomonas reinhardtii.
Abstract Cold stress imposes a great impact on the growth of nearly all photosynthetic organisms, including Chlamydomonas reinhardtii (C. reinhardtii). Despite prior studies on the mechanism of stress acclimation in plants, little has been done on the early events of cold sensing in C. reinhardtii. Here, we used C. reinhardtii as a model to study early events of cold signal transduction. By analyzing transcriptomic changes of C. reinhardtii exposed to cold, we found that 3471 genes were differentially expressed after 1 h of cold exposure. These genes were associated with a wide range of biological events and pro...
Source: Genomics - June 25, 2019 Category: Genetics & Stem Cells Authors: Li L, Peng H, Tan S, Zhou J, Fang Z, Hu Z, Gao L, Li T, Zhang W, Chen L Tags: Genomics Source Type: research

Comparative genomic analysis identifies small open reading frames (sORFs) with peptide-encoding features in avian 16S rDNA.
amp C Abstract The mitochondrial genome (mt-DNA) functional repertoire has recently been enriched in mammals by the identification of functional small open reading frames (sORFs) embedded in ribosomal DNAs. Through comparative genomic analyses the presence of putatively functional sORFs was investigated in birds. Alignment of available avian mt-DNA sequences revealed highly conserved regions containing four putative sORFs that presented low insertion/deletion polymorphism rate (80% of species. Detected sORFs included avian homologs of human Humanin and Short-Humanin-Like-Peptide 6 and two new sORFs not yet describ...
Source: Genomics - June 24, 2019 Category: Genetics & Stem Cells Authors: Mortz M, Dégletagne C, Romestaing C, Duchamp C Tags: Genomics Source Type: research

Transcriptome profiling and dimorphic expression of sex-related genes in fifth-instar nymphs of Sogatella furcifera, an important rice pest.
This study provided transcriptome resource as a fundamental support for future functional studies to elucidate the sex determination regulatory networks governing sexual dimorphism of S. furcifera. PMID: 31247330 [PubMed - as supplied by publisher] (Source: Genomics)
Source: Genomics - June 24, 2019 Category: Genetics & Stem Cells Authors: Lin J, He J, Liang A, Wang F Tags: Genomics Source Type: research

Gene networks and toxicity/detoxification pathways in juvenile largemouth bass (Micropterus salmoides) liver induced by acute lead stress.
Abstract Lead (Pb) is a nonessential heavy metal that can be bioconcentrated to highly toxic levels in the environment. To understand the genes and toxicity/detoxification pathways of juvenile largemouth bass, liver transcriptomes were investigated in this fish after acute 96 h Pb exposure (Pb nitrate 0, 17.8, or 100 mg/L). Acute Pb exposure induced an immune response and apoptosis pathway activation in the liver. A number of transcripts related to complement and coagulation cascades were significantly increased. Up- and downregulated genes were significantly enriched in numerous pathways, including the natura...
Source: Genomics - June 24, 2019 Category: Genetics & Stem Cells Authors: Qian B, Xue L, Qi X, Bai Y, Wu Y Tags: Genomics Source Type: research

Bioinformatic analysis suggests potential mechanisms underlying parasitoid venom evolution and function.
Abstract Hymenopteran parasitoid wasps are a diverse collection of species that infect arthropod hosts and use factors found in their venoms to manipulate host immune responses, physiology, and behaviour. Whole parasitoid venoms have been profiled using proteomic approaches, and here we present a bioinformatic characterization of the venom protein content from Ganaspis sp. 1, a parasitoid that infects flies of the genus Drosophila. We find evidence that diverse evolutionary processes including multifunctionalization, co-option, gene duplication, and horizontal gene transfer may be acting in concert to drive venom ...
Source: Genomics - June 24, 2019 Category: Genetics & Stem Cells Authors: Alvarado G, Holland SR, DePerez-Rasmussen J, Jarvis BA, Telander T, Wagner N, Waring AL, Anast A, Davis B, Frank A, Genenbacher K, Larson J, Mathis C, Oates AE, Rhoades NA, Scott L, Young J, Mortimer NT Tags: Genomics Source Type: research

Comparative transcriptome analysis of rhizome nodes and internodes in Panax. japonicus var. major reveals candidate genes involved in the biosynthesis of triterpenoid saponins.
PMID: 31242451 [PubMed - as supplied by publisher] (Source: Genomics)
Source: Genomics - June 23, 2019 Category: Genetics & Stem Cells Authors: Zhang S, Wang G, Zuo T, Zhang X, Xu R, Zhu W, You J, Wang R, Chen P Tags: Genomics Source Type: research

Close encounters between Trypanosoma cruzi and the host mammalian cell: Lessons from genome-wide expression studies.
Abstract Trypanosoma cruzi is the etiologic agent of Chagas disease, a life-threatening disease that affects different tissues. Within its mammalian host, T. cruzi develops molecular strategies for successful invasion of different cell types and adaptation to the intracellular environment. Conversely, the host cell responds to the infection by activating intracellular pathways to control parasite replication. Here, we reviewed genome-wide expression studies based on microarray and RNA-seq data from both parasite and host genes generated from animal models of infection as well as from Chagas disease patients. As ex...
Source: Genomics - June 20, 2019 Category: Genetics & Stem Cells Authors: Oliveira AER, Silva VG, Ferreira LRP, Teixeira SMR Tags: Genomics Source Type: research

Dominance of Wolbachia sp. in the deep-sea sediment bacterial metataxonomic sequencing analysis in the Bay of Bengal, Indian Ocean.
Abstract The Bay of Bengal, located in the north-eastern part of the Indian Ocean is world's largest bay occupying an area of ~8,39,000 mile2. The variability in bacterial community structure and function in sediment ecosystems of the Bay of Bengal is examined by Illumina high-throughput metagenomic sequencing. Of five metataxonomics data sets presented, two (SD1 and SD2) were from stations close to the shore and three (SD4, SD5, and SD6) were from the deep-sea (~3000 m depth). Phylum Proteobacteria (90.27 to 92.52%) dominated the deep-sea samples, whereas phylum Firmicutes (65.35 to 90.98%) dominated the coasta...
Source: Genomics - June 20, 2019 Category: Genetics & Stem Cells Authors: Ammini P, Vijayan J, Krishna AV, Sreekumar A, Vinod Kumar N, Jyothibabu R Tags: Genomics Source Type: research

Deregulation of H19 is associated with cervical carcinoma.
Abstract CACX is one of the most common cancer affecting women world-wide. Here, expression microarray analysis revealed 8 over-expressed transcribed pseudogenes (GBP1P1, HLA-DRB6, HLAH, SLC6A10P, NAPSB, KRT16P2, PTTG3P and RNF126P1), down-regulated 7 lincRNAs (H19, MIR100HG, MEG3, DIO3OS, HOXA11-AS, CD27-AS1 and EPB41L4A-AS) and 6 snoRNAs (SNORD97, SNORD3A, SNORD3C, SNORD3D, SNORA12 and SCARNA9) as DEncGs (log2 fold-change ≥ ±1.0) in CACX. Consequently, down-regulation of lincRNA MEG3 and over-expression of pseudogenes, GBP1P1 and PTTG3P in the microarray analysis were found concordant with the real...
Source: Genomics - June 20, 2019 Category: Genetics & Stem Cells Authors: Roychowdhury A, Samadder S, Das P, Mazumder DI, Chatterjee A, Addya S, Mondal R, Roy A, Roychoudhury S, Panda CK Tags: Genomics Source Type: research

The complete genome sequence of Bifidobacterium longum LTBL16, a potential probiotic strain from healthy centenarians with strong antioxidant activity.
Abstract B. longum LTBL16 is a potential probiotic strain that was isolated from healthy centenarians in Bama, China. In vitro experiments show that B. longum LTBL16 has a strong antioxidant activity and the complete genome of B. longum LTBL16 was sequenced in this work. The genome consists of one 2,430,682 bp circular chromosome that is plasmid free. The circular chromosome has a GC content of 61.23% and contains 2071 coding sequences (CDSs), 4 rRNA manipulators and 55 tRNA coding genes. Genetic analysis showed that at least five protein-coding genes were associated with antioxidant activity, and the abundance ...
Source: Genomics - June 18, 2019 Category: Genetics & Stem Cells Authors: Huang G, Pan H, Zhu Z, Li Q Tags: Genomics Source Type: research

lncRNA SNHG16 promotes glioma tumorigenicity through miR-373/EGFR axis by activating PI3K/AKT pathway.
Abstract Glioma is one of the most common and aggressive malignant primary brain tumor with invariably poor 5-year survival rates. Because of the high recurrence rate and mortality rate, effective therapies for glioma are still weak. Recently, several studies has been proved that long non-coding RNAs (lncRNAs) have been identified to play regulatory mediators in the tumorigenesis of glioma. Nevertheless, the role of lncRNAs and their downstream transcripts are still elusive in the progression of glioma. Small nucleolar RNA host gene 16 (SNHG16), a newly identified lncRNA, has been verified to be up-regulated in hu...
Source: Genomics - June 18, 2019 Category: Genetics & Stem Cells Authors: Zhou XY, Liu H, Ding ZB, Xi HP, Wang GW Tags: Genomics Source Type: research

Phylogenetic determinants of toxin gene distribution in genomes of Brevibacillus laterosporus.
Abstract Brevibacillus laterosporus is a globally ubiquitous, spore forming bacterium, strains of which have shown toxic activity against invertebrates and microbes and several have been patented due to their commercial potential. Relatively little is known about this bacterium. Here, we examined the genomes of six published and five newly determined genomes of B. laterosporus, with an emphasis on the relationships between known and putative toxin encoding genes, as well as the phylogenetic relationships between strains. Phylogenetically, strain relationships are similar using average nucleotide identity (ANI) val...
Source: Genomics - June 18, 2019 Category: Genetics & Stem Cells Authors: Glare TR, Durrant A, Berry C, Palma L, Ormskirk MM, Cox MP Tags: Genomics Source Type: research

Drug databases and their contributions to drug repurposing.
Abstract Drug repurposing is an interesting field in the drug discovery scope because of reducing time and cost. It is also considered as an appropriate method for finding medications for orphan and rare diseases. Hence, many researchers have proposed novel methods based on databases which contain different information. Thus, a suitable organization of data which facilitates the repurposing applications and provides a tool or a web service can be beneficial. In this review, we categorize drug databases and discuss their advantages and disadvantages. Surprisingly, to the best of our knowledge, the importance and po...
Source: Genomics - June 18, 2019 Category: Genetics & Stem Cells Authors: Masoudi-Sobhanzadeh Y, Omidi Y, Amanlou M, Masoudi-Nejad A Tags: Genomics Source Type: research

Genome wide association study (GWAS) and identification of candidate genes for yield and oil yield related traits in oil palm (Eleaeis guineensis) using SNPs by genotyping-based sequencing.
Abstract The genotyping-based sequencing (GBS) method used for GWAS of four yield and seven oil yield related traits on highly diverse African oil palm germplasm. GBS generated 325 million-reads covering 50.78Gb of sequence data, with an average of 3.4 million-reads per sample. Finally, 4031 fully informative SNPs with a range between 157 on chromosome 15 to 455 on chromosome 1 were used for GWAS. Association mapping resulted in identification of 40 highly significant loci, where more genetic loci were found to be associated with oil to bunch (OB), followed by average bunch weight (ABW). The loci, SGI|593,593|link...
Source: Genomics - June 18, 2019 Category: Genetics & Stem Cells Authors: Babu BK, Mathur RK, Ravichandran G, Anita P, Venu MVB Tags: Genomics Source Type: research

Prophages contribute to remarkable genome plasticity of Klebsiella pneumoniae and may involve the chromosomal integration of ARGs in CG258.
This study showed prophages contribute to remarkable genome plasticity of K. pneumoniae. The strains of CG258 possess several conserved prophages including the couple of P2-P4 prophages. CRISPR-Cas system has limited impact on the presence of prophages. The strong MLST-depended distribution of CRISPR-Cas and prophages and the high proportion of strains with self-targeting spacers may be the causes. Four core ARGs (blaSHV, fosA and oqxAB) were detected on almost all the chromosomes, but the acquired ARGs were only found in CG258 and CRISPR-positive strains. The factors influencing the chromosomal integration of ARGs in CG25...
Source: Genomics - June 17, 2019 Category: Genetics & Stem Cells Authors: Shen J, Zhou J, Xu Y, Xiu Z Tags: Genomics Source Type: research

Development of SNVs and indels markers mined out of the first multi-organ transcriptomes from Hypancistrus zebra (Loricariidae), an endangered Amazonian catfish.
te TE Abstract Hypancistrus zebra is a catfish, endemic from the Xingu River, threatened with extinction due to the impacts of Belo Monte dam, of its illegal capture, of gold mining activities and of climate change. Currently, there are three nucleotide sequences from this species in GenBank, what impedes the development of genetic markers to assist on its conservation. A total of 217 million RNA-Seq reads from seven organs were sequenced and used to assemble 566,607 transcripts, including 98% of BUSCO vertebrates orthologs, 11,321 transcripts with SNVs and 1724 transcripts with indels. Three transcripts with SNVs...
Source: Genomics - June 17, 2019 Category: Genetics & Stem Cells Authors: Magalhães MGP, Moreira DA, Furtado C, Parente TE Tags: Genomics Source Type: research

Metataxonomics of Tunisian phosphogypsum based on five bioinformatics pipelines: Insights for bioremediation.
Abstract Phosphogypsum (PG) is an acidic by-product from the phosphate fertilizer industry and it is characterized by a low nutrient availability and the presence of radionuclides and heavy metals which pose a serious problem in its management. Here, we have applied Illumina MiSeq sequencing technology and five bioinformatics pipelines to explore the phylogenetic communities in Tunisian PG. Taking One Codex as a reference method, we present the results of 16S-rDNA-gene-based metataxonomics abundances with four other alternative bioinformatics pipelines (MetaGenome Rapid Annotation using Subsystem Technology (MG-RA...
Source: Genomics - June 17, 2019 Category: Genetics & Stem Cells Authors: Trifi H, Najjari A, Achouak W, Barakat M, Ghedira K, Mrad F, Saidi M, Sghaier H Tags: Genomics Source Type: research

Genomic analysis of a lignocellulose degrading strain from the underexplored genus Meridianimaribacter.
In this study, Meridianimaribacter sp. strain CL38, a lignocellulose degrading halophile was isolated from mangrove soil. The genome of strain CL38 was sequenced and analyzed. The assembled genome contains 17 contigs with 3.33 Mbp, a GC content of 33.13% and a total of 2982 genes predicted. Lignocellulose degrading enzymes such as cellulases (GH3, 5, 9, 16, 74 and 144), xylanases (GH43 and CE4) and mannanases (GH5, 26, 27 and 130) are encoded in the genome. Furthermore, strain CL38 demonstrated its ability to decompose empty fruit bunch, a lignocellulosic waste residue arising from palm oil industry. The genome information...
Source: Genomics - June 12, 2019 Category: Genetics & Stem Cells Authors: Lam MQ, Oates NC, Thevarajoo S, Tokiman L, Goh KM, McQueen-Mason SJ, Bruce NC, Chong CS Tags: Genomics Source Type: research

Screening and evaluating of long non-coding RNAs in prenatal and postnatal pituitary gland of sheep.
In this study, we identified 1755 lncRNAs (545 annotated lncRNAs and 1210 novel lncRNAs) from RNA-seq data in the pituitary gland of embryonic and adult sheep. A total of 235 lncRNAs were differentially expressed between embryonic and adult group. We verified the presence of some lncRNAs using RT-PCR and DNA sequencing, and identified some differentially expressed lncRNAs using qPCR. We also investigated the role of cis-acting lncRNAs on target genes. GO and KEGG enrichment analysis revealed that the target genes of lncRNAs were involved in the regulation of hormones secretion and some signaling pathways in the sheep pitui...
Source: Genomics - June 11, 2019 Category: Genetics & Stem Cells Authors: Li X, Li C, Wureli H, Ni W, Zhang M, Li H, Xu Y, Rizabek K, Bolatkhan M, Askar D, Gulzhan K, Hou X, Hu S Tags: Genomics Source Type: research

Identification of novel alternative transcripts of the human Ribonuclease κ (RNASEK) gene using 3' RACE and high-throughput sequencing approaches.
Identification of novel alternative transcripts of the human Ribonuclease κ (RNASEK) gene using 3' RACE and high-throughput sequencing approaches. Genomics. 2019 Jun 11;: Authors: Adamopoulos PG, Kontos CK, Scorilas A, Sideris DC Abstract The human RNASEK gene encodes Ribonuclease κ, an endoribonuclease that belongs to a highly conserved protein family of metazoans. Recent evidence suggests that the mRNA levels of the RNASEK gene possess biomarker attributes in patients with prostate cancer. In the present study, we used 3' RACE and next-generation sequencing (NGS) to detect and identify n...
Source: Genomics - June 11, 2019 Category: Genetics & Stem Cells Authors: Adamopoulos PG, Kontos CK, Scorilas A, Sideris DC Tags: Genomics Source Type: research

Genetic polymorphism of angiotensin converting enzyme and angiotensin II type 1 receptors and their impact on the outcome of acute coronary syndrome.
This study aims to investigate the impact of ACE (rs4343) and AT1R (rs 5182) genetic polymorphisms on the outcome of acute coronary syndrome (ACS) in patients on captopril. Two hundred and fifty participants with ACS were included in this study (Group 1 (120) participants on captopril 25 mg twice daily and Group 2 (130) participants received no captopril (control study)). Participants were genotyped for ACE (rs4343) and AT1R (rs5182) polymorphisms and the phenotype was determined. ACE polymorphism (rs 4343) GG and GA genotypes are more related to STEMI (OR = 1.7, 1.5 respectively) and NSTEMI (OR = 3, 3.8 respecti...
Source: Genomics - June 10, 2019 Category: Genetics & Stem Cells Authors: Ghafil FA, Mohammad BI, Al-Janabi HS, Hadi NR, Al-Aubaidy HA Tags: Genomics Source Type: research

Prediction of lysine formylation sites using the composition of k-spaced amino acid pairs via Chou's 5-steps rule and general pseudo components.
In this study, a novel bioinformatics tool named CKSAAP_FormSite is proposed to predict lysine formylation sites. An effective feature extraction method, the composition of k-spaced amino acid pairs, is employed to encode formylation sites. Moreover, a biased support vector machine algorithm is proposed to solve the class imbalance problem in the prediction of formylation sites. As illustrated by 10-fold cross-validation, CKSAAP_FormSite achieves an satisfactory performance with an AUC of 0.8234. Therefore, CKSAAP_FormSite can be a useful bioinformatics tool for the prediction of formylation sites. Feature analysis shows t...
Source: Genomics - June 5, 2019 Category: Genetics & Stem Cells Authors: Ju Z, Wang SY Tags: Genomics Source Type: research

Identification and genetic analysis of alternative splicing of long non-coding RNAs in tomato initial flowering stage.
This study was designed to investigate the AS pattern of lncRNAs in tomato flower, leaf, and root tissues at the initial flowering stage. Using RNA-Seq, we found that 72.55% of lncRNAs underwent AS in these tissues, yielding a total of 16,995 AS events. Among them, the main type of AS event is alternative first exon (AFE), followed by retained intron (RI). We performed candidate target genes analysis on tissue-specific AS lncRNA, and the results indicated that the candidate target genes of these lncRNAs may be involved in the regulation of circadian rhythm, plant immunity, cellulose synthesis and phosphate-containing compo...
Source: Genomics - June 5, 2019 Category: Genetics & Stem Cells Authors: Yang Z, Yang Z, Yang C, Wang Z, Chen D, Xie Y, Wu Y Tags: Genomics Source Type: research

Whole-genome sequence of Arthrinium phaeospermum, a globally distributed pathogenic fungus.
This study aimed to develop genomic resources for A. phaeospermum to provide solid data and a theoretical basis for further studies of its pathogenesis, transcriptomics, proteomics, metabolomics and RNA genomics. The genome was obtained from the mycelia of the strain AP-Z13 using a combination of analyses with the high-throughput Illumina HiSeq 4000 system and PacBio RSII LongRead sequencing platform. Functional annotation was performed by BLASTing protein sequences against those in different publicly available databases to obtain their corresponding annotations. The genome is 48.45 Mb in size, with an N90 scaffold size ...
Source: Genomics - June 5, 2019 Category: Genetics & Stem Cells Authors: Li S, Tang Y, Fang X, Qiao T, Han S, Zhu T Tags: Genomics Source Type: research

Global integrated omics expression analyses of abiotic stress signaling HSF transcription factor genes in Oryza sativa L.: An in silico approach.
Abstract Among the significant transcription factors (TFs), HSF proteins play pivotal roles in the regulation of hormonal signal transduction and different abiotic stress (AbS) responses. Hence considering its importance, global omics expression analysis of HSF candidates was performed in rice (OsHSF). The current study identified 25 HSF family members and physically plotted them against the rice genome. These proteins were systematically analyzed for their physicochemical features, organization and expression signatures. Further, heatmap of both spatio-temporal and global plant hormones revealed the developmental...
Source: Genomics - June 5, 2019 Category: Genetics & Stem Cells Authors: Muthuramalingam P, Jeyasri R, Bharathi RKAS, Suba V, Pandian STK, Ramesh M Tags: Genomics Source Type: research

De novo assembly and annotation of the Ganoderma australe genome.
ez JF Abstract The Ganoderma genus represents clear biotechnological potential, due to the large quantity of molecules with biological activity that could be explored. However, available information regarding the biotechnological importance of species within Ganoderma, other than G. lucidum, is quite limited. Genomic studies of little-known species can contribute to the knowledge thereof, as well as the search for metabolic pathways and the identification of genes which code for proteins that may be of biotechnological relevance. Therefore, the objective of the present study was to obtain the G. australe genome, t...
Source: Genomics - June 5, 2019 Category: Genetics & Stem Cells Authors: Agudelo-Valencia D, Uribe-Echeverry PT, Betancur-Pérez JF Tags: Genomics Source Type: research

Characterization of the complete mitochondrial genome of Uca lacteus and comparison with other Brachyuran crabs.
In this study, the complete mitochondrial genome (mitogenome) of Uca lacteus (Ocypodoidea, Ocypodidae) was sequenced, annotated, and compared with those of other Brachyuran crabs. The circular mitogenome of U. lacteus is 15,661 base pairs long and contains the entire set of 37 genes and an A + T-rich region typically observed in decapod mitogenomes. Secondary structures of several tRNAs are partly missing (trnS1), and the number of bases is significantly decreased (trnD and trnF), as discovered in many other metazoans. We compared the gene order of U. lacteus with other species of Ocypodidae and found that they are con...
Source: Genomics - June 5, 2019 Category: Genetics & Stem Cells Authors: Wang Z, Shi X, Guo H, Tang D, Bai Y, Wang Z Tags: Genomics Source Type: research

Insight into the epigenetic landscape of a currently endogenizing gammaretrovirus in mule deer (Odocoileus hemionus).
Abstract Endogenous retroviruses (ERVs) constitute a significant part of vertebrate genomes. They originated from past retroviral infections and some of them retain transcriptional activity. The key mechanism avoiding uncontrolled ERV transcription is DNA methylation-mediated epigenetic silencing. Despite numerous studies describing the involvement of ERV activity in cellular processes, epigenetic regulation of ERVs is still poorly understood. We previously described a cervid endogenous retrovirus (CrERV) in the mule deer genome. This virus exhibits massive insertional polymorphism, suggesting recent activity. Her...
Source: Genomics - June 5, 2019 Category: Genetics & Stem Cells Authors: Hron T, Fabryova H, Elleder D Tags: Genomics Source Type: research

Whole-genome resequencing reveals selection signatures associated with milk production traits in African Kenana dairy zebu cattle.
In this study, we aimed at detecting signatures of positive selection in Kenana, known as one of the high milk production African indigenous zebu cattle, using next-generation sequencing data. To detect genomic signatures of positive selection, we applied three methods based on population comparison, fixation index (FST), cross population composite likelihood ratio (XP-CLR) and nucleotide diversity (Pi). Further analysis showed that several candidate genes such as CSN3, IGFBP-2, RORA, ABCG2, B4GALT1 and GHR are positively selected for milk production traits in Kenana cattle. The candidate genes and enriched pathways identi...
Source: Genomics - June 3, 2019 Category: Genetics & Stem Cells Authors: Nanaei HA, Qanatqestani MD, Esmailizadeh A Tags: Genomics Source Type: research

Effect of the key histone modifications on the expression of genes related to breast cancer.
Abstract Abnormal histone modifications (HMs) and transcription factors (TFs) can alter the expression of cancer-related genes to promote tumorigenesis. We studied the variations of 11 HMs and 2 TFs in human breast cancer cells (MCF-7) compared to human normal mammary epithelial cells (HMEC), and the effects of HMs/TFs in various regions of the genome on the expression changes of breast cancer-related genes. Based on HMs and TFs signals' differences between MCF-7 and HMEC flanking TSSs, the up- and down-regulated genes in MCF-7 were predicted by Random Forest, and important HMs and regions were found. Results indi...
Source: Genomics - June 3, 2019 Category: Genetics & Stem Cells Authors: Jin W, Li QZ, Liu Y, Zuo YC Tags: Genomics Source Type: research

Gene expression profiling and identification of hub genes in Nellore cattle with different marbling score levels.
The objective of this study was to use RNA-Seq to identify differentially expressed genes (DEGs) in muscle tissue (longissimus thoracis) of Nellore cattle divergently ranked on marbling, in order to increase our understanding of genes involved in the expression of this trait. The results revealed 49 DEGs and three hub genes (CISH, UFM1, TSHZ1), all of them involved in insulin and diabetes mellitus metabolism. These results indicating key genes and pathways, which may help to develop strategies designed to select animals with greater marbling. PMID: 31170441 [PubMed - as supplied by publisher] (Source: Genomics)
Source: Genomics - June 3, 2019 Category: Genetics & Stem Cells Authors: Fonseca LFS, Dos Santos Silva DB, Gimenez DFJ, Baldi F, Ferro JA, Chardulo LAL, de Albuquerque LG Tags: Genomics Source Type: research

Effects of PRSS1-PRSS2 rs10273639, CLDN2 rs7057398 and MORC4 rs12688220 polymorphisms on individual susceptibility to pancreatitis: A meta-analysis.
CONCLUSIONS: Our findings suggested that rs7057398, rs12688220 and rs10273639 polymorphisms could be used to identify individuals at an elevated susceptibility to acute pancreatitis in Caucasians. Moreover, rs12688220 and rs10273639 polymorphisms could be used to identify individuals at an elevated susceptibility chronic pancreatitis in Asians. PMID: 31163246 [PubMed - as supplied by publisher] (Source: Genomics)
Source: Genomics - June 1, 2019 Category: Genetics & Stem Cells Authors: Deng Y, Li Z Tags: Genomics Source Type: research

Glioma stages prediction based on machine learning algorithm combined with protein-protein interaction networks.
CONCLUSION: Machine learning combined with PPI networks, GO and KEGG analyses of selected DEGs improve our understanding of the biological functions involved in glioma growth. PMID: 31150762 [PubMed - as supplied by publisher] (Source: Genomics)
Source: Genomics - May 28, 2019 Category: Genetics & Stem Cells Authors: Niu B, Liang C, Lu Y, Zhao M, Chen Q, Zhang Y, Zheng L, Chou KC Tags: Genomics Source Type: research

Copy number variation detection in Chinese indigenous cattle by whole genome sequencing.
In this study, a comprehensive genomic analysis was performed on 75 cattle individuals including six Chinese indigenous cattle breeds and two non-native specialized beef cattle breeds. Based on the 11,486 CNVRs discovered, population analysis was performed, showed that all the cattle breeds clustered in to three clades, consistent with their lineages Bos taurus, Bos taurus × Bos indicus and Bos indicus. Importantly, a set of CNVRs related genes were found to be associated with the traits of interest, which include meat production or quality (CAST, ACTC1, etc.), adaption (BLA-DQB, EGLN2, etc.) and coat color (KIT, MIT...
Source: Genomics - May 27, 2019 Category: Genetics & Stem Cells Authors: Mei C, Junjvlieke Z, Raza SHA, Wang H, Cheng G, Zhao C, Zhu W, Zan L Tags: Genomics Source Type: research

Gibberellin causes wide transcriptional modifications in the early stage of grape cluster development.
Abstract Yaghooti grape of Sistan is seedless, early ripening but has compact clusters. To study gibberellin effect on cluster compactness of Yaghooti grape, it has been studied transcriptomic changes in three developmental stages (cluster formation, berry formation and final size of cluster). We found out that 5409 of 22,756 genes in cluster tissue showed significant changes under gibberellin. Finally, it was showed that 2855, 2862 and 497 genes have critically important role on above developmental stages, respectively. GO enrichment analysis showed that gibberellin enhances biochemical pathways activity. Moreove...
Source: Genomics - May 25, 2019 Category: Genetics & Stem Cells Authors: Shiri Y, Solouki M, Ebrahimie E, Emamjomeh A, Zahiri J Tags: Genomics Source Type: research

Potential miRNA-disease association prediction based on kernelized Bayesian matrix factorization.
In this study, we presented a neoteric Bayesian model (KBMFMDA) that combines kernel-based nonlinear dimensionality reduction, matrix factorization and binary classification. The main idea of KBMFMDA is to project miRNAs and disease into a unified subspace and estimating the association network in that subspace. KBMFMDA obtained the AUCs of 0.9132, 0.8708, 0.9008±0.0044 in global and local leave-one-out and five-fold cross validation. Moreover, KBMFMDA was applied to three important human cancers in three different kinds of case studies and most of the top 50 potential disease-related miRNAs were confirmed by many e...
Source: Genomics - May 25, 2019 Category: Genetics & Stem Cells Authors: Chen X, Li SX, Yin J, Wang CC Tags: Genomics Source Type: research

Draft genome sequence of marine sediment-derived red pigmented bacteria Zooshikella sp. strain S2.1 with potential biomedical applications.
Abstract The present study is aimed to determine the draft genome of novel species of Zooshikella strain S2.1, a potential red pigmented strain isolated recently from the coastal sediment of Andaman and Nicobar Islands, India. This Gram negative, rod shaped aerobic bacterium produces pink, yellowish-red and dark red with metallic green sheen pigmentation on agar plates. It is able to grow under NaCl concentrations of 1 to 9%. This species has antimicrobial, antioxidant, dye and food colorant applications. Whole genomes sequence analysis revealed that strain S2.1 represents a novel species of the genus Zooshikella....
Source: Genomics - May 22, 2019 Category: Genetics & Stem Cells Authors: Ramesh C, Anwesh M, Vinithkumar NV, Kirubagaran R Tags: Genomics Source Type: research

Molecular characterization, genomic structure and expression analysis of a gene (CATL1/CPT1C) encoding a third member of the human carnitine acyltransferase family.
Abstract Τhe carnitine palmitoyltransferase (CPT) system is responsible for transporting long-chain acyl-CoAs from cytoplasm into the mitochondria. This system consists of two l-carnitine acyltransferases (CPT1 and CPT2) and the carnitine acylcarnitine translocase. In mammals, two CPT1 homologs (CPT1A and CPT1B) were previously described. By using positional cloning gene approaches, RT-PCR, and next-generation sequencing (NGS), we sought to identify novel human genes that might be involved in fatty acid metabolism. Thus, we discovered a third CPT1 homolog (CATL1/CPT1C), transcribed into two major protein-codin...
Source: Genomics - May 22, 2019 Category: Genetics & Stem Cells Authors: Adamopoulos PG, Kontos CK, Scorilas A Tags: Genomics Source Type: research

Comparative transcriptome analysis of different stages of Plasmodium falciparum to explore vaccine and drug candidates.
Abstract Malaria is a life-threatening disease causes huge burden on human health. Every year>200 million cases of malaria are reported globally. Researchers have carried out research on transcriptome of different stages of Plasmodium species to understand complex pathology of pathogens and to discover therapeutics. Researchers are targeting different stages of Plasmodium falciparum separately. Hence, to target all stages of Plasmodium simultaneously comparative transcriptome analysis of different stages was carried out and 44 commonly expressed proteins from different stages of Plasmodium were identified. Thes...
Source: Genomics - May 22, 2019 Category: Genetics & Stem Cells Authors: Vandana, Jaiswal V Tags: Genomics Source Type: research

Genome-wide identification and expression analysis of R2R3, 3R- and 4R-MYB transcription factors during lignin biosynthesis in flax (Linum usitatissimum).
Abstract MYB transcription factors (TFs) have vital roles in regulating lignin or fiber development. Flax (Linum usitatissimum) is known as one of the plants with high fiber production capacity. However, no studies have been conducted to identify and characterize MYB TFs in the flax genome. Results showed that flax genome harbours 167 R2R3, seven 3R, and one 4R-type MYB TFs. 22 MYB genes (%13) were estimated to be tandem duplicated dated around 13.3-86.98 Mya. 130 flax MYB members have apparent orthologous with Arabidopsis, in which 17 R2R3 MYBs are associated with lignin biosynthesis. MYB062, MYB072, MYB096, MYB1...
Source: Genomics - May 22, 2019 Category: Genetics & Stem Cells Authors: Tombuloglu H Tags: Genomics Source Type: research

Transcriptional response of Caenorhabditis elegans when exposed to Shigella flexneri.
This study aims to further develop this model using RNA-sequencing to understand which pathways/cellular characteristics are affected and potentially cause death in Shigella-exposed worms. We identified 1631 differentially expressed genes in Shigella-exposed worms (6 h exposure). A number of these genes encode proteins involved in fatty-acid β-oxidation (FAO), antioxidant defense and autophagy. The down-regulation of acyl-CoA dehydrogenases would impede FAO, reducing the overall energy to combat Shigella in the worm's intestinal tract. This is potentially coupled with the production of reactive oxygen species (ROS) ...
Source: Genomics - May 21, 2019 Category: Genetics & Stem Cells Authors: Somasiri P, Behm CA, Adamski M, Wen J, Verma NK Tags: Genomics Source Type: research

Special issue on fish transcriptomics.
Shi Q PMID: 31121245 [PubMed - as supplied by publisher] (Source: Genomics)
Source: Genomics - May 20, 2019 Category: Genetics & Stem Cells Authors: Ortí G, Lovejoy NR, Shi Q Tags: Genomics Source Type: research

Identification, characterization, and expressions profile analysis of growth hormone receptors (GHR1 and GHR2) in Hybrid grouper (Epinephelus fuscoguttatus ♀ × Epinephelus polyphekadion ♂).
Identification, characterization, and expressions profile analysis of growth hormone receptors (GHR1 and GHR2) in Hybrid grouper (Epinephelus fuscoguttatus ♀ × Epinephelus polyphekadion ♂). Genomics. 2019 May 20;: Authors: Amenyogbe E, Chen G, Wang Z Abstract Growth hormone is an essential hormone that plays essential roles in growth, metabolism, cellular differentiation, immunity and reproduction in fish, by means of the growth hormone receptors. The encoding cDNA growth hormone receptors (GHR1 and GHR2) were cloned and characterized from Hybrid grouper (Epinephelus fuscoguttatus♀ &...
Source: Genomics - May 20, 2019 Category: Genetics & Stem Cells Authors: Amenyogbe E, Chen G, Wang Z Tags: Genomics Source Type: research