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Genomics

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https://www.readbyqxmd.com/read/27913251/unmapped-reads-from-cattle-rnaseq-data-a-source-for-missing-and-misassembled-sequences-in-the-reference-assemblies-and-for-detection-of-pathogens-in-the-host
#1
Tahir Usman, Frieder Hadlich, Wiebke Demasius, Rosemarie Weikard, Christa Kühn
Usually, reads from transcriptome sequencing data unmapped to the target species reference genome are disregarded. A recent RNAseq project on the new fatal disease Bovine Neonatal Pancytopenia had indicated an unexplained immune response signature to a double stranded RNA virus. To unravel its background, contigs were de novo assembled from unmapped RNAseq reads and aligned against the bovine genome assemblies and multispecies NCBI databases. Lack of genuine virus sequence contigs rejected the hypothesis of a live virus being causal for the unexplained immune response...
November 29, 2016: Genomics
https://www.readbyqxmd.com/read/27913250/identification-of-non-coding-and-coding-rnas-in-porcine-endometrium
#2
Yueying Wang, Tao Hu, Lihang Wu, Xiaoran Liu, Songyi Xue, Minggang Lei
One of the most critical periods of embryonic loss in pig is day 12 of pregnancy, when implantation begins. Here, we analyzed the gene expression on day 12 of pregnancy and non-pregnancy in the porcine endometrium using RNA sequencing (RNA-seq). 237 mRNAs, 34 lncRNAs and 1 miRNA were significantly differentially expressed between the two groups. Further functional analyses were conducted to identify these differentially expressed transcripts. The results demonstrated that they participate in various biological processes, such as cell adhesion, binding, nucleic and metabolic processes...
November 29, 2016: Genomics
https://www.readbyqxmd.com/read/27913249/comparison-of-the-transcriptomic-profile-of-hepatic-human-induced-pluripotent-stem-like-cells-cultured-in-plates-and-in-a-3d-microscale-dynamic-environment
#3
Eric Leclerc, Keiichi Kimura, Marie Shinohara, Mathieu Danoy, Morgane Le Gall, Taketomo Kido, Atsushi Miyajima, Teruo Fujii, Yasuyuki Sakai
We have compared the transcriptomic profiles of human induced pluripotent stem cells after their differentiation in hepatocytes like cells in plates and microfluidic biochips. The biochips provided a 3D and dynamic support during the cell differentiation when compared to the 2D static cultures in plates. The microarray have demonstrated the up regulation of important pathway related to liver development and maturation during the culture in biochips. Furthermore, the results of the transcriptomic profile, coupled with immunostaining, and RTqPCR analysis have shown typical biomarkers illustrating the presence of responders of biliary like cells, hepatocytes like cells, and endothelial like cells...
November 29, 2016: Genomics
https://www.readbyqxmd.com/read/27867104/identification-of-transcripts-involved-in-digestion-detoxification-and-immune-response-from-transcriptome-of-empoasca-vitis-hemiptera-cicadellidae-nymphs
#4
En-Si Shao, Gui-Fang Lin, Si-Jun Liu, Xiao-Li Ma, Ming-Feng Chen, Li Lin, Song-Qing Wu, Li Sha, Zhao-Xia Liu, Xiao-Hua Hu, Xiong Guan, Ling-Ling Zhang
Tea production has been significantly impacted by the false-eye leafhopper, Empoasca vitis (Göthe), around Asia. To identify the key genes which are responsible for nutrition absorption, xenobiotic metabolism and immune response, the transcriptome of either alimentary tracts or bodies minus alimentary tract of E. vitis was sequenced and analyzed. Over 31 million reads were obtained from Illumina sequencing. De novo sequence assembly resulted in 52,182 unigenes with a mean size of 848nt. The assembled unigenes were then annotated using various databases...
November 17, 2016: Genomics
https://www.readbyqxmd.com/read/27856225/correlations-of-vdr-and-vdbp-genetic-polymorphisms-with-susceptibility-to-adolescent-idiopathic-scoliosis-and-efficacy-of-brace-treatment
#5
Yu Wang, Zhi-Qiang Cui, Tian-Bao Luo, Long Liu
OBJECTIVE: This paper aimed to elucidate the correlations of VDR and VDBP polymorphisms with susceptibility to adolescent idiopathic scoliosis (AIS) and efficacy of brace treatment. METHODS: AIS patients and healthy controls were enrolled. Lumbar spine bone mineral density (LSBMD) and femoral neck bone mineral density (FNBMD) were detected by dual energy X-ray absorptiometry. VDR and VDBP polymorphisms were detected by PCR-RFLP. Efficacy of brace treatment was evaluated by Cobb measurement...
November 14, 2016: Genomics
https://www.readbyqxmd.com/read/27856224/tid-standalone-software-for-mining-putative-drug-targets-from-bacterial-proteome
#6
Reena Gupta, Dibyabhaba Pradhan, Arun Kumar Jain, Chandra Shekhar Rai
TiD is a standalone application, which relies on basic assumption that a protein must be essential for pathogens survival and non-homologous with host to qualify as putative target. With an input bacterial proteome, TiD removes paralogous proteins, picks essential ones, and excludes proteins homologous with host organisms. The targets illustrate non-homology with at least 40 out of 84 gut microbes, considered safe for human. TiD classifies proposed targets as known, novel and virulent. Users can perform pathway analysis, choke point analysis, interactome analysis, subcellular localization and functional annotations through web servers cross-referenced with the application...
November 14, 2016: Genomics
https://www.readbyqxmd.com/read/27851990/genetic-variants-associated-with-primary-open-angle-glaucoma-in-indian-population
#7
REVIEW
Sunil Kumar, Manzoor Ahmad Malik, Sooraj K, Ramanjit Sihota, Jasbir Kaur
Glaucoma is a very common disorder of the eye wherein the disturbance of the structural or functional integrity of the optic nerve causes characteristic atrophic changes in the optic nerve, which may lead to specific visual field defects over time. Primary open angle glaucoma (POAG) is most frequent among the three principle glaucoma subtypes. With well-established role of genes like Myocilin (MYOC), Optineurin (OPTN) and WD repeat Domain 36, (WDR36), at least 29 genetic loci have been found till date to be linked to POAG...
November 13, 2016: Genomics
https://www.readbyqxmd.com/read/27829169/slc44a2-single-nucleotide-polymorphisms-isoforms-and-expression-association-with-severity-of-meniere-s-disease
#8
Thankam S Nair, Pavan K Kommareddi, Maria M Galano, Danielle M Miller, Bala Naveen Kakaraparthi, Steven A Telian, H Alex Arts, Hussam El-Kashlan, Alyse Kilijanczyk, Amy Anne D Lassig, Martin P Graham, Susan G Fisher, Stefan W Stoll, Rajan P Nair, James T Elder, Thomas E Carey
SLC44A2 was discovered as the target of an antibody that causes hearing loss. Knockout mice develop age related hearing loss, loss of sensory cells and spiral ganglion neurons. SLC44A2 has polymorphic sites implicated in human disease. Transfusion related acute lung injury (TRALI) is linked to rs2288904 and genome wide association studies link rs2288904 and rs9797861 to venous thromboembolism (VTE), coronary artery disease and stroke. Here we report linkage disequilibrium of rs2288904 with rs3087969 and the association of these SLC44A2 SNPs with Meniere's disease severity...
November 6, 2016: Genomics
https://www.readbyqxmd.com/read/27826049/methylation-status-of-homeobox-genes-in-common-human-cancers
#9
REVIEW
Maria Fernanda Setúbal Destro Rodrigues, Carina Magalhães Esteves, Flávia Caló Aquino Xavier, Fabio Daumas Nunes
Approximately 300 homeobox loci were identified in the euchromatic regions of the human genome, of which 235 are probable functional genes and 65 are likely pseudogenes. Many of these genes play important roles in embryonic development and cell differentiation. Dysregulation of homeobox gene expression is a frequent occurrence in cancer. Accumulating evidence suggests that as genetics disorders, epigenetic modifications alter the expression of oncogenes and tumor suppressor genes driving tumorigenesis and perhaps play a more central role in the evolution and progression of this disease...
November 4, 2016: Genomics
https://www.readbyqxmd.com/read/27816578/distinctive-gene-expression-profile-in-women-with-history-of-postpartum-depression
#10
Anna Landsman, Rafael Aidelman, Yoav Smith, Matthew Boyko, Chaya Greenberger
Postpartum depression (PPD) is a disease which incorporates a variety of depressive states differing in nature and severity. To assist in the understanding of the pathogenesis of the disease, we aimed to ascertain a molecular mechanism underlying PPD development. We applied microarray technology to characterize gene expression of euthymic women with a history of PPD and compared the results with healthy controls. Our study demonstrated that women who considered euthymic on a clinical level, in fact, had an altered molecular profile when compared to participants with no PPD history...
November 2, 2016: Genomics
https://www.readbyqxmd.com/read/27810268/identification-and-characterization-of-micrornas-in-maize-endosperm-response-to-exogenous-sucrose-using-small-rna-sequencing
#11
Huanhuan Huang, Jiao Long, Lanjie Zheng, Yangping Li, Yufeng Hu, Guowu Yu, Hanmei Liu, Yinghong Liu, Zhi Huang, Junjie Zhang, Yubi Huang
Sucrose acts as a signaling molecule for genes critical to starch biosynthesis in maize endosperm. Previously, we showed that sucrose could regulate starch biosynthesis in maize via transcription factors. To better understand the complex regulation of starch biosynthesis, the 10days after pollination endosperm from Zea mays L. B73 inbred line was collected and treated with sucrose for small RNA sequencing. The sequencing results revealed that 24 known miRNAs and 190 novel miRNAs were significantly differentially expressed in response to sucrose...
November 1, 2016: Genomics
https://www.readbyqxmd.com/read/27789319/genome-wide-regulatory-dynamics-of-g-quadruplexes-in-human-malaria-parasite-plasmodium-falciparum
#12
Deeksha Bhartiya, Vandna Chawla, Sourav Ghosh, Ravi Shankar, Niti Kumar
The AT-rich genome of P. falciparum has uniquely localized G-rich stretches that have propensity to form G-quadruplexes. However, their global occurrence and potential biological roles in the parasite are poorly explored. Our genome-wide analysis revealed unique enrichment of quadruplexes in P. falciparum genome which was remarkably different from other Plasmodium species. A distinct predominance of quadruplexes was observed in nuclear and organellar genes that participate in antigenic variation, pathogenesis, DNA/RNA regulation, metabolic and protein quality control processes...
October 24, 2016: Genomics
https://www.readbyqxmd.com/read/27746014/a-pubmed-wide-study-of-endometriosis
#13
Ji-Long Liu, Miao Zhao
Endometriosis affects 5-10% of women in reproductive age, leading to dysmenorrhea, pelvic pain and infertility; however, our understanding on the pathogenesis of this disease remains incomplete. In the present study, we performed a systematic analysis of endometriosis-related genes using text mining. Taking text mining results as input, we subsequently generated a filtered gene set by computing the likelihood of finding more than expected occurrences for every gene across the disease-centered subset of the PubMed database...
October 13, 2016: Genomics
https://www.readbyqxmd.com/read/27732888/tissue-specific-transcriptome-characterization-for-developing-tadpoles-of-the-northern-leopard-frog-lithobates-pipiens
#14
Jeffrey R Row, Michael E Donaldson, Jessica N Longhi, Barry J Saville, Dennis L Murray
A potential cause of amphibian population declines are the impacts of environmental degradation on tadpole development. We conducted RNA sequencing on developing northern leopard frog tadpoles and through de novo transcriptome assembly we annotated a large number of open reading frames comparable in number and extent to genes identified in Xenopus. Using our transcriptome, we found transcript level changes between early (Gosner 26-31) and late (Gosner 36-41) stage tadpoles were the greatest in the tail, which is reabsorbed throughout development...
October 11, 2016: Genomics
https://www.readbyqxmd.com/read/27720826/the-ciona-intestinalis-cleavage-clock-is-independent-of-dna-methylation
#15
Miho M Suzuki, Tomoko Mori, Noriyuki Satoh
The initiation of embryonic gene expression in ascidian embryos appears to be tightly regulated by the number of DNA replication cycles. DNA methylation is thought to contribute to the clock mechanism that counts the rounds of DNA replication. We used mass spectrometry and whole genome bisulfite sequencing to characterize DNA methylation changes that occur in early developmental stages of the ascidian, Ciona intestinalis. We found that global DNA methylation in early Ciona development was static, and a base-wise comparison between the genomes of consecutive developmental stages found no DNA demethylation that was related to zygotic gene activation...
October 5, 2016: Genomics
https://www.readbyqxmd.com/read/27702613/insights-in-human-epigenomic-dynamics-through-comparative-primate-analysis
#16
Christopher G Bell
Epigenomic analysis gives a molecular insight into cell-specific genomic activity. It provides a detailed functional plan to dissect an organism, tissue by tissue. Therefore comparative epigenomics may increase understanding of human-acquired traits, by revealing regulatory changes in systems such as the neurological, musculoskeletal, and immunological. Enhancer loci evolve fast by hijacking elements from other tissues or rewiring and amplifying existing units for human-specific function. Promoters by contrast often require a CpG dense genetic infrastructure...
October 1, 2016: Genomics
https://www.readbyqxmd.com/read/27621057/transcriptomic-response-of-drosophila-melanogaster-pupae-developed-in-hypergravity
#17
Shannon Hateley, Ravikumar Hosamani, Shilpa R Bhardwaj, Lior Pachter, Sharmila Bhattacharya
Altered gravity can perturb normal development and induce corresponding changes in gene expression. Understanding this relationship between the physical environment and a biological response is important for NASA's space travel goals. We use RNA-Seq and qRT-PCR techniques to profile changes in early Drosophila melanogaster pupae exposed to chronic hypergravity (3g, or three times Earth's gravity). During the pupal stage, D. melanogaster rely upon gravitational cues for proper development. Assessing gene expression changes in the pupae under altered gravity conditions helps highlight gravity-dependent genetic pathways...
September 10, 2016: Genomics
https://www.readbyqxmd.com/read/27613113/characterize-the-relationship-between-essential-and-tata-containing-genes-for-s-cerevisiae-by-network-topologies-in-the-perturbation-sensitivity-network
#18
Lei Yang, Shiyuan Wang, Meng Zhou, Xiaowen Chen, Yongchun Zuo, Yingli Lv
Essential genes are those that are indispensable for the survival and propagation of an organism. TATA-containing genes are associated with responses to various stresses and are highly regulated. Although both essential genes and TATA genes are very important in the function of biological systems, their relationship remains unclear because they have typically been researched independently. In this study, to investigate the relationship between essential genes and TATA genes, S. cerevisiae genes were classified as: essential TATA-containing, non-essential TATA-containing, essential non-TATA, and non-essential non-TATA genes...
September 6, 2016: Genomics
https://www.readbyqxmd.com/read/27580967/genomic-features-of-human-limb-specific-enhancers
#19
Shahid Ali, Bibi Amina, Saneela Anwar, Rashid Minhas, Nazia Parveen, Uzma Nawaz, Syed Sikandar Azam, Amir Ali Abbasi
To elucidate important cellular and molecular interactions that regulate patterning and skeletal development, vertebrate limbs served as a model organ. A growing body of evidence from detailed studies on a subset of limb regulators like the HOXD cluster or SHH, reveals the importance of enhancers in limb related developmental and disease processes. Exploiting the recent genome-wide availability of functionally confirmed enhancer dataset, this study establishes regulatory interactions for dozens of human limb developmental genes...
August 28, 2016: Genomics
https://www.readbyqxmd.com/read/27538895/numerical-encoding-of-dna-sequences-by-chaos-game-representation-with-application-in-similarity-comparison
#20
Tung Hoang, Changchuan Yin, Stephen S-T Yau
Numerical encoding plays an important role in DNA sequence analysis via computational methods, in which numerical values are associated with corresponding symbolic characters. After numerical representation, digital signal processing methods can be exploited to analyze DNA sequences. To reflect the biological properties of the original sequence, it is vital that the representation is one-to-one. Chaos Game Representation (CGR) is an iterative mapping technique that assigns each nucleotide in a DNA sequence to a respective position on the plane that allows the depiction of the DNA sequence in the form of image...
August 15, 2016: Genomics
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