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Genomics & Informatics

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https://www.readbyqxmd.com/read/28638312/in-silico-signature-prediction-modeling-in-cytolethal-distending-toxin-producing-escherichia-coli-strains
#1
Maryam Javadi, Mana Oloomi, Saeid Bouzari
In this study, cytolethal distending toxin (CDT) producer isolates genome were compared with genome of pathogenic and commensal Escherichia coli strains. Conserved genomic signatures among different types of CDT producer E. coli strains were assessed. It was shown that they could be used as biomarkers for research purposes and clinical diagnosis by polymerase chain reaction, or in vaccine development. cdt genes and several other genetic biomarkers were identified as signature sequences in CDT producer strains...
June 2017: Genomics & Informatics
https://www.readbyqxmd.com/read/28638311/a-variant-in-runx3-is-associated-with-the-risk-of-ankylosing-spondylitis-in-koreans
#2
Sung-Min Cho, Seung-Hyun Jung, Yeun-Jun Chung
Ankylosing spondylitis (AS) is a chronic autoinflammatory disease that affects the spine and sacroiliac joints. Regarding its etiology, although HLA-B27 is known to be the strongest genetic factor of AS, much evidence suggests the potential contribution of non-MHC genes to the susceptibility to AS. Most of these non-MHC genes have been discovered in non-Asian populations; however, just some of them have been validated in Koreans. In this study, we aimed to identify additional AS-associated single-nucleotide polymorphism (SNP) candidates by replicating the candidate SNPs in Korean AS patients and healthy controls...
June 2017: Genomics & Informatics
https://www.readbyqxmd.com/read/28638310/analysis-of-gene-expression-in-human-dermal-fibroblasts-treated-with-senescence-modulating-cox-inhibitors
#3
Jeong A Han, Jong-Il Kim
We have previously reported that NS-398, a cyclooxygenase-2 (COX-2)-selective inhibitor, inhibited replicative cellular senescence in human dermal fibroblasts and skin aging in hairless mice. In contrast, celecoxib, another COX-2-selective inhibitor, and aspirin, a non-selective COX inhibitor, accelerated the senescence and aging. To figure out causal factors for the senescence-modulating effect of the inhibitors, we here performed cDNA microarray experiment and subsequent Gene Set Enrichment Analysis. The data showed that several senescence-related gene sets were regulated by the inhibitor treatment...
June 2017: Genomics & Informatics
https://www.readbyqxmd.com/read/28638309/editor-s-introduction-to-this-issue-g-i-15-2-2017
#4
EDITORIAL
Yeun-Jun Chung
No abstract text is available yet for this article.
June 2017: Genomics & Informatics
https://www.readbyqxmd.com/read/28416950/trapr-r-package-for-statistical-analysis-and-visualization-of-rna-seq-data
#5
Jae Hyun Lim, Soo Youn Lee, Ju Han Kim
High-throughput transcriptome sequencing, also known as RNA sequencing (RNA-Seq), is a standard technology for measuring gene expression with unprecedented accuracy. Numerous bioconductor packages have been developed for the statistical analysis of RNA-Seq data. However, these tools focus on specific aspects of the data analysis pipeline, and are difficult to appropriately integrate with one another due to their disparate data structures and processing methods. They also lack visualization methods to confirm the integrity of the data and the process...
March 2017: Genomics & Informatics
https://www.readbyqxmd.com/read/28416949/circulating-tumor-dna-in-a-breast-cancer-patient-s-plasma-represents-driver-alterations-in-the-tumor-tissue
#6
Jieun Lee, Sung-Min Cho, Min Sung Kim, Sug Hyung Lee, Yeun-Jun Chung, Seung-Hyun Jung
Tumor tissues from biopsies or surgery are major sources for the next generation sequencing (NGS) study, but these procedures are invasive and have limitation to overcome intratumor heterogeneity. Recent studies have shown that driver alterations in tumor tissues can be detected by liquid biopsy which is a less invasive technique capable of both capturing the tumor heterogeneity and overcoming the difficulty in tissue sampling. However, it is still unclear whether the driver alterations in liquid biopsy can be detected by targeted NGS and how those related to the tissue biopsy...
March 2017: Genomics & Informatics
https://www.readbyqxmd.com/read/28416948/comparative-analysis-of-predicted-gene-expression-among-crenarchaeal-genomes
#7
Shibsankar Das, Brajadulal Chottopadhyay, Satyabrata Sahoo
Research into new methods for identifying highly expressed genes in anonymous genome sequences has been going on for more than 15 years. We presented here an alternative approach based on modified score of relative codon usage bias to identify highly expressed genes in crenarchaeal genomes. The proposed algorithm relies exclusively on sequence features for identifying the highly expressed genes. In this study, a comparative analysis of predicted highly expressed genes in five crenarchaeal genomes was performed using the score of Modified Relative Codon Bias Strength (MRCBS) as a numerical estimator of gene expression level...
March 2017: Genomics & Informatics
https://www.readbyqxmd.com/read/28416947/dna-methylation-profiles-of-blood-cells-are-distinct-between-early-onset-obese-and-control-individuals
#8
Je-Keun Rhee, Jin-Hee Lee, Hae Kyung Yang, Tae-Min Kim, Kun-Ho Yoon
Obesity is a highly prevalent, chronic disorder that has been increasing in incidence in young patients. Both epigenetic and genetic aberrations may play a role in the pathogenesis of obesity. Therefore, in-depth epigenomic and genomic analyses will advance our understanding of the detailed molecular mechanisms underlying obesity and aid in the selection of potential biomarkers for obesity in youth. Here, we performed microarray-based DNA methylation and gene expression profiling of peripheral white blood cells obtained from six young, obese individuals and six healthy controls...
March 2017: Genomics & Informatics
https://www.readbyqxmd.com/read/28416946/use-of-graph-database-for-the-integration-of-heterogeneous-biological-data
#9
Byoung-Ha Yoon, Seon-Kyu Kim, Seon-Young Kim
Understanding complex relationships among heterogeneous biological data is one of the fundamental goals in biology. In most cases, diverse biological data are stored in relational databases, such as MySQL and Oracle, which store data in multiple tables and then infer relationships by multiple-join statements. Recently, a new type of database, called the graph-based database, was developed to natively represent various kinds of complex relationships, and it is widely used among computer science communities and IT industries...
March 2017: Genomics & Informatics
https://www.readbyqxmd.com/read/28416945/a-chip-seq-data-analysis-pipeline-based-on-bioconductor-packages
#10
Seung-Jin Park, Jong-Hwan Kim, Byung-Ha Yoon, Seon-Young Kim
Nowadays, huge volumes of chromatin immunoprecipitation-sequencing (ChIP-Seq) data are generated to increase the knowledge on DNA-protein interactions in the cell, and accordingly, many tools have been developed for ChIP-Seq analysis. Here, we provide an example of a streamlined workflow for ChIP-Seq data analysis composed of only four packages in Bioconductor: dada2, QuasR, mosaics, and ChIPseeker. 'dada2' performs trimming of the high-throughput sequencing data. 'QuasR' and 'mosaics' perform quality control and mapping of the input reads to the reference genome and peak calling, respectively...
March 2017: Genomics & Informatics
https://www.readbyqxmd.com/read/28416944/evaluation-of-digital-pcr-as-a-technique-for-monitoring-acute-rejection-in-kidney-transplantation
#11
Hyeseon Lee, Young-Mi Park, Yu-Mee We, Duck Jong Han, Jung-Woo Seo, Haena Moon, Yu-Ho Lee, Yang-Gyun Kim, Ju-Young Moon, Sang-Ho Lee, Jong-Keuk Lee
Early detection and proper management of kidney rejection are crucial for the long-term health of a transplant recipient. Recipients are normally monitored by serum creatinine measurement and sometimes with graft biopsies. Donor-derived cell-free deoxyribonucleic acid (cfDNA) in the recipient's plasma and/or urine may be a better indicator of acute rejection. We evaluated digital PCR (dPCR) as a system for monitoring graft status using single nucleotide polymorphism (SNP)-based detection of donor DNA in plasma or urine...
March 2017: Genomics & Informatics
https://www.readbyqxmd.com/read/28416943/editor-s-introduction-to-this-issue-g-i-15-1-2017
#12
EDITORIAL
Yeun-Jun Chung
No abstract text is available yet for this article.
March 2017: Genomics & Informatics
https://www.readbyqxmd.com/read/28154519/mining-the-proteome-of-fusobacterium-nucleatum-subsp-nucleatum-atcc-25586-for-potential-therapeutics-discovery-an-in-silico-approach
#13
Abdul Musaweer Habib, Md Saiful Islam, Md Sohel, Md Habibul Hasan Mazumder, Mohd Omar Faruk Sikder, Shah Md Shahik
The plethora of genome sequence information of bacteria in recent times has ushered in many novel strategies for antibacterial drug discovery and facilitated medical science to take up the challenge of the increasing resistance of pathogenic bacteria to current antibiotics. In this study, we adopted subtractive genomics approach to analyze the whole genome sequence of the Fusobacterium nucleatum, a human oral pathogen having association with colorectal cancer. Our study divulged 1,499 proteins of F. nucleatum, which have no homolog's in human genome...
December 2016: Genomics & Informatics
https://www.readbyqxmd.com/read/28154518/drug-target-identification-and-elucidation-of-natural-inhibitors-for-bordetella-petrii-an-in-silico-study
#14
Surya Narayan Rath, Manisha Ray, Animesh Pattnaik, Sukanta Kumar Pradhan
Environmental microbes like Bordetella petrii has been established as a causative agent for various infectious diseases in human. Again, development of drug resistance in B. petrii challenged to combat against the infection. Identification of potential drug target and proposing a novel lead compound against the pathogen has a great aid and value. In this study, bioinformatics tools and technology have been applied to suggest a potential drug target by screening the proteome information of B. petrii DSM 12804 (accession No...
December 2016: Genomics & Informatics
https://www.readbyqxmd.com/read/28154517/tissue-specific-expression-levels-of-apoptosis-involved-genes-have-correlations-with-codon-and-amino-acid-usage
#15
Mohammadreza Hajjari, Iman Sadeghi, Abbas Salavaty, Habib Nasiri, Maryam Tahmasebi Birgani
Different mechanisms, including transcriptional and post transcriptional processes, regulate tissue specific expression of genes. In this study, we report differences in gene/protein compositional features between apoptosis involved genes selectively expressed in human tissues. We found some correlations between codon/amino acid usage and tissue specific expression level of genes. The findings can be significant for understanding the translational selection on these features. The selection may play an important role in the differentiation of human tissues and can be considered for future studies in diagnosis of some diseases such as cancer...
December 2016: Genomics & Informatics
https://www.readbyqxmd.com/read/28154516/demographic-trends-in-korean-native-cattle-explained-using-bovine-snp50-beadchip
#16
Aditi Sharma, Dajeong Lim, Han-Ha Chai, Bong-Hwan Choi, Yongmin Cho
Linkage disequilibrium (LD) is the non-random association between the loci and it could give us a preliminary insight into the genetic history of the population. In the present study LD patterns and effective population size (Ne) of three Korean cattle breeds along with Chinese, Japanese and Mongolian cattle were compared using the bovine Illumina SNP50 panel. The effective population size (Ne) is the number of breeding individuals in a population and is particularly important as it determines the rate at which genetic variation is lost...
December 2016: Genomics & Informatics
https://www.readbyqxmd.com/read/28154515/metabolic-pathways-associated-with-kimchi-a-traditional-korean-food-based-on-in-silico-modeling-of-published-data
#17
Ga Hee Shin, Byeong-Chul Kang, Dai Ja Jang
Kimchi is a traditional Korean food prepared by fermenting vegetables, such as Chinese cabbage and radishes, which are seasoned with various ingredients, including red pepper powder, garlic, ginger, green onion, fermented seafood (Jeotgal), and salt. The various unique microorganisms and bioactive components in kimchi show antioxidant activity and have been associated with an enhanced immune response, as well as anti-cancer and anti-diabetic effects. Red pepper inhibits decay due to microorganisms and prevents food from spoiling...
December 2016: Genomics & Informatics
https://www.readbyqxmd.com/read/28154514/identification-of-a-copy-number-variation-on-chromosome-20q13-12-associated-with-osteoporotic-fractures-in-the-korean-population
#18
Tae-Joon Park, Mi Yeong Hwang, Sanghoon Moon, Joo-Yeon Hwang, Min Jin Go, Bong-Jo Kim
Osteoporotic fractures (OFs) are critical hard outcomes of osteoporosis and are characterized by decreased bone strength induced by low bone density and microarchitectural deterioration in bone tissue. Most OFs cause acute pain, hospitalization, immobilization, and slow recovery in patients and are associated with increased mortality. A variety of genetic studies have suggested associations of genetic variants with the risk of OF. Genome-wide association studies have reported various single-nucleotide polymorphisms and copy number variations (CNVs) in European and Asian populations...
December 2016: Genomics & Informatics
https://www.readbyqxmd.com/read/28154513/investigation-of-splicing-quantitative-trait-loci-in-arabidopsis-thaliana
#19
Wonseok Yoo, Sungkyu Kyung, Seonggyun Han, Sangsoo Kim
The alteration of alternative splicing patterns has an effect on the quantification of functional proteins, leading to phenotype variation. The splicing quantitative trait locus (sQTL) is one of the main genetic elements affecting splicing patterns. Here, we report the results of genome-wide sQTLs across 141 strains of Arabidopsis thaliana with publicly available next generation sequencing datasets. As a result, we found 1,694 candidate sQTLs in Arabidopsis thaliana at a false discovery rate of 0.01. Furthermore, among the candidate sQTLs, we found 25 sQTLs that overlapped with the list of previously examined trait-associated single nucleotide polymorphisms (SNPs)...
December 2016: Genomics & Informatics
https://www.readbyqxmd.com/read/28154512/interleukin-10-polymorphisms-in-association-with-prognosis-in-patients-with-b-cell-lymphoma-treated-by-r-chop
#20
Min Kyeong Kim, Kyong-Ah Yoon, Eun Young Park, Jungnam Joo, Eun Young Lee, Hyeon-Seok Eom, Sun-Young Kong
Interleukin-10 (IL10) plays an important role in initiating and maintaining an appropriate immune response to non-Hodgkin lymphoma (NHL). Previous studies have revealed that the transcription of IL10 mRNA and its protein expression may be infl uenced by several single-nucleotide polymorphisms in the promoter and intron regions, including rs1800896, rs1800871, and rs1800872. However, the impact of polymorphisms of the IL10 gene on NHL prognosis has not been fully elucidated. Here, we investigated the association between IL10 polymorphisms and NHL prognosis...
December 2016: Genomics & Informatics
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