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International Journal of Genomics

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https://www.readbyqxmd.com/read/28929106/common-expression-quantitative-trait-loci-shared-by-histone-genes
#1
Hanseol Kim, Yujin Suh, Chaeyoung Lee
A genome-wide association study (GWAS) was conducted to examine expression quantitative trait loci (eQTLs) for histone genes. We examined common eQTLs for multiple histone genes in 373 European lymphoblastoid cell lines (LCLs). A linear regression model was employed to identify single-nucleotide polymorphisms (SNPs) associated with expression of the histone genes, and the number of eQTLs was determined by linkage disequilibrium analysis. Additional associations of the identified eQTLs with other genes were also examined...
2017: International Journal of Genomics
https://www.readbyqxmd.com/read/28929105/havec-an-efficient-de-bruijn-graph-construction-algorithm-for-genome-assembly
#2
Md Mahfuzer Rahman, Ratul Sharker, Sajib Biswas, M Sohel Rahman
BACKGROUND: The rapid advancement of sequencing technologies has made it possible to regularly produce millions of high-quality reads from the DNA samples in the sequencing laboratories. To this end, the de Bruijn graph is a popular data structure in the genome assembly literature for efficient representation and processing of data. Due to the number of nodes in a de Bruijn graph, the main barrier here is the memory and runtime. Therefore, this area has received significant attention in contemporary literature...
2017: International Journal of Genomics
https://www.readbyqxmd.com/read/28913347/haplotypes-for-type-degree-and-rate-of-marbling-in-cattle-are-syntenic-with-human-muscular-dystrophy
#3
Sally S Lloyd, Edward J Steele, Jose L Valenzuela, Roger L Dawkins
Traditional analyses of a QTL on Bota 19 implicate a surfeit of candidates, but each is of marginal significance in explaining the deposition of healthy, low melting temperature fat within marbled muscle of Wagyu cattle. As an alternative approach, we have used genomic, multigenerational segregation to identify 14 conserved, ancestral 20 Mb haplotypes. These determine the degree and rate of marbling in Wagyu and other breeds of cattle. The melting temperature of intramuscular fat is highly heritable and traceable by haplotyping...
2017: International Journal of Genomics
https://www.readbyqxmd.com/read/28900619/aquatic-plant-genomics-advances-applications-and-prospects
#4
REVIEW
Shiqi Hu, Gaojie Li, Jingjing Yang, Hongwei Hou
Genomics is a discipline in genetics that studies the genome composition of organisms and the precise structure of genes and their expression and regulation. Genomics research has resolved many problems where other biological methods have failed. Here, we summarize advances in aquatic plant genomics with a focus on molecular markers, the genes related to photosynthesis and stress tolerance, comparative study of genomes and genome/transcriptome sequencing technology.
2017: International Journal of Genomics
https://www.readbyqxmd.com/read/28900618/comparative-genomic-in-situ-hybridization-and-the-possible-role-of-retroelements-in-the-karyotypic-evolution-of-three-akodontini-species
#5
Naiara Pereira Araújo, Gustavo Campos Silva Kuhn, Flávia Nunes Vieira, Thaís Queiroz Morcatty, Adriano Pereira Paglia, Marta Svartman
South American Akodontini rodents are characterized by a large number of chromosome rearrangements. Among them, the genus Akodon has been extensively analyzed with classical and molecular cytogenetics, which allowed the identification of a large number of intra- and interspecific chromosomal variation due to Robertsonian rearrangements, pericentric inversions, and heterochromatin additions/deletions. In order to shed some light on the cause of these rearrangements, we comparatively analyzed the karyotypes of three Akodontini species, Akodon cursor (2n = 14, FN = 19), A...
2017: International Journal of Genomics
https://www.readbyqxmd.com/read/28900617/serum-and-brain-metabolomic-variations-reveal-perturbation-of-sleep-deprivation-on-rats-and-ameliorate-effect-of-total-ginsenoside-treatment
#6
Xiao-Jun Gou, Fang Cen, Zi-Quan Fan, Ying Xu, Hong-Yi Shen, Ming-Mei Zhou
Sleep loss or sleep deprivation (SD) refers to shorter sleep than average baseline need, and SD has been a serious problem of modern societies which affects health and well-being. Panax ginseng is a well-known traditional Chinese medicine (TCM). Our previous study has demonstrated that total ginsenosides (GS), the extracts from Panax ginseng, could effectively improve cognition and behavior on SD rats. However, little is known about its metabolomic study. In this study, serum and brain metabolomic method based on gas chromatography coupled with mass spectrometry (GC/MS) was employed to evaluate the efficacy and study the mechanism of GS on a rat model of SD...
2017: International Journal of Genomics
https://www.readbyqxmd.com/read/28894747/mirna-expression-profile-and-effect-of-wenxin-granule-in-rats-with-ligation-induced-myocardial-infarction
#7
Aiming Wu, Lixia Lou, Jianying Zhai, Dongmei Zhang, Limin Chai, Bo Nie, Haiyan Zhu, Yonghong Gao, Hongcai Shang, Mingjing Zhao
Wenxin Granule (WXKL) is a traditional Chinese medicine used for treatment of myocardial infarction (MI) and arrhythmias. However, the genomic pathological mechanisms of MI and mechanisms of WXKL are largely unknown. This study aims to investigate a comprehensive miRNA expression profile, and the predicted correlation pathways to be targeted by differentially expressed miRNAs in MI, and mechanisms of WXKL from a gene level. MI rat model was established by a coronary artery ligation surgery. miRNA expression microarrays were performed and the data were deposited in Gene Expression Omnibus (GEO number GSE95855)...
2017: International Journal of Genomics
https://www.readbyqxmd.com/read/28890892/microrna-profiling-in-cartilage-ageing
#8
Panagiotis Balaskas, Katarzyna Goljanek-Whysall, Peter Clegg, Yongxiang Fang, Andy Cremers, Pieter Emans, Tim Welting, Mandy Peffers
Osteoarthritis (OA) is the most common age-related joint disorder in man. MicroRNAs (miRNA), a class of small noncoding RNAs, are potential therapeutic targets for regulating molecular mechanisms in both disease and ageing. Whilst there is an increasing amount of research on the roles of miRNAs in ageing, there has been scant research on age-related changes in miRNA in a cartilage. We undertook a microarray study on young and old human cartilages. Findings were validated in an independent cohort. Contrasts between these samples identified twenty differentially expressed miRNAs in a cartilage from old donors, derived from an OA environment which clustered based on OA severity...
2017: International Journal of Genomics
https://www.readbyqxmd.com/read/28884117/the-role-of-mirnas-as-biomarkers-for-pregnancy-outcomes-a-comprehensive-review
#9
REVIEW
Martina Barchitta, Andrea Maugeri, Annalisa Quattrocchi, Ottavia Agrifoglio, Antonella Agodi
Several studies showed that altered expression of the miRNA-ome in maternal circulation or in placental tissue may reflect not only gestational disorders, such as preeclampsia, spontaneous abortion, preterm birth, low birth weight, or macrosomia, but also prenatal exposure to environmental pollutants. Generally, the relationships between environmental exposure, changes in miRNA expression, and gestational disorders are explored separately, producing conflicting findings. However, validation of tissue-accessible biomarkers for the monitoring of adverse pregnancy outcomes needs a systematic methodological approach that takes also into account early-life environmental exposure...
2017: International Journal of Genomics
https://www.readbyqxmd.com/read/28848760/transcriptome-analysis-of-two-different-developmental-stages-of-paeonia-lactiflora-seeds
#10
Yonglei Ma, Jinqiu Cui, Xiujun Lu, Lijie Zhang, Zhijing Chen, Riwen Fei, Xiaomei Sun
Paeonia lactiflora is a herbaceous flower in the family Paeoniaceae with both hypocotyl and epicotyl dormant seeds. We used high-throughput transcriptome sequencing on two different developmental stages of P. lactiflora seeds to identify seed dormancy and germination-related genes. We performed de novo assembly and annotated a total of 123,577 unigenes, which encoded 24,688 putative proteins with 47 GO categories. A total of 10,714 unigenes were annotated in the KEGG database, and 258 pathways were involved in the annotations...
2017: International Journal of Genomics
https://www.readbyqxmd.com/read/28848759/the-promise-of-genomic-studies-on-human-diseases-from-basic-science-to-clinical-application
#11
EDITORIAL
Lam C Tsoi, Bethany Wolf, Y Ann Chen
No abstract text is available yet for this article.
2017: International Journal of Genomics
https://www.readbyqxmd.com/read/28845431/mapping-qtl-for-root-and-shoot-morphological-traits-in-a-durum-wheat%C3%A2-%C3%A3-%C3%A2-t-dicoccum-segregating-population-at-seedling-stage
#12
Anna Iannucci, Daniela Marone, Maria Anna Russo, Pasquale De Vita, Vito Miullo, Pina Ferragonio, Antonio Blanco, Agata Gadaleta, Anna Maria Mastrangelo
A segregating population of 136 recombinant inbred lines derived from a cross between the durum wheat cv. "Simeto" and the T. dicoccum accession "Molise Colli" was grown in soil and evaluated for a number of shoot and root morphological traits. A total of 17 quantitative trait loci (QTL) were identified for shoot dry weight, number of culms, and plant height and for root dry weight, volume, length, surface area, and number of forks and tips, on chromosomes 1B, 2A, 3A, 4B, 5B, 6A, 6B, and 7B. LODs were 2.1 to 21...
2017: International Journal of Genomics
https://www.readbyqxmd.com/read/28840121/a-pilot-genome-wide-association-study-in-postmenopausal-mexican-mestizo-women-implicates-the-rmnd1-ccdc170-locus-is-associated-with-bone-mineral-density
#13
Marisela Villalobos-Comparán, Rogelio F Jiménez-Ortega, Karol Estrada, Alma Y Parra-Torres, Anahí González-Mercado, Nelly Patiño, Manuel Castillejos-López, Manuel Quiterio, Juan Carlos Fernandez-López, Bertha Ibarra, Sandra Romero-Hidalgo, Jorge Salmerón, Rafael Velázquez-Cruz
To identify genetic variants influencing bone mineral density (BMD) in the Mexican-Mestizo population, we performed a GWAS for femoral neck (FN) and lumbar spine (LS) in Mexican-Mestizo postmenopausal women. In the discovery sample, 300,000 SNPs were genotyped in a cohort of 411 postmenopausal women and seven SNPs were analyzed in the replication cohort (n = 420). The combined results of a meta-analysis from the discovery and replication samples identified two loci, RMND1 (rs6904364, P = 2.77 × 10(-4)) and CCDC170 (rs17081341, P = 1...
2017: International Journal of Genomics
https://www.readbyqxmd.com/read/28831389/uncover-the-underlying-mechanism-of-drug-induced-myopathy-by-using-systems-biology-approaches
#14
Dong Li, Aixin Li, Hairui Zhou, Xi Wang, Peng Li, Sheng Bi, Yang Teng
Drug-induced myopathy (DIM) is a rare side effect; however, the consequence could be fatal. There are few reports to systematically assess the underlying mechanism of DIM. In this study, we curated the comprehensive DIM drug list based on structured labeling products (SPLs) and carried out the analysis based on chemical structure space, drug protein interaction, side effect space, and transcriptomic profiling space. Some key features are enriched from each of analysis. Specifically, the similarity of DIM drugs is more significant than random chance, which shows that the chemical structure could distinguish the DIM-positive drugs from negatives...
2017: International Journal of Genomics
https://www.readbyqxmd.com/read/28831388/a-new-network-based-strategy-for-predicting-the-potential-mirna-mrna-interactions-in-tumorigenesis
#15
Jiwei Xue, Fanfan Xie, Junmei Xu, Yuan Liu, Yu Liang, Zhining Wen, Menglong Li
MicroRNA (miRNA) plays an important role in the degradation and inhibition of mRNAs and is a kind of essential drug targets for cancer therapy. To facilitate the clinical cancer research, we proposed a network-based strategy to identify the cancer-related miRNAs and to predict their targeted genes based on the gene expression profiles. The strategy was validated by using the data sets of acute myeloid leukemia (AML), breast invasive carcinoma (BRCA), and kidney renal clear cell carcinoma (KIRC). The results showed that in the top 20 miRNAs ranked by their degrees, 90...
2017: International Journal of Genomics
https://www.readbyqxmd.com/read/28808654/genome-wide-identification-and-transcriptional-expression-analysis-of-cucumber-superoxide-dismutase-sod-family-in-response-to-various-abiotic-stresses
#16
Yong Zhou, Lifang Hu, Hao Wu, Lunwei Jiang, Shiqiang Liu
Superoxide dismutase (SOD) proteins are widely present in the plant kingdom and play important roles in different biological processes. However, little is known about the SOD genes in cucumber. In this study, night SOD genes were identified from cucumber (Cucumis sativus) using bioinformatics-based methods, including 5 Cu/ZnSODs, 3 FeSODs, and 1 MnSOD. Gene structure and motif analysis indicated that most of the SOD genes have relatively conserved exon/intron arrangement and motif composition. Phylogenetic analyses with SODs from cucumber and several other species revealed that these SOD proteins can be traced back to two ancestral SODs before the divergence of monocot and dicot plants...
2017: International Journal of Genomics
https://www.readbyqxmd.com/read/28791299/differential-microrna-analyses-of-burkholderia-pseudomallei-and-francisella-tularensis-exposed-hpbmcs-reveal-potential-biomarkers
#17
Regina Z Cer, J Enrique Herrera-Galeano, Kenneth G Frey, Kevin L Schully, Truong V Luu, John Pesce, Vishwesh P Mokashi, Andrea M Keane-Myers, Kimberly A Bishop-Lilly
Increasing evidence that microRNAs (miRNAs) play important roles in the immune response against infectious agents suggests that miRNA might be exploitable as signatures of exposure to specific infectious agents. In order to identify potential early miRNA biomarkers of bacterial infections, human peripheral blood mononuclear cells (hPBMCs) were exposed to two select agents, Burkholderia pseudomallei K96243 and Francisella tularensis SHU S4, as well as to the nonpathogenic control Escherichia coli DH5α. RNA samples were harvested at three early time points, 30, 60, and 120 minutes postexposure, then sequenced...
2017: International Journal of Genomics
https://www.readbyqxmd.com/read/28770220/transcriptome-based-modeling-reveals-that-oxidative-stress-induces-modulation-of-the-atfa-dependent-signaling-networks-in-aspergillus-nidulans
#18
Erzsébet Orosz, Károly Antal, Zoltán Gazdag, Zsuzsa Szabó, Kap-Hoon Han, Jae-Hyuk Yu, István Pócsi, Tamás Emri
To better understand the molecular functions of the master stress-response regulator AtfA in Aspergillus nidulans, transcriptomic analyses of the atfA null mutant and the appropriate control strains exposed to menadione sodium bisulfite- (MSB-), t-butylhydroperoxide- and diamide-induced oxidative stresses were performed. Several elements of oxidative stress response were differentially expressed. Many of them, including the downregulation of the mitotic cell cycle, as the MSB stress-specific upregulation of FeS cluster assembly and the MSB stress-specific downregulation of nitrate reduction, tricarboxylic acid cycle, and ER to Golgi vesicle-mediated transport, showed AtfA dependence...
2017: International Journal of Genomics
https://www.readbyqxmd.com/read/28758108/blood-transcriptional-signatures-for-disease-progression-in-a-rat-model-of-osteoarthritis
#19
Michał Korostyński, Natalia Małek, Marcin Piechota, Katarzyna Starowicz
Biomarkers of osteoarthritis (OA) that can accurately diagnose the disease at the earliest stage would significantly support efforts to develop treatments for prevention and early intervention. We have sought to determine the time course of alterations in peripheral blood gene expression profile associated with the development of OA. Blood samples were collected from a tail vein of individual rats with monosodium iodoacetate- (MIA-) induced OA (2, 14, 21, and 28 days after the treatment). We used whole-genome microarrays to reveal OA-related transcriptional alterations of 72 transcripts...
2017: International Journal of Genomics
https://www.readbyqxmd.com/read/28713819/differential-analysis-of-genetic-epigenetic-and-cytogenetic-abnormalities-in-aml
#20
Mirazul Islam, Zahurin Mohamed, Yassen Assenov
Acute myeloid leukemia (AML) is a haematological malignancy characterized by the excessive proliferation of immature myeloid cells coupled with impaired differentiation. Many AML cases have been reported without any known cytogenetic abnormalities and carry no mutation in known AML-associated driver genes. In this study, 200 AML cases were selected from a publicly available cohort and differentially analyzed for genetic, epigenetic, and cytogenetic abnormalities. Three genes (FLT3, DNMT3A, and NPMc) are found to be predominantly mutated...
2017: International Journal of Genomics
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