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International Journal of Genomics

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https://www.readbyqxmd.com/read/28630856/chimeric-genes-in-deletions-and-duplications-associated-with-intellectual-disability
#1
Sonia Mayo, Sandra Monfort, Mónica Roselló, Carmen Orellana, Silvestre Oltra, Alfonso Caro-Llopis, Francisco Martínez
We report on three nonrelated patients with intellectual disability and CNVs that give rise to three new chimeric genes. All the genes forming these fusion transcripts may have an important role in central nervous system development and/or in gene expression regulation, and therefore not only their deletion or duplication but also the resulting chimeric gene may contribute to the phenotype of the patients. Deletions and duplications are usually pathogenic when affecting dose-sensitive genes. Alternatively, a chimeric gene may also be pathogenic by different gain-of-function mechanisms that are not restricted to dose-sensitive genes: the emergence of a new polypeptide that combines functional domains from two different genes, the deregulated expression of any coding sequence by the promoter region of a neighboring gene, and/or a putative dominant-negative effect due to the preservation of functional domains of partially truncated proteins...
2017: International Journal of Genomics
https://www.readbyqxmd.com/read/28620613/evidence-of-divergent-amino-acid-usage-in-comparative-analyses-of-r5-and-x4-associated-hiv-1-vpr-sequences
#2
Gregory C Antell, Will Dampier, Benjamas Aiamkitsumrit, Michael R Nonnemacher, Vanessa Pirrone, Wen Zhong, Katherine Kercher, Shendra Passic, Jean Williams, Yucheng Liu, Tony James, Jeffrey M Jacobson, Zsofia Szep, Brian Wigdahl, Fred C Krebs
Vpr is an HIV-1 accessory protein that plays numerous roles during viral replication, and some of which are cell type dependent. To test the hypothesis that HIV-1 tropism extends beyond the envelope into the vpr gene, studies were performed to identify the associations between coreceptor usage and Vpr variation in HIV-1-infected patients. Colinear HIV-1 Env-V3 and Vpr amino acid sequences were obtained from the LANL HIV-1 sequence database and from well-suppressed patients in the Drexel/Temple Medicine CNS AIDS Research and Eradication Study (CARES) Cohort...
2017: International Journal of Genomics
https://www.readbyqxmd.com/read/28567415/neurodevelopmental-disorders-and-environmental-toxicants-epigenetics-as-an-underlying-mechanism
#3
REVIEW
Nguyen Quoc Vuong Tran, Kunio Miyake
The increasing prevalence of neurodevelopmental disorders, especially autism spectrum disorders (ASD) and attention deficit hyperactivity disorder (ADHD), calls for more research into the identification of etiologic and risk factors. The Developmental Origin of Health and Disease (DOHaD) hypothesizes that the environment during fetal and childhood development affects the risk for many chronic diseases in later stages of life, including neurodevelopmental disorders. Epigenetics, a term describing mechanisms that cause changes in the chromosome state without affecting DNA sequences, is suggested to be the underlying mechanism, according to the DOHaD hypothesis...
2017: International Journal of Genomics
https://www.readbyqxmd.com/read/28555190/evolution-of-the-apicomplexan-sugar-transporter-gene-family-repertoire
#4
Ousman Mahmud, Jessica C Kissinger
Apicomplexan protist parasites utilize host sugars transported into the parasite by sugar transporter proteins for use as an energy source. We performed a phylum-wide phylogenetic analysis of the apicomplexan sugar transporter repertoire. Phylogenetic analyses revealed six major subfamilies of apicomplexan sugar transporters. Transporters in one subfamily have undergone expansions in Piroplasma species and Gregarina niphandrodes, while other subfamilies are highly divergent and contain genes found in only one or two species...
2017: International Journal of Genomics
https://www.readbyqxmd.com/read/28553643/comparative-transcriptome-analyses-of-resistant-and-susceptible-near-isogenic-wheat-lines-following-inoculation-with-blumeria-graminis-f-sp-tritici
#5
Piyi Xing, Xueying Zhang, Yinguang Bao, Yuhai Wang, Honggang Wang, Xingfeng Li
Powdery mildew is one of the most important diseases of wheat. In this study, the leaf RNA samples of wheat NILs carrying powdery mildew resistant and susceptible Pm2 alleles (L031 and Chancellor) and its F1 hybrid at two time points (16 h and 96 h postinoculation) were used for RNA-seq analysis. We carry comparison between similar materials at different times and between different materials at same times. The overlapping DEGs between the dominant phenotypes (L031 and F1 hybrid) and the recessive phenotype (Chancellor) were 1028 and 2214 DEGs, which were clearly lower than those between the dominant and recessive parents and thus could provide relatively accurate and valuable information...
2017: International Journal of Genomics
https://www.readbyqxmd.com/read/28487862/naturally-occurring-canine-invasive-urinary-bladder-cancer-a-complementary-animal-model-to-improve-the-success-rate-in-human-clinical-trials-of-new-cancer-drugs
#6
REVIEW
Christopher M Fulkerson, Deepika Dhawan, Timothy L Ratliff, Noah M Hahn, Deborah W Knapp
Genomic analyses are defining numerous new targets for cancer therapy. Therapies aimed at specific genetic and epigenetic targets in cancer cells as well as expanded development of immunotherapies are placing increased demands on animal models. Traditional experimental models do not possess the collective features (cancer heterogeneity, molecular complexity, invasion, metastasis, and immune cell response) critical to predict success or failure of emerging therapies in humans. There is growing evidence, however, that dogs with specific forms of naturally occurring cancer can serve as highly relevant animal models to complement traditional models...
2017: International Journal of Genomics
https://www.readbyqxmd.com/read/28487861/genome-wide-identification-of-bzip-family-genes-involved-in-drought-and-heat-stresses-in-strawberry-fragaria-vesca
#7
Xiao-Long Wang, Xinlu Chen, Tian-Bao Yang, Qunkang Cheng, Zong-Ming Cheng
Basic leucine zipper (bZIP) genes are known to play a crucial role in response to various processes in plant as well as abiotic or biotic stress challenges. We have performed an identification and characterization of 50 bZIP genes across the woodland strawberry (Fragaria vesca) genome, which were divided into 10 clades according to the phylogenetic relationship of the strawberry bZIP proteins with those in Arabidopsis and rice. Five categories of intron patterns were observed within basic and hinge regions of the bZIP domains...
2017: International Journal of Genomics
https://www.readbyqxmd.com/read/28487860/chromosome-1-sequence-analysis-of-c57bl-6j-chr1-km-mouse-strain
#8
Fuyi Xu, Tianzhu Chao, Yiyin Zhang, Shixian Hu, Yuxun Zhou, Hongyan Xu, Junhua Xiao, Kai Li
The Chinese Kunming (KM) mouse is a widely used outbred mouse stock in China. However, its genetic structure remains unclear. In this study, we sequenced the genome of the C57BL/6J-Chr1(KM) (B6-Chr1(KM)) strain, the chromosome 1 (Chr 1) of which was derived from one KM mouse. With 36.6× average coverage of the entire genome, 0.48 million single nucleotide polymorphisms (SNPs) and 96,679 indels were detected on Chr 1 through comparison with reference strain C57BL/6J. Moreover, 46,590 of them were classified as novel mutations...
2017: International Journal of Genomics
https://www.readbyqxmd.com/read/28480217/an-integrating-approach-for-genome-wide-screening-of-microrna-polymorphisms-mediated-drug-response-alterations
#9
Xianyue Wang, Hong Jiang, Wei Wu, Rongxin Zhang, Lingxiang Wu, Huan Chen, Pengping Li, Yumin Nie, Jiaofang Shao, Yan Li, Xue Lin, Sali Lv, Qh Wang, Jie Hu
MicroRNAs (miRNAs) are a class of evolutionarily conserved small noncoding RNAs, ~22 nt in length, and found in diverse organisms and play important roles in the regulation of mRNA translation and degradation. It was shown that miRNAs were involved in many key biological processes through regulating the expression of targets. Genetic polymorphisms in miRNA target sites may alter miRNA regulation and therefore result in the alterations of the drug targets. Recent studies have demonstrated that SNPs in miRNA target sites can affect drug efficiency...
2017: International Journal of Genomics
https://www.readbyqxmd.com/read/28470009/transcriptome-analysis-of-orange-head-chinese-cabbage-brassica-rapa-l-ssp-pekinensis-and-molecular-marker-development
#10
Jingjuan Li, Yihui Zhang, Qian Ding, Huayin Li, Lifeng Liu, Fengde Wang, Jianwei Gao
Due to the visual appearance and high carotenoid content, orange inner leaves are a desirable trait for the Chinese cabbage. To understand the molecular mechanism underlying the formation of orange inner leaves, the BrCRTISO (Bra031539) gene, as the Br-or candidate gene, was analyzed among the white and orange varieties, and 7 single nucleotide polymorphisms (SNPs) were identified. However, only one SNP (C(952) to T(952)) altered the amino acid sequence, resulting in a mutation from Leu(318) to Phe(318) in the orange varieties...
2017: International Journal of Genomics
https://www.readbyqxmd.com/read/28459054/application-of-genomic-in-situ-hybridization-in-horticultural-science
#11
REVIEW
Fahad Ramzan, Adnan Younis, Ki-Byung Lim
Molecular cytogenetic techniques, such as in situ hybridization methods, are admirable tools to analyze the genomic structure and function, chromosome constituents, recombination patterns, alien gene introgression, genome evolution, aneuploidy, and polyploidy and also genome constitution visualization and chromosome discrimination from different genomes in allopolyploids of various horticultural crops. Using GISH advancement as multicolor detection is a significant approach to analyze the small and numerous chromosomes in fruit species, for example, Diospyros hybrids...
2017: International Journal of Genomics
https://www.readbyqxmd.com/read/28409151/temporal-changes-in-gene-expression-profile-during-mature-adipocyte-dedifferentiation
#12
Julie Anne Côté, Frédéric Guénard, Julie Lessard, Marc Lapointe, Simon Biron, Marie-Claude Vohl, André Tchernof
Objective. To characterize changes in gene expression profile during human mature adipocyte dedifferentiation in ceiling culture. Methods. Subcutaneous (SC) and omental (OM) adipose tissue samples were obtained from 4 participants paired for age and BMI. Isolated adipocytes were dedifferentiated in ceiling culture. Gene expression analysis at days 0, 4, 7, and 12 of the cultures was performed using Affymetrix Human Gene 2.0 STvi arrays. Hierarchical clustering according to similarity of expression changes was used to identify overrepresented functions...
2017: International Journal of Genomics
https://www.readbyqxmd.com/read/28367438/the-promise-of-agriculture-genomics
#13
EDITORIAL
Wenqin Wang, Xuan H Cao, Mihai Miclăuș, Jianhong Xu, Wenwei Xiong
No abstract text is available yet for this article.
2017: International Journal of Genomics
https://www.readbyqxmd.com/read/28352639/racial-differences-in-expression-levels-of-mirna-machinery-related-genes-dicer-drosha-dgcr8-and-ago2-in-asian-korean-papillary-thyroid-carcinoma-and-comparative-validation-using-the-cancer-genome-atlas
#14
Jaegil Kim, Woo-Jae Park, Kwang-Joon Jeong, Sun Hee Kang, Sun Young Kwon, Shin Kim, Jong-Wook Park
Aberrant regulation of microRNA (miRNA) machinery components is associated with various human cancers, including papillary thyroid carcinoma (PTC), which is the most common type of thyroid cancer, and a higher prevalent female malignancy. The purpose of this study is to investigate racial differences in mRNA expression levels of four miRNA machinery components, Dicer, Drosha, DGCR8, and AGO2, and their correlations with clinicopathological characteristics. Forty PTC samples from female Asian Korean PTC patients were enrolled...
2017: International Journal of Genomics
https://www.readbyqxmd.com/read/28331849/a-review-of-recent-advancement-in-integrating-omics-data-with-literature-mining-towards-biomedical-discoveries
#15
REVIEW
Kalpana Raja, Matthew Patrick, Yilin Gao, Desmond Madu, Yuyang Yang, Lam C Tsoi
In the past decade, the volume of "omics" data generated by the different high-throughput technologies has expanded exponentially. The managing, storing, and analyzing of this big data have been a great challenge for the researchers, especially when moving towards the goal of generating testable data-driven hypotheses, which has been the promise of the high-throughput experimental techniques. Different bioinformatics approaches have been developed to streamline the downstream analyzes by providing independent information to interpret and provide biological inference...
2017: International Journal of Genomics
https://www.readbyqxmd.com/read/28326315/genomewide-expression-and-functional-interactions-of-genes-under-drought-stress-in-maize
#16
Nepolean Thirunavukkarasu, Rinku Sharma, Nidhi Singh, Kaliyugam Shiriga, Sweta Mohan, Swati Mittal, Shikha Mittal, Mallana Gowdra Mallikarjuna, Atmakuri Ramakrishna Rao, Prasanta Kumar Dash, Firoz Hossain, Hari Shanker Gupta
A genomewide transcriptome assay of two subtropical genotypes of maize was used to observe the expression of genes at seedling stage of drought stress. The number of genes expressed differentially was greater in HKI1532 (a drought tolerant genotype) than in PC3 (a drought sensitive genotype), indicating primary differences at the transcriptional level in stress tolerance. The global coexpression networks of the two genotypes differed significantly with respect to the number of modules and the coexpression pattern within the modules...
2017: International Journal of Genomics
https://www.readbyqxmd.com/read/28326314/case-study-of-somaclonal-variation-in-resistance-genes-mlo-and-pme3-in-flaxseed-linum-usitatissimum-l-induced-by-nanoparticles
#17
Inese Kokina, Ilona Mickeviča, Marija Jermaļonoka, Linda Bankovska, Vjačeslavs Gerbreders, Andrejs Ogurcovs, Inese Jahundoviča
Nanoparticles influence on genome is investigated worldwide. The appearance of somaclonal variation is a cause of great concern for any micropropagation system. Somaclonal variation describes the tissue-culture-induced phenotypic and genotypic variations. This paper shows the results of somaclonal variation in two resistance genes pectin methylesterase and Mlo-like protein in all tissue culture development stages, as donor plant, calluses, and regenerants of Linum usitatissimum induced by gold and silver nanoparticles...
2017: International Journal of Genomics
https://www.readbyqxmd.com/read/28316974/exploration-of-nitrate-reductase-metabolic-pathway-in-corynebacterium-pseudotuberculosis
#18
Sintia Almeida, Cassiana Sousa, Vinícius Abreu, Carlos Diniz, Elaine M S Dorneles, Andrey P Lage, Debmalya Barh, Vasco Azevedo
Based on the ability of nitrate reductase synthesis, Corynebacterium pseudotuberculosis is classified into two biovars: Ovis and Equi. Due to the presence of nitrate reductase, the Equi biovar can survive in absence of oxygen. On the other hand, Ovis biovar that does not have nitrate reductase is able to adapt to various ecological niches and can grow on certain carbon sources. Apart from these two biovars, some other strains are also able to carry out the reduction of nitrate. The enzymes that are involved in electron transport chain are also identified by in silico methods...
2017: International Journal of Genomics
https://www.readbyqxmd.com/read/28280724/integrating-biological-covariates-into-gene-expression-based-predictors-of-radiation-sensitivity
#19
Vidya P Kamath, Javier F Torres-Roca, Steven A Eschrich
The use of gene expression-based classifiers has resulted in a number of promising potential signatures of patient diagnosis, prognosis, and response to therapy. However, these approaches have also created difficulties in trying to use gene expression alone to predict a complex trait. A practical approach to this problem is to integrate existing biological knowledge with gene expression to build a composite predictor. We studied the problem of predicting radiation sensitivity within human cancer cell lines from gene expression...
2017: International Journal of Genomics
https://www.readbyqxmd.com/read/28265566/whole-genome-characteristics-and-polymorphic-analysis-of-vietnamese-rice-landraces-as-a-comprehensive-information-resource-for-marker-assisted-selection
#20
Hien Trinh, Khoa Truong Nguyen, Lam Van Nguyen, Huy Quang Pham, Can Thu Huong, Tran Dang Xuan, La Hoang Anh, Mario Caccamo, Sarah Ayling, Nguyen Thuy Diep, Cuong Nguyen, Khuat Huu Trung, Tran Dang Khanh
Next generation sequencing technologies have provided numerous opportunities for application in the study of whole plant genomes. In this study, we present the sequencing and bioinformatic analyses of five typical rice landraces including three indica and two japonica with potential blast resistance. A total of 688.4 million 100 bp paired-end reads have yielded approximately 30-fold coverage to compare with the Nipponbare reference genome. Among them, a small number of reads were mapped to both chromosomes and organellar genomes...
2017: International Journal of Genomics
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