journal
MENU ▼
Read by QxMD icon Read
search

International Journal of Genomics

journal
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
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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
#9
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
#10
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
#11
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
#12
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
#13
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
#14
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
#15
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
https://www.readbyqxmd.com/read/28265565/the-draft-genome-and-transcriptome-of-the-atlantic-horseshoe-crab-limulus-polyphemus
#16
Stephen D Simpson, Jordan S Ramsdell, Winsor H Watson Iii, Christopher C Chabot
The horseshoe crab, Limulus polyphemus, exhibits robust circadian and circatidal rhythms, but little is known about the molecular mechanisms underlying those rhythms. In this study, horseshoe crabs were collected during the day and night as well as high and low tides, and their muscle and central nervous system tissues were processed for genome and transcriptome sequencing, respectively. The genome assembly resulted in 7.4 × 10(5) contigs with N50 of 4,736, while the transcriptome assembly resulted in 9.3 × 10(4) contigs and N50 of 3,497...
2017: International Journal of Genomics
https://www.readbyqxmd.com/read/28265564/the-numerical-predominance-and-large-transcriptome-differences-of-neutrophils-in-peripheral-blood-together-inevitably-account-for-a-reported-pulmonary-tuberculosis-signature
#17
Kang Wu, Ka-Wing Wong, Wang-Long Deng, Hao Zhang, Jing Li, Douglas B Lowrie, Xiao-Yong Fan
Previous transcriptomic analysis revealed a 393-transcript signature (PTBsig), which is dominated by interferon inducible genes, in whole blood of pulmonary tuberculosis (PTB) patients. Comparisons with a limited set of interferon-driven genes among separated monocytes, CD4+ T cells, CD8+ T cells, and neutrophils indicated that the signature is due to changes in neutrophils, the overwhelmingly predominant cell type. By extending the analysis to the entire 393 transcripts of PTBsig and by switching the cell proportions between separated monocytes, CD4+ T cells, CD8+ T cells, and neutrophils, we create putative PTBsig for whole blood (pPTBsig) in which CD4+ or CD8+ T cells or monocytes predominated or in which the cell proportions were unchanged...
2017: International Journal of Genomics
https://www.readbyqxmd.com/read/28265563/characteristics-and-validation-techniques-for-pca-based-gene-expression-signatures
#18
Anders E Berglund, Eric A Welsh, Steven A Eschrich
Background. Many gene-expression signatures exist for describing the biological state of profiled tumors. Principal Component Analysis (PCA) can be used to summarize a gene signature into a single score. Our hypothesis is that gene signatures can be validated when applied to new datasets, using inherent properties of PCA. Results. This validation is based on four key concepts. Coherence: elements of a gene signature should be correlated beyond chance. UNIQUENESS: the general direction of the data being examined can drive most of the observed signal...
2017: International Journal of Genomics
https://www.readbyqxmd.com/read/28261603/genetic-diversity-and-association-analysis-for-solvent-retention-capacity-in-the-accessions-derived-from-soft-wheat-ningmai-9
#19
Peng Jiang, Ping-Ping Zhang, Xu Zhang, Hong-Xiang Ma
Solvent retention capacity (SRC) test is an effective method for quality evaluation of soft wheat. Ningmai 9 is a founder in soft wheat breeding. The SRC and genotype of Ningmai 9 and its 117 derivatives were tested. Association mapping was employed to identify the quantitative trait loci (QTL) associated with SRCs. Ningmai 9 had the allele frequency of 75.60% and 67.81% to its first- and second-generation derivatives, respectively, indicating higher contribution than theoretical expectation. Neighbor-joining cluster based on the genotyping data showed that Ningmai 9 and most of its first-generation derivatives were clustered together, whereas its second-generation derivatives were found in another group...
2017: International Journal of Genomics
https://www.readbyqxmd.com/read/28246590/the-utilization-of-formalin-fixed-paraffin-embedded-specimens-in-high-throughput-genomic-studies
#20
REVIEW
Pan Zhang, Brian D Lehmann, Yu Shyr, Yan Guo
High throughput genomic assays empower us to study the entire human genome in short time with reasonable cost. Formalin fixed-paraffin-embedded (FFPE) tissue processing remains the most economical approach for longitudinal tissue specimen storage. Therefore, the ability to apply high throughput genomic applications to FFPE specimens can expand clinical assays and discovery. Many studies have measured the accuracy and repeatability of data generated from FFPE specimens using high throughput genomic assays. Together, these studies demonstrate feasibility and provide crucial guidance for future studies using FFPE specimens...
2017: International Journal of Genomics
journal
journal
47642
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"