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International Journal of Genomics

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https://www.readbyqxmd.com/read/30211214/whole-exome-sequencing-uncovers-germline-variants-of-cancer-related-genes-in-sporadic-pheochromocytoma
#1
Milena Urbini, Margherita Nannini, Annalisa Astolfi, Valentina Indio, Valentina Vicennati, Matilde De Luca, Giuseppe Tarantino, Federica Corso, Maristella Saponara, Lidia Gatto, Donatella Santini, Guido Di Dalmazi, Uberto Pagotto, Renato Pasquali, Andrea Pession, Guido Biasco, Maria A Pantaleo
Background: Pheochromocytomas (PCCs) show the highest degree of heritability in human neoplasms. However, despite the wide number of alterations until now reported in PCCs, it is likely that other susceptibility genes remain still unknown, especially for those PCCs not clearly syndromic. Methods: Whole exome sequencing of tumor DNA was performed on a set of twelve PCCs clinically defined as sporadic. Results: About 50% of PCCs examined had somatic mutations on the known susceptibility VHL , NF1 , and RET genes...
2018: International Journal of Genomics
https://www.readbyqxmd.com/read/30211213/metagenomic-approaches-for-understanding-new-concepts-in-microbial-science
#2
REVIEW
Luana de Fátima Alves, Cauã Antunes Westmann, Gabriel Lencioni Lovate, Guilherme Marcelino Viana de Siqueira, Tiago Cabral Borelli, María-Eugenia Guazzaroni
Over the past thirty years, since the dawn of metagenomic studies, a completely new (micro) universe was revealed, with the potential to have profound impacts on many aspects of the society. Remarkably, the study of human microbiome provided a new perspective on a myriad of human traits previously regarded as solely (epi-) genetically encoded, such as disease susceptibility, immunological response, and social and nutritional behaviors. In this context, metagenomics has established a powerful framework for understanding the intricate connections between human societies and microbial communities, ultimately allowing for the optimization of both human health and productivity...
2018: International Journal of Genomics
https://www.readbyqxmd.com/read/30159320/meta-analysis-of-genome-wide-association-studies-identifies-novel-functional-cpg-snps-associated-with-bone-mineral-density-at-lumbar-spine
#3
Chuan Qiu, Hui Shen, Xiaoying Fu, Chao Xu, Hongwen Deng
Osteoporosis is a serious public health issue, which is mostly characterized by low bone mineral density (BMD). To search for additional genetic susceptibility loci underlying BMD variation, an effective strategy is to focus on testing of specific variants with high potential of functional effects. Single nucleotide polymorphisms (SNPs) that introduce or disrupt CpG dinucleotides (CpG-SNPs) may alter DNA methylation levels and thus represent strong candidate functional variants. Here, we performed a targeted GWAS for 63,627 potential functional CpG-SNPs that may affect DNA methylation in bone-related cells, in five independent cohorts ( n = 5905)...
2018: International Journal of Genomics
https://www.readbyqxmd.com/read/30155473/protein-engineering-strategies-to-expand-crispr-cas9-applications
#4
REVIEW
Lucas F Ribeiro, Liliane F C Ribeiro, Matheus Q Barreto, Richard J Ward
The development of precise and modulated methods for customized manipulation of DNA is an important objective for the study and engineering of biological processes and is essential for the optimization of gene therapy, metabolic flux, and synthetic gene networks. The clustered regularly interspaced short palindromic repeat- (CRISPR-) associated protein 9 is an RNA-guided site-specific DNA-binding complex that can be reprogrammed to specifically interact with a desired DNA sequence target. CRISPR-Cas9 has been used in a wide variety of applications ranging from basic science to the clinic, such as gene therapy, gene regulation, modifying epigenomes, and imaging chromosomes...
2018: International Journal of Genomics
https://www.readbyqxmd.com/read/30148158/the-effect-of-citalopram-on-genome-wide-dna-methylation-of-human-cells
#5
Riya R Kanherkar, Bruk Getachew, Joseph Ben-Sheetrit, Sudhir Varma, Thomas Heinbockel, Yousef Tizabi, Antonei B Csoka
Commonly used pharmaceutical drugs might alter the epigenetic state of cells, leading to varying degrees of long-term repercussions to human health. To test this hypothesis, we cultured HEK-293 cells in the presence of 50  μ M citalopram, a common antidepressant, for 30 days and performed whole-genome DNA methylation analysis using the NimbleGen Human DNA Methylation 3x720K Promoter Plus CpG Island Array. A total of 626 gene promoters, out of a total of 25,437 queried genes on the array (2.46%), showed significant differential methylation ( p < 0...
2018: International Journal of Genomics
https://www.readbyqxmd.com/read/30116731/discovery-of-novel-caeridins-from-the-skin-secretion-of-the-australian-white-s-tree-frog-litoria-caerulea
#6
Lei Li, Qing Wu, Xi Wang, Huimin Lu, Xinping Xi, Mei Zhou, Chris J Watson, Tianbao Chen, Lei Wang
Abundant biologically active peptides have been discovered from frog skin secretions, a rich natural source of bioactive compounds with great potential in drug discovery. In this study, three Caeridin peptides, namely, Caeridin-1, S5-Caeridin-1, and Caeridin-a1, were discovered from the skin secretion of the Australian White's tree frog, Litoria caerulea , for the first time, by means of combining transcriptomic and peptidomic analyses. It also represents the first report on bioactive Caeridins since this family of peptides was initially studied 20 years ago...
2018: International Journal of Genomics
https://www.readbyqxmd.com/read/30116730/detecting-differentially-variable-micrornas-via-model-based-clustering
#7
Xuan Li, Yuejiao Fu, Xiaogang Wang, Dawn L DeMeo, Kelan Tantisira, Scott T Weiss, Weiliang Qiu
Identifying differentially variable (DV) genomic probes is becoming a new approach to detect novel genomic risk factors for complex human diseases. The F test is the standard equal-variance test in statistics. For high-throughput genomic data, the probe-wise F test has been successfully used to detect biologically relevant DNA methylation marks that have different variances between two groups of subjects (e.g., cases versus controls). In addition to DNA methylation, microRNA (miRNA) is another important mechanism of epigenetics...
2018: International Journal of Genomics
https://www.readbyqxmd.com/read/30116729/exploring-long-noncoding-rnas-in-glioblastoma-regulatory-mechanisms-and-clinical-potentials
#8
REVIEW
Tao Zeng, Lei Li, Yan Zhou, Liang Gao
Gliomas are primary brain tumors presumably derived from glial cells. The WHO grade IV glioblastoma (GBM), characterized by rapid cell proliferation, easily recrudescent, high morbidity, and mortality, is the most common, devastating, and lethal gliomas. Molecular mechanisms underlying the pathogenesis and progression of GBMs with potential diagnostic and therapeutic value have been explored industriously. With the advent of high-throughput technologies, numerous long noncoding RNAs (lncRNAs) aberrantly expressed in GBMs were discovered recently, some of them probably involved in GBM initiation, malignant progression, relapse and resistant to therapy, or showing diagnostic and prognostic value...
2018: International Journal of Genomics
https://www.readbyqxmd.com/read/30057905/expanding-the-mirna-transcriptome-of-human-kidney-and-renal-cell-carcinoma
#9
Adam P Sage, Brenda C Minatel, Erin A Marshall, Victor D Martinez, Greg L Stewart, Katey S S Enfield, Wan L Lam
Despite advancements in therapeutic strategies, diagnostic and prognostic molecular markers of kidney cancer remain scarce, particularly in patients who do not harbour well-defined driver mutations. Recent evidence suggests that a large proportion of the human noncoding transcriptome has escaped detection in early genomic explorations. Here, we undertake a large-scale analysis of small RNA-sequencing data from both clear cell renal cell carcinoma (ccRCC) and nonmalignant samples to generate a robust set of miRNAs that remain unannotated in kidney tissues...
2018: International Journal of Genomics
https://www.readbyqxmd.com/read/30057904/identification-of-novel-arsa-mutations-in-chinese-patients-with-metachromatic-leukodystrophy
#10
Li Chen, Huifang Yan, Binbin Cao, Ye Wu, Qiang Gu, Jiangxi Xiao, Yanling Yang, Huixia Yang, Zhen Shi, Zhixian Yang, Hong Pan, Xingzhi Chang, Junya Chen, Yu Sun, Yuehua Zhang, Xiru Wu, Yuwu Jiang, Jingmin Wang
Objective: Metachromatic leukodystrophy (MLD) is an inherited disease caused by a deficiency of the enzyme arylsulfatase A (ARSA) that leads to severe physiologic and developmental problems. Our study is aimed at elucidating the clinical and genetic characteristics of Chinese MLD patients. Methods: Clinical data of 21 MLD patients was collected. All coding exons of ARSA and their flanking intronic sequences were amplified by polymerase chain reaction and subjected to direct sequencing...
2018: International Journal of Genomics
https://www.readbyqxmd.com/read/30046585/cerebellar-lncrna-expression-profile-analysis-of-sca3-mjd-mice
#11
Zhe Long, Tianjiao Li, Zhao Chen, Yun Peng, Chunrong Wang, Xiaocan Hou, Hongyu Yuan, Puzhi Wang, Yue Xie, Lang He, Xin Zhou, Huirong Peng, Rong Qiu, Kun Xia, Beisha Tang, Hong Jiang
Spinocerebellar ataxia type 3 (SCA3) or Machado-Joseph disease (MJD) is the most common autosomal dominant spinocerebellar ataxia in China with highly clinical heterogeneity, such as progressive cerebellar ataxia, dysarthria, pyramidal signs, external ophthalmoplegia, dysphagia, and distal muscle atrophy. It is caused by the abnormal expansion of CAG repeats in a coding region of ATXN3 . However, by focusing on the ATXN3 itself cannot fully explain the heterogeneous clinical features of SCA3/MJD. With the discovery of the increasing number of long noncoding RNAs (lncRNAs) that are believed to be involved in spinocerebellar ataxia type 8 (SCA8) and Huntington disease (HD), we wonder whether the lncRNAs are differentially expressed in the SCA3/MJD patients compared to the nonpatients...
2018: International Journal of Genomics
https://www.readbyqxmd.com/read/30027094/expression-analysis-of-nitrogen-metabolism-related-genes-reveals-differences-in-adaptation-to-low-nitrogen-stress-between-two-different-barley-cultivars-at-seedling-stage
#12
Zhiwei Chen, Chenghong Liu, Yifei Wang, Ting He, Runhong Gao, Hongwei Xu, Guimei Guo, Yingbo Li, Longhua Zhou, Ruiju Lu, Jianhua Huang
The excess use of nitrogen fertilizers causes many problems, including higher costs of crop production, lower nitrogen use efficiency, and environmental damage. Crop breeding for low-nitrogen tolerance, especially molecular breeding, has become the major route to solving these issues. Therefore, in crops such as barley ( Hordeum vulgare L.), it is crucial to understand the mechanisms of low-nitrogen tolerance at the molecule level. In the present study, two barley cultivars, BI-04 (tolerant to low nitrogen) and BI-45 (sensitive to low nitrogen), were used for gene expression analysis under low-nitrogen stress, including 10 genes related to primary nitrogen metabolism...
2018: International Journal of Genomics
https://www.readbyqxmd.com/read/30009162/topological-characterization-of-human-and-mouse-m-5-c-epitranscriptome-revealed-by-bisulfite-sequencing
#13
Zhen Wei, Subbarayalu Panneerdoss, Santosh Timilsina, Jingting Zhu, Tabrez A Mohammad, Zhi-Liang Lu, João Pedro de Magalhães, Yidong Chen, Rong Rong, Yufei Huang, Manjeet K Rao, Jia Meng
Background: Compared with the well-studied 5-methylcytosine (m5 C) in DNA, the role and topology of epitranscriptome m5 C remain insufficiently characterized. Results: Through analyzing transcriptome-wide m5 C distribution in human and mouse, we show that the m5 C modification is significantly enriched at 5' untranslated regions (5'UTRs) of mRNA in human and mouse. With a comparative analysis of the mRNA and DNA methylome, we demonstrate that, like DNA methylation, transcriptome m5 C methylation exhibits a strong clustering effect...
2018: International Journal of Genomics
https://www.readbyqxmd.com/read/30003085/nonredundant-highly-connected-micrornas-control-functionality-in-breast-cancer-networks
#14
Guillermo de Anda-Jáuregui, Jesús Espinal-Enríquez, Diana Drago-García, Enrique Hernández-Lemus
Alterations to transcriptional regulation are an important factor in breast cancer. Noncoding RNA, such as microRNA (miR), have very influential roles in the transcriptional regulation of genes. Transcriptional regulation can be successfully modeled and analyzed using complex network theory. Particularly, interactions between two distinct classes of biological elements, such as miR and genes, can be approached through the bipartite network formalism. Based on bipartite network properties, it is possible to identify highly influential miRs in the network, such as those that have a large number of connections indicating regulation of a large set of genes...
2018: International Journal of Genomics
https://www.readbyqxmd.com/read/29977903/the-genetic-diversity-and-geographic-differentiation-of-the-wild-soybean-in-northeast-china-based-on-nuclear-microsatellite-variation
#15
Hongkun Zhao, Yumin Wang, Fu Xing, Xiaodong Liu, Cuiping Yuan, Guangxun Qi, Jixun Guo, Yingshan Dong
In this study, the genetic diversity and population structure of 205 wild soybean core collections in Northeast China from nine latitude populations and nine longitude populations were evaluated using SSR markers. A total of 973 alleles were detected by 43 SSR loci, and the average number of alleles per locus was 22.628. The mean Shannon information index ( I ) and the mean expected heterozygosity were 2.528 and 0.879, respectively. At the population level, the regions of 42°N and 124°E had the highest genetic diversity among all latitudes and longitudes...
2018: International Journal of Genomics
https://www.readbyqxmd.com/read/29967765/transcriptome-and-expression-profiling-analysis-of-recalcitrant-tea-camellia-sinensis-l-seeds-sensitive-to-dehydration
#16
Xiaofang Jin, Dandan Liu, Linlong Ma, Ziming Gong, Dan Cao, Yanli Liu, Yeyun Li, Changjun Jiang
The tea plant ( Camellia sinensis (L.) O. Kuntze) is an economically important woody perennial nonalcoholic health beverage crop. Tea seeds are categorized as recalcitrant and are sensitive to dehydration treatment. However, the molecular basis of this phenomenon has not been investigated. Thus, we analyzed the genome-wide expression profiles of three dehydration stages using RNA-Seq and digital gene expression (DGE) technologies. We performed de novo assembly and obtained a total of 91,925 nonredundant unigenes, of which 58,472 were extensively annotated...
2018: International Journal of Genomics
https://www.readbyqxmd.com/read/29951522/overexpression-of-a-new-zinc-finger-protein-transcription-factor-osctzfp8-improves-cold-tolerance-in-rice
#17
Yong-Mei Jin, Rihua Piao, Yong-Feng Yan, Mojun Chen, Ling Wang, Hongxia He, Xiaoxiao Liu, Xing-Ai Gao, Wenzhu Jiang, Xiu-Feng Lin
Cold stress is one of the most important abiotic stresses in rice. C2 H2 zinc finger proteins play important roles in response to abiotic stresses in plants. In the present study, we isolated and functionally characterized a new C2 H2 zinc finger protein transcription factor OsCTZFP8 in rice. OsCTZFP8 encodes a C2 H2 zinc finger protein, which contains a typical zinc finger motif, as well as a potential nuclear localization signal (NLS) and a leucine-rich region (L-box). Expression of OsCTZFP8 was differentially induced by several abiotic stresses and was strongly induced by cold stress...
2018: International Journal of Genomics
https://www.readbyqxmd.com/read/29951521/advancing-genomics-for-drug-development-and-safety-evaluation
#18
EDITORIAL
Zhichao Liu, Joshua Xu, Zhining Wen
No abstract text is available yet for this article.
2018: International Journal of Genomics
https://www.readbyqxmd.com/read/29888248/whole-exome-sequencing-identifies-one-de-novo-variant-in-the-fgd6-gene-in-a-thai-family-with-autism-spectrum-disorder
#19
Chuphong Thongnak, Areerat Hnoonual, Duangkamol Tangviriyapaiboon, Suchaya Silvilairat, Apichaya Puangpetch, Ekawat Pasomsub, Wasun Chantratita, Pornprot Limprasert, Chonlaphat Sukasem
Autism spectrum disorder (ASD) has a strong genetic basis, although the genetics of autism is complex and it is unclear. Genetic testing such as microarray or sequencing was widely used to identify autism markers, but they are unsuccessful in several cases. The objective of this study is to identify causative variants of autism in two Thai families by using whole-exome sequencing technique. Whole-exome sequencing was performed with autism-affected children from two unrelated families. Each sample was sequenced on SOLiD 5500xl Genetic Analyzer system followed by combined bioinformatics pipeline including annotation and filtering process to identify candidate variants...
2018: International Journal of Genomics
https://www.readbyqxmd.com/read/29888247/insights-into-the-genome-sequence-of-chromobacterium-amazonense-isolated-from-a-tropical-freshwater-lake
#20
Alexandre Bueno Santos, Patrícia Silva Costa, Anderson Oliveira do Carmo, Gabriel da Rocha Fernandes, Larissa Lopes Silva Scholte, Jeronimo Ruiz, Evanguedes Kalapothakis, Edmar Chartone-Souza, Andréa Maria Amaral Nascimento
Members of the genus Chromobacterium have been isolated from geographically diverse ecosystems and exhibit considerable metabolic flexibility, as well as biotechnological and pathogenic properties in some species. This study reports the draft assembly and detailed sequence analysis of Chromobacterium amazonense strain 56AF. The de novo-assembled genome is 4,556,707 bp in size and contains 4294 protein-coding and 95 RNA genes, including 88 tRNA, six rRNA, and one tmRNA operon. A repertoire of genes implicated in virulence, for example, hemolysin, hemolytic enterotoxins, colicin V, lytic proteins, and Nudix hydrolases, is present...
2018: International Journal of Genomics
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