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https://www.readbyqxmd.com/read/28431355/genome-wide-identification-and-analysis-of-the-populus-trichocarpa-tify-gene-family
#1
Yue Wang, Feng Pan, Danmei Chen, Wenyuan Chu, Huanlong Liu, Yan Xiang
The plant-specific TIFY proteins are widely present in land plants and play the important roles in the regulation of plant stress-responses. In this study, we carried out a bioinformatics analysis of TIFY genes in Populus trichocarpa by determining the phylogenetic relationship, chromosomal location and gene structure and expression profiles analysis under stresses. The 24 TIFY genes were identified and classified into four subfamilies (ZML, JAZ, PPD and TIFY). The 24 TIFY genes were irregularly located on 13 of the 19 chromosomes; ten gene pairs were involved in large-scale interchromosomal segmental duplication events; we identified 17 collinear TIFY gene pairs in the Populus trichocarpa genome...
April 13, 2017: Plant Physiology and Biochemistry: PPB
https://www.readbyqxmd.com/read/28427330/pan-genome-and-crispr-analyses-of-the-bacterial-fish-pathogen-moritella-viscosa
#2
Christian Karlsen, Erik Hjerde, Terje Klemetsen, Nils Peder Willassen
BACKGROUND: Winter-ulcer Moritella viscosa infections continue to be a significant burden in Atlantic salmon (Salmo salar L.) farming. M. viscosa comprises two main clusters that differ in genetic variation and phenotypes including virulence. Horizontal gene transfer through acquisition and loss of mobile genetic elements (MGEs) is a major driving force of bacterial diversification. To gain insight into genomic traits that could affect sublineage evolution within this bacterium we examined the genome sequences of twelve M...
April 20, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28426276/integrative-epigenetic-and-genetic-pan-cancer-somatic-alteration-portraits
#3
Lucas A Salas, Kevin C Johnson, Devin C Koestler, Dylan E O'Sullivan, Brock C Christensen
Genetic and epigenetic alterations are required for carcinogenesis and the mutation burden across tumor types has been investigated. Here, we investigate epigenetic alterations with a novel measure of global DNA methylation dysregulation, the methylation dysregulation index (MDI), across 14 cancer types in The Cancer Genome Atlas (TCGA) database. DNA methylation data-obtained using Illumina HumanMethylation450 BeadChip-was accessed from TCGA. We calculated the MDI in 14 tumor types (n = 5,592 tumors), using adjacent normal tissues (n = 701) from each tumor site...
April 20, 2017: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/28424525/genome-wide-detection-of-copy-number-variation-in-chinese-indigenous-sheep-using-an-ovine-high-density-600%C3%A2-k-snp-array
#4
Qing Ma, Xuexue Liu, Jianfei Pan, Lina Ma, Yuehui Ma, Xiaohong He, Qianjun Zhao, Yabin Pu, Yingkang Li, Lin Jiang
Copy number variants (CNVs) represent a form of genomic structural variation underlying phenotypic diversity. In this study, we used the Illumina Ovine SNP 600 K BeadChip array for genome-wide detection of CNVs in 48 Chinese Tan sheep. A total of 1,296 CNV regions (CNVRs), ranging from 1.2 kb to 2.3 Mb in length, were detected, representing approximately 4.7% of the entire ovine genome (Oar_v3.1). We combined our findings with five existing CNVR reports to generate a composite genome-wide dataset of 4,321 CNVRs, which revealed 556 (43%) novel CNVRs...
April 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28421459/rapid-progression-to-glioblastoma-in-a-subset-of-idh-mutated-astrocytomas-a-genome-wide-analysis
#5
Timothy E Richardson, Matija Snuderl, Jonathan Serrano, Matthias A Karajannis, Adriana Heguy, Dwight Oliver, Jack M Raisanen, Elizabeth A Maher, Edward Pan, Samuel Barnett, Chunyu Cai, Amyn A Habib, Robert M Bachoo, Kimmo J Hatanpaa
According to the recently updated World Health Organization (WHO) classification (2016), grade II-III astrocytomas are divided into IDH-wildtype and IDH-mutant groups, the latter being significantly less aggressive in terms of both progression-free and total survival. We identified a small cohort of WHO grade II-III astrocytomas that harbored the IDH1 R132H mutation, as confirmed by both immunohistochemistry and molecular sequence analysis, which nonetheless had unexpectedly rapid recurrence and subsequent progression to glioblastoma...
April 18, 2017: Journal of Neuro-oncology
https://www.readbyqxmd.com/read/28421090/comparative-genomics-and-phylogenomics-of-east-asian-tulips-amana-liliaceae
#6
Pan Li, Rui-Sen Lu, Wu-Qin Xu, Tetsuo Ohi-Toma, Min-Qi Cai, Ying-Xiong Qiu, Kenneth M Cameron, Cheng-Xin Fu
The genus Amana Honda (Liliaceae), when it is treated as separate from Tulipa, comprises six perennial herbaceous species that are restricted to China, Japan and the Korean Peninsula. Although all six Amana species have important medicinal and horticultural uses, studies focused on species identification and molecular phylogenetics are few. Here we report the nucleotide sequences of six complete Amana chloroplast (cp) genomes. The cp genomes of Amana range from 150,613 bp to 151,136 bp in length, all including a pair of inverted repeats (25,629-25,859 bp) separated by the large single-copy (81,482-82,218 bp) and small single-copy (17,366-17,465 bp) regions...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28420516/prenatal-diagnosis-and-molecular-cytogenetic-characterization-of%C3%A2-low-level-mosaic-trisomy-12-at-amniocentesis-associated-with%C3%A2-a%C3%A2-favorable-pregnancy-outcome
#7
Chih-Ping Chen, Chen-Ju Lin, Schu-Rern Chern, Peih-Shan Wu, Yen-Ni Chen, Shin-Wen Chen, Chen-Wen Pan, Chien-Wen Yang, Wayseen Wang
OBJECTIVE: We present prenatal diagnosis of low-level mosaic trisomy 12. CASE REPORT: A 40-year-old woman underwent amniocentesis at 18 weeks of gestation because of advanced maternal age, which revealed a karyotype of 47,XX,+12[5]/46,XX[24] consistent with 17.2% (5/29) mosaicism for trisomy 12. Repeat amniocentesis performed at 21 weeks of gestation revealed a karyotype of 47,XX,+12[4]/46,XX[6] consistent with 40% (4/10) mosaicism for trisomy 12. Interphase fluorescence in situ hybridization (FISH) on 112 uncultured amniocytes detected 23 cells with trisomy 12 consistent with 20...
April 2017: Taiwanese Journal of Obstetrics & Gynecology
https://www.readbyqxmd.com/read/28420511/prenatal-diagnosis-and-molecular-cytogenetic-characterization-of-concomitant-familial-small-supernumerary-marker-chromosome-derived-from-chromosome-4q-4q11-1-q13-2-and-5q13-2-microdeletion-with-no-apparent-phenotypic-abnormality
#8
Chih-Ping Chen, Schu-Rern Chern, Yen-Ni Chen, Shin-Wen Chen, Peih-Shan Wu, Chien-Wen Yang, Chen-Chi Lee, Meng-Shan Lee, Chen-Wen Pan, Wayseen Wang
OBJECTIVE: We present prenatal diagnosis and molecular cytogenetic characterization of concomitant familial small supernumerary marker chromosome 4 [sSMC(4)] derived from 4q11.1-q12 and q13.2, and 5q13.2 microdeletion with no apparent phenotypic abnormality. MATERIALS AND METHODS: A 32-year-old woman underwent amniocentesis at 21 weeks of gestation because of absent nasal bone on fetal ultrasound. Amniocentesis revealed a karyotype of 47,XX,+mar[13]/46,XX[3]. Array comparative genomic hybridization analysis on the cultured amniocytes revealed a 2...
April 2017: Taiwanese Journal of Obstetrics & Gynecology
https://www.readbyqxmd.com/read/28416776/clinical-value-of-mir-101-3p-and-biological-analysis-of-its-prospective-targets-in-breast-cancer-a-study-based-on-the-cancer-genome-atlas-tcga-and-bioinformatics
#9
Chun-Yao Li, Dan-Dan Xiong, Chun-Qin Huang, Rong-Quan He, Hai-Wei Liang, Deng-Hua Pan, Han-Lin Wang, Yi-Wen Wang, Hua-Wei Zhu, Gang Chen
BACKGROUND MiR-101-3p can promote apoptosis and inhibit proliferation, invasion, and metastasis in breast cancer (BC) cells. However, its mechanisms in BC are not fully understood. Therefore, a comprehensive analysis of the target genes, pathways, and networks of miR-101-3p in BC is necessary. MATERIAL AND METHODS The miR-101 profiles for 781 patients with BC from The Cancer Genome Atlas (TCGA) were analyzed. Gene expression profiling of GSE31397 with miR-101-3p transfected MCF-7 cells and scramble control cells was downloaded from Gene Expression Omnibus (GEO), and the differentially expressed genes (DEGs) were identified...
April 18, 2017: Medical Science Monitor: International Medical Journal of Experimental and Clinical Research
https://www.readbyqxmd.com/read/28415739/high-tgf-%C3%AE-1-expression-predicts-poor-disease-prognosis-in-hepatocellular-carcinoma-patients
#10
Li Peng, Xiao-Qing Yuan, Chao-Yang Zhang, Fei Ye, Hui-Fang Zhou, Wen-Ling Li, Zhao-Yang Liu, Ya-Qin Zhang, Xi Pan, Guan-Cheng Li
Transforming growth factor beta (TGF-β) promotes the pathogenesis of hepatocellular carcinoma (HCC). We evaluated the associations between TGF-β1 expression and clinicopathological parameters in HCC patients from The Cancer Genome Atlas (TCGA), as well as the prognostic power of TGF-β1 expression. Eligible studies were retrieved from several databases, and effects (hazard ratios (HRs) with 95% confidence intervals (CIs)) for overall survival (OS), disease-free survival (DFS), recurrence-free survival (RFS), metastasis-free survival (MFS), and progression-free survival (PFS) were pooled to assess the prognostic ability of TGF-β1 expression in HCC patients...
March 13, 2017: Oncotarget
https://www.readbyqxmd.com/read/28415565/rad52-deficiency-decreases-development-of-lung-squamous-cell-carcinomas-by-enhancing-immuno-surveillance
#11
Rachel Lieberman, Jing Pan, Qi Zhang, Ming You
RAD52 is involved in homologous recombination and DNA repair. This study focuses on lung cancer progression and how the DNA repair gene, Rad52, enables tumor cells to have sufficient genome integrity, i.e., the ability to repair lethal DNA damage, to avoid cell death. In this report, we analyze the phenotypic differences between wild type and Rad52-/- in inhibition of tumor phenotypes including cell growth, viability, cytolysis, and immune profiling. We demonstrated that loss of Rad52 not only increases the death of cells undergoing carcinogen-induced transformation in vivo, but that Rad52 loss also augments in vivo antitumor activity through an enhanced capacity for direct killing of LLC tumor cells by stimulated Rad52-/- NK and CD8+ T cells...
March 18, 2017: Oncotarget
https://www.readbyqxmd.com/read/28414739/an-in-silico-pan-genomic-probe-for-the-molecular-traits-behind-lactobacillus-ruminis-gut-autochthony
#12
Ravi Kant, Airi Palva, Ingemar von Ossowski
As an ecological niche, the mammalian intestine provides the ideal habitat for a variety of bacterial microorganisms. Purportedly, some commensal genera and species offer a beneficial mix of metabolic, protective, and structural processes that help sustain the natural digestive health of the host. Among these sort of gut inhabitants is the Gram-positive lactic acid bacterium Lactobacillus ruminis, a strict anaerobe with both pili and flagella on its cell surface, but also known for being autochthonous (indigenous) to the intestinal environment...
2017: PloS One
https://www.readbyqxmd.com/read/28414633/genome-wide-analysis-provides-evidence-on-the-genetic-relatedness-of-the-emergent-xylella-fastidiosa-genotype-in-italy-to-isolates-from-central-america
#13
Annalisa Giampetruzzi, Maria Saponari, Giuliana Loconsole, Donato Boscia, Vito Nicola Savino, Rodrigo Almeida, Stefania Zicca, Blanca Landa, Carlos Chacon Diaz, Pasquale Saldarelli
Xylella fastidiosa is a plant pathogenic bacterium recently introduced in Europe that is causing decline in olive trees in the South of Italy. Genetic studies have consistently shown that the bacterial genotype recovered from infected olive trees belongs to the sequence type ST53 within subspecies pauca. This genotype, ST53, has also been reported to occur in Costa Rica. The ancestry of ST53 was recently clarified, showing it contains alleles which are monophyletic with those of subsp. pauca in South America...
April 17, 2017: Phytopathology
https://www.readbyqxmd.com/read/28410234/the-ovarian-cancer-oncobiome
#14
Sagarika Banerjee, Tian Tian, Zhi Wei, Natalie Shih, Michael D Feldman, George Coukos, James C Alwine, Erle S Robertson
Humans and other mammals are colonized by microbial agents across the kingdom which can represent a unique microbiome pattern. Dysbiosis of the microbiome has been associated with pathology including cancer. We have identified a microbiome signature unique to ovarian cancers, one of the most lethal malignancies of the female reproductive system, primarily because of its asymptomatic nature during the early stages in development. We screened ovarian cancer samples along with matched, and non-matched control samples using our pan-pathogen array (PathoChip), combined with capture-next generation sequencing...
March 30, 2017: Oncotarget
https://www.readbyqxmd.com/read/28410203/exploring-the-key-genes-and-pathways-in-enchondromas-using-a-gene-expression-microarray
#15
Zhongju Shi, Hengxing Zhou, Bin Pan, Lu Lu, Yi Kang, Lu Liu, Zhijian Wei, Shiqing Feng
Enchondromas are the most common primary benign osseous neoplasms that occur in the medullary bone; they can undergo malignant transformation into chondrosarcoma. However, enchondromas are always undetected in patients, and the molecular mechanism is unclear. To identify key genes and pathways associated with the occurrence and development of enchondromas, we downloaded the gene expression dataset GSE22855 and obtained the differentially expressed genes (DEGs) by analyzing high-throughput gene expression in enchondromas...
March 30, 2017: Oncotarget
https://www.readbyqxmd.com/read/28408461/whole-genome-non-coding-sequence-analysis-in-t-cell-acute-lymphoblastic-leukemia-identifies-oncogene-enhancer-mutations
#16
Shaoyan Hu, Maoxiang Qian, Hui Zhang, Yu Guo, Jin Yang, Xujie Zhao, Hailong He, Jun Lu, Jian Pan, Meimei Chang, Guoqing Du, Ting-Nien Lin, Shirley Kow-Yin Kham, Thuan Chong Quah, Hany Ariffin, Ah-Moy Tan, Yong Cheng, Chunliang Li, Allen Eng-Juh Yeoh, Ching-Hon Pui, Anders Jacobsen Skanderup, Jun J Yang
No abstract text is available yet for this article.
April 13, 2017: Blood
https://www.readbyqxmd.com/read/28406802/distinct-subtype-distribution-and-somatic-mutation-spectrum-of-lymphomas-in-east-asia
#17
Weicheng Ren, Wei Li, Xiaofei Ye, Hui Liu, Qiang Pan-Hammarström
PURPOSE OF REVIEW: Here, we give an updated overview of the subtype distribution of lymphomas in East Asia and also present the genome sequencing data on two major subtypes of these tumors. RECENT FINDINGS: The distribution of lymphoma types/subtypes among East Asian countries is very similar, with a lower proportion of B-cell malignancies and a higher proportion of T/natural killer (NK)-cell lymphomas as compared to Western populations. Extranodal NK/T-cell lymphoma is more frequently observed in East Asia, whereas follicular lymphoma and chronic lymphocytic leukemia, are proportionally lower...
April 13, 2017: Current Opinion in Hematology
https://www.readbyqxmd.com/read/28405512/high-expression-of-pd-1-ligands-is-associated-with-kataegis-mutational-signature-and-apobec3-alterations
#18
Amélie Boichard, Igor F Tsigelny, Razelle Kurzrock
Immunotherapy with checkpoint inhibitors, such as antibodies blocking the programmed cell-death receptor-1 (PD-1), has resulted in remarkable responses in patients having traditionally refractory cancers. Although response to PD-1 inhibitors correlates with PD-1 ligand (PD-L1 or PD-L2) expression, PD-1 ligand positivity represents only a part of the predictive model necessary for selecting patients predisposed to respond to immunotherapy. We used all genomic, transcriptomic, proteomic and phenotypic data related to 8,475 pan-cancer samples available in The Cancer Genome Atlas (TCGA) and conducted a logistic regression analysis based on a large set of variables, such as microsatellite instability (MSI-H), mismatch repair (MMR) alterations, polymerase δ (POLD1) and polymerase ε (POLE) mutations, activation-induced/apolipoprotein-B editing cytidine deaminases (AID/APOBEC) alterations, lymphocyte markers and mutation burden estimates to determine independent factors that associate with PD-1 ligand overexpression...
2017: Oncoimmunology
https://www.readbyqxmd.com/read/28404963/tumor-socs3-methylation-status-predicts-the-treatment-response-to-tace-and-prognosis-in-hcc-patients
#19
Bei-Ge Jiang, Neng Wang, Jian Huang, Yuan Yang, Liang-Liang Sun, Ze-Ya Pan, Wei-Ping Zhou
BACKGROUND: Suppressor of cytokine signaling (SOCS) 1 and 3 methylation have been associated with clinical features and outcomes of cancer patients. However, their roles in determining the treatment response to transarterial chemoembolization (TACE) in patients with hepatocellular carcinoma (HCC) remain unknown. RESULTS: We found that presence of SOCS3 methylation is significantly associated with the major clinical features of HCC patients, including tumor stage, lymph node and vascular invasion...
March 13, 2017: Oncotarget
https://www.readbyqxmd.com/read/28399795/pan-cancer-analysis-of-systematic-batch-effects-on-somatic-sequence-variations
#20
Ji-Hye Choi, Seong-Eui Hong, Hyun Goo Woo
BACKGROUND: The Cancer Genome Atlas (TCGA) is a comprehensive database that includes multi-layered cancer genome profiles. Large-scale collection of data inevitably generates batch effects introduced by differences in processing at various stages from sample collection to data generation. However, batch effects on the sequence variation and its characteristics have not been studied extensively. RESULTS: We systematically evaluated batch effects on somatic sequence variations in pan-cancer TCGA data, revealing 999 somatic variants that were batch-biased with statistical significance (P < 0...
April 11, 2017: BMC Bioinformatics
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