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https://www.readbyqxmd.com/read/28231309/improving-molecular-diagnosis-of-aniridia-and-wagr-syndrome-using-customized-targeted-array-based-cgh
#1
Fiona Blanco-Kelly, María Palomares, Elena Vallespín, Cristina Villaverde, Rubén Martín-Arenas, Camilo Vélez-Monsalve, Isabel Lorda-Sánchez, Julián Nevado, María José Trujillo-Tiebas, Pablo Lapunzina, Carmen Ayuso, Marta Corton
Chromosomal deletions at 11p13 are a frequent cause of congenital Aniridia, a rare pan-ocular genetic disease, and of WAGR syndrome, accounting up to 30% of cases. First-tier genetic testing for newborn with aniridia, to detect 11p13 rearrangements, includes Multiplex Ligation-dependent Probe Amplification (MLPA) and karyotyping. However, neither of these approaches allow obtaining a complete picture of the high complexity of chromosomal deletions and breakpoints in aniridia. Here, we report the development and validation of a customized targeted array-based comparative genomic hybridization, so called WAGR-array, for comprehensive high-resolution analysis of CNV in the WAGR locus...
2017: PloS One
https://www.readbyqxmd.com/read/28230926/association-between-high-expression-of-phosphorylated-akt-and-mammalian-target-of-rapamycin-and-improved-survival-in-salivary-gland-adenoid-cystic-carcinoma
#2
Dai-Qiao Ouyang, Li-Zhong Liang, Zun-Fu Ke, Guang-Sen Zheng, De-Sheng Weng, Wei-Fa Yang, Yu-Xiong Su, Gui-Qing Liao
BACKGROUND: Previous genomic studies revealed phosphotidylinositol-3-kinase (PI3K)/Akt pathway mutation in human salivary gland adenoid cystic carcinoma (ACC). No validation of its prognostic value has been reported. METHODS: P-Akt, pan-Akt, phosphorylated-mammalian target of rapamycin (p-mTOR), PI3K, and insulin-like growth factor-1 receptor beta (IGF-1Rβ) were detected on 120 salivary gland ACC/adjacent salivary gland pairs immunohistochemically and were correlated with clinicopathological data...
February 23, 2017: Head & Neck
https://www.readbyqxmd.com/read/28230808/genome-sequence-of-rhodoferax-antarcticus-ant-br-t-a-psychrophilic-purple-nonsulfur-bacterium-from-an-antarctic-microbial-mat
#3
Jennifer M Baker, Carli J Riester, Blair M Skinner, Austin W Newell, Wesley D Swingley, Michael T Madigan, Deborah O Jung, Marie Asao, Min Chen, Patrick C Loughlin, Hao Pan, Yuankui Lin, Yaqiong Li, Jacob Shaw, Mindy Prado, Chris Sherman, Joseph Kuo-Hsiang Tang, Robert E Blankenship, Tingting Zhao, Jeffrey W Touchman, W Matthew Sattley
Rhodoferax antarcticus is an Antarctic purple nonsulfur bacterium and the only characterized anoxygenic phototroph that grows best below 20 °C. We present here a high-quality draft genome of Rfx. antarcticus strain ANT.BR(T), isolated from an Antarctic microbial mat. The circular chromosome (3.8 Mbp) of Rfx. antarcticus has a 59.1% guanine + cytosine (GC) content and contains 4036 open reading frames. In addition, the bacterium contains a sizable plasmid (198.6 kbp, 48.4% GC with 226 open reading frames) that comprises about 5% of the total genetic content...
February 21, 2017: Microorganisms
https://www.readbyqxmd.com/read/28230775/prec-and-c-regions-of-woodchuck-hepatitis-virus-facilitate-persistent-expression-of-surface-antigen-of-chimeric-whv-hbv-virus-in-the-hydrodynamic-injection-balb-c-mouse-model
#4
Weimin Wu, Yan Liu, Yong Lin, Danzhen Pan, Dongliang Yang, Mengji Lu, Yang Xu
In the hydrodynamic injection (HI) BALB/c mouse model with the overlength viral genome, we have found that woodchuck hepatitis virus (WHV) could persist for a prolonged period of time (up to 45 weeks), while hepatitis B virus (HBV) was mostly cleared at week four. In this study, we constructed a series of chimeric genomes based on HBV and WHV, in which the individual sequences of a 1.3-fold overlength HBV genome in pBS-HBV1.3 were replaced by their counterparts from WHV. After HI with the WHV-HBV chimeric constructs in BALB/c mice, serum viral antigen, viral DNA (vDNA), and intrahepatic viral antigen expression were analyzed to evaluate the persistence of the chimeric genomes...
February 21, 2017: Viruses
https://www.readbyqxmd.com/read/28229505/a-variant-in-a-cis-regulatory-element-enhances-claudin-14-expression-and-is-associated-with-pediatric-onset-hypercalciuria-and-kidney-stones
#5
Megan E Ure, Emma Heydari, Wanling Pan, Ajay Ramesh, Sabah Rehman, Catherine Morgan, Maury Pinsk, Robin Erickson, Johannes M Herrmann, Henrik Dimke, Emmanuelle Cordat, Mathieu Lemaire, Michael Walter, R Todd Alexander
The greatest risk factor for kidney stones is hypercalciuria, the etiology of which is largely unknown. A recent genome-wide association study (GWAS) linked hypercalciuria and kidney stones to a claudin-14 (CLDN14) risk haplotype. However, the underlying molecular mechanism was not delineated. Recently, renal CLDN14 expression was found to increase in response to increased plasma calcium, thereby inducing calciuria. We hypothesized therefore that some children with hypercalciuria and kidney stones harbor a CLDN14 variant that inappropriately increases gene expression...
February 22, 2017: Human Mutation
https://www.readbyqxmd.com/read/28228523/vpx-overcomes-a-samhd1-independent-block-to-hiv-reverse-transcription-that-is-specific-to-resting-cd4-t-cells
#6
Hanna-Mari Baldauf, Lena Stegmann, Sarah-Marie Schwarz, Ina Ambiel, Maud Trotard, Margarethe Martin, Manja Burggraf, Gina M Lenzi, Helena Lejk, Xiaoyu Pan, Oliver I Fregoso, Efrem S Lim, Libin Abraham, Laura A Nguyen, Frank Rutsch, Renate König, Baek Kim, Michael Emerman, Oliver T Fackler, Oliver T Keppler
Early after entry into monocytes, macrophages, dendritic cells, and resting CD4 T cells, HIV encounters a block, limiting reverse transcription (RT) of the incoming viral RNA genome. In this context, dNTP triphosphohydrolase SAM domain and HD domain-containing protein 1 (SAMHD1) has been identified as a restriction factor, lowering the concentration of dNTP substrates to limit RT. The accessory lentiviral protein X (Vpx) proteins from the major simian immunodeficiency virus of rhesus macaque, sooty mangabey, and HIV-2 (SIVsmm/SIVmac/HIV-2) lineage packaged into virions target SAMHD1 for proteasomal degradation, increase intracellular dNTP pools, and facilitate HIV cDNA synthesis...
February 22, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28224116/persistence-of-functional-protein-domains-in-mycoplasma-species-and-their-role-in-host-specificity-and-synthetic-minimal-life
#7
Tjerko Kamminga, Jasper J Koehorst, Paul Vermeij, Simen-Jan Slagman, Vitor A P Martins Dos Santos, Jetta J E Bijlsma, Peter J Schaap
Mycoplasmas are the smallest self-replicating organisms and obligate parasites of a specific vertebrate host. An in-depth analysis of the functional capabilities of mycoplasma species is fundamental to understand how some of simplest forms of life on Earth succeeded in subverting complex hosts with highly sophisticated immune systems. In this study we present a genome-scale comparison, focused on identification of functional protein domains, of 80 publically available mycoplasma genomes which were consistently re-annotated using a standardized annotation pipeline embedded in a semantic framework to keep track of the data provenance...
2017: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/28222377/identification-of-autophagy-related-genes-lc3-and-atg4-from-yellow-catfish-pelteobagrus-fulvidraco-and-their-transcriptional-responses-to-waterborne-and-dietborne-zinc-exposure
#8
Chuan-Chuan Wei, Zhi Luo, Yu-Feng Song, Ya-Xiong Pan, Kun Wu, Wen-Jing You
Autophagy mediates the regulation of lipid metabolism. Moreover, our recent study indicated that waterborne and dietborne zinc (Zn) exposure differentially influenced lipid metabolism in a fish species of significance for aquaculture, yellow catfish Pelteobagrus fulvidraco, but further mechanism remained unknown. The hypothesis of the present study is that autophagy mediated the Zn-induced changes of lipid metabolism of yellow catfish subjected to different exposure pathways. To this end, we cloned key genes involved in autophagy in yellow catfish, explored their mRNA expressions in responses to different Zn exposure pathways...
February 8, 2017: Chemosphere
https://www.readbyqxmd.com/read/28219438/genomic-insights-into-divergence-and-dual-domestication-of-cultivated-allotetraploid-cottons
#9
Lei Fang, Hao Gong, Yan Hu, Chunxiao Liu, Baoliang Zhou, Tao Huang, Yangkun Wang, Shuqi Chen, David D Fang, Xiongming Du, Hong Chen, Jiedan Chen, Sen Wang, Qiong Wang, Qun Wan, Bingliang Liu, Mengqiao Pan, Lijing Chang, Huaitong Wu, Gaofu Mei, Dan Xiang, Xinghe Li, Caiping Cai, Xiefei Zhu, Z Jeffrey Chen, Bin Han, Xiaoya Chen, Wangzhen Guo, Tianzhen Zhang, Xuehui Huang
BACKGROUND: Cotton has been cultivated and used to make fabrics for at least 7000 years. Two allotetraploid species of great commercial importance, Gossypium hirsutum and Gossypium barbadense, were domesticated after polyploidization and are cultivated worldwide. Although the overall genetic diversity between these two cultivated species has been studied with limited accessions, their population structure and genetic variations remain largely unknown. RESULTS: We resequence the genomes of 147 cotton accessions, including diverse wild relatives, landraces, and modern cultivars, and construct a comprehensive variation map to provide genomic insights into the divergence and dual domestication of these two important cultivated tetraploid cotton species...
February 20, 2017: Genome Biology
https://www.readbyqxmd.com/read/28218778/identification-and-cloning-of-golden2-like1-glk1-a-transcription-factor-associated-with-chloroplast-development-in-brassica-napus-l
#10
Y L Pan, Y Pan, C M Qu, C G Su, J H Li, X G Zhang
Photosynthesis is the process by which dry matter accumulates, which affects rapeseed yield. In this study, we identified GOLDEN2-LIKE1 (GLK1), located on chromosome A07 and 59.2 kb away from the single nucleotide polymorphism marker SNP16353A07, which encodes a transcription factor associated with the rate of photosynthesis in leaves. We then identified 96 GLK1 family members from 53 species using a hidden Markov model (HMM) search and found 24 of these genes, which were derived from 17 Brassicaceae species...
February 16, 2017: Genetics and Molecular Research: GMR
https://www.readbyqxmd.com/read/28217118/genomic-characterization-of-dairy-associated-leuconostoc-species-and-diversity-of-leuconostocs-in-undefined-mixed-mesophilic-starter-cultures
#11
Cyril A Frantzen, Witold Kot, Thomas B Pedersen, Ylva M Ardö, Jeff R Broadbent, Horst Neve, Lars H Hansen, Fabio Dal Bello, Hilde M Østlie, Hans P Kleppen, Finn K Vogensen, Helge Holo
Undefined mesophilic mixed (DL-type) starter cultures are composed of predominantly Lactococcus lactis subspecies and 1-10% Leuconostoc spp. The composition of the Leuconostoc population in the starter culture ultimately affects the characteristics and the quality of the final product. The scientific basis for the taxonomy of dairy relevant leuconostocs can be traced back 50 years, and no documentation on the genomic diversity of leuconostocs in starter cultures exists. We present data on the Leuconostoc population in five DL-type starter cultures commonly used by the dairy industry...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28215484/establishment-and-characterization-of-a-new-human-acinar-cell-carcinoma-cell-line-faraz-icr-from-pancreas
#12
Marzieh Rezaei, Ahmad Hosseini, Saman Nikeghbalian, Abbas Ghaderi
OBJECTIVES: Basic research in the field of acinar cell carcinoma (ACC) as a rare neoplasm of the pancreas is dependent on the availability of pragmatic model such as new pancreatic cancer cell lines. Thus, establishment and characterization of new pancreatic cancer cell lines from ACC origin are deemed important. METHODS: Faraz-ICR cell line was derived from a 58-years old woman with pancreatic acinar cell carcinoma by the collagenase digestion protocol. We characterized the cell line by examining its morphology and cytostructural and functional profile...
February 8, 2017: Pancreatology: Official Journal of the International Association of Pancreatology (IAP) ... [et Al.]
https://www.readbyqxmd.com/read/28215215/the-mitochondrial-genome-of-ancylostoma-tubaeforme-from-cats-in-china
#13
X L Shi, Y Q Fu, A Y Abdullahi, M W Wang, F Yang, X G Yu, W D Pan, X X Yan, J X Hang, P Zhang, G Q Li
Ancylostoma tubaeforme may infect canids, felids and humans, and pose a potential risk to public health. Polymerase chain reaction (PCR) techniques were used to amplify the complete mitochondrial (mt) genome sequence of A. tubaeforme from cats and to analyse its sequence characteristics after molecular identification based on the internal transcribed spacer ITS1+ sequence. The results show that the complete mt genome sequence (GenBank accession number KY070315) of A. tubaeforme from cats was 13,730 bp in length, including 12 protein-coding genes, 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, two non-coding regions and an AT-rich region...
February 20, 2017: Journal of Helminthology
https://www.readbyqxmd.com/read/28214218/implication-of-downregulation-and-prospective-pathway-signaling-of-microrna-375-in-lung-squamous-cell-carcinoma
#14
Wen-Jie Chen, Ting-Qing Gan, Hui Qin, Su-Ning Huang, Li-Hua Yang, Ye-Ying Fang, Zu-Yun Li, Lin-Jiang Pan, Gang Chen
BACKGROUND: Lung cancer is one of the most typical cancers in the world. Altered expression profiles of microRNA-375(miR-375) are linked to many diseases including lung cancer. However, the relationship between miR-375 and lung squamous cell carcinoma (LUSC) is controversial. METHODS: We first evaluated the 23 LUSCs and the paired normal lung tissues by qRT-PCR. Then we analyzed the LUSC samples with miR-375 expression based on The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO)...
January 22, 2017: Pathology, Research and Practice
https://www.readbyqxmd.com/read/28212573/dynamic-variations-in-epithelial-to-mesenchymal-transition-emt-atm-and-slfn11-govern-response-to-parp-inhibitors-and-cisplatin-in-small-cell-lung-cancer
#15
C Allison Stewart, Pan Tong, Robert J Cardnell, Triparna Sen, Lerong Li, Carl M Gay, Fatemah Masrorpour, You Fan, Rasha O Bara, Ying Feng, Yuanbin Ru, Junya Fujimoto, Samrat T Kundu, Leonard E Post, Karen Yu, Yuqiao Shen, Bonnie S Glisson, Ignatio Wistuba, John V Heymach, Don L Gibbons, Jing Wang, Lauren Averett Byers
Small cell lung cancer (SCLC) is one of the most aggressive forms of cancer, with a 5-year survival <7%. A major barrier to progress is the absence of predictive biomarkers for chemotherapy and novel targeted agents such as PARP inhibitors. Using a high-throughput, integrated proteomic, transcriptomic, and genomic analysis of SCLC patient-derived xenografts (PDXs) and profiled cell lines, we identified biomarkers of drug sensitivity and determined their prevalence in patient tumors. In contrast to breast and ovarian cancer, PARP inhibitor response was not associated with mutations in homologous recombination (HR) genes (e...
February 15, 2017: Oncotarget
https://www.readbyqxmd.com/read/28205648/identification-of-a-novel-nampt-inhibitor-by-crispr-cas9-chemogenomic-profiling-in-mammalian-cells
#16
David Estoppey, Jeffrey W Hewett, Chantale T Guy, Edmund Harrington, Jason R Thomas, Markus Schirle, Rachel Cuttat, Annick Waldt, Bertran Gerrits, Zinger Yang, Sven Schuierer, Xuewen Pan, Kevin Xie, Walter Carbone, Judith Knehr, Alicia Lindeman, Carsten Russ, Elizabeth Frias, Gregory R Hoffman, Malini Varadarajan, Nadire Ramadan, John S Reece-Hoyes, Qiong Wang, Xin Chen, Gregory McAllister, Guglielmo Roma, Tewis Bouwmeester, Dominic Hoepfner
Chemogenomic profiling is a powerful and unbiased approach to elucidate pharmacological targets and the mechanism of bioactive compounds. Until recently, genome-wide, high-resolution experiments of this nature have been limited to fungal systems due to lack of mammalian genome-wide deletion collections. With the example of a novel nicotinamide phosphoribosyltransferase (NAMPT) inhibitor, we demonstrate that the CRISPR/Cas9 system enables the generation of transient homo- and heterozygous deletion libraries and allows for the identification of efficacy targets and pathways mediating hypersensitivity and resistance relevant to the compound mechanism of action...
February 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28202506/recurrent-patterns-of-dna-copy-number-alterations-in-tumors-reflect-metabolic-selection-pressures
#17
Nicholas A Graham, Aspram Minasyan, Anastasia Lomova, Ashley Cass, Nikolas G Balanis, Michael Friedman, Shawna Chan, Sophie Zhao, Adrian Delgado, James Go, Lillie Beck, Christian Hurtz, Carina Ng, Rong Qiao, Johanna Ten Hoeve, Nicolaos Palaskas, Hong Wu, Markus Müschen, Asha S Multani, Elisa Port, Steven M Larson, Nikolaus Schultz, Daniel Braas, Heather R Christofk, Ingo K Mellinghoff, Thomas G Graeber
Copy number alteration (CNA) profiling of human tumors has revealed recurrent patterns of DNA amplifications and deletions across diverse cancer types. These patterns are suggestive of conserved selection pressures during tumor evolution but cannot be fully explained by known oncogenes and tumor suppressor genes. Using a pan-cancer analysis of CNA data from patient tumors and experimental systems, here we show that principal component analysis-defined CNA signatures are predictive of glycolytic phenotypes, including (18)F-fluorodeoxy-glucose (FDG) avidity of patient tumors, and increased proliferation...
February 15, 2017: Molecular Systems Biology
https://www.readbyqxmd.com/read/28198668/comparative-analysis-of-corynebacterium-glutamicum-genomes-a-new-perspective-for-the-industrial-production-of-amino-acids
#18
Junjie Yang, Sheng Yang
BACKGROUND: Corynebacterium glutamicum is a non-pathogenic bacterium widely used in industrial amino acid production and metabolic engineering research. Although the genome sequences of some C. glutamicum strains are available, comprehensive comparative genome analyses of these species have not been done. Six wild type C. glutamicum strains were sequenced using next-generation sequencing technology in our study. Together with 20 previously reported strains, we present a comprehensive comparative analysis of C...
January 25, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28197164/isolation-characterization-and-transcriptome-analysis-of-a-cytokinin-receptor-mutant-osckt1-in-rice
#19
Wona Ding, Huishan Tong, Wenjuan Zheng, Jing Ye, Zhichong Pan, Botao Zhang, Shihua Zhu
Cytokinins play important roles in regulating plant development, including shoot and root meristems, leaf longevity, and grain yield. However, the in planta functions of rice cytokinin receptors have not been genetically characterized yet. Here we isolated a rice mutant, Osckt1, with enhanced tolerance to cytokinin treatment. Further analysis showed that Osckt1 was insensitive to aromatic cytokinins but responded normally to isoprenoid and phenylurea-type cytokinins. Map-based cloning revealed that the mutation occurred in a putative cytokinin receptor gene, histidine kinase 6 (OsHK6)...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28196101/de-novo-assembly-characterization-and-annotation-for-the-transcriptome-of-sarcocheilichthys-sinensis
#20
Chuankun Zhu, Zhengjun Pan, Hui Wang, Guoliang Chang, Nan Wu, Huaiyu Ding
The Chinese lake gudgeon Sarcocheilichthys sinensis is a small cyprinid fish with great aquaculture potential both for its edible and ornamental values. Nevertheless, available genomic and transcriptomic information for this fish is extremely deficient. In this study, a normalized cDNA library was constructed using 13 mixed tissues of an adult male S. sinensis, and was sequenced by the Illumina HiSeq2500 platform. De novo assembly was performed using 38,911,511 obtained clean reads, and a total of 147,282 unigenes with an average length of 900 bp were finally achieved...
2017: PloS One
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