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https://www.readbyqxmd.com/read/28927094/genomic-markers-of-ovarian-adenocarcinoma-and-its-relevancy-to-the-effectiveness-of-chemotherapy
#1
Monika Englert-Golon, Bartosz Burchardt, Bartlomiej Budny, Szymon Dębicki, Blanka Majchrzycka, Elzbieta Wrotkowska, Piotr Jasiński, Katarzyna Ziemnicka, Radosław Słopień, Marek Ruchała, Stefan Sajdak
Ovarian cancer is the eighth most common cancer and the seventh highest cause of cancer-associated mortality in women worldwide. It is the second highest cause of mortality among female reproductive malignancies. The current standard first-line treatment for advanced ovarian cancer includes a combination of surgical debulking and standard systemic platinum-based chemotherapy with carboplatin and paclitaxel. Although a deeper understanding of this disease has been attained, relapse occurs in 70% of patients 18 months subsequent to the first-line treatment...
September 2017: Oncology Letters
https://www.readbyqxmd.com/read/28926727/early-pregnancy-intrauterine-fetal-exposure-to-maternal-smoking-and-impact-on-fetal-telomere-length
#2
Hooman Mirzakhani, Immaculata De Vivo, J Steven Leeder, Roger Gaedigk, Carrie A Vyhlidal, Scott T Weiss, Kelan Tantisira
BACKGROUND: Reduced telomere length, or its accelerated attrition, has been implicated in aging, mortality, and several human diseases, including respiratory diseases. Age dependent manifestation of telomere-mediated disease during life span indicates the role of developmental stage in these diseases and highlights the importance of fetal developmental process in utero and at earlier life stages. Environmental determinants during developmental and later stages of life could affect telomere length...
September 14, 2017: European Journal of Obstetrics, Gynecology, and Reproductive Biology
https://www.readbyqxmd.com/read/28926565/a-snp-panel-and-online-tool-for-checking-genotype-concordance-through-comparing-qr-codes
#3
Yonghong Du, Joshua S Martin, John McGee, Yuchen Yang, Eric Yi Liu, Yingrui Sun, Matthias Geihs, Xuejun Kong, Eric Lingfeng Zhou, Yun Li, Jie Huang
In the current precision medicine era, more and more samples get genotyped and sequenced. Both researchers and commercial companies expend significant time and resources to reduce the error rate. However, it has been reported that there is a sample mix-up rate of between 0.1% and 1%, not to mention the possibly higher mix-up rate during the down-stream genetic reporting processes. Even on the low end of this estimate, this translates to a significant number of mislabeled samples, especially over the projected one billion people that will be sequenced within the next decade...
2017: PloS One
https://www.readbyqxmd.com/read/28925595/determination-of-crassphage-in-water-samples-and-applicability-for-tracking-human-faecal-pollution
#4
Cristina García-Aljaro, Elisenda Ballesté, Maite Muniesa, Juan Jofre
In recent decades, considerable effort has been devoted to finding microbial source-tracking (MST) markers that are suitable to assess the health risks of faecally polluted waters, with no universal marker reported so far. In this study, the abundance and prevalence of a crAssphage-derived DNA marker in wastewaters of human and animal origins were studied by a new qPCR assay with the ultimate aim of assessing its potential as an MST marker. crAssphage showed up to 10(6) GC/ml in the sewage samples of human origin, in both the total DNA and the viral DNA fraction...
September 19, 2017: Microbial Biotechnology
https://www.readbyqxmd.com/read/28925386/5-hydroxymethylcytosine-signatures-in-circulating-cell-free-dna-as-diagnostic-biomarkers-for-human-cancers
#5
Wenshuai Li, Xu Zhang, Xingyu Lu, Lei You, Yanqun Song, Zhongguang Luo, Jun Zhang, Ji Nie, Wanwei Zheng, Diannan Xu, Yaping Wang, Yuanqiang Dong, Shulin Yu, Jun Hong, Jianping Shi, Hankun Hao, Fen Luo, Luchun Hua, Peng Wang, Xiaoping Qian, Fang Yuan, Lianhuan Wei, Ming Cui, Taiping Zhang, Quan Liao, Menghua Dai, Ziwen Liu, Ge Chen, Katherine Meckel, Sarbani Adhikari, Guifang Jia, Marc B Bissonnette, Xinxiang Zhang, Yupei Zhao, Wei Zhang, Chuan He, Jie Liu
DNA modifications such as 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) are epigenetic marks known to affect global gene expression in mammals. Given their prevalence in the human genome, close correlation with gene expression and high chemical stability, these DNA epigenetic marks could serve as ideal biomarkers for cancer diagnosis. Taking advantage of a highly sensitive and selective chemical labeling technology, we report here the genome-wide profiling of 5hmC in circulating cell-free DNA (cfDNA) and in genomic DNA (gDNA) of paired tumor and adjacent tissues collected from a cohort of 260 patients recently diagnosed with colorectal, gastric, pancreatic, liver or thyroid cancer and normal tissues from 90 healthy individuals...
September 19, 2017: Cell Research
https://www.readbyqxmd.com/read/28925155/-analysis-on-dna-methylation-of-mosaic-and-moxa-type-leaves-of-aconitum-carmichaeli-by-msap
#6
Huan Wen, Cheng Peng, Chao-Long Rao, Da-Yan Zhang, Xiao-Fang Xie, Ji-Hai Gao
An MSAP analysis method was established for detecting DNA methylation of Aconitum carmichaeli leaves, and the DNA methylation of different leaf shapes and different leaf position was analyzed by MSAP. The study made experiments on the leaves of different position of mosaic and moxa leaf type A. carmichaeli, researched the effects of restriction digestion of genomic DNA by using two restriction enzymes, screened the suitable selective amplification primers, and analyzed the methylation differences of leaves by calculating the 6% acrylamide gel electrophoresis bands and lane...
October 2016: Zhongguo Zhong Yao za Zhi, Zhongguo Zhongyao Zazhi, China Journal of Chinese Materia Medica
https://www.readbyqxmd.com/read/28924976/spontaneous-generation-of-a-novel-foetal-human-retinal-pigment-epithelium-rpe-cell-line-available-for-investigation-on-phagocytosis-and-morphogenesis
#7
Zhihua Shao, Haiyun Wang, Xuejian Zhou, Baosen Guo, Xuehu Gao, Zengrong Xiao, Meng Liu, Jihong Sha, Chunlian Jiang, Yuping Luo, Zhixue Liu, Siguang Li
OBJECTIVES: Primary retinal pigment epithelium (RPE) cells have a limited capacity to re-establish epithelial morphology and to maintain native RPE function in vitro, and all commercially available RPE cell lines have drawbacks of morphology or function; therefore, the establishment of new RPE cell lines with typical characteristics of RPE would be helpful in further understanding of their physiological and pathological mechanisms. Here, we firstly report a new spontaneously generated RPE line, fhRPE-13A, from a 13-week aborted foetus...
September 18, 2017: Cell Proliferation
https://www.readbyqxmd.com/read/28923591/transcriptome-profiling-based-on-protein-protein-interaction-networks-provides-a-core-set-of-genes-for-understanding-blood-immune-response-mechanisms-against-edwardsiella-tarda-infection-in-japanese-flounder-paralichthys-olivaceus
#8
Zan Li, Xiumei Liu, Jinxiang Liu, Kai Zhang, Haiyang Yu, Yan He, Xubo Wang, Jie Qi, Zhigang Wang, Quanqi Zhang
Marine organisms are commonly under threat from various pathogens. Edwardsiella tarda is one of the fish pathogens that can infect both cultured and wild fish species. E. tarda can also infect other vertebrates, including amphibians, reptiles, and mammals. Bacteremia caused by E. tarda can be a fatal disease in humans. Blood acts as a pipeline for the fish immune system. Generating blood transcriptomic resources from fish challenged by E. tarda is crucial for understanding molecular mechanisms underlying blood immune response process...
September 15, 2017: Developmental and Comparative Immunology
https://www.readbyqxmd.com/read/28923158/isotopic-self-organization-as-an-informational-factor-in-biological-systems
#9
Alexander A Berezin, Vladimir V Gridin
We outline possible effects of isotopic randomness and isotopic self-organization (isotopicity) for biology, genetics, neurodynamics and conscious-ness. Prime ideas are (a) isotopic genetic code based on isotopic permutations in genomes, and (b) catalytic effects of decays of radioactive isotopes in physiology and psychology. We discuss the reasons why these ideas are presently severely under-appreciated by the biomedical research community. We propose some steps to foster interest in isotopic effects in biology...
October 2017: Nonlinear Dynamics, Psychology, and Life Sciences
https://www.readbyqxmd.com/read/28923016/5-hydroxymethylcytosine-is-highly-dynamic-across-human-fetal-brain-development
#10
Helen Spiers, Eilis Hannon, Leonard C Schalkwyk, Nicholas J Bray, Jonathan Mill
BACKGROUND: Epigenetic processes play a key role in orchestrating transcriptional regulation during the development of the human central nervous system. We previously described dynamic changes in DNA methylation (5mC) occurring during human fetal brain development, but other epigenetic processes operating during this period have not been extensively explored. Of particular interest is DNA hydroxymethylation (5hmC), a modification that is enriched in the human brain and hypothesized to play an important role in neuronal function, learning and memory...
September 18, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28922742/glytoucan-an-accessible-glycan-structure-repository
#11
Michael Tiemeyer, Kazuhiro Aoki, James Paulson, Richard D Cummings, William S York, Niclas G Karlsson, Frederique Lisacek, Nicolle H Packer, Matthew P Campbell, Nobuyuki P Aoki, Akihiro Fujita, Masaaki Matsubara, Daisuke Shinmachi, Shinichiro Tsuchiya, Issaku Yamada, Michael Pierce, René Ranzinger, Hisashi Narimatsu, Kiyoko F Aoki-Kinoshita
Rapid and continued growth in the generation of glycomic data has revealed the need for enhanced development of basic infrastructure for presenting and interpreting these datasets in a manner that engages the broader biomedical research community. Early in their growth, the genomic and proteomic fields implemented mechanisms for assigning unique gene and protein identifiers that were essential for organizing data presentation and for enhancing bioinformatic approaches to extracting knowledge. Similar unique identifiers are currently absent from glycomic data...
October 1, 2017: Glycobiology
https://www.readbyqxmd.com/read/28922347/pearl-millet-genome-sequence-provides-a-resource-to-improve-agronomic-traits-in-arid-environments
#12
Rajeev K Varshney, Chengcheng Shi, Mahendar Thudi, Cedric Mariac, Jason Wallace, Peng Qi, He Zhang, Yusheng Zhao, Xiyin Wang, Abhishek Rathore, Rakesh K Srivastava, Annapurna Chitikineni, Guangyi Fan, Prasad Bajaj, Somashekhar Punnuri, S K Gupta, Hao Wang, Yong Jiang, Marie Couderc, Mohan A V S K Katta, Dev R Paudel, K D Mungra, Wenbin Chen, Karen R Harris-Shultz, Vanika Garg, Neetin Desai, Dadakhalandar Doddamani, Ndjido Ardo Kane, Joann A Conner, Arindam Ghatak, Palak Chaturvedi, Sabarinath Subramaniam, Om Parkash Yadav, Cécile Berthouly-Salazar, Falalou Hamidou, Jianping Wang, Xinming Liang, Jérémy Clotault, Hari D Upadhyaya, Philippe Cubry, Bénédicte Rhoné, Mame Codou Gueye, Ramanjulu Sunkar, Christian Dupuy, Francesca Sparvoli, Shifeng Cheng, R S Mahala, Bharat Singh, Rattan S Yadav, Eric Lyons, Swapan K Datta, C Tom Hash, Katrien M Devos, Edward Buckler, Jeffrey L Bennetzen, Andrew H Paterson, Peggy Ozias-Akins, Stefania Grando, Jun Wang, Trilochan Mohapatra, Wolfram Weckwerth, Jochen C Reif, Xin Liu, Yves Vigouroux, Xun Xu
Pearl millet [Cenchrus americanus (L.) Morrone] is a staple food for more than 90 million farmers in arid and semi-arid regions of sub-Saharan Africa, India and South Asia. We report the ∼1.79 Gb draft whole genome sequence of reference genotype Tift 23D2B1-P1-P5, which contains an estimated 38,579 genes. We highlight the substantial enrichment for wax biosynthesis genes, which may contribute to heat and drought tolerance in this crop. We resequenced and analyzed 994 pearl millet lines, enabling insights into population structure, genetic diversity and domestication...
September 18, 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/28921870/detection-and-genetic-characterization-of-porcine-circovirus-type-3-in-italy
#13
S Faccini, I Barbieri, A Gilioli, G Sala, L R Gibelli, A Moreno, C Sacchi, C Rosignoli, G Franzini, A Nigrelli
Porcine circovirus type 3 (PCV3) was recently proposed as a new porcine circovirus. It has been described by researchers in the USA and China and associated with porcine dermatitis and nephropathy syndrome, reproductive failure and systemic inflammation disease. The study reports the occurrence of the new virus in Italy. PCV3 was detected in the tissues of foetuses and stillborn piglets coming from two farms located in the Po Valley. The genome sequences of the two Italian strains share 99.7% to 97.8% of nucleotide identity with those available in GenBank...
September 17, 2017: Transboundary and Emerging Diseases
https://www.readbyqxmd.com/read/28921760/genome-wide-association-study-of-a-nicotine-metabolism-biomarker-in-african-american-smokers-impact-of-chromosome-19-genetic-influences
#14
Meghan J Chenoweth, Jennifer J Ware, Andy Z X Zhu, Christopher B Cole, Lisa Sanderson Cox, Nikki Nollen, Jasjit S Ahluwalia, Neal L Benowitz, Robert A Schnoll, Larry W Hawk, Paul M Cinciripini, Tony P George, Caryn Lerman, Joanne Knight, Rachel F Tyndale
BACKGROUND AND AIMS: The activity of CYP2A6, the major nicotine-inactivating enzyme, is measurable in smokers using the nicotine metabolite ratio (NMR; 3'hydroxycotinine/cotinine). Due to its role in nicotine clearance, the NMR is associated with smoking behaviours and response to pharmacotherapies. The NMR is highly heritable (~80%), and on average lower in African Americans (AA) versus Whites. We previously identified several reduce and loss-of-function CYP2A6 variants common in individuals of African descent...
September 16, 2017: Addiction
https://www.readbyqxmd.com/read/28920716/transposons-moving-forward-from-preclinical-studies-to-clinical-trials
#15
Jaitip Tipanee, Thierry VandenDriessche, Marinee K Chuah
Transposons have emerged as promising vectors for gene therapy that can potentially overcome some of the limitations of commonly used viral vectors. Transposons stably integrate into the target cell genome, enabling persistent expression of therapeutic genes. Transposons have evolved from being used as basic tools in biomedical research to bona fide therapeutics. Currently, the most promising transposons for gene therapy applications are derived from Sleeping Beauty (SB) or piggyBac (PB). Stable transposition requires co-delivery of the transposon DNA with the corresponding transposase gene, mRNA, or protein...
August 22, 2017: Human Gene Therapy
https://www.readbyqxmd.com/read/28920489/primer-in-genetics-and-genomics-article-5-further-defining-the-concepts-of-genotype-and-phenotype-and-exploring-genotype-phenotype-associations
#16
Fay Wright, Kristen Fessele
As nurses begin to incorporate genetic and genomic sciences into clinical practice, education, and research, it is essential that they have a working knowledge of the terms foundational to the science. The first article in this primer series provided brief definitions of the basic terms (e.g., genetics and genomics) and introduced the concept of phenotype during the discussion of Mendelian inheritance. These terms, however, are inconsistently used in publications and conversations, and the linkage between genotype and phenotype requires clarification...
October 2017: Biological Research for Nursing
https://www.readbyqxmd.com/read/28919992/molecular-and-clinical-characterization-of-tim-3-in-glioma-through-1-024-samples
#17
Guanzhang Li, Zheng Wang, Chuanbao Zhang, Xing Liu, Jinquan Cai, Zhiliang Wang, Huimin Hu, Fan Wu, Zhaoshi Bao, Yanwei Liu, Liang Zhao, Tingyu Liang, Fan Yang, Ruoyu Huang, Wei Zhang, Tao Jiang
Background: Researches on immunotherapy of glioma has been increasing exponentially in recent years. However, autoimmune-like side effects of current immune checkpoint blockade hindered the clinical application of immunotherapy in glioma. The discovery of the TIM-3, a tumor-specific immune checkpoint, has shed a new light on solution of this dilemma. We aimed at investigating the role of TIM-3 at transcriptome level and its relationship with clinical practice in glioma. Methods: A cohort of 325 glioma patients with RNA-seq data from Chinese Glioma Genome Atlas (CGGA project) was analyzed, and the results were well validated in TCGA RNA-seq data of 699 gliomas...
2017: Oncoimmunology
https://www.readbyqxmd.com/read/28919981/regulation-of-cancer-epigenomes-with-a-histone-binding-synthetic-transcription-factor
#18
David B Nyer, Rene M Daer, Daniel Vargas, Caroline Hom, Karmella A Haynes
Chromatin proteins have expanded the mammalian synthetic biology toolbox by enabling control of active and silenced states at endogenous genes. Others have reported synthetic proteins that bind DNA and regulate genes by altering chromatin marks, such as histone modifications. Previously, we reported the first synthetic transcriptional activator, the "Polycomb-based transcription factor" (PcTF) that reads histone modifications through a protein-protein interaction between the polycomb chromodomain motif and trimethylated lysine 27 of histone H3 (H3K27me3)...
2017: NPJ Genomic Medicine
https://www.readbyqxmd.com/read/28919972/cytogenetic-maps-of-homoeologous-chromosomes-a-h01-and-d-h01-and-their-integration-with-the-genome-assembly-in-gossypium-hirsutum
#19
Yuling Liu, Zhen Liu, Renhai Peng, Yuhong Wang, Zhongli Zhou, Xiaoyan Cai, Xingxing Wang, Zhenmei Zhang, Kunbo Wang, Fang Liu
Cytogenetic maps of Gossypium hirsutum (Linnaeus, 1753) homoeologous chromosomes Ah01 and Dh01 were constructed by fluorescence in situ hybridization (FISH), using eleven homoeologous-chromosomes-shared bacterial artificial chromosomes (BACs) clones and one chromosome-specific BAC clone respectively. We compared the cytogenetic maps with the genetic linkage and draft genome assembly maps based on a standardized map unit, relative map position (RMP), which allowed a global view of the relationship of genetic and physical distances along each chromosome, and assembly quality of the draft genome assembly map...
2017: Comparative Cytogenetics
https://www.readbyqxmd.com/read/28919449/genome-editing-in-fishes-and-their-applications
#20
Bo Zhu, Wei Ge
There have been revolutionary progresses in genome engineering in the past few years. The newly-emerged genome editing technologies including zinc-finger nuclease (ZFN), transcription activator-like effector nuclease (TALEN) and clustered regularly interspaced short palindromic repeats associated with Cas9 (CRISPR/Cas9) have enabled biological scientists to perform efficient and precise targeted genome editing in different species. Fish represent the largest group of vertebrates with many species having values for both scientific research and aquaculture industry...
September 14, 2017: General and Comparative Endocrinology
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