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https://www.readbyqxmd.com/read/28823137/survey-of-genetic-structure-of-geese-using-novel-microsatellite-markers
#1
Fang-Yu Lai, Po-An Tu, Shih-Torng Ding, Min-Jung Lin, Shen-Chang Chang, En-Chung Lin, Ling-Ling Lo, Pei-Hwa Wang
Objective: The aim of this study was to create a set of microsatellite markers with high polymorphism for the genetic monitoring and genetic structure analysis of local goose populations. Methods: Novel microsatellite markers were isolated from the genomic DNA of white Roman geese using short tandem repeated probes. The DNA segments, including short tandem repeats, were tested for their variability among four populations of geese from the Changhua Animal Propagation Station (CAPS)...
August 16, 2017: Asian-Australasian Journal of Animal Sciences
https://www.readbyqxmd.com/read/28823121/characterization-of-the-porcine-nanog-5-flanking-region
#2
Azra Memon, Ki-Duk Song, Woon Kyu Lee
Objective: Nanog, a homeodomain protein, has been investigated in humans and mice using ESCs. Because of the limited availability of ESCs, few studies have reported the function and role of Nanog in porcine ESCs. Therefore, in this study, we investigated the location of the porcine Nanog chromosome and its basal promoter activity, which might have potential applications in development of ESs specific marker as well as understanding its operating systems in the porcine. Methods: To characterize the porcine Nanog promoter, the 5'-flanking region of Nanog was isolated from cells of mini-pig ears...
August 16, 2017: Asian-Australasian Journal of Animal Sciences
https://www.readbyqxmd.com/read/28823120/deoxynivalenol-and-zearalenone-contaminated-feeds-alter-gene-expression-profiles-in-the-livers-of-piglets
#3
Kondreddy Eswar Reddy, Jin Young Jeong, Yookyung Lee, Hyun-Jeong Lee, Min Seok Kim, Dong-Wook Kim, Hyun Jung Jung, Changyong Choe, Young Kyoon Oh, Sung Dae Lee
Objective: The Fusarium mycotoxins of deoxynivalenol (DON) and zerolenone (ZEN) cause health hazards for both humans and farm animals. Therefore, the main intention of this study was to reveal DON and ZEN effects on the mRNA expression of pro-inflammatory cytokines and other immune related genes in the liver of piglets. Methods: In the present study, 15 six-week-old piglets were randomly assigned to the following three different dietary treatments for 4 weeks: control diet, diet containing 8 mg DON/kg feed, and diet containing 0...
August 16, 2017: Asian-Australasian Journal of Animal Sciences
https://www.readbyqxmd.com/read/28822857/exploring-associations-of-clinical-and-social-parameters-with-violent-behaviors-among-psychiatric-patients
#4
Hong-Jie Dai, Emily Chia-Yu Su, Mohy Uddin, Jitendra Jonnagaddala, Chi-Shin Wu, Shabbir Syed-Abdul
Evidence has revealed interesting associations of clinical and social parameters with violent behaviors of patients with psychiatric disorders. Men are more violent preceding and during hospitalization, whereas women are more violent than men throughout the 3 days following a hospital admission. It has also been proven that mental disorders may be a consistent risk factor for the occurrence of violence. In order to better understand violent behaviors of patients with psychiatric disorders, it is important to investigate both the clinical symptoms and psychosocial factors that accompany violence in these patients...
August 16, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28822827/host-genes-regulate-transcription-of-sperm-introduced-hepatitis-b-virus-genes-in-embryo
#5
Ying Zhong, Dong-Ling Liu, Mohamed Morsi M Ahmed, Peng-Hao Li, Xiao-Ling Zhou, Qing-Dong Xie, Xiao-Qing Xu, Ting-Ting Han, Zhi-Wei Hou, Chen-Yao Zhong, Ji-Hua Huang, Fei Zeng, Tian-Hua Huang
Hepatitis B virus (HBV) can invade the male germline, and sperm-introduced HBV genes could be transcribed in embryo. This study was to explore whether viral gene transcription is regulated by host genes. Embryos were produced by in vitro fertilization of hamster oocytes with human sperm containing the HBV genome. Total RNA extracted from test and control embryos were subjected to SMART-PCR, SSH, microarray hybridization, sequencing and BLAST analysis. Twenty-nine sequences showing significant identity to five human gene families were identified, with CSH2, EIF4G2, PCBD2, PSG4 and TTN selected to represent target genes...
August 16, 2017: Reproductive Toxicology
https://www.readbyqxmd.com/read/28822795/strategies-for-analyzing-bisulfite-sequencing-data
#6
Katarzyna Wreczycka, Alexander Gosdschan, Dilmurat Yusuf, Björn Grüning, Yassen Assenov, Altuna Akalin
DNA methylation is one of the main epigenetic modifications in the eukaryotic genome; it has been shown to play a role in cell-type specific regulation of gene expression, and therefore cell-type identity. Bisulfite sequencing is the gold-standard for measuring methylation over the genomes of interest. Here, we review several techniques used for the analysis of high-throughput bisulfite sequencing. We introduce specialized short-read alignment techniques as well as pre/post-alignment quality check methods to ensure data quality...
August 16, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28822783/the-expression-induction-and-pharmacological-activity-of-cyp1a2-are-post-transcriptionally-regulated-by-microrna-hsa-mir-132-5p
#7
Yinting Chen, Linjuan Zeng, Yong Wang, William H Tolleson, Bridgett Knox, Si Chen, Zhen Ren, Lei Guo, Nan Mei, Feng Qian, Kaihong Huang, David Liu, Weida Tong, Dianke Yu, Baitang Ning
Cytochrome P450 1A2 (CYP1A2) is one of the most abundant and important drug metabolizing enzymes in human liver. However, little is known about the post-transcriptional regulation of CYP1A2, especially the mechanisms involving microRNAs (miRNAs). This study applied a systematic approach to investigate the post-transcriptional regulation of CYP1A2 by miRNAs. Candidate miRNAs targeting the 3'-untranslated region (3'-UTR) of CYP1A2 were screened in silico, resulting in the selection of sixty-two potential miRNAs for further analysis...
August 16, 2017: Biochemical Pharmacology
https://www.readbyqxmd.com/read/28822753/the-genepattern-notebook-environment
#8
Michael Reich, Thorin Tabor, Ted Liefeld, Helga Thorvaldsdóttir, Barbara Hill, Pablo Tamayo, Jill P Mesirov
Interactive analysis notebook environments promise to streamline genomics research through interleaving text, multimedia, and executable code into unified, sharable, reproducible "research narratives." However, current notebook systems require programming knowledge, limiting their wider adoption by the research community. We have developed the GenePattern Notebook environment (http://www.genepattern-notebook.org), to our knowledge the first system to integrate the dynamic capabilities of notebook systems with an investigator-focused, easy-to-use interface that provides access to hundreds of genomic tools without the need to write code...
August 14, 2017: Cell Systems
https://www.readbyqxmd.com/read/28822700/full-length-genome-of-a-novel-genotype-3-hepatitis-e-virus-strain-obtained-from-domestic-pigs-in-japan
#9
Putu Prathiwi Primadharsini, Masao Miyake, Satoshi Kunita, Tsutomu Nishizawa, Masaharu Takahashi, Shigeo Nagashima, Tanggis, Hiroshi Ohnishi, Tominari Kobayashi, Takashi Nishiyama, Suljid Jirintai, Hiroaki Okamoto
Hepatitis E virus (HEV) causes acute or chronic hepatitis in humans and can be transmitted via the fecal-oral route. Pigs are one of the main reservoirs for this infection. Sixty pigs, 4-5 months of age, on a swine herd in Japan had detectable anti-HEV IgG antibodies, and five (8.3%) of them had ongoing infection of genotype 3 HEV. Five HEV strains obtained from the viremic pigs shared 98.8-100% nucleotide identity, and one representative strain (swHE1606845), whose entire genomic sequence was determined in this study, differed by 14...
August 16, 2017: Virus Research
https://www.readbyqxmd.com/read/28822699/extent-and-evolution-of-gene-duplication-in-dna-viruses
#10
Yuxia Gao, Huayao Zhao, Yin Jin, Xiaoyu Xu, Guan-Zhu Han
Gene duplication is the main source of genomic novelties and complexities for both eukaryotes and prokaryotes. In contrast, gene duplication appears to be infrequent in the RNA viruses. However, the extent and evolution of gene duplication in DNA viruses remains obscure. Here we perform a genome-wide analysis of gene duplication in the genomes of 250 DNA viruses that represent all known DNA viral genera. While no gene duplication event is identified in single stranded DNA (ssDNA) or reverse transcribing DNA viruses, gene duplication is frequent among double stranded DNA (dsDNA) viruses...
August 16, 2017: Virus Research
https://www.readbyqxmd.com/read/28822625/landscaping-crossover-interference-across-a-genome
#11
REVIEW
Lidan Sun, Jing Wang, Mengmeng Sang, Libo Jiang, Bingyu Zhao, Tangran Cheng, Qixiang Zhang, Rongling Wu
The evolutionary success of eukaryotic organisms crucially depends on the capacity to produce genetic diversity through reciprocal exchanges of each chromosome pair, or crossovers (COs), during meiosis. It has been recognized that COs arise more evenly across a given chromosome than at random. This phenomenon, termed CO interference, occurs pervasively in eukaryotes and may confer a selective advantage. We describe here a multipoint linkage analysis procedure for segregating families to quantify the strength of CO interference over the genome, and extend this procedure to illustrate the landscape of CO interference in natural populations...
August 16, 2017: Trends in Plant Science
https://www.readbyqxmd.com/read/28822012/mtor-co-targeting-strategies-for-head-and-neck-cancer-therapy
#12
Zhiyong Wang, Juan Callejas Valera, Xuefeng Zhao, Qianming Chen, J Silvio Gutkind
Head and neck squamous cell carcinoma (HNSCC) is the sixth most common malignancy worldwide. There is an urgent need to develop effective therapeutic approaches to prevent and treat HNSCC. Recent deep sequencing of the HNSCC genomic landscape revealed a multiplicity and diversity of genetic alterations in this malignancy. Although a large variety of specific molecules were found altered in each individual tumor, they all participate in only a handful of driver signaling pathways. Among them, the PI3K/mTOR pathway is the most frequently activated, which plays a central role in cancer initiation and progression...
August 18, 2017: Cancer Metastasis Reviews
https://www.readbyqxmd.com/read/28821952/genome-wide-association-study-and-gene-set-analysis-for-understanding-candidate-genes-involved-in-salt-tolerance-at-the-rice-seedling-stage
#13
Jie Yu, Weiguo Zao, Qiang He, Tae-Sung Kim, Yong-Jin Park
Salt is the major factor limiting crop productivity in saline soils and is controlled by various genes. The development of salt-tolerant rice through molecular breeding methods is important to meet the needs of rice breeding. We used 295 accessions to perform a genome-wide association study (GWAS) of salt tolerance-related phenotypes in rice at the seedling stage and obtained 93 candidate genes with high association peaks across six phenotypes. We constructed a protein interaction network using the candidate genes identified here, and 33 genes were associated...
August 18, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28821798/unconventional-mapk-gsk-3%C3%AE-pathway-behind-atypical-epithelial-mesenchymal-transition-in-hepatocellular-carcinoma
#14
Sana Parveen, Dhiviya Vedagiri, Hitha Gopalan Nair, Haripriya Parthasarathy, Krishnan Harinivas Harshan
We recently reported an atypical epithelial mesenchymal transition (EMT) in human hepatoma cell culture Huh7.5, which was non-responsive to the canonical EMT-transcription factors. Here we characterize major pathways regulating this atypical EMT through whole genome transcriptome profiling and molecular analysis, and identify a unique regulation of EMT by GSK-3β. Our analysis reveals remarkable suppression of several key liver-specific markers in Huh7.5M cells indicating that EMT not only changes the epithelial properties, but alters the characteristics associated with hepatocytes as well...
August 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28821784/high-copy-and-stable-expression-of-the-xylanase-xynhb-in-saccharomyces-cerevisiae-by-rdna-mediated-integration
#15
Cheng Fang, Qinhong Wang, Jonathan Nimal Selvaraj, Yuling Zhou, Lixin Ma, Guimin Zhang, Yanhe Ma
Xylanase is a widely-used additive in baking industry for enhancing dough and bread quality. Several xylanases used in baking industry were expressed in different systems, but their expression in antibiotic free vector system is highly essential and safe. In the present study, an alternative rDNA-mediated technology was developed to increase the copy number of target gene by integrating it into Saccharomyces cerevisiae genome. A xylanase-encoding gene xynHB from Bacillus sp. was cloned into pHBM367H and integrated into S...
August 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28821745/metabolomics-and-genomics-combine-to-unravel-the-pathway-for-the-presence-of-fragrance-in-rice
#16
Venea Dara Daygon, Mariafe Calingacion, Louise C Forster, James J De Voss, Brett D Schwartz, Ben Ovenden, David E Alonso, Susan R McCouch, Mary J Garson, Melissa A Fitzgerald
Since it was first characterised in 1983, 2-acetyl-1-pyrroline (2AP) has been considered to be the most important aroma compound in rice. In this study, we show four other amine heterocycles: 6-methyl, 5-oxo-2,3,4,5-tetrahydropyridine (6M5OTP), 2-acetylpyrrole, pyrrole and 1-pyrroline, that correlate strongly with the production of 2AP, and are present in consistent proportions in a set of elite aromatic rice varieties from South East Asia and Australia as well as in a collection of recombinant inbred lines (RILs) derived from indica Jasmine-type varieties, Australian long grain varieties (temperate japonica) and Basmati-type rice (Grp V)...
August 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28821723/structural-and-developmental-expression-of-ss-riok-2-an-rio-protein-kinase-encoding-gene-of-strongyloides-stercoralis
#17
Wei-Qiang Lei, James B Lok, Wang Yuan, Yue-Zhou Zhang, Jonathan D Stoltzfus, Robin B Gasser, Si-Yuan He, Huan Zhou, Rui Zhou, Jun-Long Zhao, Min Hu
RIO kinases are essential atypical protein kinases in diverse prokaryotic and eukaryotic organisms, playing significant roles in yeast and humans. However, little is known about their functions in parasitic nematodes. In the present study, we have isolated and characterized the full-length cDNA, gDNA and a putative promoter of a RIOK-2 protein kinase (Ss-RIOK-2) encoding gene (Ss-riok-2) from Strongyloides stercoralis, a medically important parasitic nematode (Order Rhabditida). A three-dimensional structure (3D) model of Ss-RIOK-2 was generated using the Chaetomium thermophilum RIOK-2 protein kinase (Ct-RIOK-2) crystal structure 4GYG as a template...
August 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28821669/transcriptomic-analysis-of-ribosome-bound-mrna-in-cortical-neurites-in-vivo
#18
Rebecca Ouwenga, Allison M Lake, David O'Brien, Amit Mogha, Adish Dani, Joseph D Dougherty
Localized translation in neurites helps regulate synaptic strength and development. Dysregulation of local translation is associated with many neurological disorders. However, due to technical limitations, study of this phenomenon has largely been limited to brain regions with laminar organization of dendrites such as the hippocampus or cerebellum. It has not been examined in the cortex, a region of importance for most neurological disorders, where dendrites of each neuronal population are densely intermingled with cell bodies of others...
August 8, 2017: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
https://www.readbyqxmd.com/read/28821607/two-plant-derived-aporphinoid-alkaloids-exert-their-antifungal-activity-by-disrupting-mitochondrial-iron-sulfur-cluster-biosynthesis
#19
Siddharth K Tripathi, Tao Xu, Qin Feng, Bharathi Avula, Xiaomin Shi, Xuewen Pan, Melanie M Mask, Scott R Baerson, Melissa R Jacob, Ranga Rao Ravu, Shabana I Khan, Xing-Cong Li, Ikhlas A Khan, Alice M Clark, Ameeta K Agarwal
Eupolauridine and liriodenine are plant-derived aporphinoid alkaloids that exhibit potent inhibitory activity against the opportunistic fungal pathogens Candida albicans and Cryptococcus neoformans However, the molecular mechanism of this antifungal activity is unknown. In this study, we show that eupolauridine 9591 (E9591), a synthetic analog of eupolauridine, and liriodenine methiodide (LMT), a methiodide salt of liriodenine, mediate their antifungal activities by disrupting mitochondrial iron-sulfur (Fe-S) cluster synthesis...
August 18, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28821592/global-analysis-of-gene-expression-in-response-to-whole-chromosome-aneuploidy-in-hexaploid-wheat
#20
Ai Zhang, Ning Li, Lei Gong, Xiaowan Gou, Bin Wang, Xin Deng, Changping Li, Qianli Dong, Huakun Zhang, Bao Liu
Aneuploidy, a condition of unbalanced chromosome content, represents a large-effect mutation that bears significant relevancy to human health and microbe adaptation. As such, extensive studies of aneuploidy have been conducted in unicellular model organisms and cancer cells. Aneuploidy also frequently is associated with plant polyploidization, but its impact on gene expression and relevance to polyploid genome evolution/functional innovation remain largely unknown. Here, we used a panel of diverse types of whole-chromosome aneuploidy of hexaploid wheat, all under the common genetic background of cv...
August 18, 2017: Plant Physiology
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