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Genomic selection

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https://www.readbyqxmd.com/read/29332211/testosterone-mediated-upregulation-of-delayed-rectifier-potassium-channel-in-cardiomyocytes-causes-abbreviation-of-qt-intervals-in-rats
#1
Kimiko Masuda, Hiroki Takanari, Masaki Morishima, FangFang Ma, Yan Wang, Naohiko Takahashi, Katsushige Ono
Men have shorter rate-corrected QT intervals (QTc) than women, especially at the period of adolescence or later. The aim of this study was to elucidate the long-term effects of testosterone on cardiac excitability parameters including electrocardiogram (ECG) and potassium channel current. Testosterone shortened QT intervals in ECG in castrated male rats, not immediately after, but on day 2 or later. Expression of Kv7.1 (KCNQ1) mRNA was significantly upregulated by testosterone in cardiomyocytes of male and female rats...
January 13, 2018: Journal of Physiological Sciences: JPS
https://www.readbyqxmd.com/read/29332164/skewing-of-the-genetic-architecture-at-the-zmym3-human-specific-5-utr-short-tandem-repeat-in-schizophrenia
#2
F Alizadeh, A Bozorgmehr, J Tavakkoly-Bazzaz, M Ohadi
Differential expansion of a number of human short tandem repeats (STRs) at the critical core promoter and 5' untranslated region (UTR) support the hypothesis that at least some of these STRs may provide a selective advantage in human evolution. Following a genome-wide screen of all human protein-coding gene 5' UTRs based on the Ensembl database ( http://www.ensembl.org ), we previously reported that the longest STR in this interval is a (GA)32, which belongs to the X-linked zinc finger MYM-type containing 3 (ZMYM3) gene...
January 13, 2018: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/29332151/1h-13c-and-15n-backbone-and-partial-side-chain-resonance-assignments-of-the-c-terminal-domain-of-hiv-1-pr55gag-encompassed-in-ncp15
#3
Valéry Larue, Marjorie Catala, Anissa Belfetmi, Loussiné Zargarian, Olivier Mauffret, Carine Tisné
During HIV-1 assembly, the Pr55Gag polyprotein precursor (Gag) interacts with the genomic RNA, with lipids of the plasma membrane, with host proteins (ALIX, TSG101) through the ESCRT complex, with the viral protein Vpr and are involved in intermolecular interactions with other Pr55Gag proteins. This network of interactions is responsible for the formation of the viral particle, the selection of genomic RNA and the packaging of Vpr. The C-terminal domain of Gag encompassed in NCp15 is involved in the majority of these interactions, either by its nucleocapsid or its p6 domains...
January 13, 2018: Biomolecular NMR Assignments
https://www.readbyqxmd.com/read/29331751/comprehensive-genomic-profiling-of-head-and-neck-squamous-cell-carcinoma-reveals-fgfr1-amplifications-and-tumour-genomic-alterations-burden-as-prognostic-biomarkers-of-survival
#4
C Dubot, V Bernard, M P Sablin, S Vacher, W Chemlali, A Schnitzler, G Pierron, K Ait Rais, N Bessoltane, E Jeannot, J Klijanienko, O Mariani, T Jouffroy, V Calugaru, C Hoffmann, M Lesnik, N Badois, F Berger, C Le Tourneau, M Kamal, I Bieche
BACKGROUND: We aimed at identifying deleterious genomic alterations from untreated head and neck squamous cell carcinoma (HNSCC) patients, and assessing their prognostic value. PATIENTS AND METHODS: We retrieved 122 HNSCC patients who underwent primary surgery. Targeted NGS was used to analyse a panel of 100 genes selected among the most frequently altered genes in HNSCC and potential therapeutic targets. We selected only deleterious (activating or inactivating) single nucleotide variations, and copy number variations for analysis...
January 10, 2018: European Journal of Cancer
https://www.readbyqxmd.com/read/29331527/construction-of-sake-yeast-with-low-production-of-dimethyl-trisulfide-precursor-by-a-self-cloning-method
#5
Yuriko Ikeda, Atsuko Isogai, Yuta Moriyoshi, Ryoko Kanda, Kazuhiro Iwashita, Tsutomu Fujii
Dimethyl trisulfide (DMTS) is the primary component responsible for "hineka", the stale aroma of Japanese sake. Deletion of the MRI1 or MDE1 gene of sake yeast, encoding 5'-methylthioribose-1-phosphate isomerase and 5'-methylthioribulose-1-phosphate dehydratase, respectively, has been reported to greatly reduce the amount of DMTS precursor (DMTS-P1) in sake and to suppress the formation of DMTS during storage. In this study, we constructed sake yeast strains lacking MRI1 gene function by a self-cloning method...
January 10, 2018: Journal of Bioscience and Bioengineering
https://www.readbyqxmd.com/read/29331471/symposium-review-novel-strategies-to-genetically-improve-mastitis-resistance-in-dairy-cattle
#6
P Martin, H W Barkema, L F Brito, S G Narayana, F Miglior
Mastitis is a disease of major economic importance to the dairy cattle sector because of the high incidence of clinical mastitis and prevalence of subclinical mastitis and, consequently, the costs associated with treatment, production losses, and reduced animal welfare. Disease-recording systems compiling data from a large number of farms are still not widely implemented around the world; thus, selection for mastitis resistance is often based on genetically correlated indicator traits such as somatic cell count (SCC), udder depth, and fore udder attachment...
January 10, 2018: Journal of Dairy Science
https://www.readbyqxmd.com/read/29331465/genome-wide-association-study-for-milk-infrared-wavenumbers
#7
Qiuyu Wang, Henk Bovenhuis
Individual wavenumbers of the infrared (IR) spectra of bovine milk have been shown to be moderately to highly heritable. The objective of this study was to identify genomic regions associated with individual milk IR wavenumbers. This is expected to provide information about the genetic background of milk composition and give insight in the relation between IR wavenumbers and milk components. For this purpose, a genome-wide association study was performed for a selected set of 50 individual IR wavenumbers measured on 1,748 Dutch Holstein cows...
January 10, 2018: Journal of Dairy Science
https://www.readbyqxmd.com/read/29331262/can-interrogation-of-tumour-characteristics-lead-us-to-safely-omit-adjuvant-radiotherapy-in-patients-with-early-breast-cancer
#8
I S Bhattacharya, A M Kirby, J M Bliss, C E Coles
Adjuvant radiotherapy after breast-conserving surgery has been an important component of the standard of care for early breast cancer. Improvements in breast cancer care have resulted in a substantial reduction in local relapse rates over recent decades. Although the proportional benefits of adjuvant radiotherapy are similar for different prognostic risk groups of patients, the absolute benefits depend on the risk of relapse and therefore vary considerably between prognostic groups. Radiotherapy is not without risk and for some patients at very low risk of relapse the risks of radiotherapy may outweigh the benefit, leading to potential overtreatment...
January 10, 2018: Clinical Oncology: a Journal of the Royal College of Radiologists
https://www.readbyqxmd.com/read/29331019/cis-regulator-runaway-and-divergence-in-asexuals
#9
Frédéric Fyon, Thomas Lenormand
With the advent of new sequencing technologies, the evolution of gene expression is becoming a subject of intensive genomic research, with sparking debates upon the role played by these kinds of changes in adaptive evolution and speciation. In this paper, we model expression evolution in species differing by their reproductive systems. We consider different rates of sexual versus asexual reproduction and the different type of parthenogenesis (apomixis and the various modes of automixis). We show that competition for expression leads to two selective processes on cis-regulatory regions that act independently to organism-level adaptation...
January 13, 2018: Evolution; International Journal of Organic Evolution
https://www.readbyqxmd.com/read/29330918/leptosphaeria-maculans-avrlm9-a-new-player-in-the-game-of-hide-and-seek-with-avrlm4-7
#10
Kaveh Ghanbarnia, Lisong Ma, Nicholas J Larkan, Parham Haddadi, W G Dilantha Fernando, M Hossein Borhan
Blackleg disease of Brassica napus caused by Leptosphaeria maculans (Lm) is largely controlled by deploying race-specific resistance (R) genes. However, selection pressure exerted by R genes causes Lm to adapt and give rise to new virulent strains through mutation and deletion of effector genes. Therefore, knowledge of effector gene function is necessary for effective management of the disease. Here we report cloning of Lm effector AvrLm9 that is recognised by the resistance gene Rlm9 in B. napus cultivar Goéland...
January 13, 2018: Molecular Plant Pathology
https://www.readbyqxmd.com/read/29330893/mitogenomic-differences-between-the-normal-and-tumour-cells-of-colorectal-cancer-patients
#11
Katarzyna Skonieczna, Boris Malyarchuk, Arkadiusz Jawień, Andrzej Marszałek, Zbigniew Banaszkiewicz, Paweł Jarmocik, Tomasz Grzybowski
So far, a reliable spectrum of mitochondrial DNA mutations in colorectal cancer cells is still unknown, and neither is their significance in carcinogenesis. Indeed, it remains debatable whether mtDNA mutations are "drivers" or "passengers" of colorectal carcinogenesis. Thus, we analyzed 200 mitogenomes from normal and cancer tissues of 100 colorectal cancer patients. Minority variant mutations were detected at the 1% level. We showed that somatic mutations frequently occur in colorectal cancer cells (75%) and are randomly distributed across the mitochondrial genome...
January 12, 2018: Human Mutation
https://www.readbyqxmd.com/read/29330726/ultra-deep-genomic-sequencing-of-hcv-ns5a-resistance-associated-substitutions-in-hcv-hiv-coinfected-patients
#12
Enass A Abdel-Hameed, Susan D Rouster, Ceejay L Boyce, Xiang Zhang, Jacek Biesiada, Mario Medvedovic, Kenneth E Sherman
BACKGROUND AND AIMS: The prevalence of naturally occurring HCV-NS5A resistance-associated substitutions (RAS) to DAA drugs might affect the response to treatment in HCV/HIV coinfected subjects. There are limited data on the frequency of HCV-NS5A naturally occurring drug-RAS at baseline in HCV/HIV coinfected patients when ultra-deep sequencing methodologies are applied. METHODS: HCV-NS5A-RAS were evaluated among 25 subjects in each group. Patients were matched by age, gender, and hepatic fibrosis stage category to control for selection bias...
January 12, 2018: Digestive Diseases and Sciences
https://www.readbyqxmd.com/read/29330722/location-of-low-copy-genes-in-chromosomes-of-brachiaria-spp
#13
Thaís Furtado Nani, James C Schnable, Jacob D Washburn, Patrice Albert, Welison Andrade Pereira, Fausto Souza Sobrinho, James A Birchler, Vânia Helena Techio
Repetitive DNA sequences have been widely used in cytogenetic analyses. The use of gene sequences with a low-copy-number, however, is little explored especially in plants. To date, the karyotype details in Brachiaria spp. are limited to the location of rDNA sites. The challenge lies in developing new probes based on incomplete sequencing data for the genus or complete sequencing of related species, since there are no model species with a sequenced genome in Brachiaria spp. The present study aimed at the physical location of conserved genes in chromosomes of Brachiaria ruziziensis, Brachiaria brizantha, and Brachiaria decumbens using RNAseq data, as well as sequences of Setaria italica and Sorghum bicolor through the fluorescent in situ hybridization technique...
January 12, 2018: Molecular Biology Reports
https://www.readbyqxmd.com/read/29330664/an-iranian-genomic-sequence-of-beet-mosaic-virus-provides-insights-into-diversity-and-evolution-of-the-world-population
#14
Musa Mohammadi, Adrian J Gibbs, Ahmad Hosseini, Samin Hosseini
Beet mosaic virus (BtMV), the only Potyvirus known to infect sugar beet, occurs worldwide in beet crops. The full genome sequencing of a BtMV isolate from Iran (Ir-VRU), enabled us to better understand the evolutionary history of this virus. Selection analysis suggested that BtMV evolution is mainly under negative selection but its strength varies in different proteins with the multifunctional proteins under strongest selection. Recombination has played a major role in the evolution of the BtMVs; only the Ir-VRU and USA isolates show no evidence of recombination...
January 12, 2018: Virus Genes
https://www.readbyqxmd.com/read/29330592/genomic-characterization-of-key-bacteriophages-to-formulate-the-potential-biocontrol-agent-to-combat-enteric-pathogenic-bacteria
#15
Krupa M Parmar, Nishant A Dafale, Hitesh Tikariha, Hemant J Purohit
Combating bacterial pathogens has become a global concern especially when the antibiotics and chemical agents are failing to control the spread due to its resistance. Bacteriophages act as a safe biocontrol agent by selectively lysing the bacterial pathogens without affecting the natural beneficial microflora. The present study describes the screening of prominent enteric pathogens NDK1, NDK2, NDK3, and NDK4 (Escherichia, Klebsiella, Enterobacter, and Serratia) mostly observed in domestic wastewater; against which KNP1, KNP2, KNP3, and KNP4 phages were isolated...
January 12, 2018: Archives of Microbiology
https://www.readbyqxmd.com/read/29330493/development-of-versatile-non-homologous-end-joining-based-knock-in-module-for-genome-editing
#16
Shun Sawatsubashi, Yudai Joko, Seiji Fukumoto, Toshio Matsumoto, Shigeo S Sugano
CRISPR/Cas9-based genome editing has dramatically accelerated genome engineering. An important aspect of genome engineering is efficient knock-in technology. For improved knock-in efficiency, the non-homologous end joining (NHEJ) repair pathway has been used over the homology-dependent repair pathway, but there remains a need to reduce the complexity of the preparation of donor vectors. We developed the versatile NHEJ-based knock-in module for genome editing (VIKING). Using the consensus sequence of the time-honored pUC vector to cut donor vectors, any vector with a pUC backbone could be used as the donor vector without customization...
January 12, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29330484/single-cell-rna-sequencing-resolves-self-antigen-expression-during-mtec-development
#17
Ricardo J Miragaia, Xiuwei Zhang, Tomás Gomes, Valentine Svensson, Tomislav Ilicic, Johan Henriksson, Gozde Kar, Tapio Lönnberg
The crucial capability of T cells for discrimination between self and non-self peptides is based on negative selection of developing thymocytes by medullary thymic epithelial cells (mTECs). The mTECs purge autoreactive T cells by expression of cell-type specific genes referred to as tissue-restricted antigens (TRAs). Although the autoimmune regulator (AIRE) protein is known to promote the expression of a subset of TRAs, its mechanism of action is still not fully understood. The expression of TRAs that are not under the control of AIRE also needs further characterization...
January 12, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29330432/developing-genome-wide-snps-and-constructing-an-ultrahigh-density-linkage-map-in-oil-palm
#18
Bin Bai, Le Wang, Ying Jun Zhang, May Lee, Rahmadsyah Rahmadsyah, Yuzer Alfiko, Bao Qing Ye, Sigit Purwantomo, Antonius Suwanto, Nam-Hai Chua, Gen Hua Yue
Oil palm (Elaeis guineensis Jacq.) is the leading oil-producing crops and the most important edible oil resource worldwide. DNA markers and genetic linkage maps are essential resources for marker-assisted selection to accelerate genetic improvement. We conducted RAD-seq on an Illumina NextSeq500 to discover genome-wide SNPs, and used the SNPs to construct a linkage map for an oil palm (Tenera) population derived from a cross between a Deli Dura and an AVROS Pisifera. The RAD-seq produced 1,076 million single-end reads across the breeding population containing 155 trees...
January 12, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29330349/pharmacologic-inhibition-of-phospholipase-c-in-the-brain-attenuates-early-memory-formation-in-the-honeybee-apis-mellifera-l
#19
Shota Suenami, Shiori Iino, Takeo Kubo
Although the molecular mechanisms involved in learning and memory in insects have been studied intensively, the intracellular signaling mechanisms involved in early memory formation are not fully understood. We previously demonstrated that phospholipase C epsilon (PLCe), whose product is involved in calcium signaling, is almost selectively expressed in the mushroom bodies, a brain structure important for learning and memory in the honeybee. Here, we pharmacologically examined the role of phospholipase C (PLC) in learning and memory in the honeybee...
January 12, 2018: Biology Open
https://www.readbyqxmd.com/read/29330297/characterization-and-evidence-of-the-mir-888-cluster-as-a-novel-cancer-network-in-prostate
#20
Tsuyoshi Hasegawa, Garrison Glavich, Mary Pahuski, Aleena M Short, Oliver John Semmes, Lifang Yang, Vitold Galkin, Richard R Drake, Aurora Esquela-Kerscher
Prostate cancer afflicts 1 in 7 men and is the second leading cause of male cancer-related deaths in the United States. MicroRNAs (miRNAs), an extensive class of ~22 nucleotide non-coding RNAs, are often aberrantly expressed in tissues and fluids from prostate cancer patients but the mechanism of how specific miRNAs regulate prostate tumorigenesis and metastasis are poorly understood. Here, miR-888 was identified as a novel prostate factor that promotes proliferation and migration. miR-888 resides within a genomic cluster of 7 miRNA genes (mir-892c, mir-890, mir-888, mir-892a, mir-892b, mir-891b, mir-891a) on human chromosome Xq27...
January 12, 2018: Molecular Cancer Research: MCR
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