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https://www.readbyqxmd.com/read/29475126/snp-rs403212791-in-exon-2-of-the-mtnr1a-gene-is-associated-with-reproductive-seasonality-in-the-rasa-aragonesa-sheep-breed
#1
J H Calvo, M Serrano, A Martinez-Royo, B Lahoz, P Sarto, A Ibañez-Deler, J Folch, J L Alabart
The aim of this study was to characterize and identify causative SNPs in the MTNR1A gene responsible for the reproductive seasonality traits in the Rasa aragonesa sheep breed. A total of 290 ewes (155, 84 and 51 mature, young and ewe lambs, respectively) from one flock were controlled from January to August. The following three reproductive seasonality traits were considered: the total days of anoestrus (TDA) and the progesterone cycling months (P4CM); both ovarian function seasonality traits based on blood progesterone levels; and the oestrus cycling months (OCM) based on oestrous detection, which indicate behavioural signs of oestrous...
February 12, 2018: Theriogenology
https://www.readbyqxmd.com/read/29475118/kockdown-of-oip5-as1-expression-inhibits-proliferation-metastasis-and-emt-progress-in-hepatoblastoma-cells-through-up-regulating-mir-186a-5p-and-down-regulating-zeb1
#2
Ze Zhang, Feng Liu, Fan Yang, Yahui Liu
Long non-coding RNA OIP5-AS1 has been studied in human diseases, including several kinds of cancers. It was not studied or reported in hepatoblastoma, so we chose it to do our research in hepatoblastoma. We thought OIP5-AS1 was oncogenic in hepatoblastoma for the high expression of it in hepatoblastoma tissues and cells. OIP5-AS1 knockdown was carried out in cancer cells. Unsurprisingly, this action was verified to be able to inhibit cell proliferation, metastasis and EMT progress in hepatoblastoma. We then measured the low expression level of miR-186a-5p and the high expression level of ZEB1 in hepatoblastoma tissues and cells...
February 20, 2018: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
https://www.readbyqxmd.com/read/29474933/an-optimised-multi-arm-multi-stage-clinical-trial-design-for-unknown-variance
#3
Michael J Grayling, James M S Wason, Adrian P Mander
Multi-arm multi-stage trial designs can bring notable gains in efficiency to the drug development process. However, for normally distributed endpoints, the determination of a design typically depends on the assumption that the patient variance in response is known. In practice, this will not usually be the case. To allow for unknown variance, previous research explored the performance of t-test statistics, coupled with a quantile substitution procedure for modifying the stopping boundaries, at controlling the familywise error-rate to the nominal level...
February 20, 2018: Contemporary Clinical Trials
https://www.readbyqxmd.com/read/29474928/lncrna-hottip-promotes-papillary-thyroid-carcinoma-cell-proliferation-invasion-and-migration-by-regulating-mir-637
#4
Qingling Yuan, Yang Liu, Yuxia Fan, Zheng Liu, Xiaoming Wang, Meng Jia, Zushi Geng, Jing Zhang, Xiubo Lu
BACKGROUND: Papillary thyroid carcinoma (PTC) is the most common thyroid malignancy. Besides, increasing evidence has demonstrated that long non-coding RNA (lncRNA) HOTTIP played a crucial role in cancer pathogenesis. MiR-637-mediated Akt1 was involved in cell growth, invasion and migration in various malignancies. This study was aimed to investigate the potential biological effect and regulatory mechanism of HOTTIP on cell proliferation, invasion and migration in PTC. METHODS: Expression of HOTTIP, miR-637 and Akt1 were determined by quantitative RT-PCR (qRT-PCR) and western blotting in PTC tissues, normal tissues, PTC cells (TPC-1 and HTH83) or non-tumor thyroid cells (Nthy-ori 3-1)...
February 20, 2018: International Journal of Biochemistry & Cell Biology
https://www.readbyqxmd.com/read/29474915/solving-mendelian-mysteries-the-non-coding-genome-may-hold-the-key
#5
Enza Maria Valente, Kailash P Bhatia
Despite revolutionary advances in sequencing approaches, many mendelian disorders have remained unexplained. In this issue of Cell, Aneichyk et al. combine genomic and cell-type-specific transcriptomic data to causally link a non-coding mutation in the ubiquitous TAF1 gene to X-linked dystonia-parkinsonism.
February 22, 2018: Cell
https://www.readbyqxmd.com/read/29474877/the-grp78-bip-inhibitor-ha15-synergizes-with-mitotane-action-against-adrenocortical-carcinoma-cells-through-convergent-activation-of-er-stress-pathways
#6
Carmen Ruggiero, Mabrouka Doghman-Bouguerra, Cyril Ronco, Rachid Benhida, Stéphane Rocchi, Enzo Lalli
Many types of cancer cells present constitutively activated ER stress pathways because of their significant burden of misfolded proteins coded by mutated and rearranged genes. Further increase of ER stress by pharmacological intervention may shift the balance towards cell death and can be exploited therapeutically. Recent studies have shown that an important component in the mechanism of action of mitotane, the only approved drug for the medical treatment of adrenocortical carcinoma (ACC), is represented by activation of ER stress through inhibition of the SOAT1 enzyme and accumulation of toxic lipids...
February 20, 2018: Molecular and Cellular Endocrinology
https://www.readbyqxmd.com/read/29474815/complete-mitochondrial-genome-of-the-tea-looper-caterpillar-ectropis-obliqua-lepidoptera-geometridae-with-a-phylogenetic-analysis-of-geometridae
#7
Li Qian, Wang Xiaoxi, Chen Xuexin, Han Baoyu
The complete mitochondrial genome (mitogenome) of the Ectropis obliqua (Lepidoptera: Geometridae) was sequenced and compared with other species of Geometridae. The mitochondrial genome of E. obliqua is 15,475 bp long and contains 37 genes including 13 protein coding genes (PCGs), 22 transfer RNA genes, 2 ribosomal RNA genes and an A + T-rich region. Gene cluster trnI-trnQ-trnM rearranged to trnM-trnI-trnQ comparing with the ancestral mitogenome of insects. All tRNA genes have typical cloverleaf secondary structure except for trnS (AGN)...
February 20, 2018: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/29474735/mads-box-genes-and-crop-domestication-the-jack-of-all-traits
#8
Susanne Schilling, Sirui Pan, Alice Kennedy, Rainer Melzer
MADS-box genes are key regulators of virtually every aspect of plant reproductive development. They play especially prominent roles in flowering time control, inflorescence architecture, floral organ identity determination, and seed development. The developmental and evolutionary importance of MADS-box genes is widely acknowledged. However, their role during flowering plant domestication is less well recognized. Here, we provide an overview illustrating that MADS-box genes have been important targets of selection during crop domestication and improvement...
February 21, 2018: Journal of Experimental Botany
https://www.readbyqxmd.com/read/29474700/content-analysis-of-twitter-chatter-about-indoor-tanning
#9
Molly E Waring, Katie Baker, Anthony Peluso, Christine N May, Sherry L Pagoto
Twitter may be useful for learning about indoor tanning behavior and attitudes. The objective of this study was to analyze the content of tweets about indoor tanning to determine the extent to which tweets are posted by people who tan, and to characterize the topics of tweets. We extracted 4,691 unique tweets from Twitter using the terms "tanning bed" or "tanning salon" over 7 days in March 2016. We content analyzed a random selection of 1,000 tweets, double-coding 20% of tweets (κ = 0...
February 21, 2018: Translational Behavioral Medicine
https://www.readbyqxmd.com/read/29474694/a-monte-carlo-tool-for-multi-target-nanodosimetry
#10
A Selva, V Conte, P Colautti
A Monte Carlo simulation tool has been developed, based on the physical models of the Geant4-DNA extension of Geant4, to study the ionisation pattern of charged particles in a multi-target environment. The tool allows to code easily the geometry to build a simulation with multiple targets, since several parameters can be changed interactively and independently via macro commands. In this work a set of nanometric target spheres is embedded in a cylindrical water phantom 20 nm in height and 40 nm in diameter...
February 21, 2018: Radiation Protection Dosimetry
https://www.readbyqxmd.com/read/29474643/cross-sections-measured-by-quasi-monoenergetic-neutrons
#11
Mitja Majerle, Martin Ansorge, Pavel Bém, Jan Novák, Eva Šimecková, Milan Štefánik
197Au, 209Bi, 59Co, natFe and 169Tm samples were irradiated several times with quasi-monoenergetic neutrons from the p+7Li reaction in the energy range of 18-34 MeV. The activities of the samples were measured with the HPGe detector and the reaction rates were calculated. The cross sections were extracted using the SAND-II code with the reference cross sections from the IRDFF database.
February 21, 2018: Radiation Protection Dosimetry
https://www.readbyqxmd.com/read/29474641/improvements-in-the-thermal-neutron-calibration-unit-tnf2-at-lnmri-ird
#12
A Astuto, S S Fernandes, K C S Patrão, E S Fonseca, W W Pereira, R T Lopes
The standard thermal neutron flux unit, TNF2, in the Brazilian National Ionizing Radiation Metrology Laboratory was rebuilt. Fluence is still achieved by moderating of four 241Am-Be sources with 0.6 TBq each. The facility was again simulated and redesigned with graphite core and paraffin added graphite blocks surrounding it. Simulations using the MCNPX code on different geometric arrangements of moderator materials and neutron sources were performed. The resulting neutron fluence quality in terms of intensity, spectrum and cadmium ratio was evaluated...
February 21, 2018: Radiation Protection Dosimetry
https://www.readbyqxmd.com/read/29474580/recently-evolved-tumor-suppressor-transcript-tp73-as1-functions-as-sponge-of-human-specific-mir-941
#13
Haiyang Hu, Jian-Mei Liu, Zhenyu Hu, Xi Jiang, Xiaode Yang, Jiangxia Li, Yao Zhang, Haijing Yu, Philipp Khaitovich
MicroRNA (miRNA) sponges are vital components of posttranscriptional gene regulation. Yet, only a limited number of miRNA sponges have been identified. Here, we show that the recently evolved non-coding tumor suppressor transcript, antisense RNA to TP73 gene (TP73-AS1), functions as a natural sponge of human-specific miRNA miR-941. We find unusually nine high-affinity miR-941 binding sites clustering within 1kb region on TP73-AS1, which forms miR-941 sponge region. This sponge region displays increased sequence constraint only in humans, and its formation can be traced to the tandem expansion of a 71-nt-long sequence containing a single miR-941 binding site in old world monkeys...
February 20, 2018: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29474560/a-genetic-survey-of-pyrethroid-insecticide-resistance-in-aphids-in-new-brunswick-canada-with-particular-emphasis-on-aphids-as-vectors-of-potato-virus-y
#14
Tyler D B MacKenzie, Irin Arju, René Poirier, Mathuresh Singh
Aphids are viral vectors in potatoes, most importantly of Potato virus Y (PVY), and insecticides are frequently used to reduce viral spread during the crop season. Aphids collected from the potato belt of New Brunswick, Canada, in 2015 and 2016 were surveyed for known and novel mutations in the Na-channel (para) gene, coding for the target of synthetic pyrethroid insecticides. Specific genetic mutations known to confer resistance (kdr and skdr) were found in great abundance in Myzus persicae (Sulzer) (Hemiptera: Aphididae), which rose from 76% in 2015 to 96% in 2016...
February 21, 2018: Journal of Economic Entomology
https://www.readbyqxmd.com/read/29474557/penndiff-detecting-differential-alternative-splicing-and-transcription-by-rna-sequencing
#15
Yu Hu, Jennie Lin, Jian Hu, Gang Hu, Kui Wang, Hanrui Zhang, Muredach P Reilly, Mingyao Li
Motivation: Alternative splicing and alternative transcription are a major mechanism for generating transcriptome diversity. Differential alternative splicing and transcription (DAST), which describe different usage of transcript isoforms across different conditions, can complement differential expression in characterizing gene regulation. However, the analysis of DAST is challenging because only a small fraction of RNA-seq reads is informative for isoforms. Several methods have been developed to detect exon-based and gene-based DAST, but they suffer from power loss for genes with many isoforms...
February 20, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29474529/epic-coge-managing-and-analyzing-genomic-data
#16
Andrew D L Nelson, Asher K Haug-Baltzell, Sean Davey, Brian D Gregory, Eric Lyons
Summary: The EPIC-CoGe browser is a web-based genome visualization utility that integrates the GMOD JBrowse genome browser with the extensive CoGe genome database (currently containing over 30,000 genomes). In addition, the EPIC-CoGe browser boasts many additional features over basic JBrowse, including enhanced search capability and on-the-fly analyses for comparisons and analyses between all types of functional and diversity genomics data. There is no installation required and data (genome, annotation, functional genomic, and diversity data) can be loaded by following a simple point and click wizard, or using a REST API, making the browser widely accessible and easy to use by researchers of all computational skill levels...
February 20, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29474523/progressive-approach-for-snp-calling-and-haplotype-assembly-using-single-molecular-sequencing-data
#17
Fei Guo, Dan Wang, Lusheng Wang
Motivation: Haplotype information is essential to the complete description and interpretation of genomes, genetic diversity and genetic ancestry. The new technologies can provide Single Molecular Sequencing (SMS) data that cover about 90% of positions over chromosomes. However, the SMS data has a higher error rate comparing to 1% error rate for short reads. Thus, it becomes very difficult for SNP calling and haplotype assembly using SMS reads. Most existing technologies do not work properly for the SMS data...
February 19, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29474519/victree-an-automated-framework-for-taxonomic-classification-from-protein-sequences
#18
Sejal Modha, Anil Thanki, Susan F Cotmore, Andrew J Davison, Joseph Hughes
Motivation: The increasing rate of submission of genetic sequences into public databases is providing a growing resource for classifying the organisms that these sequences represent. To aid viral classification, we have developed ViCTree, which automatically integrates the relevant sets of sequences in NCBI GenBank and transforms them into an interactive maximum likelihood phylogenetic tree that can be updated automatically. ViCTree incorporates ViCTreeView, which is a JavaScript-based visualisation tool that enables the tree to be explored interactively in the context of pairwise distance data...
February 20, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29474517/cost-function-network-based-design-of-protein-protein-interactions-predicting-changes-in-binding-affinity
#19
Clément Viricel, Simon de Givry, Thomas Schiex, Sophie Barbe
Motivation: Accurate and economic methods to predict change in protein binding free energy upon mutation are imperative to accelerate the design of proteins for a wide range of applications. Free energy is defined by enthalpic and entropic contributions. Following the recent progresses of Artificial Intelligence-based algorithms for guaranteed NP-hard energy optimization and partition function computation, it becomes possible to quickly compute minimum energy conformations and to reliably estimate the entropic contribution of side-chains in the change of free energy of large protein interfaces...
February 20, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29474446/physicell-an-open-source-physics-based-cell-simulator-for-3-d-multicellular-systems
#20
Ahmadreza Ghaffarizadeh, Randy Heiland, Samuel H Friedman, Shannon M Mumenthaler, Paul Macklin
Many multicellular systems problems can only be understood by studying how cells move, grow, divide, interact, and die. Tissue-scale dynamics emerge from systems of many interacting cells as they respond to and influence their microenvironment. The ideal "virtual laboratory" for such multicellular systems simulates both the biochemical microenvironment (the "stage") and many mechanically and biochemically interacting cells (the "players" upon the stage). PhysiCell-physics-based multicellular simulator-is an open source agent-based simulator that provides both the stage and the players for studying many interacting cells in dynamic tissue microenvironments...
February 23, 2018: PLoS Computational Biology
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