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https://www.readbyqxmd.com/read/28197171/genome-wide-microrna-binding-site-variation-between-extinct-wild-aurochs-and-modern-cattle-identifies-candidate-microrna-regulated-domestication-genes
#1
Martin Braud, David A Magee, Stephen D E Park, Tad S Sonstegard, Sinead M Waters, David E MacHugh, Charles Spillane
The domestication of cattle from the now-extinct wild aurochs (Bos primigenius) involved selection for physiological and behavioral traits, with underlying genetic factors that remain largely unknown. Non-coding microRNAs have emerged as key regulators of the spatio-temporal expression of target genes controlling mammalian growth and development, including in livestock species. During the domestication process, selection of mutational changes in miRNAs and/or miRNA binding sites could have provided a mechanism to generate some of the traits that differentiate domesticated cattle from wild aurochs...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28194377/comparative-study-between-lateral-decubitus-and-traction-table-for-treatment-of-pertrochanteric-fractures-with-cephalomedullary-nails
#2
Eric Fernando de Souza, José Octávio Soares Hungria, Lucas Romano Sampaio Rezende, Davi Gabriel Bellan, Jonas Aparecido Borracini
OBJECTIVE: To perform a retrospective radiographic assessment of the reduction and implant position in the femoral head in patients with pertrochanteric fractures treated with cephalomedullary nailing in the lateral position versus traction table. METHODS: Radiographs of patients with pertrochanteric fracture of the femur treated with cephalomedullary nailing in the lateral position and traction table were retrospectively evaluated. For the evaluation we used the anteroposterior radiographic view of the pelvis and the lateral view of the affected side...
January 2017: Revista Brasileira de Ortopedia
https://www.readbyqxmd.com/read/28172841/systematic-profiling-of-short-tandem-repeats-in-the-cattle-genome
#3
Lingyang Xu, Ryan J Haasl, Jiajie Sun, Yang Zhou, Derek M Bickhart, Junya Li, Jiuzhou Song, Tad S Sonstegard, Curtis P Van Tassell, Harris A Lewin, George E Liu
No abstract text is available yet for this article.
January 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28168148/protein-functionalized-dna-nanostructures-as-tools-to-control-transcription-in-zebrafish-embryos
#4
Alessandro Angelin, Olivier Kassel, Sepand Rastegar, Uwe Strähle, Christof M Niemeyer
The unique structure-directing properties of DNA origami nanostructures (DONs) show great potential to specifically manipulate intracellular processes. We report an innovative concept to selectively activate the transcription of a single gene in the developing zebrafish embryo. We reason that engineering a designer transcription factor in which a rigid DON imposes a fixed distance between the DNA-binding domain (DBD) and the transactivation domain (TAD) would allow the selective activation of a gene harboring the same distance between the corresponding transcription factor binding site and the core promoter...
February 2017: ChemistryOpen
https://www.readbyqxmd.com/read/28167501/comprehensive-characterization-of-neutrophil-genome-topology
#5
Yina Zhu, Ke Gong, Matthew Denholtz, Vivek Chandra, Mark P Kamps, Frank Alber, Cornelis Murre
Neutrophils are responsible for the first line of defense against invading pathogens. Their nuclei are uniquely structured as multiple lobes that establish a highly constrained nuclear environment. Here we found that neutrophil differentiation was not associated with large-scale changes in the number and sizes of topologically associating domains (TADs). However, neutrophil genomes were enriched for long-range genomic interactions that spanned multiple TADs. Population-based simulation of spherical and toroid genomes revealed declining radii of gyration for neutrophil chromosomes...
February 6, 2017: Genes & Development
https://www.readbyqxmd.com/read/28157500/a-finer-print-than-tads-prc1-mediated-domains
#6
Elena Torlai Triglia, Tiago Rito, Ana Pombo
Polycomb proteins are well-known epigenetic repressors with unexplained roles in chromatin folding. In this issue of Molecular Cell, Kundu et al. (2017) investigate the structures of PRC1-mediated domains in stem cells and probe their changes upon differentiation and in PRC knockouts.
February 2, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28151083/bird-feeders-as-locations-for-skunk-uptake-of-oral-rabies-vaccine-baits
#7
Tad Theimer, Tisheena Talk, Shylo Johnson, David L Bergman
Significantly more (54%, P=0.003) placebo baits placed under 26 bird feeders in Arizona were removed by striped skunks ( Mephitis mephitis ) than at paired, nonfeeder locations (19%). Baiting at bird feeders could supplement traditional oral rabies vaccine bait placement in urban-suburban areas while engaging the public in rabies control efforts.
February 2, 2017: Journal of Wildlife Diseases
https://www.readbyqxmd.com/read/28139425/factors-influencing-the-food-purchases-of-early-care-and-education-providers
#8
Jennifer J Otten, Tad Hirsch, Catherine Lim
BACKGROUND: With the majority of US children enrolled in some form of early care and education, the settings for early care and education represent a valuable opportunity to positively impact young children's diets and their interactions with food. Little evidence exists on how early care and education providers make food purchasing and service decisions for this population of young children. OBJECTIVE: Our aim was to explore the factors that influence early care and education providers' food purchasing and service decisions...
January 27, 2017: Journal of the Academy of Nutrition and Dietetics
https://www.readbyqxmd.com/read/28137286/chrom3d-three-dimensional-genome-modeling-from-hi-c-and-nuclear-lamin-genome-contacts
#9
Jonas Paulsen, Monika Sekelja, Anja R Oldenburg, Alice Barateau, Nolwenn Briand, Erwan Delbarre, Akshay Shah, Anita L Sørensen, Corinne Vigouroux, Brigitte Buendia, Philippe Collas
Current three-dimensional (3D) genome modeling platforms are limited by their inability to account for radial placement of loci in the nucleus. We present Chrom3D, a user-friendly whole-genome 3D computational modeling framework that simulates positions of topologically-associated domains (TADs) relative to each other and to the nuclear periphery. Chrom3D integrates chromosome conformation capture (Hi-C) and lamin-associated domain (LAD) datasets to generate structure ensembles that recapitulate radial distributions of TADs detected in single cells...
January 30, 2017: Genome Biology
https://www.readbyqxmd.com/read/28133708/tadalafil-improves-lean-mass-and-endothelial-function-in-nonobese-men-with-mild-ed-luts-in-vivo-and-in-vitro-characterization
#10
Antonio Aversa, Simona Fittipaldi, Davide Francomano, Viviana M Bimonte, Emanuela A Greco, Clara Crescioli, Luigi Di Luigi, Andrea Lenzi, Silvia Migliaccio
PURPOSE: Phosphodiesterase type-5 inhibitor administration in diabetic men with erectile dysfunction (ED) is associated with reduced waist circumference. We evaluated potential effects of daily tadalafil administration on body composition and investigated its possible mechanism(s) of action in C2C12 skeletal muscle cells in vitro. METHODS: Forty-three men on stable caloric intake (mean age 48.5 ± 7; BMI 25.5 ± 0.9 kg/m(2)) complaining mild ED and/or low urinary tract symptoms (LUTS) were randomly assigned to receive tadalafil (TAD) 5 mg/daily (once-a-day=OAD-TAD; n = 23) or 20 mg on-demand (on-demand=OD-TAD; n = 20) for 2 months...
January 30, 2017: Endocrine
https://www.readbyqxmd.com/read/28123046/pde5-inhibitor-tadalafil-and-hydroxychloroquine-co-treatment-provides-synergistic-protection-against-type-2-diabetes-and-myocardial-infarction-in-mice
#11
Rui Wang, Lei Xi, Rakesh C Kukreja
Diabetes is associated with high risk of ischemic heart disease. We previously showed that phosphodiesterase 5 inhibitor - tadalafil (TAD) induces cardioprotection against ischemia/ reperfusion (I/R) injury in diabetic mice. Hydroxychloroquine (HCQ) is a widely used antimalarial and anti-inflammatory drug, which was reported to reduce hyperglycemia in diabetic patients. Therefore we hypothesized that combination of TAD and HCQ may induce synergistic cardioprotection in diabetes. We also investigated the role of insulin-Akt-mTOR signaling, which regulates protein synthesis and cell survival...
January 25, 2017: Journal of Pharmacology and Experimental Therapeutics
https://www.readbyqxmd.com/read/28108933/modelling-genome-wide-topological-associating-domains-in-mouse-embryonic-stem-cells
#12
REVIEW
Y Zhan, L Giorgetti, G Tiana
Chromosome conformation capture (3C)-based techniques such as chromosome conformation capture carbon copy (5C) and Hi-C revealed that the folding of mammalian chromosomes is highly hierarchical. A fundamental structural unit in the hierarchy is represented by topologically associating domains (TADs), sub-megabase regions of the genome within which the chromatin fibre preferentially interacts. 3C-based methods provide the mean contact probabilities between chromosomal loci, averaged over a large number of cells, and do not give immediate access to the single-cell conformations of the chromatin fibre...
January 20, 2017: Chromosome Research
https://www.readbyqxmd.com/read/28107684/non-invasive-brain-stimulation-targeting-the-right-fusiform-gyrus-selectively-increases-working-memory-for-faces
#13
Tad T Brunyé, Joseph M Moran, Amanda Holmes, Caroline R Mahoney, Holly A Taylor
The human extrastriate cortex contains a region critically involved in face detection and memory, the right fusiform gyrus. The present study evaluated whether transcranial direct current stimulation (tDCS) targeting this anatomical region would selectively influence memory for faces versus non-face objects (houses). Anodal tDCS targeted the right fusiform gyrus (Brodmann's Area 37), with the anode at electrode site PO10, and cathode at FP2. Two stimulation conditions were compared in a repeated-measures design: 0...
January 17, 2017: Brain and Cognition
https://www.readbyqxmd.com/read/28104665/draft-genome-sequences-of-three-aeromonas-hydrophila-isolates-from-catfish-and-tilapia
#14
Hasan C Tekedar, Salih Kumru, Safak Kalindamar, Attila Karsi, Geoffrey C Waldbieser, Tad Sonstegard, Steven G Schroeder, Mark R Liles, Matt J Griffin, Mark L Lawrence
Aeromonas hydrophila is a Gram-negative bacterium that is particularly adapted to freshwater environments and can cause severe infections in fish and humans. Here, we report the draft genomes of three A. hydrophila catfish and tilapia isolates.
January 19, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28094609/ecological-potential-for-rabies-virus-transmission-via-scavenging-of-dead-bats-by-mesocarnivores
#15
Tad C Theimer, Annie C Dyer, Brian W Keeley, Amy T Gilbert, David L Bergman
Multiple species of bats are reservoirs of rabies virus in the Americas and are occasionally the source of spillover infections into mesocarnivore species. Although rabies transmission generally is assumed to occur via bite, laboratory studies have demonstrated the potential for rabies transmission via ingestion of rabid animals. We investigated the ecological potential for this mode of transmission by assessing mesocarnivore scavenging behavior of dead bats in suburban habitats of Flagstaff, Arizona. In autumn 2013, summer 2014, and autumn 2015, we placed 104 rabies-negative bat carcasses either near buildings, in wildland areas, or in residential yards and then monitored them with trail cameras for 5 d...
January 17, 2017: Journal of Wildlife Diseases
https://www.readbyqxmd.com/read/28087711/ctcf-mediated-topological-boundaries-during-development-foster-appropriate-gene-regulation
#16
Varun Narendra, Milica Bulajić, Job Dekker, Esteban O Mazzoni, Danny Reinberg
The genome is organized into repeating topologically associated domains (TADs), each of which is spatially isolated from its neighbor by poorly understood boundary elements thought to be conserved across cell types. Here, we show that deletion of CTCF (CCCTC-binding factor)-binding sites at TAD and sub-TAD topological boundaries that form within the HoxA and HoxC clusters during differentiation not only disturbs local chromatin domain organization and regulatory interactions but also results in homeotic transformations typical of Hox gene misregulation...
December 15, 2016: Genes & Development
https://www.readbyqxmd.com/read/28087402/accuracy-is-in-the-eyes-of-the-pathologist-the-visual-interpretive-process-and-diagnostic-accuracy-with-digital-whole-slide-images
#17
Tad T Brunyé, Ezgi Mercan, Donald L Weaver, Joann G Elmore
Digital whole slide imaging is an increasingly common medium in pathology, with application to education, telemedicine, and rendering second opinions. It has also made it possible to use eye tracking devices to explore the dynamic visual inspection and interpretation of histopathological features of tissue while pathologists review cases. Using whole slide images, the present study examined how a pathologist's diagnosis is influenced by fixed case-level factors, their prior clinical experience, and their patterns of visual inspection...
January 10, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28087167/lingering-questions-about-enhancer-rna-and-enhancer-transcription-coupled-genomic-instability
#18
REVIEW
Gerson Rothschild, Uttiya Basu
Intergenic and intragenic enhancers found inside topologically associated regulatory domains (TADs) express noncoding RNAs, known as enhancer RNAs (eRNAs). Recent studies have indicated these eRNAs play a role in gene regulatory networks by controlling promoter and enhancer interactions and topology of higher-order chromatin structure. Misregulation of enhancer and promoter associated noncoding RNAs (ncRNAs) could stabilize deleterious secondary DNA structures, noncoding RNA associated DNA/RNA hybrid formation, and promote collisions of transcription complexes with replisomes...
February 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28070687/predicting-chromatin-architecture-from-models-of-polymer-physics
#19
REVIEW
Simona Bianco, Andrea M Chiariello, Carlo Annunziatella, Andrea Esposito, Mario Nicodemi
We review the picture of chromatin large-scale 3D organization emerging from the analysis of Hi-C data and polymer modeling. In higher mammals, Hi-C contact maps reveal a complex higher-order organization, extending from the sub-Mb to chromosomal scales, hierarchically folded in a structure of domains-within-domains (metaTADs). The domain folding hierarchy is partially conserved throughout differentiation, and deeply correlated to epigenomic features. Rearrangements in the metaTAD topology relate to gene expression modifications: in particular, in neuronal differentiation models, topologically associated domains (TADs) tend to have coherent expression changes within architecturally conserved metaTAD niches...
January 9, 2017: Chromosome Research
https://www.readbyqxmd.com/read/28069653/the-molecular-epidemiology-of-pf-k13-mutations-in-senegal-using-targeted-amplicon-deep-sequencing
#20
Eldin Talundzic, Yaye D Ndiaye, Awa B Deme, Christian Olsen, Dhruviben S Patel, Shweta Biliya, Rachel Daniels, Fredrik O Vannberg, Sarah K Volkman, Venkatachalam Udhayakumar, Daouda Ndiaye
The emergence of Plasmodium falciparum (Pf) resistance to artemisinin in Southeast Asia threatens malaria control and elimination activities worldwide. Multiple polymorphisms in the Pf kelch gene found in chromosome 13 (Pfk13) have been associated with artemisinin resistance. Surveillance of potential drug resistance loci within a population that may emerge under increasing drug pressure is an important public health activity. In this context, P. falciparum infections from an observational surveillance study in Senegal were genotyped using targeted amplicon deep sequencing (TADS) for Pfk13 polymorphisms...
January 9, 2017: Antimicrobial Agents and Chemotherapy
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