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https://www.readbyqxmd.com/read/29023438/the-tad-pathway-for-gwas-signals
#1
Natalia Pervjakova, Inga Prokopenko
No abstract text is available yet for this article.
November 2017: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/29017057/a-p53-super-tumor-suppressor-reveals-a-tumor-suppressive-p53-ptpn14-yap-axis-in-pancreatic-cancer
#2
Stephano S Mello, Liz J Valente, Nitin Raj, Jose A Seoane, Brittany M Flowers, Jacob McClendon, Kathryn T Bieging-Rolett, Jonghyeob Lee, Danton Ivanochko, Margaret M Kozak, Daniel T Chang, Teri A Longacre, Albert C Koong, Cheryl H Arrowsmith, Seung K Kim, Hannes Vogel, Laura D Wood, Ralph H Hruban, Christina Curtis, Laura D Attardi
The p53 transcription factor is a critical barrier to pancreatic cancer progression. To unravel mechanisms of p53-mediated tumor suppression, which have remained elusive, we analyzed pancreatic cancer development in mice expressing p53 transcriptional activation domain (TAD) mutants. Surprisingly, the p53(53,54) TAD2 mutant behaves as a "super-tumor suppressor," with an enhanced capacity to both suppress pancreatic cancer and transactivate select p53 target genes, including Ptpn14. Ptpn14 encodes a negative regulator of the Yap oncoprotein and is necessary and sufficient for pancreatic cancer suppression, like p53...
October 9, 2017: Cancer Cell
https://www.readbyqxmd.com/read/28994223/multiple-taf-subunits-of-tfiid-interact-with-ino2-activation-domains-and-contribute-to-expression-of-genes-required-for-yeast-phospholipid-biosynthesis
#3
Stefan Hintze, Maike Engelhardt, Laura van Diepen, Eric Witt, Hans-Joachim Schüller
Expression of phospholipid biosynthetic genes in yeast requires activator protein Ino2 which can bind to the UAS element ICRE (inositol/choline-responsive element) and trigger activation of target genes, using two separate transcriptional activation domains, TAD1 and TAD2. However, it is still unknown which cofactors mediate activation by TADs of Ino2. Here we show that multiple subunits of basal transcription factor TFIID (TBP-associated factors Taf1, Taf4, Taf6, Taf10 and Taf12) are able to interact in vitro with activation domains of Ino2...
October 10, 2017: Molecular Microbiology
https://www.readbyqxmd.com/read/28991264/architectural-alterations-of-the-fission-yeast-genome-during-the-cell-cycle
#4
Hideki Tanizawa, Kyoung-Dong Kim, Osamu Iwasaki, Ken-Ichi Noma
Eukaryotic genomes are highly ordered through various mechanisms, including topologically associating domain (TAD) organization. We employed an in situ Hi-C approach to follow the 3D organization of the fission yeast genome during the cell cycle. We demonstrate that during mitosis, large domains of 300 kb-1 Mb are formed by condensin. This mitotic domain organization does not suddenly dissolve, but gradually diminishes until the next mitosis. By contrast, small domains of 30-40 kb that are formed by cohesin are relatively stable across the cell cycle...
October 9, 2017: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/28981529/design-and-validation-of-a-90k-snp-genotyping-assay-for-the-water-buffalo-bubalus-bubalis
#5
Daniela Iamartino, Ezequiel L Nicolazzi, Curtis P Van Tassell, James M Reecy, Eric R Fritz-Waters, James E Koltes, Stefano Biffani, Tad S Sonstegard, Steven G Schroeder, Paolo Ajmone-Marsan, Riccardo Negrini, Rolando Pasquariello, Paola Ramelli, Angelo Coletta, José F Garcia, Ahmad Ali, Luigi Ramunno, Gianfranco Cosenza, Denise A A de Oliveira, Marcela G Drummond, Eduardo Bastianetto, Alessandro Davassi, Ali Pirani, Fiona Brew, John L Williams
BACKGROUND: The availability of the bovine genome sequence and SNP panels has improved various genomic analyses, from exploring genetic diversity to aiding genetic selection. However, few of the SNP on the bovine chips are polymorphic in buffalo, therefore a panel of single nucleotide DNA markers exclusive for buffalo was necessary for molecular genetic analyses and to develop genomic selection approaches for water buffalo. The creation of a 90K SNP panel for river buffalo and testing in a genome wide association study for milk production is described here...
2017: PloS One
https://www.readbyqxmd.com/read/28977568/computational-characterization-of-chromatin-domain-boundary-associated-genomic-elements
#6
Seungpyo Hong, Dongsup Kim
Topologically associated domains (TADs) are 3D genomic structures with high internal interactions that play important roles in genome compaction and gene regulation. Their genomic locations and their association with CCCTC-binding factor (CTCF)-binding sites and transcription start sites (TSSs) were recently reported. However, the relationship between TADs and other genomic elements has not been systematically evaluated. This was addressed in the present study, with a focus on the enrichment of these genomic elements and their ability to predict the TAD boundary region...
August 23, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28977529/hitad-detecting-the-structural-and-functional-hierarchies-of-topologically-associating-domains-from-chromatin-interactions
#7
Xiao-Tao Wang, Wang Cui, Cheng Peng
A current question in the high-order organization of chromatin is whether topologically associating domains (TADs) are distinct from other hierarchical chromatin domains. However, due to the unclear TAD definition in tradition, the structural and functional uniqueness of TAD is not well studied. In this work, we refined TAD definition by further constraining TADs to the optimal separation on global intra-chromosomal interactions. Inspired by this constraint, we developed a novel method, called HiTAD, to detect hierarchical TADs from Hi-C chromatin interactions...
August 24, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28977418/developmentally-regulated-higher-order-chromatin-interactions-orchestrate-b-cell-fate-commitment
#8
Ravi Boya, Anurupa Devi Yadavalli, Sameena Nikhat, Sreenivasulu Kurukuti, Dasaradhi Palakodeti, Jagan M R Pongubala
Genome organization in 3D nuclear-space is important for regulation of gene expression. However, the alterations of chromatin architecture that impinge on the B cell-fate choice of multi-potent progenitors are still unclear. By integrating in situ Hi-C analyses with epigenetic landscapes and genome-wide expression profiles, we tracked the changes in genome architecture as the cells transit from a progenitor to a committed state. We identified the genomic loci that undergo developmental switch between A and B compartments during B-cell fate determination...
August 17, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28975416/habitual-exercise-is-associated-with-cognitive-control-and-cognitive-reappraisal-success
#9
Grace E Giles, Julie A Cantelon, Marianna D Eddy, Tad T Brunyé, Heather L Urry, Caroline R Mahoney, Robin B Kanarek
Habitual exercise is associated with enhanced domain-general cognitive control, such as inhibitory control, selective attention, and working memory, all of which rely on the frontal cortex. However, whether regular exercise is associated with more specific aspects of cognitive control, such as the cognitive control of emotion, remains relatively unexplored. The present study employed a correlational design to determine whether level of habitual exercise was related to performance on the Stroop test measuring selective attention and response inhibition, the cognitive reappraisal task measuring cognitive reappraisal success, and associated changes in prefrontal cortex (PFC) oxygenation using functional near-infrared spectroscopy...
October 3, 2017: Experimental Brain Research. Experimentelle Hirnforschung. Expérimentation Cérébrale
https://www.readbyqxmd.com/read/28965826/transfusion-associated-hypoxemia-in-pediatric-patients-with-solid-tumors-after-autologous-peripheral-blood-stem-cell-transplantation
#10
Ryu Yanagisawa, Seiki Abe, Ikuko Fujihara, Kazutoshi Komori, Yoshiaki Kondo, Kazuo Sakashita, Tomohiko Nakamura
BACKGROUND: Although several types of transfusion-related adverse reactions (TRARs) have been reported, one of the most important involves respiratory features during and after blood transfusion. Transfusion-related acute lung injury (TRALI) and transfusion-associated circulatory overload (TACO) are the most severe adverse events following blood transfusion, whereas transfusion-associated dyspnea (TAD) is a less severe respiratory distress. However, there exists little evidence of these factors in pediatric populations...
September 20, 2017: Transfusion and Apheresis Science
https://www.readbyqxmd.com/read/28965202/interleukin-6-downregulated-vascular-smooth-muscle-cell-contractile-proteins-via-atg4b-mediated-autophagy-in-thoracic-aortic-dissection
#11
Zhao An, Fan Qiao, Qijue Lu, Ye Ma, Yang Liu, Fanglin Lu, Zhiyun Xu
Interleukin-6 (IL-6) overexpression played an important role in the pathogenesis of thoracic aortic dissection (TAD). Our previous study found enhanced autophagy accompanying with contractile proteins α smooth muscle actin (α-SMA) and smooth muscle 22α (SM22α) degradation in TAD aortic vascular smooth muscle cells (VSMCs). Autophagy is an important way for intracellular proteins degradation, while IL-6 has been found as a contributing factor of autophagy in some cancers. These indicated IL-6 might contribute to the occurrence of TAD by promoting autophagy-induced contractile proteins degradation, which has not been investigated...
September 30, 2017: Heart and Vessels
https://www.readbyqxmd.com/read/28965118/nuclear-repositioning-of-the-non-translocated-hlxb9-allele-in-the-leukaemia-cell-line-gdm-1-harbouring-a-t-6-7-q23-q36
#12
Concetta Federico, Claudia G Leotta, Francesca Bruno, Anna M Longo, Temitayo Owoka, Sabrina Tosi, Salvatore Saccone
Transcriptionally active and inactive topologically associated domains (TADs) occupy different areas in the cell nucleus, and chromosomal rearrangements relocating TADs could determine ectopic expression of the repositioned genes. In this study, we investigated the HLXB9 gene in a myeloid leukaemia cell line, GDM-1, known to harbour a rearrangement involving chromosome 7 with a breakpoint distal to HLXB9, highly expressed in these cells. We used FISH to target the regions involved in the translocation and to distinguish the translocated chromosome from the non-translocated one in interphase nuclei...
September 29, 2017: Cytogenetic and Genome Research
https://www.readbyqxmd.com/read/28962727/comparison-of-in-vivo-failure-of-single-thread-and-dual-thread-temporary-anchorage-devices-over-18%C3%A2-months-a-split-mouth-randomized-controlled-trial
#13
Owais Khalid Durrani, Sohrab Shaheed, Arsalan Khan, Ulfat Bashir
INTRODUCTION: The purpose of this study was to compare the in-vivo failure rates of single-thread and dual-thread temporary anchorage device (TAD) designs over 18 months. METHODS: Thirty patients with skeletal Class II Division 1 malocclusion requiring anchorage from TADs for retraction of maxillary incisors into the extracted premolar space were recruited in this parallel group, split-mouth, randomized controlled trial. A block randomization sequence was generated with Random Allocation Software (version 2...
October 2017: American Journal of Orthodontics and Dentofacial Orthopedics
https://www.readbyqxmd.com/read/28956183/effectiveness-of-time-related-interventions-in-children-with-adhd-aged-9-15%C3%A2-years-a-randomized-controlled-study
#14
Birgitta Wennberg, Gunnel Janeslätt, Anette Kjellberg, Per A Gustafsson
Specific problems with time and timing that affect daily routines, homework, school work, and social relations have been recognized in children with ADHD. The primary treatments for children with ADHD do not specifically focus on time-related difficulties. The aim of this randomized controlled study (RCT) was to investigate how multimodal interventions, consisting of training in time-processing ability (TPA) and compensation with time-assistive devices (TAD), affect TPA and daily time management (DTM) in children with ADHD and time difficulties, compared with only educational intervention...
September 27, 2017: European Child & Adolescent Psychiatry
https://www.readbyqxmd.com/read/28950143/comparison-of-pre-and-inter-stage-aerobic-treatment-of-wastewater-sludge-effects-on-biogas-production-and-cod-removal
#15
Charlotte Rennuit, Jin Mi Triolo, Søren Eriksen, Julie Jimenez, Hélène Carrère, Sasha D Hafner
The aim of this study was to investigate thermophilic (55°C) aerobic digestion (TAD) as pre- and inter-stage treatment of sludge anaerobic digestion and to analyse the change in organic matter accessibility and complexity. Pre-treatment decreased methane yield (up to -70%), due to oxidation losses whereas inter-stage treatment slightly improved overall methane yield (+2.6%) and total COD removal (+5%) compared to control. Anaerobic degradability and COD removal in the second anaerobic stage significantly increased, by 13-40%...
August 24, 2017: Bioresource Technology
https://www.readbyqxmd.com/read/28946939/an-nmr-study-on-the-intrinsically-disordered-core-transactivation-domain-of-human-glucocorticoid-receptor
#16
Do-Hyoung Kim, Anthony Wright, Kyou-Hoon Han
A large number of transcriptional activation domains (TADs) are intrinsically unstructured, meaning they are devoid of a three-dimensional structure. The fact that these TADs are transcriptionally active without forming a 3-D structure raises the question of what features in these domains enable them to function. One of two TADs in human glucocorticoid receptor (hGR) is located at its N-terminus and is responsible for ~70% of the transcriptional activity of hGR. This 58-residue intrinsically-disordered TAD, named tau1c in an earlier study, was shown to form three helices under trifluoroethanol, which might be important for its activity...
September 26, 2017: BMB Reports
https://www.readbyqxmd.com/read/28938092/ctcf-mediated-enhancer-promoter-interaction-is-a-critical-regulator-of-cell-to-cell-variation-of-gene-expression
#17
Gang Ren, Wenfei Jin, Kairong Cui, Joseph Rodrigez, Gangqing Hu, Zhiying Zhang, Daniel R Larson, Keji Zhao
Recent studies indicate that even a homogeneous population of cells display heterogeneity in gene expression and response to environmental stimuli. Although promoter structure critically influences the cell-to-cell variation of gene expression in bacteria and lower eukaryotes, it remains unclear what controls the gene expression noise in mammals. Here we report that CTCF decreases cell-to-cell variation of expression by stabilizing enhancer-promoter interaction. We show that CTCF binding sites are interwoven with enhancers within topologically associated domains (TADs) and a positive correlation is found between CTCF binding and the activity of the associated enhancers...
September 21, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28936982/optimization-and-quality-control-of-genome-wide-hi-c-library-preparation
#18
Xiang-Yuan Zhang, Chao He, Bing-Yu Ye, De-Jian Xie, Ming-Lei Shi, Yan Zhang, Wen-Long Shen, Ping Li, Zhi-Hu Zhao
Highest-throughput chromosome conformation capture (Hi-C) is one of the key assays for genome- wide chromatin interaction studies. It is a time-consuming process that involves many steps and many different kinds of reagents, consumables, and equipments. At present, the reproducibility is unsatisfactory. By optimizing the key steps of the Hi-C experiment, such as crosslinking, pretreatment of digestion, inactivation of restriction enzyme, and in situ ligation etc., we established a robust Hi-C procedure and prepared two biological replicates of Hi-C libraries from the GM12878 cells...
September 20, 2017: Yi Chuan, Hereditas
https://www.readbyqxmd.com/read/28913417/parasite-biodiversity-faces-extinction-and-redistribution-in-a-changing-climate
#19
Colin J Carlson, Kevin R Burgio, Eric R Dougherty, Anna J Phillips, Veronica M Bueno, Christopher F Clements, Giovanni Castaldo, Tad A Dallas, Carrie A Cizauskas, Graeme S Cumming, Jorge Doña, Nyeema C Harris, Roger Jovani, Sergey Mironov, Oliver C Muellerklein, Heather C Proctor, Wayne M Getz
Climate change is a well-documented driver of both wildlife extinction and disease emergence, but the negative impacts of climate change on parasite diversity are undocumented. We compiled the most comprehensive spatially explicit data set available for parasites, projected range shifts in a changing climate, and estimated extinction rates for eight major parasite clades. On the basis of 53,133 occurrences capturing the geographic ranges of 457 parasite species, conservative model projections suggest that 5 to 10% of these species are committed to extinction by 2070 from climate-driven habitat loss alone...
September 2017: Science Advances
https://www.readbyqxmd.com/read/28910577/subnuclear-distribution-of-proteins-links-with-genome-architecture
#20
Fouziya R Shah, Younus A Bhat, Ajazul H Wani
Metazoan genomes have a hierarchal 3-dimensional (3D) organization scaling from nucleosomes, loops, topologically associating domains (TADs), compartments, to chromosome territories. The 3D organization of genome has been linked with development, differentiation and disease. However, the principles governing the 3D chromatin architecture are just beginning to get unraveled. The nucleus has very high concentration of proteins and these proteins are either diffusely distributed throughout the nucleus, or aggregated in the form of foci/bodies/clusters/speckles or in combination of both...
September 14, 2017: Nucleus
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