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https://www.readbyqxmd.com/read/27911722/dawn-of-the-in-vivo-rna-structurome-and-interactome
#1
REVIEW
Chun Kit Kwok
RNA is one of the most fascinating biomolecules in living systems given its structural versatility to fold into elaborate architectures for important biological functions such as gene regulation, catalysis, and information storage. Knowledge of RNA structures and interactions can provide deep insights into their functional roles in vivo For decades, RNA structural studies have been conducted on a transcript-by-transcript basis. The advent of next-generation sequencing (NGS) has enabled the development of transcriptome-wide structural probing methods to profile the global landscape of RNA structures and interactions, also known as the RNA structurome and interactome, which transformed our understanding of the RNA structure-function relationship on a transcriptomic scale...
October 15, 2016: Biochemical Society Transactions
https://www.readbyqxmd.com/read/27889101/highly-heterogeneous-genomic-landscape-of-uterine-leiomyomas-by%C3%A2-whole-exome-sequencing-and-genome-wide-arrays
#2
Svetlana A Yatsenko, Priya Mittal, Michelle A Wood-Trageser, Mirka W Jones, Urvashi Surti, Robert P Edwards, Anil K Sood, Aleksandar Rajkovic
OBJECTIVE: To determine the genomic signatures of human uterine leiomyomas and prevalence of MED12 mutations in human uterine leiomyosarcomas. DESIGN: Retrospective cohort study. SETTING: Not applicable. PATIENT(S): This study included a set of 16 fresh frozen leiomyoma and corresponding unaffected myometrium specimens as well as 153 leiomyosarcomas collected from women diagnosed with uterine leiomyomas or leiomyosarcomas who underwent clinically indicated abdominal hysterectomy...
November 23, 2016: Fertility and Sterility
https://www.readbyqxmd.com/read/27881085/the-ebola-outbreak-catalyzing-a-shift-in-global-health-governance
#3
Tim K Mackey
BACKGROUND: As the 2014 Ebola virus disease outbreak (EVD) transitions to its post-endemic phase, its impact on the future of global public health, particularly the World Health Organization (WHO), is the subject of continued debate. Criticism of WHO's performance grew louder in the outbreak's wake, placing this international health UN-specialized agency in the difficult position of navigating a complex series of reform recommendations put forth by different stakeholders. Decisions on WHO governance reform and the broader role of the United Nations could very well shape the future landscape of 21st century global health and how the international community responds to health emergencies...
November 24, 2016: BMC Infectious Diseases
https://www.readbyqxmd.com/read/27873369/the-genetic-architecture-of-novel-trophic-specialists-higher-effect-sizes-are-associated-with-exceptional-oral-jaw-diversification-in-a-pupfish-adaptive-radiation
#4
Christopher H Martin, Priscilla A Erickson, Craig T Miller
The genetic architecture of adaptation is fundamental to understanding the mechanisms and constraints governing diversification. However, most case studies focus on loss of complex traits or parallel speciation in similar environments. It is still unclear how the genetic architecture of these local adaptive processes compares to the architecture of evolutionary transitions contributing to morphological and ecological novelty. Here we identify quantitative trait loci (QTL) between two trophic specialists in an excellent case study for examining the origins of ecological novelty: a sympatric radiation of pupfishes endemic to San Salvador Island, Bahamas containing a large-jawed scale-eater and a short-jawed molluscivore with a skeletal nasal protrusion...
November 22, 2016: Molecular Ecology
https://www.readbyqxmd.com/read/27863252/the-allelic-landscape-of-human-blood-cell-trait-variation-and-links-to-common-complex-disease
#5
William J Astle, Heather Elding, Tao Jiang, Dave Allen, Dace Ruklisa, Alice L Mann, Daniel Mead, Heleen Bouman, Fernando Riveros-Mckay, Myrto A Kostadima, John J Lambourne, Suthesh Sivapalaratnam, Kate Downes, Kousik Kundu, Lorenzo Bomba, Kim Berentsen, John R Bradley, Louise C Daugherty, Olivier Delaneau, Kathleen Freson, Stephen F Garner, Luigi Grassi, Jose Guerrero, Matthias Haimel, Eva M Janssen-Megens, Anita Kaan, Mihir Kamat, Bowon Kim, Amit Mandoli, Jonathan Marchini, Joost H A Martens, Stuart Meacham, Karyn Megy, Jared O'Connell, Romina Petersen, Nilofar Sharifi, Simon M Sheard, James R Staley, Salih Tuna, Martijn van der Ent, Klaudia Walter, Shuang-Yin Wang, Eleanor Wheeler, Steven P Wilder, Valentina Iotchkova, Carmel Moore, Jennifer Sambrook, Hendrik G Stunnenberg, Emanuele Di Angelantonio, Stephen Kaptoge, Taco W Kuijpers, Enrique Carrillo-de-Santa-Pau, David Juan, Daniel Rico, Alfonso Valencia, Lu Chen, Bing Ge, Louella Vasquez, Tony Kwan, Diego Garrido-Martín, Stephen Watt, Ying Yang, Roderic Guigo, Stephan Beck, Dirk S Paul, Tomi Pastinen, David Bujold, Guillaume Bourque, Mattia Frontini, John Danesh, David J Roberts, Willem H Ouwehand, Adam S Butterworth, Nicole Soranzo
Many common variants have been associated with hematological traits, but identification of causal genes and pathways has proven challenging. We performed a genome-wide association analysis in the UK Biobank and INTERVAL studies, testing 29.5 million genetic variants for association with 36 red cell, white cell, and platelet properties in 173,480 European-ancestry participants. This effort yielded hundreds of low frequency (<5%) and rare (<1%) variants with a strong impact on blood cell phenotypes. Our data highlight general properties of the allelic architecture of complex traits, including the proportion of the heritable component of each blood trait explained by the polygenic signal across different genome regulatory domains...
November 17, 2016: Cell
https://www.readbyqxmd.com/read/27863239/ever-changing-landscapes-transcriptional-enhancers-in-development-and-evolution
#6
REVIEW
Hannah K Long, Sara L Prescott, Joanna Wysocka
A class of cis-regulatory elements, called enhancers, play a central role in orchestrating spatiotemporally precise gene-expression programs during development. Consequently, divergence in enhancer sequence and activity is thought to be an important mediator of inter- and intra-species phenotypic variation. Here, we give an overview of emerging principles of enhancer function, current models of enhancer architecture, genomic substrates from which enhancers emerge during evolution, and the influence of three-dimensional genome organization on long-range gene regulation...
November 17, 2016: Cell
https://www.readbyqxmd.com/read/27856745/unreasonable-effectiveness-of-learning-neural-networks-from-accessible-states-and-robust-ensembles-to-basic-algorithmic-schemes
#7
Carlo Baldassi, Christian Borgs, Jennifer T Chayes, Alessandro Ingrosso, Carlo Lucibello, Luca Saglietti, Riccardo Zecchina
In artificial neural networks, learning from data is a computationally demanding task in which a large number of connection weights are iteratively tuned through stochastic-gradient-based heuristic processes over a cost function. It is not well understood how learning occurs in these systems, in particular how they avoid getting trapped in configurations with poor computational performance. Here, we study the difficult case of networks with discrete weights, where the optimization landscape is very rough even for simple architectures, and provide theoretical and numerical evidence of the existence of rare-but extremely dense and accessible-regions of configurations in the network weight space...
November 29, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27846889/using-expert-decision-making-to-establish-indicators-of-urban-friendliness-for-walking-environments-a-multidisciplinary-assessment
#8
Yen-Cheng Chiang, Han-Yu Lei
BACKGROUND: Numerous studies have suggested that friendly walking environments positively affect physical activity and health. Creating friendly walking environments in urban areas is a complex and wide-ranging topic, and no study has yet established a set of assessment indicators by drawing on the expertise of various disciplines. This study uses a multiple-criteria decision-making technique to elucidate the environmental factors that affect the friendliness of the walking environment...
November 15, 2016: International Journal of Health Geographics
https://www.readbyqxmd.com/read/27767303/coarse-grained-simulations-complemented-by-atomistic-molecular-dynamics-provide-new-insights-into-folding-of-human-telomeric-g-quadruplexes
#9
Petr Stadlbauer, Liuba Mazzanti, Tristan Cragnolini, David J Wales, Philippe Derreumaux, Samuela Pasquali, Jiri Sponer
G-quadruplexes are the most important non-canonical DNA architectures. Many quadruplex-forming sequences, including the human telomeric sequence d(GGGTTA)n, have been investigated due to their implications in cancer and other diseases, and because of their potential in DNA-based nanotechnology. Despite availability of atomistic structural studies of folded G-quadruplexes, their folding pathways remain mysterious, and mutually contradicting models of folding coexist in the literature. Recent experiments convincingly demonstrated that G-quadruplex folding often takes days to reach the thermodynamics equilibrium...
October 21, 2016: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/27762135/contribution-of-mass-spectrometry-based-proteomics-to-the-understanding-of-tnf-%C3%AE-signaling
#10
Rodolfo Ciuffa, Etienne Caron, Alexander Leitner, Federico Uliana, Matthias Gstaiger, Ruedi Aebersold
NF-κB is a family of ubiquitous dimeric transcription factors that play a role in a myriad of cellular processes, ranging from differentiation to stress response and immunity. In inflammation, activation of NF-κB is mediated by pro-inflammatory cytokines, in particular the prototypic cytokines IL-1β and TNF-α, which trigger the activation of complex signaling cascades. In spite of decades of research, the system level understanding of TNF-α signaling is still incomplete. This is partially due to the limited knowledge at the proteome level...
October 20, 2016: Journal of Proteome Research
https://www.readbyqxmd.com/read/27730478/action-observation-training-modifies-brain-gray-matter-structure-in-healthy-adult-individuals
#11
Maria A Rocca, Silvia Fumagalli, Elisabetta Pagani, Roberto Gatti, Gianna C Riccitelli, Paolo Preziosa, Giancarlo Comi, Andrea Falini, Massimo Filippi
Action observation training (AOT) is thought to facilitate motor system function. We applied voxelwise methods to assess the regional modifications of brain gray matter (GM) volumes and white matter (WM) architecture in healthy subjects following AOT and their correlations with improvements at motor and cognitive functional scales. Forty-two righ-handed healthy subjects were randomized into an experimental (AOT-G, n = 20) and a control (C-G, n = 22) group. The training lasted 2 weeks and consisted of 10 sessions of 45 min each during which subjects watched videos of daily-life actions (AOT-G) or landscapes (C-G), alternated by the execution with the right hand of actions presented in the AOT-G videos...
October 11, 2016: Brain Imaging and Behavior
https://www.readbyqxmd.com/read/27702596/dna-damage-induced-inflammation-and-nuclear-architecture
#12
Kalliopi Stratigi, Ourania Chatzidoukaki, George A Garinis
Nuclear architecture and the chromatin state affect most-if not all- DNA-dependent transactions, including the ability of cells to sense DNA lesions and restore damaged DNA back to its native form. Recent evidence points to functional links between DNA damage sensors, DNA repair mechanisms and the innate immune responses. The latter raises the question of how such seemingly disparate processes operate within the intrinsically complex nuclear landscape and the chromatin environment. Here, we discuss how DNA damage-induced immune responses operate within chromatin and the distinct sub-nuclear compartments highlighting their relevance to chronic inflammation...
October 1, 2016: Mechanisms of Ageing and Development
https://www.readbyqxmd.com/read/27692923/genomic-energy-landscapes
#13
Bin Zhang, Peter G Wolynes
Energy landscape theory, developed in the context of protein folding, provides, to our knowledge, a new perspective on chromosome architecture. We review what has been learned concerning the topology and structure of both the interphase and mitotic chromosomes from effective energy landscapes constructed using Hi-C data. Energy landscape thinking raises new questions about the nonequilibrium dynamics of the chromosome and gene regulation.
September 30, 2016: Biophysical Journal
https://www.readbyqxmd.com/read/27692891/sustainable-infrastructure-a-review-and-a-research-agenda
#14
Antônio Márcio Tavares Thomé, Paula Santos Ceryno, Annibal Scavarda, Arne Remmen
This paper proposes a taxonomy of themes and a research agenda on sustainable infrastructure, with a focus on sustainable buildings (SB) and green infrastructure (GI). The citation databases of Web of Science formed the basis for a novel strategic thematic analysis of co-citation and co-occurrence of keywords with a longitudinal identification of themes during the last two decades (from 1995 to 2015) of an emerging and ever growing research area. SI is a multidisciplinary endeavour, including a diversified array of disciplines as general engineering, environmental ecology, construction, architecture, urban planning, and geography...
September 29, 2016: Journal of Environmental Management
https://www.readbyqxmd.com/read/27688758/transferable-model-for-chromosome-architecture
#15
Michele Di Pierro, Bin Zhang, Erez Lieberman Aiden, Peter G Wolynes, José N Onuchic
In vivo, the human genome folds into a characteristic ensemble of 3D structures. The mechanism driving the folding process remains unknown. We report a theoretical model for chromatin (Minimal Chromatin Model) that explains the folding of interphase chromosomes and generates chromosome conformations consistent with experimental data. The energy landscape of the model was derived by using the maximum entropy principle and relies on two experimentally derived inputs: a classification of loci into chromatin types and a catalog of the positions of chromatin loops...
October 25, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27678043/maternal-depression-research-socioeconomic-analysis-and-density-equalizing-mapping-of-the-global-research-architecture
#16
Dörthe Brüggmann, Christina Wagner, Doris Klingelhöfer, Norman Schöffel, Michael Bendels, Frank Louwen, Jenny Jaque, David A Groneberg
Maternal depression can be accounted for one of the most common complications during pregnancy and the postpartum period affecting women all over the world. So far, no detailed map of the worldwide maternal depression research architecture has been constructed, which encompasses aspects of research activity, quality, and also socioeconomic features. Using the NewQIS platform, density-equalizing mapping projections, scientometric techniques, and economic benchmarking procedures were applied to evaluate global maternal depression research for the period between 1900 and 2012...
September 27, 2016: Archives of Women's Mental Health
https://www.readbyqxmd.com/read/27647397/-multiregion-sequencing-reveals-intratumor-heterogeneity-in-esophageal-squamous-cell-carcinoma
#17
W Cao, W Wu, M Yan, F Tian, H S Liu, J W Wang, Q W Zhang, Y J Li, M Li
Objective: To study the intratumor heterogeneity of esophageal squamous cell carcinoma (ESCC). Methods: We used whole-exome sequencing and array-based comparative genomic hybridization to profile mutations and changes in copy number from 11 regions within 2 cases of ESCC and from the metastatic lymph nodes. Results: The numbers of somatic single nuclear polymorphisms (SNPs) in 4 regions within the tumors in case 1 and case 2 were 93±17 and 124±28, respectively. The majority of SNPs were non synonymous mutations, synonymous mutations, nonsense mutations and splicing junction mutations...
September 23, 2016: Zhonghua Zhong Liu za Zhi [Chinese Journal of Oncology]
https://www.readbyqxmd.com/read/27642047/real-time-tracking-of-parental-histones-reveals-their-contribution-to-chromatin-integrity-following-dna-damage
#18
Salomé Adam, Juliette Dabin, Odile Chevallier, Olivier Leroy, Céline Baldeyron, Armelle Corpet, Patrick Lomonte, Olivier Renaud, Geneviève Almouzni, Sophie E Polo
Chromatin integrity is critical for cell function and identity but is challenged by DNA damage. To understand how chromatin architecture and the information that it conveys are preserved or altered following genotoxic stress, we established a system for real-time tracking of parental histones, which characterize the pre-damage chromatin state. Focusing on histone H3 dynamics after local UVC irradiation in human cells, we demonstrate that parental histones rapidly redistribute around damaged regions by a dual mechanism combining chromatin opening and histone mobilization on chromatin...
October 6, 2016: Molecular Cell
https://www.readbyqxmd.com/read/27598692/effects-of-polymer-conjugation-on-hybridization-thermodynamics-of-oligonucleic-acids
#19
Ahmadreza F Ghobadi, Arthi Jayaraman
In this work, we perform coarse-grained (CG) and atomistic simulations to study the effects of polymer conjugation on hybridization/melting thermodynamics of oligonucleic acids (ONAs). We present coarse-grained Langevin molecular dynamics simulations (CG-NVT) to assess the effects of the polymer flexibility, length, and architecture on hybridization/melting of ONAs with different ONA duplex sequences, backbone chemistry, and duplex concentration. In these CG-NVT simulations, we use our recently developed CG model of ONAs in implicit solvent, and treat the conjugated polymer as a CG chain with purely repulsive Weeks-Chandler-Andersen interactions with all other species in the system...
September 15, 2016: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/27585846/promoter-architecture-and-sex-specific-gene-expression-in-daphnia-pulex
#20
R Taylor Raborn, Ken Spitze, Volker P Brendel, Michael Lynch
Large-scale transcription start site (TSS) profiling produces a high-resolution, quantitative picture of transcription initiation and core promoter locations within a genome. However, application of TSS profiling to date has largely been restricted to a small set of prominent model systems. We sought to characterize the cis-regulatory landscape of the water flea Daphnia pulex, an emerging model arthropod that reproduces both asexually (via parthenogenesis) and sexually (via meiosis). We performed Cap Analysis of Gene Expression (CAGE) with RNA isolated from D...
October 2016: Genetics
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