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https://www.readbyqxmd.com/read/27924036/folding-and-misfolding-pathways-of-g-quadruplex-dna
#1
Adrien Marchand, Valérie Gabelica
G-quadruplexes adopt various folding topologies, but information on their folding pathways remains scarce. Here, we used electrospray mass spectrometry to detect and quantify the specifically bound potassium ions, and circular dichroism to characterize the stacking topology of each ensemble. For human telomeric (hTel) sequences containing the d((GGGTTA)3GGG) core, K(+) binding affinity and cooperativity strongly depends on the chosen construct. The shortest sequences bind only one K(+) at low KCl concentration, and this 2-quartet G-quadruplex is antiparallel...
October 19, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27923409/geographical-landscape-and-host-associations-of-trypanosoma-cruzi-dtus-and-lineages
#2
Amaia Izeta-Alberdi, Carlos N Ibarra-Cerdeña, David A Moo-Llanes, Janine M Ramsey
BACKGROUND: The evolutionary history and ecological associations of Trypanosoma cruzi, the need to identify genetic markers that can distinguish parasite subpopulations, and understanding the parasite's evolutionary and selective processes have been the subject of a significant number of publications since 1998, the year when the first DNA sequence analysis for the species was published. METHODS: The current analysis systematizes and re-analyzes this original research, focusing on critical methodological and analytical variables and results that have given rise to interpretations of putative patterns of genetic diversity and diversification of T...
December 7, 2016: Parasites & Vectors
https://www.readbyqxmd.com/read/27923066/somatic-genomics-and-clinical-features-of-lung-adenocarcinoma-a-retrospective-study
#3
Jianxin Shi, Xing Hua, Bin Zhu, Sarangan Ravichandran, Mingyi Wang, Cu Nguyen, Seth A Brodie, Alessandro Palleschi, Marco Alloisio, Gianluca Pariscenti, Kristine Jones, Weiyin Zhou, Aaron J Bouk, Joseph Boland, Belynda Hicks, Adam Risch, Hunter Bennett, Brian T Luke, Lei Song, Jubao Duan, Pengyuan Liu, Takashi Kohno, Qingrong Chen, Daoud Meerzaman, Crystal Marconett, Ite Laird-Offringa, Ian Mills, Neil E Caporaso, Mitchell H Gail, Angela C Pesatori, Dario Consonni, Pier Alberto Bertazzi, Stephen J Chanock, Maria Teresa Landi
BACKGROUND: Lung adenocarcinoma (LUAD) is the most common histologic subtype of lung cancer and has a high risk of distant metastasis at every disease stage. We aimed to characterize the genomic landscape of LUAD and identify mutation signatures associated with tumor progression. METHODS AND FINDINGS: We performed an integrative genomic analysis, incorporating whole exome sequencing (WES), determination of DNA copy number and DNA methylation, and transcriptome sequencing for 101 LUAD samples from the Environment And Genetics in Lung cancer Etiology (EAGLE) study...
December 2016: PLoS Medicine
https://www.readbyqxmd.com/read/27920956/grassland-productivity-in-response-to-nutrient-additions-and-herbivory-is-scale-dependent
#4
Erica A H Smithwick, Douglas C Baldwin, Kusum J Naithani
Vegetation response to nutrient addition can vary across space, yet studies that explicitly incorporate spatial pattern into experimental approaches are rare. To explore whether there are unique spatial scales (grains) at which grass response to nutrients and herbivory is best expressed, we imposed a large (∼3.75 ha) experiment in a South African coastal grassland ecosystem. In two of six 60 × 60 m grassland plots, we imposed a scaled sampling design in which fertilizer was added in replicated sub-plots (1 × 1 m, 2 × 2 m, and 4 × 4 m)...
2016: PeerJ
https://www.readbyqxmd.com/read/27918925/biosphere-reserves-attributes-for-success
#5
Chu Van Cuong, Peter Dart, Marc Hockings
Biosphere reserves established under the UNESCO Man and the Biosphere Program aim to harmonise biodiversity conservation and sustainable development. Concerns over the extent to which the reserve network was living up to this ideal led to the development of a new strategy in 1995 (the Seville Strategy) to enhance the operation of the network of reserves. An evaluation of effectiveness of management of the biosphere reserve network was called for as part of this strategy. Expert opinion was assembled through a Delphi Process to identify successful and less successful reserves and investigate common factors influencing success or failure...
December 2, 2016: Journal of Environmental Management
https://www.readbyqxmd.com/read/27917986/the-cultural-heritage-of-pastoralism-local-knowledge-state-identity-and-the-global-perspective-the-example-of-local-breeds-in-morocco
#6
Y Ben Hounet, A-M Brisebarre, S Guinand
Over the past few decades, the heritage designation process has come to impact on the way of life of many nomadic pastoralists across the world. Since the Convention Concerning the Protection of the World Cultural and Natural Heritage was adopted in 1972, policies for the conservation of protected areas have been implemented under the aegis of the United Nations Educational, Scientific and Cultural Organization (UNESCO), especially in countries of the South, with a varying impact on the practices and perceptions of pastoral communities...
November 2016: Revue Scientifique et Technique
https://www.readbyqxmd.com/read/27917863/dna-intercalation-optimized-by-two-step-molecular-lock-mechanism
#7
Ali A Almaqwashi, Johanna Andersson, Per Lincoln, Ioulia Rouzina, Fredrik Westerlund, Mark C Williams
The diverse properties of DNA intercalators, varying in affinity and kinetics over several orders of magnitude, provide a wide range of applications for DNA-ligand assemblies. Unconventional intercalation mechanisms may exhibit high affinity and slow kinetics, properties desired for potential therapeutics. We used single-molecule force spectroscopy to probe the free energy landscape for an unconventional intercalator that binds DNA through a novel two-step mechanism in which the intermediate and final states bind DNA through the same mono-intercalating moiety...
December 5, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27914793/challenges-in-translational-development-of-pharmaceutical-cocrystals
#8
Dnyaneshwar P Kale, Sandeep S Zode, Arvind K Bansal
The last 2 decades have witnessed increased research in the area of cocrystals resulting in deeper scientific understanding, increase in intellectual property landscape, and evolution in the regulatory environment. Pharmaceutical cocrystals have received significant attention as a new solid form on account of their ability to modulate poor physicochemical properties of drug molecules. However, pharmaceutical development of cocrystals could be challenging, thus limiting their translation into viable drug products...
November 30, 2016: Journal of Pharmaceutical Sciences
https://www.readbyqxmd.com/read/27912015/invasion-in-patchy-landscapes-is-affected-by-dispersal-mortality-and-mate-finding-failure
#9
Jonathan A Walter, Ariel L Firebaugh, Patrick C Tobin, Kyle J Haynes
Range expansions are a function of population growth and dispersal, and nascent populations often must overcome demographic Allee effects (positive density dependence at low population densities) driven by factors such as mate-finding failure. Given the importance of individual movement to mate finding, links between landscape structure and movement may be critical to range expansion; however, landscape effects on other factors including mortality may be equally or more important. In one of the most comprehensive investigations of the interactions of these processes to date, we combined field experiments, simulation modeling, and analysis of empirical spread patterns to investigate how landscape structure affected the spread of the gypsy moth in Virginia and West Virginia...
December 2016: Ecology
https://www.readbyqxmd.com/read/27911789/design-principles-for-nonequilibrium-self-assembly
#10
Michael Nguyen, Suriyanarayanan Vaikuntanathan
We consider an important class of self-assembly problems, and using the formalism of stochastic thermodynamics, we derive a set of design principles for growing controlled assemblies far from equilibrium. The design principles constrain the set of configurations that can be obtained under nonequilibrium conditions. Our central result provides intuition for how equilibrium self-assembly landscapes are modified under finite nonequilibrium drive.
November 22, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27908108/dual-hydrogen-bonding-motifs-in-complexes-formed-between-tropolone-and-formic-acid
#11
Deacon J Nemchick, Michael K Cohen, Patrick H Vaccaro
The near-ultraviolet π(*)←π absorption system of weakly bound complexes formed between tropolone (TrOH) and formic acid (FA) under cryogenic free-jet expansion conditions has been interrogated by exploiting a variety of fluorescence-based laser-spectroscopic probes, with synergistic quantum-chemical calculations built upon diverse model chemistries being enlisted to unravel the structural and dynamical properties of the pertinent ground [X̃(1)A(')] and excited [Ã(1)A(')π(*)π] electronic states. For binary TrOH ⋅ FA adducts, the presence of dual hydrogen-bond linkages gives rise to three low-lying isomers designated (in relative energy order) as INT, EXT1, and EXT2 depending on whether docking of the FA ligand to the TrOH substrate takes place internal or external to the five-membered reaction cleft of tropolone...
November 28, 2016: Journal of Chemical Physics
https://www.readbyqxmd.com/read/27907252/residential-yards-as-designer-ecosystems-effects-of-yard%C3%A2-management-on-land-snail-species-composition
#12
Elizabeth A Bergey, Laura L Figueroa
Residential yards comprise the majority of green space in urban landscapes, yet are an understudied system because of access issues and because yards may be considered biologically depauperate. Yards are purposely created and managed and, hence, qualify as designer ecosystems, a term borrowed from restoration ecology. We investigated whether yard management (watering regime, mulching, and chemical use) or dog presence affected land snail assemblage composition and described the pattern of native vs. nonnative species among yards...
December 2016: Ecological Applications: a Publication of the Ecological Society of America
https://www.readbyqxmd.com/read/27899794/the-impact-of-digital-technology-on-health-of-populations-affected-by-humanitarian-crises-recent-innovations-and-current-gaps
#13
Sandra Mesmar, Reem Talhouk, Chaza Akik, Patrick Olivier, Imad H Elhajj, Shady Elbassuoni, Sarah Armoush, Joumana Kalot, Madeline Balaam, Aline Germani, Hala Ghattas
Digital technology is increasingly used in humanitarian action and promises to improve the health and social well-being of populations affected by both acute and protracted crises. We set out to (1) review the current landscape of digital technologies used by humanitarian actors and affected populations, (2) examine their impact on health and well-being of affected populations, and (3) consider the opportunities for and challenges faced by users of these technologies. Through a systematic search of academic databases and reports, we identified 50 digital technologies used by humanitarian actors, and/or populations affected by crises...
November 2016: Journal of Public Health Policy
https://www.readbyqxmd.com/read/27899642/the-ucsc-genome-browser-database-2017-update
#14
Cath Tyner, Galt P Barber, Jonathan Casper, Hiram Clawson, Mark Diekhans, Christopher Eisenhart, Clayton M Fischer, David Gibson, Jairo Navarro Gonzalez, Luvina Guruvadoo, Maximilian Haeussler, Steve Heitner, Angie S Hinrichs, Donna Karolchik, Brian T Lee, Christopher M Lee, Parisa Nejad, Brian J Raney, Kate R Rosenbloom, Matthew L Speir, Chris Villarreal, John Vivian, Ann S Zweig, David Haussler, Robert M Kuhn, W James Kent
Since its 2001 debut, the University of California, Santa Cruz (UCSC) Genome Browser (http://genome.ucsc.edu/) team has provided continuous support to the international genomics and biomedical communities through a web-based, open source platform designed for the fast, scalable display of sequence alignments and annotations landscaped against a vast collection of quality reference genome assemblies. The browser's publicly accessible databases are the backbone of a rich, integrated bioinformatics tool suite that includes a graphical interface for data queries and downloads, alignment programs, command-line utilities and more...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27898802/nutrient-cycling-in-grassed-roadside-ditches-and-lawns-in-a-suburban-watershed
#15
Lauren E McPhillips, Peter M Groffman, Rebecca L Schneider, M Todd Walter
Roadside ditches are ubiquitous in developed landscapes. They are designed to route water from roads for safety, with little consideration of water quality or biogeochemical implications in ditch design and minimal data on environmental impacts. We hypothesize that periodic saturation and nutrient influxes may make roadside ditches hotspots for nitrogen (N) removal via denitrification as well as biological production of the greenhouse gases (GHGs) nitrous oxide (NO), methane (CH), and carbon dioxide (CO). Research sites included 12 grassed ditches and adjacent lawns with varying fertilization in a suburban watershed in central New York, where lawns represented a reference with similar soils as ditches but differing hydrology...
November 2016: Journal of Environmental Quality
https://www.readbyqxmd.com/read/27892767/epigenetic-modifications-in-multiple-myeloma-recent-advances-on-the-role-of-dna-and-histone-methylation
#16
Nicola Amodio, Patrizia D'Aquila, Giuseppe Passarino, Pierfrancesco Tassone, Dina Bellizzi
Multiple Myeloma (MM) is a clonal late B-cell disorder accounting for about 13% of hematological cancers and 1% of all neoplastic diseases. Recent studies on the molecular pathogenesis and biology of MM have highlighted a complex epigenomic landscape contributing to MM onset, prognosis and high individual variability. Areas covered: We describe here the current knowledge on epigenetic events characterizing MM initiation and progression, focusing on the role of DNA and histone methylation and on the most promising epi-therapeutic approaches targeting the methylation pathway...
November 28, 2016: Expert Opinion on Therapeutic Targets
https://www.readbyqxmd.com/read/27890965/beescout-a-model-of-bee-scouting-behaviour-and-a-software-tool-for-characterizing-nectar-pollen-landscapes-for-beehave
#17
M A Becher, V Grimm, J Knapp, J Horn, G Twiston-Davies, J L Osborne
Social bees are central place foragers collecting floral resources from the surrounding landscape, but little is known about the probability of a scouting bee finding a particular flower patch. We therefore developed a software tool, BEESCOUT, to theoretically examine how bees might explore a landscape and distribute their scouting activities over time and space. An image file can be imported, which is interpreted by the model as a "forage map" with certain colours representing certain crops or habitat types as specified by the user...
November 24, 2016: Ecological Modelling
https://www.readbyqxmd.com/read/27889238/insights-into-nucleosome-organization-in-mouse-embryonic-stem-cells-through-chemical-mapping
#18
Lilien N Voong, Liqun Xi, Amy C Sebeson, Bin Xiong, Ji-Ping Wang, Xiaozhong Wang
Nucleosome organization influences gene activity by controlling DNA accessibility to transcription machinery. Here, we develop a chemical biology approach to determine mammalian nucleosome positions genome-wide. We uncovered surprising features of nucleosome organization in mouse embryonic stem cells. In contrast to the prevailing model, we observe that for nearly all mouse genes, a class of fragile nucleosomes occupies previously designated nucleosome-depleted regions around transcription start sites and transcription termination sites...
December 1, 2016: Cell
https://www.readbyqxmd.com/read/27888423/assessment-of-land-use-and-land-cover-change-using-spatiotemporal-analysis-of-landscape-case-study-in-south-of-tehran
#19
Abutaleb Sabr, Mazaher Moeinaddini, Hossein Azarnivand, Benjamin Guinot
In the recent years, dust storms originating from local abandoned agricultural lands have increasingly impacted Tehran and Karaj air quality. Designing and implementing mitigation plans are necessary to study land use/land cover change (LUCC). Land use/cover classification is particularly relevant in arid areas. This study aimed to map land use/cover by pixel- and object-based image classification methods, analyse landscape fragmentation and determine the effects of two different classification methods on landscape metrics...
December 0: Environmental Monitoring and Assessment
https://www.readbyqxmd.com/read/27887782/ambient-particulate-matter-landscape-fire-smoke-and-emergency-ambulance-dispatches-in-sydney-australia
#20
Farhad Salimi, Sarah B Henderson, Geoffrey G Morgan, Bin Jalaludin, Fay H Johnston
BACKGROUND: Emergency ambulance dispatches (EAD) are a novel outcome for evaluating the public health impacts of air pollution. We assessed the relationships between ambient particulate matter (PM) from all sources, PM from landscape fire smoke (LFS), and EADs likely to be associated with cardiorespiratory problems in the Sydney greater metropolitan region for an 11-year period from 2004 to 2015. METHODS: EAD codes are assigned at the time of the call to emergency services using standard computer assisted algorithms...
November 22, 2016: Environment International
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