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https://www.readbyqxmd.com/read/28822769/somatic-mutation-analysis-in-melanoma-using-targeted-next-generation-sequencing
#1
Allen P Miraflor, Francine B de Abreu, Jason D Peterson, Scott A Turner, Christopher I Amos, Gregory J Tsongalis, Shaofeng Yan
Advanced stage malignant melanoma often responds poorly to therapy with low survival rates. New therapeutic approaches are based upon a growing understanding of the underlying molecular abnormalities. We demonstrate the feasibility of a next generation sequencing (NGS) assay, which targets hotspots in 50 cancer genes, to assess genotypes that may influence therapeutic selection and response. DNA was extracted from formalin fixed paraffin embedded (FFPE) melanoma specimens to create multiplexed libraries which were sequenced...
August 16, 2017: Experimental and Molecular Pathology
https://www.readbyqxmd.com/read/28822491/role-of-dispersal-in-resistance-evolution-and-spread
#2
REVIEW
Nicholas J Miller, Thomas W Sappington
Gene flow via immigration affects rate of evolution of resistance to a pest management tactic, while emigration from a resistant population can spread resistance alleles spatially. Whether resistance detected across the landscape reflects ongoing de novo evolution in different hotspots or spread from a single focal population can determine the most effective mitigation strategy. Pest dispersal dynamics determine the spatio-temporal scale at which mitigation tactics must be applied to contain or reverse resistance in an area...
June 2017: Current Opinion in Insect Science
https://www.readbyqxmd.com/read/28820979/data-driven-analysis-of-nutrient-inputs-and-transfers-through-nested-catchments
#3
Lea Levi, Vladimir Cvetkovic, Georgia Destouni
A data-driven screening methodology is developed for estimating nutrient input and retention-delivery in catchments with measured water discharges and nutrient concentrations along the river network. The methodology is applied to the Sava River Catchment (SRC), a major transboundary catchment in southeast Europe, with seven monitoring stations along the main river, defining seven nested catchments and seven incremental subcatchments that are analysed and compared in this study. For the relatively large nested catchments (>40,000km(2)), characteristic regional values emerge for nutrient input per unit area of around 30T/yr/km(2) for dissolved inorganic nitrogen (DIN) and 2T/yr/km(2) for total phosphorus (TP)...
August 15, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28820883/spatial-clustering-of-patent-and-sub-patent-malaria-infections-in-northern-namibia-implications-for-surveillance-and-response-strategies-for-elimination
#4
Jennifer L Smith, Joyce Auala, Munyaradzi Tambo, Erastus Haindongo, Stark Katokele, Petrina Uusiku, Roly Gosling, Immo Kleinschmidt, Davis Mumbengegwi, Hugh J W Sturrock
BACKGROUND: Reactive case detection (RACD) around passively detected malaria cases is a strategy to identify and treat hotspots of malaria transmission. This study investigated the unproven assumption on which this approach is based, that in low transmission settings, infections cluster over small scales. METHODS: A prospective case-control study was conducted between January 2013 and August 2014 in Ohangwena and Omusati regions in north central Namibia. Patients attending health facilities who tested positive by malaria rapid diagnostic test (RDT) (index cases) were traced back to their home...
2017: PloS One
https://www.readbyqxmd.com/read/28820351/genomic-and-chromatin-features-shaping-meiotic-double-strand-break-formation-and-repair-in-mice
#5
Shintaro Yamada, Seoyoung Kim, Sam E Tischfield, Maria Jasin, Julian Lange, Scott Keeney
The SPO11-generated DNA double-strand breaks (DSBs) that initiate meiotic recombination occur non-randomly across genomes, but mechanisms shaping their distribution and repair remain incompletely understood. Here, we expand on recent studies of nucleotide-resolution DSB maps in mouse spermatocytes. We find that trimethylation of histone H3 lysine 36 around DSB hotspots is highly correlated, both spatially and quantitatively, with trimethylation of H3 lysine 4, consistent with coordinated formation and action of both PRDM9-dependent histone modifications...
August 18, 2017: Cell Cycle
https://www.readbyqxmd.com/read/28819747/word-wide-meta-analysis-of-quercus-forests-ectomycorrhizal-fungal-diversity-reveals-southwestern-mexico-as-a-hotspot
#6
Olimpia Mariana García-Guzmán, Roberto Garibay-Orijel, Edith Hernández, Elsa Arellano-Torres, Ken Oyama
Quercus is the most diverse genus of ectomycorrhizal (ECM) host plants; it is distributed in the Northern and Southern Hemispheres, from temperate to tropical regions. However, their ECM communities have been scarcely studied in comparison to those of conifers. The objectives of this study were to determine the richness of ECM fungi associated with oak forests in the Cuitzeo basin in southwestern Mexico; and to determine the level of richness, potential endemism and species similarity among ECM fungal communities associated with natural oak forests worldwide through a meta-analysis...
August 17, 2017: Mycorrhiza
https://www.readbyqxmd.com/read/28819148/analysis-and-comparative-genomics-of-r997-the-first-sxt-r391-integrative-and-conjugative-element-ice-of-the-indian-sub-continent
#7
Michael P Ryan, Patricia Armshaw, John A O'Halloran, J Tony Pembroke
The aim of this study was to analyse R997, the first integrative and conjugative element (ICE) isolated from the Indian Sub-Continent, and to determine its relationship to the SXT/R391 family of ICEs. WGS of Escherichia coli isolate AB1157 (which contains R997) was performed using Illumina sequencing technology. R997 context was assessed by de novo assembly, gene prediction and annotation tools, and compared to other SXT/R391 ICEs. R997 has a size of 85 Kb and harbours 85 ORFs. Within one of the variable regions a HMS-1 β-lactamase resistance gene is located...
August 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28819145/remote-sensing-of-seasonal-light-use-efficiency-in-temperate-bog-ecosystems
#8
R Tortini, N C Coops, Z Nesic, A Christen, S C Lee, T Hilker
Despite storing approximately half of the atmosphere's carbon, estimates of fluxes between wetlands and atmosphere under current and future climates are associated with large uncertainties, and it remains a challenge to determine human impacts on the net greenhouse gas balance of wetlands at the global scale. In this study we demonstrate that the relationship between photochemical reflectance index, derived from high spectral and temporal multi-angular observations, and vegetation light use efficiency was strong (r(2) = 0...
August 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28818662/organic-matter-quality-structures-benthic-fatty-acid-patterns-and-the-abundance-of-fungi-and-bacteria-in-temperate-lakes
#9
Robert Taube, Lars Ganzert, Hans-Peter Grossart, Gerd Gleixner, Katrin Premke
Benthic microbial communities (BMCs) play important roles in the carbon cycle of lakes, and benthic littoral zones in particular have been previously highlighted as biogeochemical hotspots. Dissolved organic matter (DOM) presents the major carbon pool in lakes, and although the effect of DOM composition on the pelagic microbial community composition is widely accepted, little is known about its effect on BMCs, particularly aquatic fungi. Therefore, we investigated the composition of benthic littoral microbial communities in twenty highly diverse lakes in northeast Germany...
August 14, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28817827/role-of-next-generation-sequencing-as-a-diagnostic-tool-for-the-evaluation-of-bone-and-soft-tissue-tumors
#10
Kinga Szurian, Karl Kashofer, Bernadette Liegl-Atzwanger
Bone and soft-tissue tumors are in general rare. Diagnosing these tumors is challenging based on the significant number of different tumor entities, the rareness of these tumors, and the considerable morphological heterogeneity which can be found within a single tumor entity. Considering that more than half of the described soft-tissue tumors and approximately 25% of the bone tumors harbor recurrent genetic alterations, the use of auxiliary molecular examinations should be strongly considered. Molecular analyses are important to confirm the diagnosis, to guide treatment, to provide information about prognosis, and to allow patient recruitment for basket trials based on the molecular signature of a tumor...
August 18, 2017: Pathobiology: Journal of Immunopathology, Molecular and Cellular Biology
https://www.readbyqxmd.com/read/28817280/x-ray-spectroscopy-uncovering-the-effects-of-cu-based-nanoparticle-concentration-and-structure-on-phaseolus-vulgaris-germination-and-seedling-development
#11
Nádia Marion Duran, Susilaine Maira Savassa, Rafael G Lima, Eduardo de Almeida, Francisco Scaglia Linhares, Cornelis A M van Gestel, Hudson W Pereira de Carvalho
Presenting fertilizers in nano form can improve their performance, but may also bring risks to the environment since the fate of nanomaterials is poorly understood. This study investigated the impact of CuO nanoparticles on the germination and seedling development of Phaseolus vulgaris L. A range of nanoparticle sizes and concentrations was covered (25, 40 and <80 nm at 1, 10, 100 and 1,000 mg Cu L-1). Nanoparticles did not affect seed germination, but seedling weight gain was promoted by 100 mg Cu L-1 and inhibited by 1,000 mg Cu L-1 of 25 nm Cu and CuSO4...
August 17, 2017: Journal of Agricultural and Food Chemistry
https://www.readbyqxmd.com/read/28817220/klk14-interactions-with-hai-1-and-hai-2-serine-protease-inhibitors-a-molecular-dynamics-and-relative-free-energy-calculations-study
#12
Christian Solís-Calero, Hernandes F Carvalho
Kallikrein 14 (KLK14) is a serine protease linked to several pathologies including prostate cancer and positively correlates with Gleason score. Though KLK14 functioning in cancer is poorly understood, it has been implicated in HGF/Met signaling, given that KLK14 proteolytically inhibits HGF activator-inhibitor 1 (HAI-1), which strongly inhibits pro-HGF activators, thereby contributing to tumor progression. In this work, KLK14 binding to either hepatocyte growth factor activator inhibitor type-1 (HAI-1) or type-2 (HAI-2) was essayed using homology modeling, molecular dynamic simulations and free-energy calculations through MM/PBSA and MM/GBSA...
August 17, 2017: Cell Biology International
https://www.readbyqxmd.com/read/28815794/finding-the-candidate-sequence-variants-for-diagnosis-of-hypertrophic-cardiomyopathy-in-east-slovak-patients
#13
Michaela Zigova, Jarmila Bernasovska, Iveta Boronova, Marta Mydlarova Blascakova, Jan Kmec
BACKGROUND: Hypertrophic cardiomyopathy is a heterogeneous myocardial disease. Mutations appearing in several genes might be a potential cause of the disease. The aim of the study was to analyze selected exons of the sarcomeric and non-sarcomeric genes, with the purpose to identify potential candidate genetic variants and to understand etiopathogenetic mechanisms of hypertrophic cardiomyopathy in East Slovak patients. METHODS: This study recruited 23 unrelated patients with hypertrophic cardiomyopathy, namely, 13 men and 10 women (mean age of 58...
August 16, 2017: Journal of Clinical Laboratory Analysis
https://www.readbyqxmd.com/read/28815591/engineering-defined-membrane-embedded-elements-of-ampa-receptor-induces-opposing-gating-modulation-by-cnih3-and-stargazin
#14
Natalie Hawken, Elena Zaika, Terunaga Nakagawa
During excitatory synaptic transmission, various structurally unrelated transmembrane auxiliary subunits control the function of AMPA receptors (AMPARs), but the underlying mechanisms remain unclear. We identified lipid-exposed residues in the transmembrane domain (TMD) of GluA2 subunit of AMPARs that are critical for the function of AMPAR auxiliary subunits, stargazin (Stg) and cornichon 3 (CNIH3). These residues are essential for stabilizing the AMPAR-CNIH3 complex in detergents and overlap with the contacts made between GluA2 TMD and Stg in the cryoEM structures...
August 17, 2017: Journal of Physiology
https://www.readbyqxmd.com/read/28813011/insights-into-the-effect-of-the-g245s-single-point-mutation-on-the-structure-of-p53-and-the-binding-of-the-protein-to-dna
#15
Marco Gaetano Lepre, Sara Ibrahim Omar, Gianvito Grasso, Umberto Morbiducci, Marco Agostino Deriu, Jack A Tuszynski
The transcription factor p53 is a potent tumor suppressor dubbed as the "guardian of the genome" because of its ability to orchestrate protective biological outputs in response to a variety of oncogenic stresses. Mutation and thus inactivation of p53 can be found in 50% of human tumors. The majority are missense mutations located in the DNA binding region. Among them, G245S is known to be a structural hotspot mutation. To understand the behaviors and differences between the wild-type and mutant, both a dimer of the wild type p53 (wt-p53) and its G245S mutant (G245S-mp53), complexed with DNA, were simulated using molecular dynamics for more than 1 μs...
August 16, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28812696/skeletal-trauma-reflects-hunting-behaviour-in-extinct-sabre-tooth-cats-and-dire-wolves
#16
Caitlin Brown, Mairin Balisi, Christopher A Shaw, Blaire Van Valkenburgh
Skeletal-injury frequency and distribution are likely to reflect hunting behaviour in predatory vertebrates and might therefore differ between species with distinct hunting modes. Two Pleistocene predators from the Rancho La Brea asphalt seeps, the sabre-tooth cat, Smilodon fatalis, and dire wolf, Canis dirus, represent ambush and pursuit predators, respectively. On the basis of a collection of over 1,900 pathological elements, the frequency of traumatic injury across skeletal elements in these two species was calculated...
April 10, 2017: Nature ecology & evolution
https://www.readbyqxmd.com/read/28812670/moment-of-truth-for-the-cerrado-hotspot
#17
Bernardo B N Strassburg, Thomas Brooks, Rafael Feltran-Barbieri, Alvaro Iribarrem, Renato Crouzeilles, Rafael Loyola, Agnieszka E Latawiec, Francisco J B Oliveira Filho, Carlos A de M Scaramuzza, Fabio R Scarano, Britaldo Soares-Filho, Andrew Balmford
No abstract text is available yet for this article.
March 23, 2017: Nature ecology & evolution
https://www.readbyqxmd.com/read/28812637/spatial-conservation-prioritization-of-biodiversity-spanning-the-evolutionary-continuum
#18
Silvia B Carvalho, Guillermo Velo-Antón, Pedro Tarroso, Ana Paula Portela, Mafalda Barata, Salvador Carranza, Craig Moritz, Hugh P Possingham
Accounting for evolutionary relationships between and within species is important for biodiversity conservation planning, but is rarely considered in practice. Here we introduce a novel framework to identify priority conservation areas accounting for phylogenetic and intraspecific diversity, integrating concepts from phylogeny, phylogeography, spatial statistics and spatial conservation prioritization. The framework allows planners to incorporate and combine different levels of evolutionary diversity and can be applied to any taxonomic group and to any region in the world...
April 28, 2017: Nature ecology & evolution
https://www.readbyqxmd.com/read/28812606/global-marine-protected-areas-to-prevent-extinctions
#19
Lindsay N K Davidson, Nicholas K Dulvy
One goal of global marine protected areas (MPAs) is to ensure they represent a breadth of taxonomic biodiversity. Ensuring representation of species in MPAs, however, would require protecting vast areas of the global oceans and does not explicitly prioritize species of conservation concern. When threatened species are considered, a recent study found that only a small fraction of their geographic ranges are within the global MPA network. Which global marine areas, and what conservation actions beyond MPAs could be prioritized to prevent marine extinctions (Convention on Biological Diversity Aichi Target 12), remains unknown...
January 23, 2017: Nature ecology & evolution
https://www.readbyqxmd.com/read/28812571/identifying-species-threat-hotspots-from-global-supply-chains
#20
Daniel Moran, Keiichiro Kanemoto
Identifying hotspots of species threat has been a successful approach for setting conservation priorities. One important challenge in conservation is that, in many hotspots, export industries continue to drive overexploitation. Conservation measures must consider not just the point of impact, but also the consumer demand that ultimately drives resource use. To understand which species threat hotspots are driven by which consumers, we have developed a new approach to link a set of biodiversity footprint accounts to the hotspots of threatened species on the IUCN Red List of Threatened Species...
January 4, 2017: Nature ecology & evolution
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