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Landscape design

Lesley S de Souza, James C Godwin, Mark A Renshaw, Eric Larson
Environmental DNA (eDNA) holds great promise for conservation applications like the monitoring of invasive or imperiled species, yet this emerging technique requires ongoing testing in order to determine the contexts over which it is effective. For example, little research to date has evaluated how seasonality of organism behavior or activity may influence detection probability of eDNA. We applied eDNA to survey for two highly imperiled species endemic to the upper Black Warrior River basin in Alabama, US: the Black Warrior Waterdog (Necturus alabamensis) and the Flattened Musk Turtle (Sternotherus depressus)...
2016: PloS One
Rachel Breyta, Doug McKenney, Tarin Tesfaye, Kotaro Ono, Gael Kurath
Surveillance and genetic typing of field isolates of a fish rhabdovirus, infectious hematopoietic necrosis virus (IHNV), has identified four dominant viral genotypes that were involved in serial viral emergence and displacement events in steelhead trout (Oncorhynchus mykiss) in western North America. To investigate drivers of these landscape-scale events, IHNV isolates designated 007, 111, 110, and 139, representing the four relevant genotypes, were compared for virulence and infectivity in controlled laboratory challenge studies in five relevant steelhead trout populations...
January 2016: Virus Evolution
E I Vanguelova, E Bonifacio, B De Vos, M R Hoosbeek, T W Berger, L Vesterdal, K Armolaitis, L Celi, L Dinca, O J Kjønaas, P Pavlenda, J Pumpanen, Ü Püttsepp, B Reidy, P Simončič, B Tobin, M Zhiyanski
Spatially explicit knowledge of recent and past soil organic carbon (SOC) stocks in forests will improve our understanding of the effect of human- and non-human-induced changes on forest C fluxes. For SOC accounting, a minimum detectable difference must be defined in order to adequately determine temporal changes and spatial differences in SOC. This requires sufficiently detailed data to predict SOC stocks at appropriate scales within the required accuracy so that only significant changes are accounted for...
November 2016: Environmental Monitoring and Assessment
Nathan A Bernhardt, Wenhui Xi, Wei Wang, Ulrich H E Hansmann
Recent experiments suggest that an amino acid sequence encodes not only the native fold of a protein but also other forms essential for its function, or important during folding or association. These various forms populate a multi-funnel folding and association landscape where mutations, changes in environment or interaction with other molecules switch between the encoded folds. We introduce replica-exchange-with- tunneling as a way to simulate efficiently switching between distinct folds of proteins and protein aggregates...
October 21, 2016: Journal of Chemical Theory and Computation
Hahnbeom Park, Philip Bradley, Per Greisen, Yuan Liu, Vikram Khipple Mulligan, David E Kim, David Baker, Frank DiMaio
Most biomolecular modeling energy functions for structure prediction, sequence design, and molecular docking, have been parameterized using existing macromolecular structural data; this contrasts molecular mechanics force fields which are largely optimized using small-molecule data. In this study, we describe an integrated method that enables optimization of a biomolecular modeling energy function simultaneously against small-molecule thermodynamic data and high-resolution macromolecular structural data. We use this approach to develop a next-generation Rosetta energy function that utilizes a new anisotropic implicit solvation model, and an improved electrostatics and Lennard-Jones model, illustrating how energy functions can be considerably improved in their ability to describe large-scale energy landscapes by incorporating both small-molecule and macromolecule data...
October 21, 2016: Journal of Chemical Theory and Computation
Vincent Ronfard, Alain Vertes, Michael May, Anne Dupraz, Mark van Dyke, Yves Bayon
"Evaluating the Past & Present of Regenerative Medicine (RM)" was the first part of an Industry Symposium dedicated to the subject during the 2015 World TERMIS Congress in Boston. This working session presented a critical review of the current RM landscape in Europe and North America with possible projections for the future. Interestingly, the RM development cycle seems to obey the Gartner hype cycle, now at the enlightenment phase, after past exaggerated expectations and discouragements, as suggested by increasing numbers of clinical trials and recent market approvals of RM solutions in both Europe (Glybera & Holoclar® from Chiesi Pharma and Strimvelis® from GSK) and Japan (Remestemcel-L from Mesoblast® )...
October 20, 2016: Tissue Engineering. Part B, Reviews
Chao-Chen Lin, Hsin-Fang Hsu, Peter Jomo Walla
The fusion of two opposing membranes is essential in biological functions such as fertilization, viral entry, membrane trafficking and synaptic transmission. Before the membrane bilayers are fully connected, at some stage a hemifusion intermediate-when the outer leaflets are merged but not the inner leaflets-is formed. However, the position of hemifusion in the energy landscape and the duration of it vary and have not been fully mapped out. To date, there has not been a way to differentiate lipid mixing of the two leaflets directly in a single experiment...
October 20, 2016: Journal of Physical Chemistry. B
Joel E Abbott, Roger L Sur
The aim of this paper was to evaluate the current technology and designs of flexible ureterorenoscopes. We will review contemporary fiberoptic and digital ureteroscopes, including a discussion on ureteroscope damage and repair, and lastly present the projected future of flexible ureterorenoscopy. Ureterorenoscopy has evolved dramatically over the past several decades, which has led to landscape reshaping of stone disease treatment and upper tract pathology. Advancements in tip control, miniaturization of scopes, introduction of a digital chip on the tip, disposable devices to augment surgery, surgical experience/familiarity and most recently single use scopes are all independent factors that have increased flexible ureterorenoscopy adoption and success...
October 19, 2016: Minerva Urologica e Nefrologica, the Italian Journal of Urology and Nephrology
Guillaume Van der Rest, Human Rezaei, Frédéric Halgand
Prion protein is involved in deadly neurodegenerative diseases. Its pathogenicity is linked to its structural conversion (α-helix to β-strand transition). However, recent studies suggest that prion protein can follow a plurality of conversion pathways, which hints towards different conformers that might coexist in solution. To gain insights on the plasticity of the ovine prion protein (PrP) monomer, wild type (A136, R154, Q171), mutants and deletions of ARQ were studied by traveling wave ion mobility experiments coupled to mass spectrometry...
October 18, 2016: Journal of the American Society for Mass Spectrometry
Daniel H Hovelson, Scott A Tomlins
Molecular biomarkers play little role in the current treatment of metastatic castration-resistant prostate cancer (CRPC). The advent of next-generation sequencing (NGS) has enabled the comprehensive molecular characterization of the genomic and transcriptomic landscape of both untreated primary prostate cancer and CRPC. Recent studies demonstrating the feasibility of interinstitution studies obtaining and NGS profiling of metastatic biopsies, targeted NGS approaches applicable to routine formalin-fixed, paraffin-embedded specimens, and NGS approaches applicable to circulating DNA and circulating tumor cells portend near-term adoption of NGS approaches in the management and treatment of CRPC...
September 2016: Cancer Journal
Sara Van Belle, Susannah H Mayhew
BACKGROUND: Improving public accountability is currently high on the global agenda. At the same time, the organisation of health services in low- and middle-income countries is taking place in fragmented institutional landscapes. State and non-state actors are involved in increasingly complex governance arrangements. This often leads to coordination problems, confusion of roles and responsibilities and possibly accountability gaps. This study aimed at assessing the governance arrangements and the accountability practices of key health actors at the level of a Ghanaian health district with the aim to understand how far public accountability is achieved...
October 12, 2016: BMC Health Services Research
Mizuki Endo, Tomoya Fukui, Sung Ho Jung, Shiki Yagai, Masayuki Takeuchi, Kazunori Sugiyasu
The significant contribution of conventional living polymerization to polymer science assures that living supramolecular polymerization will also lead to a variety of novel phenomena and applications. However, the monomer scope still remains limited in terms of the self-assembly energy landscape; a kinetic trap that retards spontaneous nucleation has to be coupled with a supramolecular polymerization pathway, which is challenging to achieve by molecular design. Herein, we report a rational approach to address this issue...
October 11, 2016: Journal of the American Chemical Society
Gennady M Verkhivker
Protein kinases are versatile molecule switches that govern functional processes in signal transduction networks and regulate fundamental biological processes of cell cycle and organism development. The continuous growth of biological information and a remarkable breath of structural, genetic, and pharmacological studies on protein kinase genes have significantly advanced our knowledge of the kinase activation, drug binding and allosteric mechanisms underlying kinase regulation and interactions in signaling cascades...
October 6, 2016: Current Medicinal Chemistry
Steven S Yu, David I Quinn, Tanya B Dorff
Clear cell (cc) renal cell carcinoma (RCC) is the most common type of cancer found in the kidney accounting for ~90% of all kidney cancers. In 2012, there were ~337,000 new cases of RCC diagnosed worldwide with an estimated 143,000 deaths, with the highest incidence and mortality in Western countries. Despite improvements in cancer control achieved with VEGF- and mTOR-targeted therapy for RCC, progression remains virtually universal and additional therapies are needed. The pivotal results of the METEOR trial led to cabozantinib's designation as a breakthrough drug by the US Food and Drug Administration and its approval for treatment of advanced RCC in 2016...
2016: OncoTargets and Therapy
Imlimaong Aier, Pritish Kumar Varadwaj, Utkarsh Raj
Polycomb group (PcG) proteins have been observed to maintain the pattern of histone by methylation of the histone tail responsible for the gene expression in various cellular processes, of which enhancer of zeste homolog 2 (EZH2) acts as tumor suppressor. Overexpression of EZH2 results in hyper activation found in a variety of cancer. Point mutation on two important residues were induced and the results were compared between the wild type and mutant EZH2. The mutation of Y641 and A677 present in the active region of the protein alters the interaction of the top ranked compound with the newly modeled binding groove of the SET domain, giving a GLIDE score of -12...
October 7, 2016: Scientific Reports
Daniel Machado, Markus J Herrgård, Isabel Rocha
Genome-scale metabolic reconstructions are currently available for hundreds of organisms. Constraint-based modeling enables the analysis of the phenotypic landscape of these organisms, predicting the response to genetic and environmental perturbations. However, since constraint-based models can only describe the metabolic phenotype at the reaction level, understanding the mechanistic link between genotype and phenotype is still hampered by the complexity of gene-protein-reaction associations. We implement a model transformation that enables constraint-based methods to be applied at the gene level by explicitly accounting for the individual fluxes of enzymes (and subunits) encoded by each gene...
October 2016: PLoS Computational Biology
Troy C Messina
Molecular dynamics of complex biological and chemical systems is possible using personal computers due to increased computer performance and improved software design. Here we describe molecular dynamics methods using Not Another Molecular Dynamics (NAMD) and Visual Molecular Dynamics (VMD) programs that aid in understanding the structural effects a mutation has on a protein. We describe in silico methods for site-specific mutation to standard and phosphorylated amino acids. Molecular dynamics equilibrations are used to provide a means for measuring structural fluctuations...
2017: Methods in Molecular Biology
Saw Thu Wah, Hathairad Hananantachai, Usanee Kerdpin, Chotiros Plabplueng, Virapong Prachayasittikul, Pornlada Nuchnoi
Cerebral malaria is still a deleterious health problem in tropical countries. The wide spread of malarial drug resistance and the lack of an effective vaccine are obstacles for disease management and prevention. Parasite and human genetic factors play important roles in malaria susceptibility and disease severity. The malaria parasite exerted a potent selective signature on the human genome, which is apparent in the genetic polymorphism landscape of genes related to pathogenesis. Currently, much genomic data and a novel body of knowledge, including the identification of microRNAs, are being increasingly accumulated for the development of laboratory testing cassettes for cerebral malaria prevention...
2016: Tropical Medicine and Health
Alberto Acerbi, Claudio Tennie, Alex Mesoudi
The extensive use of social learning is considered a major reason for the ecological success of humans. Theoretical considerations, models and experiments have explored the evolutionary basis of social learning, showing the conditions under which learning from others is more adaptive than individual learning. Here we present an extension of a previous experimental set-up, in which individuals go on simulated 'hunts' and their success depends on the features of a 'virtual arrowhead' they design. Individuals can modify their arrowhead either by individual trial and error or by copying others...
September 2016: Royal Society Open Science
Thelma S Angeles, Robert L Hudkins
Elevated lipogenesis has been associated with a variety of diseases including obesity, cancer and nonalcoholic fatty liver disease (NAFLD). Fatty acid synthase (FASN) plays a pivotal role in de novo lipogenesis, making this multi-catalytic protein an attractive target for therapeutic intervention. Recently, the first FASN inhibitor successfully advanced through the drug development process and entered clinical evaluation in oncology. Areas covered: This review discusses the biological roles of FASN in three prominent disease areas: cancer, obesity-related disorders and non-alcoholic fatty liver disease...
October 5, 2016: Expert Opinion on Drug Discovery
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