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https://www.readbyqxmd.com/read/27915230/phi-base-a-new-interface-and-further-additions-for-the-multi-species-pathogen-host-interactions-database
#1
Martin Urban, Alayne Cuzick, Kim Rutherford, Alistair Irvine, Helder Pedro, Rashmi Pant, Vidyendra Sadanadan, Lokanath Khamari, Santoshkumar Billal, Sagar Mohanty, Kim E Hammond-Kosack
The pathogen-host interactions database (PHI-base) is available at www.phi-base.org PHI-base contains expertly curated molecular and biological information on genes proven to affect the outcome of pathogen-host interactions reported in peer reviewed research articles. In addition, literature that indicates specific gene alterations that did not affect the disease interaction phenotype are curated to provide complete datasets for comparative purposes. Viruses are not included. Here we describe a revised PHI-base Version 4 data platform with improved search, filtering and extended data display functions...
December 3, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27914306/a-contactless-ultrasonic-surface-wave-approach-to-characterize-distributed-cracking-damage-in-concrete
#2
Suyun Ham, Homin Song, Michael L Oelze, John S Popovics
We describe an approach that utilizes ultrasonic surface wave backscatter measurements to characterize the volume content of relatively small distributed defects (microcrack networks) in concrete. A simplified weak scattering model is used to demonstrate that the scattered wave field projected in the direction of the surface wave propagation is relatively insensitive to scatterers that are smaller than the propagating wavelength, while the scattered field projected in the opposite direction is more sensitive to sub-wavelength scatterers...
November 9, 2016: Ultrasonics
https://www.readbyqxmd.com/read/27913588/action-categories-in-lateral-occipitotemporal-cortex-are-organized-along-sociality-and-transitivity
#3
Moritz F Wurm, Alfonso Caramazza, Angelika Lingnau
: How neural specificity for distinct conceptual knowledge categories arises is central for understanding the organization of semantic memory in the human brain. While there is a large body of research on the neural processing of distinct object categories, the organization of action categories remains largely unknown. In particular, it is unknown if different action categories follow a specific topographical organization on the cortical surface, analogously to the category-specific organization of object knowledge...
December 2, 2016: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
https://www.readbyqxmd.com/read/27912024/functional-diversity-of-non-lethal-effects-chemical-camouflage-and%C3%A2-variation-in-fish-avoidance-in-colonizing-beetles
#4
William J Resetarits, Matthew R Pintar
Predators play an extremely important role in natural communities. In freshwater systems, fish can dominate sorting both at the colonization and post-colonization stage. Specifically, for many colonizing species, fish can have non-lethal, direct effects that exceed the lethal direct effects of predation. Functionally diverse fish species with a range of predatory capabilities have previously been observed to elicit functionally equivalent responses on oviposition in tree frogs. We tested this hypothesis of functional equivalence of non-lethal effects for four predatory fish species, using naturally colonizing populations of aquatic beetles...
December 2016: Ecology
https://www.readbyqxmd.com/read/27912021/grazers-structure-the-bacterial-and-algal-diversity-of-aquatic-metacommunities
#5
Julia Birtel, Blake Matthews
Consumers can have strong effects on the biotic and abiotic dynamics of spatially-structured ecosystems. In metacommunities, dispersing consumers can alter local assembly dynamics either directly through trophic interactions or indirectly by modifying local environmental conditions. In aquatic systems, very little is known about how key grazers, such as Daphnia, structure the microbial diversity of metacommunities and influence bacterial-mediated ecosystem functions. In an outdoor mesocosm experiment with replicate metacommunities (two 300 L mesocosms), we tested how the presence and absence of Daphnia and the initial density of the microbial community (manipulated via dilution) influenced the diversity and community structure of algae and bacteria, and several ecosystem properties (e...
December 2016: Ecology
https://www.readbyqxmd.com/read/27912014/why-do-larger-mothers-produce-larger-offspring-a-test-of-classic-theory
#6
Hayley Cameron, Keyne Monro, Martino Malerba, Stephan Munch, Dustin Marshall
Across a wide range of taxa, larger mothers produce larger offspring. Theory assumes that larger, more fecund mothers create higher local densities of siblings, and so larger mothers produce larger offspring to offset sibling competition. This assumption has been debated for over 30 yr, but direct empirical tests are surprisingly rare. Here, we test two key assumptions of classic theories that predict sibling competition drives maternal-size-offspring-size (MSOS) correlations: (1) independent effects of offspring size and sibling density on offspring performance or (2) as a product of an interaction between these two factors...
December 2016: Ecology
https://www.readbyqxmd.com/read/27911361/spin-saturation-transfer-difference-nmr-sstd-nmr-a-new-tool-to-obtain-kinetic-parameters-of-chemical-exchange-processes
#7
María Teresa Quirós, Colin Macdonald, Jesús Angulo, María Paz Muñoz
This detailed protocol describes the new Spin Saturation Transfer Difference Nuclear Magnetic Resonance protocol (SSTD NMR), recently developed in our group to study processes of mutual-site chemical exchange that are difficult to analyze by traditional methods. As the name suggests, this method combines the Spin Saturation Transfer method used for small molecules, with the Saturation Transfer Difference (STD) NMR method employed for the study of protein-ligand interactions, by measuring transient spin saturation transfer along increasing saturation times (build-up curves) in small organic and organometallic molecules undergoing chemical exchange...
November 12, 2016: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/27911303/amylin-treatment-reduces-neuroinflammation-and-ameliorates-abnormal-patterns-of-gene-expression-in%C3%A2-the-cerebral-cortex-of-an-alzheimer-s-disease-mouse-model
#8
Erming Wang, Haihao Zhu, Xiaofan Wang, Adam Gower, Max Wallack, Jan Krzysztof Blusztajn, Neil Kowall, Wei Qiao Qiu
Our recent study has demonstrated that peripheral amylin treatment reduces the amyloid pathology in the brain of Alzheimer's disease (AD) mouse models, and improves their learning and memory. We hypothesized that the beneficial effects of amylin for AD was beyond reducing the amyloids in the brain, and have now directly tested the actions of amylin on other aspects of AD pathogenesis, especially neuroinflammation. A 10-week course of peripheral amylin treatment significantly reduced levels of cerebral inflammation markers, Cd68 and Iba1, in amyloid precursor protein (APP) transgenic mice...
November 28, 2016: Journal of Alzheimer's Disease: JAD
https://www.readbyqxmd.com/read/27909633/the-hidden-curriculum-exposing-the-unintended-lessons-of-medical-education
#9
Laura Hopkins, Lana Saciragic, Joanna Kim, Glenn Posner
INTRODUCTION:  The hidden curriculum is a set of ethical, moral, and value-based teachings communicated to doctors-in-training, providing a basis for their future interactions with patients, peers, and colleagues. The aim of our study is to introduce the concept of the hidden curriculum to a cohort of third-year medical students and to subsequently evaluate their understanding. In particular, we sought to measure and benchmark the degree of hidden curriculum recognition within a Canadian medical education context...
October 25, 2016: Curēus
https://www.readbyqxmd.com/read/27908641/free-energy-perturbation-calculation-of-relative-binding-free-energy-between-broadly-neutralizing-antibodies-and-the-gp120-glycoprotein-of-hiv-1
#10
Anthony J Clark, Tatyana Gindin, Baoshan Zhang, Lingle Wang, Robert Abel, Colleen S Murret, Fang Xu, Amy Bao, Nina J Lu, Tongqing Zhou, Peter D Kwong, Lawrence Shapiro, Barry Honig, Richard A Friesner
Direct calculation of relative binding affinities between antibodies and antigens is a long-sought goal. However, despite substantial efforts, no generally applicable computational method has been described. Here we describe a systematic free energy perturbation (FEP) protocol and calculate the binding affinities between the gp120 envelope glycoprotein of HIV-1 and three broadly neutralizing antibodies (bNAbs) of the VRC01 class. The protocol has been adapted from successful studies of small molecules to address the challenges associated with modeling protein-protein interactions...
November 28, 2016: Journal of Molecular Biology
https://www.readbyqxmd.com/read/27907154/pheromone-recognition-and-selectivity-by-comr-proteins-among-streptococcus-species
#11
Erin Shanker, Donald A Morrison, Antoine Talagas, Sylvie Nessler, Michael J Federle, Gerd Prehna
Natural transformation, or competence, is an ability inherent to bacteria for the uptake of extracellular DNA. This process is central to bacterial evolution and allows for the rapid acquirement of new traits, such as antibiotic resistance in pathogenic microorganisms. For the Gram-positive bacteria genus Streptococcus, genes required for competence are under the regulation of quorum sensing (QS) mediated by peptide pheromones. One such system, ComRS, consists of a peptide (ComS) that is processed (XIP), secreted, and later imported into the cytoplasm, where it binds and activates the transcription factor ComR...
December 2016: PLoS Pathogens
https://www.readbyqxmd.com/read/27907120/structural-and-functional-elucidation-of-yeast-lanosterol-14%C3%AE-demethylase-in-complex-with-agrochemical-antifungals
#12
Joel D A Tyndall, Manya Sabherwal, Alia A Sagatova, Mikhail V Keniya, Jacopo Negroni, Rajni K Wilson, Matthew A Woods, Klaus Tietjen, Brian C Monk
Azole antifungals, known as demethylase inhibitors (DMIs), target sterol 14α-demethylase (CYP51) in the ergosterol biosynthetic pathway of fungal pathogens of both plants and humans. DMIs remain the treatment of choice in crop protection against a wide range of fungal phytopathogens that have the potential to reduce crop yields and threaten food security. We used a yeast membrane protein expression system to overexpress recombinant hexahistidine-tagged S. cerevisiae lanosterol 14α-demethylase and the Y140F or Y140H mutants of this enzyme as surrogates in order characterize interactions with DMIs...
2016: PloS One
https://www.readbyqxmd.com/read/27905512/plant-phenolic-volatiles-inhibit-quorum-sensing-in-pectobacteria-and-reduce-their-virulence-by-potential-binding-to-expi-and-expr-proteins
#13
Janak Raj Joshi, Netaly Khazanov, Hanoch Senderowitz, Saul Burdman, Alexander Lipsky, Iris Yedidia
Quorum sensing (QS) is a population density-dependent regulatory system in bacteria that couples gene expression to cell density through accumulation of diffusible signaling molecules. Pectobacteria are causal agents of soft rot disease in a range of economically important crops. They rely on QS to coordinate their main virulence factor, production of plant cell wall degrading enzymes (PCWDEs). Plants have evolved an array of antimicrobial compounds to anticipate and cope with pathogens, of which essential oils (EOs) are widely recognized...
December 1, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27902891/computerized-agility-training-improves-change-of-direction-and-balance-performance-independently-of-footwear-in-young-adults
#14
Max R Paquette, Brian K Schilling, Joshua D Bravo, Shelby A Peel, Yuhua Li, Robert J Townsend
: Understanding the effects of training in different footwear on sporting performance would be useful to coaches and athletes. PURPOSE: This study compared the effects of computerized agility training using 3 types of footwear on change-of-direction and balance performance in young adults. METHOD: Thirty recreationally active young adults (Mage = 22.8 ± 3.1 years; Mheight = 1.71 ± 0.7 m; Mbodymass = 73.4 ± 10.3 kg) were randomly assigned to a 6-week computerized agility training intervention in 1 of 3 footwear groups (n = 10/group): barefoot, minimal footwear, or traditional shoes...
November 30, 2016: Research Quarterly for Exercise and Sport
https://www.readbyqxmd.com/read/27900797/evidence-for-feedback-regulation-following-cholesterol-lowering-therapy-in-a-prostate-cancer-xenograft-model
#15
Elizabeth M Masko, Mahmoud A Alfaqih, Keith R Solomon, William T Barry, Christopher B Newgard, Michael J Muehlbauer, Nikolaos A Valilis, Tameika E Phillips, Susan H Poulton, Alexis R Freedland, Stephanie Sun, Shweta K Dambal, Sergio E Sanders, Everardo Macias, Michael R Freeman, Mark W Dewhirst, Salvatore V Pizzo, Stephen J Freedland
BACKGROUND: Epidemiologic data suggest cholesterol-lowering drugs may prevent the progression of prostate cancer, but not the incidence of the disease. However, the association of combination therapy in cholesterol reduction on prostate or any cancer is unclear. In this study, we compared the effects of the cholesterol lowering drugs simvastatin and ezetimibe alone or in combination on the growth of LAPC-4 prostate cancer in vivo xenografts. METHODS: Proliferation assays were conducted by MTS solution and assessed by Student's t-test...
November 30, 2016: Prostate
https://www.readbyqxmd.com/read/27900644/elevated-levels-of-p-mnk1-p-eif4e-and-p-p70s6k-proteins-are-associated-with-tumor-recurrence-and-poor-prognosis-in-astrocytomas
#16
Weibing Fan, Weiyuan Wang, Xinfa Mao, Shuzhou Chu, Juan Feng, Desheng Xiao, Jianhua Zhou, Songqing Fan
Malignant astrocytomas are able to invade neighboring and distant areas of the normal brain. Signaling pathway alterations play important role in the development of astrocytomas. Deregulation of eukaryotic translation initiation factor 4E (eIF4E) by MAP kinase-interacting kinases (Mnk) on Ser-209 directly or PI3K/mTOR/S6K pathway indirectly has a critical effect on promoting cellular proliferation, malignant transformation and metastasis. We examined and analyzed the correlation between expression of p-Mnk1, p-eIF4E and p-p70S6K proteins and clinicopathological features in 103 astrocytomas and 54 non-tumorous brain tissues...
November 29, 2016: Journal of Neuro-oncology
https://www.readbyqxmd.com/read/27900430/visible-and-red-emissive-molecular-beacons-for-optical-temperature-measurements-and-quality-control-in-diagnostic-assays-utilizing-temperature-dependent-amplification-reactions
#17
Zerrin Fidan, Andy Wende, Ute Resch-Genger
Quality control requirements imposed on assays used in clinical diagnostics and point-of-care-diagnostic testing (POCT), utilizing amplification reactions performed at elevated temperatures of 35 to 95 °C are very stringent. As the temperature of a reaction vessel has a large impact on the specificity and sensitivity of the amplification reaction, simple tools for local in situ temperature sensing and monitoring are required for reaction and assay control. We describe here a platform of stem-and-loop structured DNA hairpins (molecular beacons, MBs), absorbing and emitting in the visible and red spectral region, rationally designed for precise temperature measurements in microfluidic assays for POCT, and their application for temperature measurements in a common DNA-based molecular biological assay utilizing thermophilic helicase-dependent amplification (tHDA)...
November 29, 2016: Analytical and Bioanalytical Chemistry
https://www.readbyqxmd.com/read/27899889/anodal-tdcs-to-right-dorsolateral-prefrontal-cortex-facilitates-performance-for-novice-jazz-improvisers-but-hinders-experts
#18
David S Rosen, Brian Erickson, Youngmoo E Kim, Daniel Mirman, Roy H Hamilton, John Kounios
Research on creative cognition reveals a fundamental disagreement about the nature of creative thought, specifically, whether it is primarily based on automatic, associative (Type-1) or executive, controlled (Type-2) processes. We hypothesized that Type-1 and Type-2 processes make differential contributions to creative production that depend on domain expertise. We tested this hypothesis with jazz pianists whose expertise was indexed by the number of public performances given. Previous fMRI studies of musical improvisation have reported that domain expertise is characterized by deactivation of the right-dorsolateral prefrontal cortex (r-DLPFC), a brain area associated with Type-2 executive processing...
2016: Frontiers in Human Neuroscience
https://www.readbyqxmd.com/read/27895529/assessing-nursing-staff-s-competences-in-mobility-support-in-nursing-home-care-development-and-psychometric-testing-of-the-kinaesthetics-competence-kc-observation-instrument
#19
Heidrun Gattinger, Helena Leino-Kilpi, Virpi Hantikainen, Sascha Köpke, Stefan Ott, Beate Senn
BACKGROUND: Between 75 and 89% of residents living in long-term care facilities have limited mobility. Nurses as well as other licensed and unlicensed personnel directly involved in resident care are in a key position to promote and maintain the mobility of care-dependent persons. This requires a certain level of competence. Kinaesthetics is a training concept used to increase nursing staff's interaction and movement support skills for assisting care-dependent persons in their daily activities...
2016: BMC Nursing
https://www.readbyqxmd.com/read/27891830/a-randomized-trial-examining-the-impact-of-communicating-genetic-and-lifestyle-risks-for-obesity
#20
Catharine Wang, Erynn S Gordon, Tricia Norkunas, Lisa Wawak, Ching-Ti Liu, Michael Winter, Rachel S Kasper, Michael F Christman, Robert C Green, Deborah J Bowen
OBJECTIVE: Genetic testing for obesity is available directly to consumers, yet little is understood about its behavioral impact and its added value to nongenetic risk communication efforts based on lifestyle factors. METHODS: A randomized trial examined the short-term impact of providing personalized obesity risk information, using a 2 × 2 factorial design. Participants were recruited from the Coriell Personalized Medicine Collaborative (CPMC) and randomized to receive (1) no risk information (control), (2) genetic risk, (3) lifestyle risk, or (4) combined genetic/lifestyle risks...
December 2016: Obesity
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