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https://www.readbyqxmd.com/read/29151349/changes-in-enzyme-structural-dynamics-studied-by-hydrogen-exchange-mass-spectrometry-ligand-binding-effects-or-catalytically-relevant-motions
#1
Courtney S Fast, Siavash Vahidi, Lars Konermann
It is believed that enzyme catalysis is facilitated by conformational dynamics of the protein scaffold that surrounds the active site. Yet, the exact nature of catalytically relevant protein motions remains largely unknown. Hydrogen/deuterium exchange (HDX) mass spectrometry (MS) reports on backbone H-bond fluctuations. HDX/MS therefore represents a promising avenue for probing the relationship between enzyme dynamics and catalysis. A seemingly straightforward strategy for such measurements involves comparative measurements during substrate turnover and in the resting state...
November 18, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/29144403/the-non-homologous-end-joining-protein-paxx-acts-to-restrict-hsv-1-infection
#2
Ben J Trigg, Katharina B Lauer, Paula Fernandes Dos Santos, Heather Coleman, Gabriel Balmus, Daniel S Mansur, Brian J Ferguson
Herpes simplex virus 1 (HSV-1) has extensive interactions with the host DNA damage response (DDR) machinery that can be either detrimental or beneficial to the virus. Proteins in the homologous recombination pathway are known to be required for efficient replication of the viral genome, while different members of the classical non-homologous end-joining (c-NHEJ) pathway have opposing effects on HSV-1 infection. Here, we have investigated the role of the recently-discovered c-NHEJ component, PAXX (Paralogue of XRCC4 and XLF), which we found to be excluded from the nucleus during HSV-1 infection...
November 16, 2017: Viruses
https://www.readbyqxmd.com/read/29138002/the-mechanism-of-hdea-unfolding-and-chaperone-activation
#3
Loïc Salmon, Frederick Stull, Sabrina Sayle, Claire Cato, Şerife Akgül, Linda Foit, Logan S Ahlstrom, Elan Z Eisenmesser, Hashim M Al-Hashimi, James C A Bardwell, Scott Horowitz
HdeA is a periplasmic chaperone that is rapidly activated upon shifting the pH to acidic conditions. This activation is thought to involve monomerization of HdeA. There is evidence that monomerization and partial unfolding allow the chaperone to bind to proteins denatured by low pH thereby protecting them from aggregation. We analyzed the acid-induced unfolding of HdeA using NMR spectroscopy and fluorescence measurements, and obtained experimental evidence suggesting a complex mechanism in HdeA's acid-induced unfolding pathway, as previously postulated from molecular dynamics simulations...
November 11, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/29136367/heptavalent-actinide-tetroxides-npo4-and-puo4-oxidation-of-pu-v-to-pu-vii-by-adding-an-electron-to-puo4
#4
John K Gibson, Wibe A de Jong, Phuong D Dau, Yu Gong
The highest known actinide oxidation states are Np(VII) and Pu(VII), both of which have been identified in solution and solid compounds. Recently a molecular Np(VII) complex, NpO3(NO3)2(-), was prepared and characterized in the gas phase. In accord with the lower stability of heptavalent Pu, no Pu(VII) molecular species has been identified. Reported here are the gas-phase syntheses and characterizations of NpO4(-) and PuO4(-). Reactivity studies and density functional theory computations indicate the heptavalent metal oxidation state in both...
November 17, 2017: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/29128881/disparities-in-geographic-accessibility-of-national-cancer-institute-cancer-centers-in-the-united-states
#5
Yanqing Xu, Cong Fu, Tracy Onega, Xun Shi, Fahui Wang
The National Cancer Institute (NCI) Cancer Centers form the backbone of the cancer care system in the United States since their inception in the early 1970s. Most studies on their geographic accessibility used primitive measures, and did not examine the disparities across urbanicity or demographic groups. This research uses an advanced accessibility method, termed "2-step floating catchment area (2SFCA)" and implemented in Geographic Information Systems (GIS), to capture the degree of geographic access to NCI Cancer Centers by accounting for competition intensity for the services and travel time between residents and the facilities...
November 11, 2017: Journal of Medical Systems
https://www.readbyqxmd.com/read/29127194/dump-the-pump-manual-aspiration-thrombectomy-mat-with-a-syringe-is-technically-effective-expeditious-and-cost-efficient
#6
Bradley A Gross, Ashutosh P Jadhav, Tudor G Jovin, Brian Thomas Jankowitz
INTRODUCTION: Syringe aspiration for manual aspiration thrombectomy (MAT) is a cost- and time-efficient alternative to an aspiration pump with likely similar efficacy. It is counterintuitive to expect the pump to perform better than direct vacuum with a syringe, as the pump must deliver vacuum additionally through a canister and meters of tubing. OBJECTIVE: To present in vitro and clinical results of MAT with a syringe. METHODS: An in vitro analysis was performed comparing vacuum pressures generated by syringe aspiration and with pump aspiration...
November 10, 2017: Journal of Neurointerventional Surgery
https://www.readbyqxmd.com/read/29119625/preparation-and-characterization-of-p2bch-ring-systems-ch-s-se-and-their-reactivity-with-n-heterocyclic-carbenes
#7
Paul J Ragogna, Cameron Graham, Clement Millet, Amy N Price, Juuso Valijus, Michael J Cowley, Heikki Tuononen
Four-membered rings with a P2BCh core (Ch = S, Se) have been synthesized via reaction of phosphinidene chalcogenide (Ar*P=Ch) and phosphaborene (Mes*P=BNR2). The mechanistic pathways towards these rings are explained by detailed computational work that confirmed the preference for the formation of P-P, not P-B, bonded systems, which seems counterintuitive given that both phosphorus atoms contain bulky ligands. The reactivity of the newly synthesized heterocycles, as well as that of the known (RPCh)n rings (n = 2, 3), was probed by the addition of N-heterocyclic carbenes, which revealed that all investigated compounds can act as sources of low-coordinate phosphorus species...
November 9, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/29118345/paradoxes-in-leaky-microbial-trade
#8
Yoav Kallus, John H Miller, Eric Libby
Microbes produce metabolic resources that are important for cell growth yet leak into the environment. Other microbes can use these resources, adjust their own metabolic production accordingly, and alter the resources available for others. We analyze a model in which metabolite concentrations, production regulation, and population frequencies coevolve in the simple case of two cell types producing two metabolites. We identify three paradoxes where changes that should intuitively benefit a cell type actually harm it...
November 8, 2017: Nature Communications
https://www.readbyqxmd.com/read/29118137/defector-clustering-is-linked-to-cooperation-in-a-pathogenic-bacterium
#9
Edward W Tekwa, Dao Nguyen, Michel Loreau, Andrew Gonzalez
Spatial clustering is thought to favour the evolution of cooperation because it puts cooperators in a position to help each other. However, clustering also increases competition. The fate of cooperation may depend on how much cooperators cluster relative to defectors, but these clustering differences have not been the focus of previous models and experiments. By competing siderophore-producing cooperator and defector strains of the opportunistic pathogen Pseudomonas aeruginosa in experimental microhabitats, we found that at the spatial scale of individual interactions, cooperator clustering lowers cooperation, but defector clustering favours cooperation...
November 15, 2017: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/29113619/parasite-mediated-host-behavioural-modifications-gyrodactylus-turnbulli-infected-trinidadian-guppies-increase-contact-rates-with-uninfected-conspecifics
#10
Michael Reynolds, Elisavet A Arapi, Jo Cable
While group formation provides antipredatory defences, increases foraging efficiency and mating opportunities, it can be counterintuitive by promoting disease transmission amongst social hosts. Upon introduction of a pathogen, uninfected individuals often modify their social preferences to reduce infection risk. Infected hosts also exhibit behavioural changes, for example, removing themselves from a group to prevent an epidemic. Conversely, here we show how Trinidadian guppies infected with a directly transmitted ectoparasite, Gyrodactylus turnbulli, significantly increase their contact rates with uninfected conspecifics...
November 8, 2017: Parasitology
https://www.readbyqxmd.com/read/29102611/regulatory-dynamics-determine-cell-fate-following-abrupt-antibiotic-exposure
#11
Daniel Schultz, Adam C Palmer, Roy Kishony
Bacterial resistance mechanisms must cope with transient fast-changing conditions. These systems are often repressed in the absence of the drug, and it is unclear how their regulation can provide a quick response when challenged. Here, we focus on the tet operon, which provides resistance to tetracycline through efflux pump TetA. We show that, somewhat counterintuitively, prompt expression of the TetA repressor TetR is key for cellular survival upon abrupt drug exposure. Tracking individual cells upon exposure, we find that differences in the rate of TetR elevation result in three distinct cell fates: recovery (high rate), death due to excess TetA (intermediate rate), and death from the drug (low rate)...
October 31, 2017: Cell Systems
https://www.readbyqxmd.com/read/29082830/hackers-against-technology-critique-and-recuperation-in-technological-cycles
#12
Maxigas
I offer an interpretation of hackers' technological choices through a theoretical framework of critique and recuperation in technological cycles, building on prior research that brings the pragmatic sociology of Boltanski and Chiapello to bear on matters in Science and Technology Studies. I argue that contextualizing technology choices in the development of capitalism through innovation illuminates their political significance. I start with the counterintuitive observation that some browser extensions popular with hackers, like RequestPolicy, make it considerably harder for them to look at websites...
October 1, 2017: Social Studies of Science
https://www.readbyqxmd.com/read/29079876/predicting-the-patterns-of-change-in-spring-onset-and-false-springs-in-china-during-the-twenty-first-century
#13
Likai Zhu, Jijun Meng, Feng Li, Nanshan You
Spring onset has generally shifted earlier in China over the past several decades in response to the warming climate. However, future changes in spring onset and false springs, which will have profound effects on ecosystems, are still not well understood. Here, we used the extended form of the Spring Indices model (SI-x) to project changes in the first leaf and first bloom dates, and predicted false springs for the historical (1950-2005) and future (2006-2100) periods based on the downscaled daily maximum/minimum temperatures under two emission scenarios from 21 General Circulation Models (GCMs) of the Coupled Model Intercomparison Project Phase 5 (CMIP5)...
October 28, 2017: International Journal of Biometeorology
https://www.readbyqxmd.com/read/29078299/finding-water-scarcity-amid-abundance-using-human-natural-system-models
#14
William K Jaeger, Adell Amos, Daniel P Bigelow, Heejun Chang, David R Conklin, Roy Haggerty, Christian Langpap, Kathleen Moore, Philip W Mote, Anne W Nolin, Andrew J Plantinga, Cynthia L Schwartz, Desiree Tullos, David P Turner
Water scarcity afflicts societies worldwide. Anticipating water shortages is vital because of water's indispensable role in social-ecological systems. But the challenge is daunting due to heterogeneity, feedbacks, and water's spatial-temporal sequencing throughout such systems. Regional system models with sufficient detail can help address this challenge. In our study, a detailed coupled human-natural system model of one such region identifies how climate change and socioeconomic growth will alter the availability and use of water in coming decades...
October 23, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29077430/roughness-facilitated-local-1-2-scaling-does-not-imply-the-onset-of-the-ultimate-regime-of-thermal-convection
#15
Xiaojue Zhu, Richard J A M Stevens, Roberto Verzicco, Detlef Lohse
In thermal convection, roughness is often used as a means to enhance heat transport, expressed in Nusselt number. Yet there is no consensus on whether the Nusselt vs Rayleigh number scaling exponent (Nu∼Ra^{β}) increases or remains unchanged. Here we numerically investigate turbulent Rayleigh-Bénard convection over rough plates in two dimensions, up to Ra≈10^{12}. Varying the height and wavelength of the roughness elements with over 200 combinations, we reveal the existence of two universal regimes. In the first regime, the local effective scaling exponent can reach up to 1/2...
October 13, 2017: Physical Review Letters
https://www.readbyqxmd.com/read/29076621/trehalose-acts-as-a-uridine-5-diphosphoglucose-competitive-inhibitor-of-trehalose-6-phosphate-synthase-in-corynebacterium-glutamicum
#16
Shinichi Oide, Masayuki Inui
A compatible solute trehalose is ubiquitous in nature. The most prevalent pathway for trehalose synthesis starts from condensation of glucose-6-phosphate (G6P) and uridine-5'-diphosphoglucose (UDPG) catalyzed by trehalose-6-phosphate synthase (TPS). A previous laboratory evolution experiment of the bacterium Corynebacterium glutamicum generated strains adapted to supraoptimal temperatures, and the R328H substitution of the TPS encoded by otsA was shown to be associated with thermotolerance acquired by the evolved strains...
October 27, 2017: FEBS Journal
https://www.readbyqxmd.com/read/29070670/ifn-%C3%AE-4-attenuates-antiviral-responses-by-enhancing-negative-regulation-of-ifn-signaling
#17
Adeola A Obajemu, Nina Rao, Kari A Dilley, Joselin M Vargas, Faruk Sheikh, Raymond P Donnelly, Reed S Shabman, Eric G Meissner, Ludmila Prokunina-Olsson, Olusegun O Onabajo
Type III IFNs are important mediators of antiviral immunity. IFN-λ4 is a unique type III IFN because it is produced only in individuals who carry a dG allele of a genetic variant rs368234815-dG/TT. Counterintuitively, those individuals who can produce IFN-λ4, an antiviral cytokine, are also less likely to clear hepatitis C virus infection. In this study, we searched for unique functional properties of IFN-λ4 that might explain its negative effect on hepatitis C virus clearance. We used fresh primary human hepatocytes (PHHs) treated with recombinant type III IFNs or infected with Sendai virus to model acute viral infection and subsequently validated our findings in HepG2 cell line models...
October 25, 2017: Journal of Immunology: Official Journal of the American Association of Immunologists
https://www.readbyqxmd.com/read/29068207/large-negative-linear-compressibility-in-inh-bdc-2-from-framework-hinging
#18
Qingxin Zeng, Kai Wang, Bo Zou
Materials with negative linear compressibility (NLC) counterintuitively expand along one specific direction coupled to the volume reduction when compressed uniformly. NLC with a large value is desired for compression and materials science. However, NLC is generally smaller than -20 TPa(-1). High-pressure X-ray diffraction experiments reveal that the β-quartz-like InH(BDC)2 generates an extreme NLC (-62.4 TPa(-1)) by framework hinging. InH(BDC)2 is much safer and lower-cost than Au(+)/Ag(+) and CN(-)-containing materials that dominated the fields of large NLC...
November 8, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/29066114/tissue-transport-affects-how-treatment-scheduling-increases-the-efficacy-of-chemotherapeutic-drugs
#19
Dan E Ganz, Briana Sexton-Stallone, Emily L Brackett, Neil S Forbes
A method to predict the effect of tissue transport on the scheduling of chemotherapeutic treatment could increase efficacy. Many drugs with desirable pharmacokinetic properties fail in vivo due to poor transport through tissue. To predict the effect of treatment schedule on drug efficacy we developed an in silico method that integrates diffusion through tissue and cell binding into a pharmacokinetic model. The model was evaluated with an array of theoretical drugs that had different rates of diffusivity, binding, and clearance...
October 21, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/29063668/anomalous-ph-dependent-nanofluidic-salinity-gradient-power
#20
Li-Hsien Yeh, Fu Chen, Yu-Ting Chiou, Yen-Shao Su
Previous studies on nanofluidic salinity gradient power (NSGP), where energy associated with the salinity gradient can be harvested with ion-selective nanopores, all suggest that nanofluidic devices having higher surface charge density should have higher performance, including osmotic power and conversion efficiency. In this manuscript, this viewpoint is challenged and anomalous counterintuitive pH-dependent NSGP behaviors are reported. For example, with equal pH deviation from its isoelectric point (IEP), the nanopore at pH < IEP is shown to have smaller surface charge density but remarkably higher NSGP performance than that at pH > IEP...
October 24, 2017: Small
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