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https://www.readbyqxmd.com/read/28636238/segmental-domain-selective-perdeuteration-and-small-angle-neutron-scattering-for-structural-analysis-of-multi-domain-proteins
#1
Miriam Sonntag, Pravin Jagtap, Bernd Simon, Marie-Sousai Appavou, Arie Geerlof, Ralf Stehle, Frank Gabel, Janosch Hennig, Michael Sattler
Multi-domain proteins play critical roles in fine-tuning essential processes in cellular signaling and gene regulation. Typically, multiple globular domains that are connected by flexible linkers undergo dynamic re-arrangements upon binding to protein, DNA or RNA ligands. RNA binding proteins (RBPs) represent an important class of multi-domain proteins, which regulate gene expression by recognizing linear or structured RNA sequence motifs. Here, we employ segmental perdeuteration of the three RNA recognition motif (RRM) domains in the RBP TIA-1 using Sortase A-mediated protein ligation...
June 21, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28635964/elastically-driven-intermittent-microscopic-dynamics-in-soft-solids
#2
Mehdi Bouzid, Jader Colombo, Lucas Vieira Barbosa, Emanuela Del Gado
Soft solids with tunable mechanical response are at the core of new material technologies, but a crucial limit for applications is their progressive aging over time, which dramatically affects their functionalities. The generally accepted paradigm is that such aging is gradual and its origin is in slower than exponential microscopic dynamics, akin to the ones in supercooled liquids or glasses. Nevertheless, time- and space-resolved measurements have provided contrasting evidence: dynamics faster than exponential, intermittency and abrupt structural changes...
June 21, 2017: Nature Communications
https://www.readbyqxmd.com/read/28634476/changes-in-n-p-supply-ratios-affect-the-ecological-stoichiometry-of-a-toxic-cyanobacterium-and-its-fungal-parasite
#3
Thijs Frenken, Joren Wierenga, Alena S Gsell, Ellen van Donk, Thomas Rohrlack, Dedmer B Van de Waal
Human activities have dramatically altered nutrient fluxes from the landscape into receiving waters. As a result, not only the concentration of nutrients in surface waters has increased, but also their elemental ratios have changed. Such shifts in resource supply ratios will alter autotroph stoichiometry, which may in turn have consequences for higher trophic levels, including parasites. Here, we hypothesize that parasite elemental composition will follow changes in the stoichiometry of its host, and that its reproductive success will decrease with host nutrient limitation...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28634300/understanding-the-mechanical-response-of-double-stranded-dna-and-rna-under-constant-stretching-forces-using-all-atom-molecular-dynamics
#4
Alberto Marin-Gonzalez, J G Vilhena, Ruben Perez, Fernando Moreno-Herrero
Multiple biological processes involve the stretching of nucleic acids (NAs). Stretching forces induce local changes in the molecule structure, inhibiting or promoting the binding of proteins, which ultimately affects their functionality. Understanding how a force induces changes in the structure of NAs at the atomic level is a challenge. Here, we use all-atom, microsecond-long molecular dynamics to simulate the structure of dsDNA and dsRNA subjected to stretching forces up to 20 pN. We determine all of the elastic constants of dsDNA and dsRNA and provide an explanation for three striking differences in the mechanical response of these two molecules: the threefold softer stretching constant obtained for dsRNA, the opposite twist-stretch coupling, and its nontrivial force dependence...
June 20, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28634294/hidden-electrostatic-basis-of-dynamic-allostery-in-a-pdz-domain
#5
Amit Kumawat, Suman Chakrabarty
Allosteric effect implies ligand binding at one site leading to structural and/or dynamical changes at a distant site. PDZ domains are classic examples of dynamic allostery without conformational changes, where distal side-chain dynamics is modulated on ligand binding and the origin has been attributed to entropic effects. In this work, we unearth the energetic basis of the observed dynamic allostery in a PDZ3 domain protein using molecular dynamics simulations. We demonstrate that electrostatic interaction provides a highly sensitive yardstick to probe the allosteric modulation in contrast to the traditionally used structure-based parameters...
June 20, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28632527/assessment-of-postoperative-analgesic-drug-efficacy-method-of-data-analysis-is-critical
#6
Lars Peter Kloster Andersen, Ismail Gögenur, Henrik Torup, Jacob Rosenberg, Mads Utke Werner
BACKGROUND: Pain intensity ratings and opioid consumption (OC) are ubiquitous indicators of pain in postoperative trials of the efficacy of interventional procedures. Unfortunately, consensus on the appropriate statistical handling of these outcomes has not been reached. The aim of this article was, therefore, to reexamine original data obtained from a postoperative analgesic drug trial, applying a collection of standard statistical methods in analgesic outcome assessments. Furthermore, a modified integrated assessment method of these outcomes was evaluated...
June 19, 2017: Anesthesia and Analgesia
https://www.readbyqxmd.com/read/28632444/the-structural-consequences-of-big-data-driven-education
#7
Elana Zeide
Educators and commenters who evaluate big data-driven learning environments focus on specific questions: whether automated education platforms improve learning outcomes, invade student privacy, and promote equality. This article puts aside separate unresolved-and perhaps unresolvable-issues regarding the concrete effects of specific technologies. It instead examines how big data-driven tools alter the structure of schools' pedagogical decision-making, and, in doing so, change fundamental aspects of America's education enterprise...
June 2017: Big Data
https://www.readbyqxmd.com/read/28632390/atomistic-simulation-derived-insight-on-the-irreversible-structural-changes-of-si-electrode-during-fast-and-slow-delithiation
#8
Kwang Jin Kim, James Wortman, Sung-Yup Kim, Yue Qi
Quantifying the irreversible chemical and structural changes of Si during cycling remains challenging. In this study, a continuous reactive molecular dynamics delithiation algorithm, with well-controlled potential gradient and delithiation rate, was developed and used to investigate the "natural" delithiation responses of an aluminum-oxide coated silicon thin-film. Fast delithiation led to the formation of dense Si network near the surface and nanoporosity inside the a-LixSi, resulting in 141 % volume dilation and significant amount of Li trapped inside (a-Li1...
June 20, 2017: Nano Letters
https://www.readbyqxmd.com/read/28632131/reciprocal-analyses-in-zebrafish-and-medaka-reveal-that-harnessing-the-immune-response-promotes-cardiac-regeneration
#9
Didier Yr Stainier, Shih-Lei Ben Lai, Rubén Marín-Juez, Pedro Luís Moura, Carsten Kuenne, Jason Kuan Han Lai, Ayele Taddese Tsedeke, Stefan Guenther, Mario Looso
Zebrafish display a distinct ability to regenerate their heart following injury. However, this ability is not shared by another teleost, the medaka. In order to identify cellular and molecular bases for this difference, we performed comparative transcriptomic analyses following cardiac cryoinjury. This comparison points to major differences in immune cell dynamics between these models. Upon closer examination, we observed delayed and reduced macrophage recruitment in medaka, along with delayed neutrophil clearance...
June 20, 2017: ELife
https://www.readbyqxmd.com/read/28631831/spatial-and-temporal-trends-and-flow-dynamics-of-glyphosate-and-other-pesticides-within-an-agricultural-watershed-in-argentina
#10
Débora J Pérez, Elena Okada, Eduardo De Gerónimo, Mirta L Menone, Virginia C Aparicio, José L Costa
In the present study, we evaluated the spatial and temporal trends of current use pesticides in surface water and sediments and to determine its relation with hydrological stream dynamics within the agricultural watershed of El Crespo stream. We sampled two contrasting sites: Site 1 (upstream) surrounded by agricultural lands, and Site 2 (downstream) surrounded by natural grasslands. Most of the applied pesticides (i.e. glyphosate, 2,4-D, atrazine, tebuconazole and imidacloprid) were detected in high frequencies in surface water samples at both sites...
June 20, 2017: Environmental Toxicology and Chemistry
https://www.readbyqxmd.com/read/28631792/nanoscopic-dynamics-of-bicontinous-microemulsions-effect-of-membrane-associated-protein
#11
V K Sharma, Douglas G Hayes, Volker S Urban, Hugh M O'Neill, M Tyagi, E Mamontov
Bicontinous microemulsions (BμE) generally consist of nanodomains formed by surfactant in a mixture of water and oil at nearly equal proportions and are potential candidates for the solubilization and purification of membrane proteins. Here we present the first time report of nanoscopic dynamics of surfactant monolayers within BμEs formed by the anionic surfactant sodium dodecyl sulfate (SDS) measured on the nanosecond to picosecond time scale using quasielastic neutron scattering (QENS). BμEs investigated herein consisted of middle phases isolated from Winsor-III microemulsion systems that were formed by mixing aqueous and oil solutions under optimal conditions...
June 20, 2017: Soft Matter
https://www.readbyqxmd.com/read/28631203/assessment-of-mri-contrast-agent-concentration-by-quantitative-susceptibility-mapping-qsm-application-to-estimation-of-cerebral-blood-volume-during-steady-state
#12
Emelie Lind, Linda Knutsson, Robin Kämpe, Freddy Ståhlberg, Ronnie Wirestam
OBJECTIVE: One major issue in dynamic susceptibility contrast MRI (DSC-MRI) is to accurately determine contrast agent (CA) concentration, since T2* relaxivity in vivo is generally unknown and varies between blood and tissue. In this study, quantitative susceptibility mapping (QSM) was used for quantification of CA concentration. MATERIALS AND METHODS: A DSC-MRI protocol, including phase data acquisition, was applied to 20 healthy volunteers in a test-retest study...
June 19, 2017: Magma
https://www.readbyqxmd.com/read/28631142/parametric-imaging-of-11-c-flumazenil-binding-in-the-rat-brain
#13
Isadora Lopes Alves, David Vállez Vállez García, Andrea Parente, Janine Doorduin, Ana Maria Marques da Silva, Michel Koole, Rudi Dierckx, Antoon Willemsen, Ronald Boellaard
PURPOSE: This study evaluates the performance of several parametric methods for assessing [(11)C]flumazenil binding distribution in the rat brain. PROCEDURES: Dynamic (60 min) positron emission tomography data with metabolite-corrected plasma input function were retrospectively analyzed (male Wistar rats, n = 10). Distribution volume (V T) images were generated from basis function method (BFM), Logan graphical analysis (Logan), and spectral analysis (SA). Using the pons as pseudo-reference tissue, binding potential (BP ND and DVR-1) images were obtained from receptor parametric imaging algorithms (RPM and SRTM2) and reference Logan (RLogan)...
June 19, 2017: Molecular Imaging and Biology: MIB: the Official Publication of the Academy of Molecular Imaging
https://www.readbyqxmd.com/read/28631079/development-of-pancreatic-cancer-is-predictable-well-in-advance-using-contrast-enhanced-ct-a-case-cohort-study
#14
Wataru Gonoi, Takana Yamakawa Hayashi, Hidemi Okuma, Masaaki Akahane, Yousuke Nakai, Suguru Mizuno, Ryosuke Tateishi, Hiroyuki Isayama, Kazuhiko Koike, Kuni Ohtomo
OBJECTIVES: To investigate the radiological findings prognostic for the development of pancreatic adenocarcinoma in a cohort of patients with hepatocellular carcinoma, using multiphasic computed tomography (CT). METHODS: A case-cohort study performed in a single university hospital. A database of patients who received hepatocellular carcinoma (HCC) treatment and trimonthly follow-up with four-phase dynamic CT was used (n = 1848). The cohort group was randomly extracted from the database (n = 103)...
June 19, 2017: European Radiology
https://www.readbyqxmd.com/read/28630473/impact-of-antigen-density-on-the-binding-mechanism-of-igg-antibodies
#15
Maya Hadzhieva, Anastas D Pashov, Srinivas Kaveri, Sébastien Lacroix-Desmazes, Hugo Mouquet, Jordan D Dimitrov
The density and distribution pattern of epitopes at the surface of pathogens have a profound impact on immune responses. Although multiple lines of evidence highlight the significance of antigen surface density for antibody binding, a quantitative description of its effect on recognition mechanisms is missing. Here, we analyzed binding kinetics and thermodynamics of six HIV-1 neutralizing antibodies as a function of the surface density of envelope glycoprotein gp120. Antibodies that recognize gp120 with low to moderate binding affinity displayed the most pronounced sensitivity to variation in antigen density, with qualitative and substantial quantitative changes in the energetics of the binding process as revealed by non-equilibrium and equilibrium thermodynamic analyses...
June 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28630277/t-cell-intracellular-antigens-and-hu-antigen-r-antagonistically-modulate-mitochondrial-activity-and-dynamics-by-regulating-optic-atrophy-1-gene-expression
#16
Isabel Carrascoso, José Alcalde, Carmen Sánchez-Jiménez, Paloma González-Sánchez, José M Izquierdo
Mitochondria undergo frequent morphological changes to control their function. We show here that T-cell intracellular antigens (TIA1b/TIARb) and Hu antigen R (HuR) have antagonistic roles in mitochondrial function by modulating the expression of mitochondrial shaping proteins. Expression of TIA1b/TIARb alters the mitochondrial dynamic network by enhancing fission and clustering, which is accompanied by a decrease in respiration. By contrast, HuR expression promotes fusion and cristae remodeling and increases respiratory activity...
June 19, 2017: Molecular and Cellular Biology
https://www.readbyqxmd.com/read/28630234/multiparametric-model-for-penumbral-flow-prediction-in-acute-stroke
#17
Michelle Livne, Tabea Kossen, Vince I Madai, Olivier Zaro-Weber, Walter Moeller-Hartmann, Kim Mouridsen, Wolf-Dieter Heiss, Jan Sobesky
BACKGROUND AND PURPOSE: Identification of salvageable penumbra tissue by dynamic susceptibility contrast magnetic resonance imaging is a valuable tool for acute stroke patient stratification for treatment. However, prior studies have not attempted to combine the different perfusion maps into a predictive model. In this study, we established a multiparametric perfusion imaging model and cross-validated it using positron emission tomography perfusion for detection of penumbral flow. METHODS: In a retrospective analysis of 17 subacute stroke patients with consecutive magnetic resonance imaging and H2O15 positron emission tomography scans, perfusion maps of cerebral blood flow, cerebral blood volume, mean transit time, time-to-maximum, and time-to-peak were constructed and combined using a generalized linear model (GLM)...
June 19, 2017: Stroke; a Journal of Cerebral Circulation
https://www.readbyqxmd.com/read/28630229/observing-clonal-dynamics-across-spatiotemporal-axes-a-prelude-to-quantitative-fitness-models-for-cancer
#18
Andrew W McPherson, Fong Chun Chan, Sohrab P Shah
The ability to accurately model evolutionary dynamics in cancer would allow for prediction of progression and response to therapy. As a prelude to quantitative understanding of evolutionary dynamics, researchers must gather observations of in vivo tumor evolution. High-throughput genome sequencing now provides the means to profile the mutational content of evolving tumor clones from patient biopsies. Together with the development of models of tumor evolution, reconstructing evolutionary histories of individual tumors generates hypotheses about the dynamics of evolution that produced the observed clones...
June 19, 2017: Cold Spring Harbor Perspectives in Medicine
https://www.readbyqxmd.com/read/28630125/communal-metabolism-of-methane-and-the-rare-earth-element-switch
#19
Zheng Yu, Ludmila Chistoserdova
Metabolism of methane is an important part of biogeochemical cycling of carbon. Methane is also a major contributor to climate change. A specialized group of microbes that consume methane, the methanotrophs, represent a natural filter preventing an even faster accumulation of methane in the atmosphere. Methanotrophy can proceed via both anaerobic and aerobic modes. The anaerobic methanotrophs, represented by both archaea and bacteria, all appear to be engaged in syntrophic interdependencies with other species, to overcome the energetic barriers of methane metabolism in the absence of oxygen...
June 19, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/28628913/age-dependent-effects-of-alk5-inhibition-and-mechanism-of-neuroprotection-in-neonatal-hypoxic-ischemic-brain-injury
#20
Brian H Kim, Mariano Guardia Clausi, Michelle Frondelli, Israel C Nnah, Chaitali Saqcena, Radek Dobrowolski, Steven W Levison
Neonatal encephalopathy due to hypoxic-ischemic (HI) brain injury triggers a wave of neuroinflammatory events attributed to causing the progressive degeneration and functional deficits seen weeks after the initial insult. In a recent set of studies, we evaluated the therapeutic efficacy of a small molecule antagonist for ALK5 (activin-like kinase 5 ), TGF-β receptor in a rat model of moderate perinatal HI and found significant improvements in neurologic outcomes. Here, we have extended those studies to evaluate the efficacy of delayed TGF-β receptor antagonism on postnatal day (P) 6 and P9 HI rat pups with and without hypothermia...
June 20, 2017: Developmental Neuroscience
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