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https://www.readbyqxmd.com/read/28538153/new-continuum-approaches-for-determining-protein-induced-membrane-deformations
#1
David Argudo, Neville P Bethel, Frank V Marcoline, Charles W Wolgemuth, Michael Grabe
The influence of the membrane on transmembrane proteins is central to a number of biological phenomena, notably the gating of stretch activated ion channels. Conversely, membrane proteins can influence the bilayer, leading to the stabilization of particular membrane shapes, topological changes that occur during vesicle fission and fusion, and shape-dependent protein aggregation. Continuum elastic models of the membrane have been widely used to study protein-membrane interactions. These mathematical approaches produce physically interpretable membrane shapes, energy estimates for the cost of deformation, and a snapshot of the equilibrium configuration...
May 23, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28533955/among-site-variability-in-the-stochastic-dynamics-of-east-african-coral-reefs
#2
Katherine A Allen, John F Bruno, Fiona Chong, Damian Clancy, Tim R McClanahan, Matthew Spencer, Kamila Żychaluk
Coral reefs are dynamic systems whose composition is highly influenced by unpredictable biotic and abiotic factors. Understanding the spatial scale at which long-term predictions of reef composition can be made will be crucial for guiding conservation efforts. Using a 22-year time series of benthic composition data from 20 reefs on the Kenyan and Tanzanian coast, we developed Bayesian vector autoregressive state-space models for reef dynamics, incorporating among-site variability, and quantified their long-term behaviour...
2017: PeerJ
https://www.readbyqxmd.com/read/28533394/nanomechanics-of-the-substrate-binding-domain-of-hsp70-determine-its-allosteric-atp-induced-conformational-change
#3
Soumit Sankar Mandal, Dale R Merz, Maximilian Buchsteiner, Ruxandra I Dima, Matthias Rief, Gabriel Žoldák
Owing to the cooperativity of protein structures, it is often almost impossible to identify independent subunits, flexible regions, or hinges simply by visual inspection of static snapshots. Here, we use single-molecule force experiments and simulations to apply tension across the substrate binding domain (SBD) of heat shock protein 70 (Hsp70) to pinpoint mechanical units and flexible hinges. The SBD consists of two nanomechanical units matching 3D structural parts, called the α- and β-subdomain. We identified a flexible region within the rigid β-subdomain that gives way under load, thus opening up the α/β interface...
May 22, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28531196/co-inheritance-of-glucose-6-phosphate-dehydrogenase-deficiency-mutations-and-hemoglobin-e-in-a-kachin-population-in-a-malaria-endemic-region-of-southeast-asia
#4
Zeshuai Deng, Fang Yang, Yao Bai, Lijun He, Qing Li, Yanrui Wu, Lan Luo, Hong Li, Limei Ma, Zhaoqing Yang, Yongshu He, Liwang Cui
Glucose-6-phosphate dehydrogenase (G6PD) deficiency and hemoglobin E (HbE, β26 Glu-Lys) are two common red cell disorders in Southeast Asia. G6PD deficiency produces hemolytic anemia, which can be triggered by certain drugs or infections. HbE is asymptomatic or is manifested as microcytic, minimally hemolytic anemia. The association between G6PD deficiency and HbE is little understood. This study aimed to investigate G6PD deficiency and HbE in a Kachin ethnic group in the China-Myanmar border area. G6PD enzyme activity was measured using a quantitative G6PD assay, G6PD variants genotyped by the SNaPshot assay, and an HbE gene mutation identified by an amplification refractory mutation system and subsequently confirmed by using a reverse dot blot hybridization assay from 100 unrelated individuals in the study area...
2017: PloS One
https://www.readbyqxmd.com/read/28529387/cross-sectional-surveys-inferring-total-eventual-time-in-current-state-using-only-elapsed-time-to-date
#5
Richard C Larson
We focus on snapshot surveying of sub-populations whose members are in a temporary state and where one of the questions asked is the elapsed time already spent in that state. From these answers we develop probabilistic and statistical procedures to estimate the distribution of total time that will eventually be spent in that state by any random individual who enters the state. The method relies on a selection bias often found in temporal sampling, sometimes called "random incidence" or "longevity bias." We develop results for several types of sampling, including random and fixed times of surveying, random and fixed times of entering the state, and sampling only those who have already spent some minimal specified time in the targeted state...
March 2017: Socio-economic Planning Sciences
https://www.readbyqxmd.com/read/28528970/the-many-faces-of-compartmentalized-pka-signalosomes
#6
REVIEW
Omar Torres-Quesada, Johanna E Mayrhofer, Eduard Stefan
Cellular signal transmission requires the dynamic formation of spatiotemporally controlled molecular interactions. At the cell surface information is received by receptor complexes and relayed through intracellular signaling platforms which organize the actions of functionally interacting signaling enzymes and substrates. The list of hormone or neurotransmitter pathways that utilize the ubiquitous cAMP-sensing protein kinase A (PKA) system is expansive. This requires that the specificity, duration, and intensity of PKA responses are spatially and temporally restricted...
May 18, 2017: Cellular Signalling
https://www.readbyqxmd.com/read/28528682/chemical-fixation-to-arrest-phospholipid-signaling-for-chemical-cytometry
#7
Angela Proctor, Christopher E Sims, Nancy L Allbritton
Chemical cytometry is a powerful tool for measuring biological processes such as enzymatic signaling at the single cell level. Among these technologies, single-cell capillary zone electrophoresis (CZE) has emerged as a powerful tool to assay a wide range of cellular metabolites. However, analysis of dynamic processes within cells remains challenging as signaling pathways are rapidly altered in response to changes in the cellular environment, including cell manipulation and storage. To address these limitations, we describe a method for chemical fixation of cells to stop the cellular reactions to preserve the integrity of key signaling molecules or reporters within the cell and to enable the cell to act as a storage reservoir for the reporter and its metabolites prior to assay by single-cell CZE...
May 10, 2017: Journal of Chromatography. A
https://www.readbyqxmd.com/read/28528636/correlative-two-photon-and-serial-block-face-scanning-electron-microscopy-in-neuronal-tissue-using-3d-near-infrared-branding-maps
#8
Robert M Lees, Christopher J Peddie, Lucy M Collinson, Michael C Ashby, Paul Verkade
Linking cellular structure and function has always been a key goal of microscopy, but obtaining high resolution spatial and temporal information from the same specimen is a fundamental challenge. Two-photon (2P) microscopy allows imaging deep inside intact tissue, bringing great insight into the structural and functional dynamics of cells in their physiological environment. At the nanoscale, the complex ultrastructure of a cell's environment in tissue can be reconstructed in three dimensions (3D) using serial block face scanning electron microscopy (SBF-SEM)...
2017: Methods in Cell Biology
https://www.readbyqxmd.com/read/28526273/the-association-of-growth-differentiation-factor-15-gene-polymorphisms-with-growth-differentiation-factor-15-serum-levels-and-risk-of-ischemic-stroke
#9
Yang Xiang, Ting Zhang, Jing Guo, You-Fan Peng, Ye-Sheng Wei
BACKGROUND: Current evidence shows that growth differentiation factor-15 (GDF-15) plays an important role in the progression of ischemic stroke (IS). The aim of this study was to investigate the association between 3 single-nucleotide polymorphisms of the GDF-15 gene and IS susceptibility in the Chinese population. MATERIALS AND METHODS: The study subjects comprised 601 Chinese individuals, including 298 stroke patients and 303 age- and gender-matched healthy controls...
May 16, 2017: Journal of Stroke and Cerebrovascular Diseases: the Official Journal of National Stroke Association
https://www.readbyqxmd.com/read/28525760/snapshot-nucleo-cytoskeletal-interactions
#10
Cátia S Janota, Francisco J Calero-Cuenca, Judite Costa, Edgar R Gomes
The nucleus is connected to the cytoskeleton, and these connections are involved in multiple functions such as nuclear positioning, shape and stiffness, cytoskeleton organization, mechanotransduction, gene expression, chromosome positioning, DNA repair, and cell migration.
May 18, 2017: Cell
https://www.readbyqxmd.com/read/28525656/a-snapshot-on-prokaryotic-diversity-of-the-solim%C3%A3%C2%B5es-river-basin-amazon-brazil
#11
D Toyama, C D Santos-Júnior, L T Kishi, T C S Oliveira, J W Garcia, H Sarmento, F P Miranda, F Henrique-Silva
The Amazon region has the largest hydrographic basin on the planet and 
is well known for its huge biodiversity of plants and animals. However, 
there is a lack of studies on aquatic microbial biodiversity in the 
Solimões River, one of its main water courses. To investigate the 
microbial biodiversity of this region, we performed 16S rRNA gene clone 
libraries from Solimões River and adjacent rivers and lakes. Our question was which microorganisms inhabit the different types of aquatic 
environments in this part of the basin, and how diversity varies among 
these environments (rivers and lakes)...
May 18, 2017: Genetics and Molecular Research: GMR
https://www.readbyqxmd.com/read/28525260/three-dimensional-visualization-and-characterization-of-polymeric-self-assemblies-by-transmission-electron-microtomography
#12
Hiroshi Jinnai, Takeshi Higuchi, Xiaodong Zhuge, Akihito Kumamoto, Kees Joost Batenburg, Yuichi Ikuhara
Self-assembling structures and their dynamical processes in polymeric systems have been investigated using three-dimensional transmission electron microscopy (3D-TEM). Block copolymers (BCPs) self-assemble into nanoscale periodic structures called microphase-separated structures, a deep understanding of which is important for creating nanomaterials with superior physical properties, such as high-performance membranes with well-defined pore size and high-density data storage media. Because microphase-separated structures have become increasingly complicated with advances in precision polymerization, characterizing these complex morphologies is becoming increasingly difficult...
May 19, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28524543/snapshot-whole-brain-t1-relaxometry-using-steady-state-prepared-spiral-multislice-variable-flip-angle-imaging
#13
Rahel Heule, Josef Pfeuffer, Oliver Bieri
PURPOSE: Variable flip angle (VFA) imaging is widely used for whole-brain T1 quantification. Because of the requirement to acquire at least two sets of MR images at different flip angles, VFA relaxometry is relatively slow. Here, whole-brain VFA T1 mapping at 1.5 T is accelerated by using efficient spiral non-Cartesian imaging METHODS: To quantify T1 in the human brain, radiofrequency spoiled gradient-echo imaging is performed at two optimized flip angles using an interleaved 2D multislice sequence with high spoiling efficiency...
May 19, 2017: Magnetic Resonance in Medicine: Official Journal of the Society of Magnetic Resonance in Medicine
https://www.readbyqxmd.com/read/28523436/hrm-and-snapshot-as-alternative-forensic-snp-genotyping-methods
#14
Bhavik Mehta, Runa Daniel, Dennis McNevin
Single nucleotide polymorphisms (SNPs) have been widely used in forensics for prediction of identity, biogeographical ancestry (BGA) and externally visible characteristics (EVCs). Single base extension (SBE) assays, most notably SNaPshot® (Thermo Fisher Scientific), are commonly used for forensic SNP genotyping as they can be employed on standard instrumentation in forensic laboratories (e.g. capillary electrophoresis). High resolution melt (HRM) analysis is an alternative method and is a simple, fast, single tube assay for low throughput SNP typing...
May 18, 2017: Forensic Science, Medicine, and Pathology
https://www.readbyqxmd.com/read/28515180/distribution-and-extent-of-electronic-medical-record-utilisation-in-eye-units-across-the-united-kingdom-a-cross-sectional-study-of-the-current-landscape
#15
Shin Bin Lim, Humma Shahid
OBJECTIVES: Ophthalmology units across the UK vary widely in their adoption of electronic medical records (EMR). There is a lack of evidence to show the extent and progress of EMR adoption. The aim of this study was to capture a snapshot of the current landscape of EMR use, as a baseline for comparison in future studies. SETTING: An electronic survey questionnaire was sent to all NHS ophthalmology Units in the UK. PARTICIPANTS: A total of 104 National Health Service (NHS) ophthalmology units participated in the survey, which was carried out over 6 months from December 2013 to June 2014...
May 17, 2017: BMJ Open
https://www.readbyqxmd.com/read/28514160/spatiotemporal-observation-of-electron-impact-dynamics-in-photovoltaic-materials-using-4d-electron-microscopy
#16
Basamat S Shaheen, Jingya Sun, Ding-Shyue Yang, Omar F Mohammed
Understanding light-triggered charge carrier dynamics near photovoltaic-material surfaces and at interfaces has been a key element and one of the major challenges for the development of real-world energy devices. Visualization of such dynamics information can be obtained using the one-of-a-kind methodology of scanning ultrafast electron microscopy (S-UEM). Here, we address the fundamental issue of how the thickness of the absorber layer may significantly affect the charge carrier dynamics on material surfaces...
May 17, 2017: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/28511665/clone-temporal-centrality-measures-for-incomplete-sequences-of-graph-snapshots
#17
Moritz Hanke, Ronja Foraita
BACKGROUND: Different phenomena like the spread of a disease, social interactions or the biological relation between genes can be thought of as dynamic networks. These can be represented as a sequence of static graphs (so called graph snapshots). Based on this graph sequences, classical vertex centrality measures like closeness and betweenness centrality have been extended to quantify the importance of single vertices within a dynamic network. An implicit assumption for the calculation of temporal centrality measures is that the graph sequence contains all information about the network dynamics over time...
May 16, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28511120/stokes-flow-patterns-induced-by-a-single-cardiac-cell
#18
Yasser Aboelkassem
Stokes flow motions induced by a beating single cardiac cell (cardiomyocyte) are obtained numerically using the method of fundamental solutions (MFS). A two-dimensional meshfree-Stokeslets computational framework is used to solve the Stokes governing equations around an isolated cardiomyocyte. An approximate beating kinematical model is derived and used to approximate the cell-length shortening over a complete cardiac cycle. The induced flow patterns have been found to be characterized by the presence of counter-rotating vortices at both cell's edges...
May 4, 2017: Computers in Biology and Medicine
https://www.readbyqxmd.com/read/28509886/an-improved-doa-estimation-approach-using-coarray-interpolation-and-matrix-denoising
#19
Muran Guo, Tao Chen, Ben Wang
Co-prime arrays can estimate the directions of arrival (DOAs) of O ( M N ) sources with O ( M + N ) sensors, and are convenient to analyze due to their closed-form expression for the locations of virtual lags. However, the number of degrees of freedom is limited due to the existence of holes in difference coarrays if subspace-based algorithms such as the spatial smoothing multiple signal classification (MUSIC) algorithm are utilized. To address this issue, techniques such as positive definite Toeplitz completion and array interpolation have been proposed in the literature...
May 16, 2017: Sensors
https://www.readbyqxmd.com/read/28508274/the-sleeping-remnant-effect-of-roux-en-y-gastric-bypass-on-plasma-levels-of-gastric-biomarkers-in-morbidly-obese-women-a-prospective-longitudinal-study
#20
Federico Marchesi, Francesco Tartamella, Giuseppina De Sario, Clarissa Forlini, Alberta Caleffi, Matteo Riccò, Francesco Di Mario
BACKGROUND: Morpho-functional modifications of the gastric remnant after Roux-en-Y gastric bypass (RYGB) have not been completely defined, due to its inaccessibility for bioptic mapping. The aim of the study is to evaluate such modifications using Gastropanel®, a non-invasive blood test cross-checking four gastric biomarkers, able to provide a snapshot of mucosa conditions. SUBJECTS AND METHODS: Twenty-four women undergoing RYGB were prospectively enrolled. Gastropanel® parameters (pepsinogens, Gastrin-17 and immunoglobulins against Helicobacter pylori), biometrical/clinical data were collected preoperatively and at 6-months follow-up...
May 15, 2017: Obesity Surgery
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