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https://www.readbyqxmd.com/read/28735170/effects-of-different-solvents-on-the-conformations-of-apoptotic-cytochrome-c-structural-insights-from-molecular-dynamics-simulation
#1
Gurusamy Muneeswaran, Subramanian Kartheeswaran, Kaliappan Muthukumar, Christopher D Dharmaraj, Chandran Karunakaran
Cytochrome c (cyt-c) upon binding with cardiolipin acquires peroxidase activity and is strictly connected to the pathogenesis of many human diseases including neurodegenerative and cardiovascular diseases. Interaction of cyt-c with cardiolipin mimics partial unfolding/conformational changes of cyt-c in different solvent environments. Dynamic pictures of these conformational changes of cyt-c are crucial in understanding their physiological roles in mitochondrial functions. Therefore, atomistic molecular dynamics (MD) simulations have been carried out to investigate the effect of different solvents (water, urea/water, MeOH and DMSO) on the structure and conformations of apoptotic cyt-c (Fe(3+))...
July 14, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28734281/hybrid-stochastic-deterministic-calculation-of-the-second-order-perturbative-contribution-of-multireference-perturbation-theory
#2
Yann Garniron, Anthony Scemama, Pierre-François Loos, Michel Caffarel
A hybrid stochastic-deterministic approach for computing the second-order perturbative contribution E((2)) within multireference perturbation theory (MRPT) is presented. The idea at the heart of our hybrid scheme-based on a reformulation of E((2)) as a sum of elementary contributions associated with each determinant of the MR wave function-is to split E((2)) into a stochastic and a deterministic part. During the simulation, the stochastic part is gradually reduced by dynamically increasing the deterministic part until one reaches the desired accuracy...
July 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28734067/range-instability-leads-to-cytonuclear-discordance-in-a-morphologically-cryptic-ground-squirrel-species-complex
#3
Mark A Phuong, Ke Bi, Craig Moritz
The processes responsible for cytonuclear discordance frequently remain unclear. Here, we employed an exon capture dataset and demographic methods to test hypotheses generated by species distribution models to examine how contrasting histories of range stability vs. fluctuation have caused cytonuclear concordance and discordance in ground squirrel lineages from the Otospermophilus beecheyi species complex. Previous studies in O. beecheyi revealed three morphologically cryptic and highly divergent mitochondrial DNA lineages (named the Northern, Central, and Southern lineages based on geography) with only the Northern lineage exhibiting concordant divergence for nuclear genes...
July 22, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28733632/3d-anatomical-and-perfusion-mri-for-longitudinal-evaluation-of-biomaterials-for-bone-regeneration-of-femoral-bone-defect-in-rats
#4
Emeline J Ribot, Clement Tournier, Rachida Aid-Launais, Neha Koonjoo, Hugo Oliveira, Aurelien J Trotier, Sylvie Rey, Didier Wecker, Didier Letourneur, Joelle Amedee Vilamitjana, Sylvain Miraux
Magnetic Resonance Imaging (MRI) appears as a good surrogate to Computed Tomography (CT) scan as it does not involve radiation. In this context, a 3D anatomical and perfusion MR imaging protocol was developed to follow the evolution of bone regeneration and the neo-vascularization in femoral bone defects in rats. For this, three different biomaterials based on Pullulan-Dextran and containing either Fucoidan or HydroxyApatite or both were implanted. In vivo MRI, ex vivo micro-CT and histology were performed 1, 3 and 5 weeks after implantation...
July 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28733616/capturing-3d-water-flow-in-rooted-soil-by-ultra-fast-neutron-tomography
#5
Christian Tötzke, Nikolay Kardjilov, Ingo Manke, Sascha E Oswald
Water infiltration in soil is not only affected by the inherent heterogeneities of soil, but even more by the interaction with plant roots and their water uptake. Neutron tomography is a unique non-invasive 3D tool to visualize plant root systems together with the soil water distribution in situ. So far, acquisition times in the range of hours have been the major limitation for imaging 3D water dynamics. Implementing an alternative acquisition procedure we boosted the speed of acquisition capturing an entire tomogram within 10 s...
July 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28733222/molecular-classification-of-hepatocellular-adenoma-in-clinical-practice
#6
REVIEW
Jean-Charles Nault, Valérie Paradis, Daniel Cherqui, Valérie Vilgrain, Jessica Zucman-Rossi
Incidental liver lesion depicted on preoperative imaging for bariatric surgery (BMI = 42) in a 34 year-old woman with oral contraceptive use of 15 years, normal blood liver tests and high CRP (11 mg/L, Nl <6). MRI showed a 6 cm liver nodule in segment V close to the gallbladder. The nodule was moderately hyperintense on T1 (in-phase) and showed a marked and heterogeneous drop in signal intensity on opposedphase sequence suggesting the presence of fat. On T2, the nodule was heterogeneous, hyperintense at the periphery and hypointense in most of the central part...
July 18, 2017: Journal of Hepatology
https://www.readbyqxmd.com/read/28732011/proteomics-analysis-reveals-a-dynamic-diurnal-pattern-of-photosynthesis-related-pathways-in-maize-leaves
#7
Dan Feng, Yanwei Wang, Tiegang Lu, Zhiguo Zhang, Xiao Han
Plant leaves exhibit differentiated patterns of photosynthesis rates under diurnal light regulation. Maize leaves show a single-peak pattern without photoinhibition at midday when the light intensity is maximized. This mechanism contributes to highly efficient photosynthesis in maize leaves. To understand the molecular basis of this process, an isobaric tag for relative and absolute quantitation (iTRAQ)-based proteomics analysis was performed to reveal the dynamic pattern of proteins related to photosynthetic reactions...
2017: PloS One
https://www.readbyqxmd.com/read/28731748/characterizing-time-irreversibility-in-disordered-fermionic-systems-by-the-effect-of-local-perturbations
#8
Shreya Vardhan, Giuseppe De Tomasi, Markus Heyl, Eric J Heller, Frank Pollmann
We study the effects of local perturbations on the dynamics of disordered fermionic systems in order to characterize time irreversibility. We focus on three different systems: the noninteracting Anderson and Aubry-André-Harper (AAH) models and the interacting spinless disordered t-V chain. First, we consider the effect on the full many-body wave functions by measuring the Loschmidt echo (LE). We show that in the extended or ergodic phase the LE decays exponentially fast with time, while in the localized phase the decay is algebraic...
July 7, 2017: Physical Review Letters
https://www.readbyqxmd.com/read/28731472/high-abundance-and-expression-of-transposases-in-bacteria-from-the-baltic-sea
#9
Theoden Vigil-Stenman, Karolina Ininbergs, Birgitta Bergman, Martin Ekman
Transposases are mobile genetic elements suggested to have an important role in bacterial genome plasticity and host adaptation but their transcriptional activity in natural bacterial communities is largely unexplored. Here we analyzed metagenomes and -transcriptomes of size fractionated (0.1-0.8, 0.8-3.0 and 3.0-200 μm) bacterial communities from the brackish Baltic Sea, and adjacent marine waters. The Baltic Sea transposase levels, up to 1.7% of bacterial genes and 2% of bacterial transcripts, were considerably higher than in marine waters and similar to levels reported for extreme environments...
July 21, 2017: ISME Journal
https://www.readbyqxmd.com/read/28731148/molecular-genetics-and-targeted-therapy-of-wnt-related-human-diseases-review
#10
Masuko Katoh, Masaru Katoh
Canonical WNT signaling through Frizzled and LRP5/6 receptors is transduced to the WNT/β-catenin and WNT/stabilization of proteins (STOP) signaling cascades to regulate cell fate and proliferation, whereas non-canonical WNT signaling through Frizzled or ROR receptors is transduced to the WNT/planar cell polarity (PCP), WNT/G protein-coupled receptor (GPCR) and WNT/receptor tyrosine kinase (RTK) signaling cascades to regulate cytoskeletal dynamics and directional cell movement. WNT/β-catenin signaling cascade crosstalks with RTK/SRK and GPCR-cAMP-PKA signaling cascades to regulate β-catenin phosphorylation and β-catenin-dependent transcription...
July 19, 2017: International Journal of Molecular Medicine
https://www.readbyqxmd.com/read/28730749/impact-of-the-dynamic-and-static-component-of-the-sport-practiced-for-electrocardiogram-analysis-in-screening-athletes
#11
Nicolas Maillot, Charles Guenancia, Nobila V Yameogo, Aurélie Gudjoncik, Fabien Garnier, Luc Lorgis, Frédéric Chagué, Yves Cottin
BACKGROUND: To interpret the electrocardiogram (ECG) of athletes, the recommendations of the ESC and the Seattle criteria define type-1 peculiarities, those induced by training, and type-2, those not induced by training, to rule out cardiomyopathy. The specificity of the screening was improved by Sheikh who definied "Refined Criteria", which includes a group of intermediate peculiarities. The aim of our study was to investigate the influence of static and dynamic components on the prevalence of different types of abnormalities...
July 21, 2017: Scandinavian Journal of Medicine & Science in Sports
https://www.readbyqxmd.com/read/28729352/optical-imaging-of-surface-chemistry-and-dynamics-in-confinement
#12
Carlos Macias-Romero, Igor Nahalka, Halil I Okur, Sylvie Roke
We imaged the interfacial structure and dynamics of water in a microscopically confined geometry in three dimensions and on millisecond time scales with a 3D structurally illuminated wide-field second harmonic microscope. Image contrast reports on the orientational order of interfacial water, induced by charge-dipole interactions between water molecules and surface charges. The images were converted into surface potential maps. Spatially resolved surface acid dissociation constant pKa,s values were determined for the silica deprotonation reaction by following pH induced chemical changes on the curved and confined surfaces of a glass micro-capillary immersed in aqueous solutions...
July 20, 2017: Science
https://www.readbyqxmd.com/read/28729294/characteristics-of-csf-velocity-time-profile-in-posttraumatic-syringomyelia
#13
J Yeo, S Cheng, S Hemley, B B Lee, M Stoodley, L Bilston
BACKGROUND AND PURPOSE: The development of syringomyelia has been associated with changes in CSF flow dynamics in the spinal subarachnoid space. However, differences in CSF flow velocity between patients with posttraumatic syringomyelia and healthy participants remains unclear. The aim of this work was to define differences in CSF flow above and below a syrinx in participants with posttraumatic syringomyelia and compare the CSF flow with that in healthy controls. MATERIALS AND METHODS: Six participants with posttraumatic syringomyelia were recruited for this study...
July 20, 2017: AJNR. American Journal of Neuroradiology
https://www.readbyqxmd.com/read/28727812/electrically-controlled-cloud-of-bulk-nanobubbles-in-water-solutions
#14
Alexander V Postnikov, Ilia V Uvarov, Mikhail V Lokhanin, Vitaly B Svetovoy
Using different experimental techniques we visualize a cloud of gas in water that is produced electrochemically by the alternating polarity process. Liquid enriched with gas does not contain bubbles strongly scattering visible light but its refractive index changes significantly near the electrodes. The change of the refractive index is a collective effect of bulk nanobubbles with a diameter smaller than 200 nm. Any alternative explanation fails to explain the magnitude of the effect. Spatial structure of the cloud is investigated with the optical lever method...
2017: PloS One
https://www.readbyqxmd.com/read/28727544/abbreviated-biparametric-prostate-mr-imaging-in-men-with-elevated-prostate-specific-antigen
#15
Christiane K Kuhl, Robin Bruhn, Nils Krämer, Sven Nebelung, Axel Heidenreich, Simone Schrading
Purpose To determine the diagnostic accuracy for clinically significant prostate cancer achieved with abbreviated biparametric prostate magnetic resonance (MR) imaging in comparison with full multiparametric contrast material-enhanced prostate MR imaging in men with elevated prostate-specific antigen (PSA) and negative transrectal ultrasonography (US)-guided biopsy findings; to determine the significant cancer detection rate of biparametric versus full multiparametric contrast-enhanced MR imaging and between-reader agreement for interpretation of biparametric MR imaging...
July 20, 2017: Radiology
https://www.readbyqxmd.com/read/28727501/validation-of-the-dominant-sequence-paradigm-and-role-of-dynamic-contrast-enhanced-imaging-in-pi-rads-version-2
#16
Matthew D Greer, Joanna H Shih, Nathan Lay, Tristan Barrett, Leonardo Kayat Bittencourt, Samuel Borofsky, Ismail M Kabakus, Yan Mee Law, Jamie Marko, Haytham Shebel, Francesca V Mertan, Maria J Merino, Bradford J Wood, Peter A Pinto, Ronald M Summers, Peter L Choyke, Baris Turkbey
Purpose To validate the dominant pulse sequence paradigm and limited role of dynamic contrast material-enhanced magnetic resonance (MR) imaging in the Prostate Imaging Reporting and Data System (PI-RADS) version 2 for prostate multiparametric MR imaging by using data from a multireader study. Materials and Methods This HIPAA-compliant retrospective interpretation of prospectively acquired data was approved by the local ethics committee. Patients were treatment-naïve with endorectal coil 3-T multiparametric MR imaging...
July 19, 2017: Radiology
https://www.readbyqxmd.com/read/28727450/carbon-nanotube-reinforced-polymer-stabilized-liquid-crystal-device-lowered-and-thermally-invariant-threshold-with-accelerated-dynamics
#17
Subbarao Krishna Prasad, Marlin Baral, Adhigan Murali, Sellamuthu N Jaisankar
Polymer stabilized liquid crystal (PSLC) devices comprise a polymer matrix in an otherwise continuous phase of liquid crystal. The fibrils of the polymer provide, even in the bulk, virtual surfaces with finite anchoring energy resulting in attractive electro-optic properties. Here we describe a novel variation of the PSLC device fabricated by reinforcing the polymer matrix with polymer-capped single-walled carbon nanotubes (CNTs). The most important outcome of this strengthening of the polymer strands is that the threshold voltage associated with the electro-optic switching becomes essentially temperature independent in marked contrast to the significant thermal variation seen in the absence of the nanotubes...
July 20, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28727249/dynamics-of-amino-acid-redistribution-in-the-carnivorous-venus-flytrap-dionaea-muscipula-after-digestion-of-13-c-15-n-labeled-prey
#18
Jörg Kruse, Peng Gao, Monika Eibelmeier, Saleh Alfarraj, Heinz Rennenberg
Amino acids represent an important component in the diet of the Venus flytrap (Dionaea muscipula), and supply plants with much needed nitrogen resources upon capture of insect prey. Little is known about the significance of prey-derived carbon backbones of amino acids for the success of Dionaea's carnivorous life-style. The present study tracked changes in plant amino acid pools and their δ(13) C- and δ(15) N-signatures, after half of all traps per plant had been fed with contrasting amounts of double-labeled insect powder (0, 5, 10 and 20 mg per trap)...
July 20, 2017: Plant Biology
https://www.readbyqxmd.com/read/28727225/intact-blood-brain-barrier-during-spontaneous-attacks-of-migraine-without-aura-a-3t-dce-mri-study
#19
F M Amin, A Hougaard, S P Cramer, C E Christensen, F Wolfram, H B W Larsson, M Ashina
BACKGROUND AND PURPOSE: The integrity of the blood-brain barrier (BBB) has been questioned in migraine, but BBB permeability has never been investigated during spontaneous migraine attacks. In the present study, BBB permeability during spontaneous attacks of migraine without aura was investigated compared to an interictal state. METHODS: Seventy-four patients suffering from migraine without aura were recruited to participate in this cross-sectional dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) study...
July 20, 2017: European Journal of Neurology: the Official Journal of the European Federation of Neurological Societies
https://www.readbyqxmd.com/read/28727185/automation-of-pattern-recognition-analysis-of-dynamic-contrast-enhanced-mri-data-to-characterize-intratumoral-vascular-heterogeneity
#20
SoHyun Han, Radka Stoyanova, Hansol Lee, Sean D Carlin, Jason A Koutcher, HyungJoon Cho, Ellen Ackerstaff
PURPOSE: To automate dynamic contrast-enhanced MRI (DCE-MRI) data analysis by unsupervised pattern recognition (PR) to enable spatial mapping of intratumoral vascular heterogeneity. METHODS: Three steps were automated. First, the arrival time of the contrast agent at the tumor was determined, including a calculation of the precontrast signal. Second, four criteria-based algorithms for the slice-specific selection of number of patterns (NP) were validated using 109 tumor slices from subcutaneous flank tumors of five different tumor models...
July 20, 2017: Magnetic Resonance in Medicine: Official Journal of the Society of Magnetic Resonance in Medicine
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