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https://www.readbyqxmd.com/read/28103588/quantifying-kinetics-from-time-series-of-single-molecule-fret-efficiency-histograms
#1
Stephan Benke, Daniel Nettels, Hagen Hofmann, Benjamin Schuler
Single-molecule fluorescence spectroscopy is a powerful approach for probing biomolecular structure and dynamics, including protein folding. For the investigation of nonequilibrium kinetics, F��rster resonance energy transfer (FRET) in combination with confocal multiparameter detection has proven particularly versatile, owing to the large number of observables and the broad range of accessible timescales, especially in combination with rapid microfluidic mixing. However, a comprehensive kinetic analysis of the resulting time series of transfer efficiency histograms and complementary observables can be challenging owing to the complexity of the data...
January 19, 2017: Nanotechnology
https://www.readbyqxmd.com/read/28103038/near-full-composition-range-high-quality-gaas1-xsbx-nanowires-grown-by-molecular-beam-epitaxy
#2
Lixia Li, Dong Pan, Yongzhou Xue, Xiaolei Wang, Miaoling Lin, Dan Su, Qinglin Zhang, Xuezhe Yu, Hyok So, Dahai Wei, Baoquan Sun, PingHeng Tan, Anlian Pan, Jianhua Zhao
Here we report on the Ga self-catalyzed growth of near full-composition-range energy-gap-tunable GaAs1-xSbx nanowires by molecular-beam epitaxy. GaAs1-xSbx nanowires with different Sb content are systematically grown by tuning the Sb and As fluxes, and the As background. We find that GaAs1-xSbx nanowires with low Sb content can be grown directly on Si (111) substrates (0 ≤ x ≤ 0.60) and GaAs nanowire stems (0 ≤ x ≤ 0.50) by tuning the Sb and As fluxes. To obtain GaAs1-xSbx nanowires with x ranging from 0...
January 19, 2017: Nano Letters
https://www.readbyqxmd.com/read/28103010/a-fluorescent-hsp90-probe-demonstrates-the-unique-association-between-extracellular-hsp90-and-malignancy-in-vivo
#3
Lauren B Crowe, Philip F Hughes, David A Alcorta, Takuya Osada, Aaron P Smith, Juliane Totzke, David R Loiselle, Isaac D Lutz, Madhusudhana Gargesha, Debasish Roy, Jose Roques, David Darr, H Kim Lyerly, Neil L Spector, Timothy Aj Haystead
Extracellular expression of heat shock protein 90 (eHsp90) by tumor cells is correlated with malignancy. Development of small molecule probes that can detect eHsp90 in vivo may therefore have utility in the early detection of malignancy. We synthesized a cell impermeable far-red fluorophore-tagged Hsp90 inhibitor to target eHsp90 in vivo. High resolution confocal and lattice light sheet microscopy show that probe-bound eHsp90 accumulates in punctate structures on the plasma membrane of breast tumor cells and is actively internalized...
January 19, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/28102671/structural-analysis-of-glycosylated-intact-hiv-1-gp120-b12-antibody-complex-using-hydroxyl-radical-protein-footprinting
#4
Xiaoyan Li, Oliver C Grant, Keigo Ito, Aaron Wallace, Shixia Wang, Peng Zhao, Lance Wells, Shan Lu, Robert J Woods, Joshua S Sharp
Glycoprotein gp120 is a surface antigen and virulence factor of the human immunodeficiency virus-1 (HIV-1). Broadly neutralizing antibodies (bNAbs) that are reactive to gp120 from a variety of HIV isolates offer hope for the development of broadly effective immunogens for vaccination purposes, if the interactions between gp120 and bNAbs can be understood. From a structural perspective, gp120 is a particularly difficult system due to its size, the presence of multiple flexible regions, and the large amount of glycosylation, all of which are important in gp120-bNAb interactions...
January 19, 2017: Biochemistry
https://www.readbyqxmd.com/read/28102667/two-different-structures-of-the-oxygen-evolving-complex-in-the-same-polypeptide-frameworks-of-photosystem-ii
#5
Ayako Tanaka, Yoshimasa Fukushima, Nobuo Kamiya
The oxygen-evolving complex (OEC) forms the heart of photosystem II (PSII) in photosynthesis. The crystal structure of PSII from Thermosynechococcus vulcanus has been reported at a resolution of 1.9 Å and at an averaged X-ray dose of 0.43 MGy. The OEC structure is suggested to be partially reduced to Mn(II) by EXAFS and DFT compu-tational studies. Recently, the "radiation-damage-free" struc-tures have been published at 1.95 Å resolution using XFEL, but reports continued to appear that the OEC is reduced to the S0-state of the Kok cycle...
January 19, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28102462/cerebellar-pathways-in-mouse-model-of-purkinje-cell-degeneration-detected-by-high-angular-resolution-diffusion-imaging-tractography
#6
Yuri Kanamaru, Jianxue Li, Natalie Stewart, Richard L Sidman, Emi Takahashi
Cerebellar MR imaging has several challenging aspects, due to the fine, repetitive layered structure of cortical folia with underlying axonal pathways. In this MR study, we imaged with high-angular resolution diffusion imaging (HARDI) abnormal cerebellar cortical structure (gray matter) and myelinated axonal pathways (white matter) of a mouse spontaneous mutation, Purkinje cell degeneration (pcd), in which almost all Purkinje neurons degenerate, mainly between postnatal days 20 and 35. Mouse brains at postnatal day 20 (P20) and at 8 months were scanned, and known or expected abnormalities, such as reduction of the white matter volume, disorganized pathways likely linked to parallel fibers, mossy fibers, and other fibers running from/to the cerebellar cortex were observed in mutant mice...
January 19, 2017: Cerebellum
https://www.readbyqxmd.com/read/28102332/dynamic-modeling-of-uteroplacental-blood-flow-in-iugr-indicates-vortices-and-elevated-pressure-in-the-intervillous-space-a-pilot-study
#7
Christian J Roth, Eva Haeussner, Tanja Ruebelmann, Franz V Koch, Christoph Schmitz, Hans-Georg Frank, Wolfgang A Wall
Ischemic placental disease is a concept that links intrauterine growth retardation (IUGR) and preeclampsia (PE) back to insufficient remodeling of uterine spiral arteries. The rheological consequences of insufficient remodeling of uterine spiral arteries were hypothesized to mediate the considerably later manifestation of obstetric disease. However, the micro-rheology in the intervillous space (IVS) cannot be examined clinically and rheological animal models of the human IVS do not exist. Thus, an in silico approach was implemented to provide in vivo inaccessible data...
January 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28102305/structure-and-membrane-interactions-of-the-homodimeric-antibiotic-peptide-homotarsinin
#8
Rodrigo M Verly, Jarbas M Resende, Eduardo F C Junior, Mariana T Q de Magalhães, Carlos F C R Guimarães, Victor H O Munhoz, Marcelo Porto Bemquerer, Fábio C L Almeida, Marcelo M Santoro, Dorila Piló-Veloso, Burkhard Bechinger
Antimicrobial peptides (AMPs) from amphibian skin are valuable template structures to find new treatments against bacterial infections. This work describes for the first time the structure and membrane interactions of a homodimeric AMP. Homotarsinin, which was found in Phyllomedusa tarsius anurans, consists of two identical cystine-linked polypeptide chains each of 24 amino acid residues. The high-resolution structures of the monomeric and dimeric peptides were determined in aqueous buffers. The dimer exhibits a tightly packed coiled coil three-dimensional structure, keeping the hydrophobic residues screened from the aqueous environment...
January 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28102296/surface-reconstructions-and-related-local-properties-of-a-bifeo3-thin-film
#9
L Jin, P X Xu, Y Zeng, L Lu, J Barthel, T Schulthess, R E Dunin-Borkowski, H Wang, C L Jia
Coupling between lattice and order parameters, such as polarization in ferroelectrics and/or polarity in polar structures, has a strong impact on surface relaxation and reconstruction. However, up to now, surface structures that involve the termination of both matrix polarization and polar atomic planes have received little attention, particularly on the atomic scale. Here, we study surface structures on a BiFeO3 thin film using atomic-resolution scanning transmission electron microscopy and spectroscopy. Two types of surface structure are found, depending on the polarization of the underlying ferroelectric domain...
January 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28102285/non-destructive-study-of-bulk-crystallinity-and-elemental-composition-of-natural-gold-single-crystal-samples-by-energy-resolved-neutron-imaging
#10
Anton S Tremsin, John Rakovan, Takenao Shinohara, Winfried Kockelmann, Adrian S Losko, Sven C Vogel
Energy-resolved neutron imaging enables non-destructive analyses of bulk structure and elemental composition, which can be resolved with high spatial resolution at bright pulsed spallation neutron sources due to recent developments and improvements of neutron counting detectors. This technique, suitable for many applications, is demonstrated here with a specific study of ~5-10 mm thick natural gold samples. Through the analysis of neutron absorption resonances the spatial distribution of palladium (with average elemental concentration of ~0...
January 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28102175/markerless-rat-head-motion-tracking-using-structured-light-for-brain-pet-imaging-of-unrestrained-awake-small-animals
#11
Alan Miranda, Steven Staelens, Sigrid Stroobants, Jeroen Verhaeghe
Preclinical positron emission tomography (PET) imaging in small animals is generally performed under anesthesia to immobilize the animal during scanning. More recently, for rat brain PET studies, methods to perform scans of unrestrained awake rats are being developed in order to avoid the unwanted effects of anesthesia on the brain response. Here, we investigate the use of a projected structure stereo camera to track the motion of the rat head during the PET scan. The motion information is then used to correct the PET data...
January 19, 2017: Physics in Medicine and Biology
https://www.readbyqxmd.com/read/28102001/evaluation-of-the-hybrid-resolution-pace-model-for-the-study-of-folding-insertion-and-pore-formation-of-membrane-associated-peptides
#12
Michael D Ward, Shivangi Nangia, Eric R May
The PACE force field presents an attractive model for conducting molecular dynamics simulations of membrane-protein systems. PACE is a hybrid model, in which lipids and solvents are coarse-grained consistent with the MARTINI mapping, while proteins are described by a united atom model. However, given PACE is linked to MARTINI, which is widely used to study membranes, the behavior of proteins interacting with membranes has only been limitedly examined in PACE. In this study, PACE is used to examine the behavior of several peptides in membrane environments, namely WALP peptides, melittin and influenza hemagglutinin fusion peptide (HAfp)...
January 19, 2017: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/28101908/recurrent-rearrangements-of-human-amylase-genes-create-multiple-independent-cnv-series
#13
Nzar A A Shwan, Sandra Louzada, Fengtang Yang, John A L Armour
The human amylase gene cluster includes the human salivary (AMY1) and pancreatic amylase genes (AMY2A and AMY2B), and is a highly variable and dynamic region of the genome. Copy number variation of AMY1 has been implicated in human dietary adaptation, and in population association with obesity, but neither of these findings has been independently replicated. Despite these functional implications, the structural genomic basis of copy number variation (CNV) has only been defined in detail very recently. In this work we use high-resolution analysis of copy number, and analysis of segregation in trios, to define new, independent allelic series of amylase CNVs in sub-Saharan Africans, including a series of higher-order expansions of a unit consisting of one copy each of AMY1, AMY2A and AMY2B...
January 19, 2017: Human Mutation
https://www.readbyqxmd.com/read/28101867/myosin-and-actin-filaments-in-muscle-structures-and-interactions
#14
John M Squire, Danielle M Paul, Edward P Morris
In the last decade, improvements in electron microscopy and image processing have permitted significantly higher resolutions to be achieved (sometimes <1 nm) when studying isolated actin and myosin filaments. In the case of actin filaments the changing structure when troponin binds calcium ions can be followed using electron microscopy and single particle analysis to reveal what happens on each of the seven non-equivalent pseudo-repeats of the tropomyosin α-helical coiled-coil. In the case of the known family of myosin filaments not only are the myosin head arrangements under relaxing conditions being defined, but the latest analysis, also using single particle methods, is starting to reveal the way that the α-helical coiled-coil myosin rods are packed to give the filament backbones...
2017: Sub-cellular Biochemistry
https://www.readbyqxmd.com/read/28101862/crystallographic-studies-of-intermediate-filament-proteins
#15
Dmytro Guzenko, Anastasia A Chernyatina, Sergei V Strelkov
Intermediate filaments (IFs), together with microtubules and actin microfilaments, are the three main cytoskeletal components in metazoan cells. IFs are formed by a distinct protein family, which is made up of 70 members in humans. Most IF proteins are tissue- or organelle-specific, which includes lamins, the IF proteins of the nucleus. The building block of IFs is an elongated dimer, which consists of a central α-helical 'rod' domain flanked by flexible N- and C-terminal domains. The conserved rod domain is the 'signature feature' of the IF family...
2017: Sub-cellular Biochemistry
https://www.readbyqxmd.com/read/28101703/differences-in-cortical-sources-of-the-event-related-p3-potential-between-young-and-old-participants-indicate-frontal-compensation
#16
R van Dinteren, R J Huster, M L A Jongsma, R P C Kessels, M Arns
The event-related P3 potential, as elicited in auditory signal detection tasks, originates from neural activity of multiple cortical structures and presumably reflects an overlap of several cognitive processes. The fact that the P3 is affected by aging makes it a potential metric for age-related cognitive change. The P3 in older participants is thought to encompass frontal compensatory activity in addition to task-related processes. The current study investigates this by decomposing the P3 using group independent component analysis (ICA)...
January 18, 2017: Brain Topography
https://www.readbyqxmd.com/read/28101421/structural-and-functional-human-retinal-imaging-with-a-fiber-based-visible-light-oct-ophthalmoscope
#17
Shau Poh Chong, Marcel Bernucci, Harsha Radhakrishnan, Vivek J Srinivasan
The design of a multi-functional fiber-based Optical Coherence Tomography (OCT) system for human retinal imaging with < 2 micron axial resolution in tissue is described. A detailed noise characterization of two supercontinuum light sources with different pulse repetition rates is presented. The higher repetition rate and lower noise source is found to enable a sensitivity of 96 dB with 0.15 mW light power at the cornea and a 98 microsecond exposure time. Using a broadband (560 ± 50 nm), 90/10, fused single-mode fiber coupler designed for visible wavelengths, the sample arm is integrated into an ophthalmoscope platform, similar to current clinical OCT systems...
January 1, 2017: Biomedical Optics Express
https://www.readbyqxmd.com/read/28101412/visualization-of-micro-capillaries-using-optical-coherence-tomography-angiography-with-and-without-adaptive-optics
#18
Matthias Salas, Marco Augustin, Laurin Ginner, Abhishek Kumar, Bernhard Baumann, Rainer Leitgeb, Wolfgang Drexler, Sonja Prager, Julia Hafner, Ursula Schmidt-Erfurth, Michael Pircher
The purpose of this work is to investigate the benefits of adaptive optics (AO) technology for optical coherence tomography angiography (OCTA). OCTA has shown great potential in non-invasively enhancing the contrast of vessels and small capillaries. Especially the capability of the technique to visualize capillaries with a lateral extension that is below the transverse resolution of the system opens unique opportunities in diagnosing retinal vascular diseases. However, there are some limitations of this technology such as shadowing and projection artifacts caused by overlying vasculature or the inability to determine the true extension of a vessel...
January 1, 2017: Biomedical Optics Express
https://www.readbyqxmd.com/read/28101411/simultaneous-multimodal-ophthalmic-imaging-using-swept-source-spectrally-encoded-scanning-laser-ophthalmoscopy-and-optical-coherence-tomography
#19
Joseph D Malone, Mohamed T El-Haddad, Ivan Bozic, Logan A Tye, Lucas Majeau, Nicolas Godbout, Andrew M Rollins, Caroline Boudoux, Karen M Joos, Shriji N Patel, Yuankai K Tao
Scanning laser ophthalmoscopy (SLO) benefits diagnostic imaging and therapeutic guidance by allowing for high-speed en face imaging of retinal structures. When combined with optical coherence tomography (OCT), SLO enables real-time aiming and retinal tracking and provides complementary information for post-acquisition volumetric co-registration, bulk motion compensation, and averaging. However, multimodality SLO-OCT systems generally require dedicated light sources, scanners, relay optics, detectors, and additional digitization and synchronization electronics, which increase system complexity...
January 1, 2017: Biomedical Optics Express
https://www.readbyqxmd.com/read/28101260/tracking-the-resolution-of-student-misconceptions-about-the-central-dogma-of-molecular-biology
#20
Amy G Briggs, Stephanie K Morgan, Seth K Sanderson, Molly C Schulting, Laramie J Wieseman
The goal of our study was to track changes in student understanding of the central dogma of molecular biology before and after taking a genetics course. Concept maps require the ability to synthesize new information into existing knowledge frameworks, and so the hypothesis guiding this study was that student performance on concept maps reveals specific central dogma misconceptions gained, lost, and retained by students. Students in a genetics course completed pre- and posttest concept mapping tasks using terms related to the central dogma...
December 2016: Journal of Microbiology & Biology Education: JMBE
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