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https://www.readbyqxmd.com/read/28643869/mechanotransduction-properties-of-the-cytoplasmic-tail-of-pecam-1
#1
Jessica L Snyder, Elena McBeath, Tamlyn N Thomas, Yi Jen Chiu, Robert L Clark, Keigi Fujiwara
BACKGROUND: Vascular endothelial cells (ECs) are a well-known cell system used in the study of mechanobiology. Using cultured ECs, we found that platelet endothelial cell adhesion molecule 1 (PECAM-1, CD31), a cell adhesion protein localized to regions of EC-EC contact, was rapidly tyrosine phosphorylated in ECs exposed to shear or cyclic stretch. Src-homology 2 domain-containing protein tyrosine phosphatase 2 (SHP2) binds phosphorylated PECAM-1 and activates the extracellular signal-regulated kinase1/2 (ERK1/2) signaling cascade, a known flow-activated signaling pathway...
June 23, 2017: Biology of the Cell
https://www.readbyqxmd.com/read/28640821/noise-reduction-in-single-time-frame-optical-dna-maps
#2
Paola C Torche, Vilhelm Müller, Fredrik Westerlund, Tobias Ambjörnsson
In optical DNA mapping technologies sequence-specific intensity variations (DNA barcodes) along stretched and stained DNA molecules are produced. These "fingerprints" of the underlying DNA sequence have a resolution of the order one kilobasepairs and the stretching of the DNA molecules are performed by surface adsorption or nano-channel setups. A post-processing challenge for nano-channel based methods, due to local and global random movement of the DNA molecule during imaging, is how to align different time frames in order to produce reproducible time-averaged DNA barcodes...
2017: PloS One
https://www.readbyqxmd.com/read/28639669/plasmon-enhanced-fluorescence-spectroscopy
#3
REVIEW
Jian-Feng Li, Chao-Yu Li, Ricardo F Aroca
Fluorescence spectroscopy with strong emitters is a remarkable tool with ultra-high sensitivity for detection and imaging down to the single-molecule level. Plasmon-enhanced fluorescence (PEF) not only offers enhanced emissions and decreased lifetimes, but also allows an expansion of the field of fluorescence by incorporating weak quantum emitters, avoiding photobleaching and providing the opportunity of imaging with resolutions significantly better than the diffraction limit. It also opens the window to a new class of photostable probes by combining metal nanostructures and quantum emitters...
June 22, 2017: Chemical Society Reviews
https://www.readbyqxmd.com/read/28639395/spatiotemporally-controllable-peptide-based-nanoassembly-in-single-living-cells-for-a-biological-self-portrait
#4
Yuanyuan Zhao, Xu Zhang, Zhipeng Li, Shuaidong Huo, Ke Zhang, Juntao Gao, Hao Wang, Xing-Jie Liang
Simultaneous precise localization and activity evaluation of a biomolecule in a single living cell is through an enzyme-specific signal-amplification process, which involves the localized, site-specific self-assembly, and activation of a presignaling molecule. The inactive presignaling tetraphenylethylene (TPE)-peptide derivative, TPE-YpYY, is nondetectable and highly biocompatible and these small molecules rapidly diffuse into living cells. Upon safely arriving at an active site, and accessing the catalytic pocket of an enzyme, TPE-YpYY immediately and quantitatively accumulates in situ in response to enzymatic activity, forms an enzyme anchor TPE-YYY nanoassembly, displays aggregation-induced emission behavior, and finally lights up the active enzyme, indicating its activity, and allowing its status in living cells to be tracked...
June 22, 2017: Advanced Materials
https://www.readbyqxmd.com/read/28637867/full-length-cellular-beta-secretase-has-a-trimeric-subunit-stoichiometry-and-its-sulfur-rich-transmembrane-interaction-site-modulates-cytosolic-copper-compartmentalization
#5
Filip Liebsch, Mark R P Aurousseau, Tobias Bethge, Hugo McGuire, Silvia Scolari, Andreas Herrmann, Rikard Blunck, Derek Bowie, Gerd Multhaup
The beta-secretase (BACE1) initiates processing of the amyloid precursor protein (APP) into Aβ peptides, which have been implicated as central players in the pathology of Alzheimer disease. BACE1 has been described as a copper-binding protein and its oligomeric state as being monomeric, dimeric, and/or multimeric, but the native cellular stoichiometry has remained elusive. Here, by using single-molecule fluorescence and in vitro cross-linking experiments with photo-activatable unnatural amino acids, we show that full-length BACE1, independently of its subcellular localization, exists as trimers in human cells...
June 21, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28637749/cell-cycle-dependent-spatial-segregation-of-telomerase-from-sites-of-dna-damage
#6
Faissal Ouenzar, Maxime Lalonde, Hadrien Laprade, Geneviève Morin, Franck Gallardo, Samuel Tremblay-Belzile, Pascal Chartrand
Telomerase can generate a novel telomere at DNA double-strand breaks (DSBs), an event called de novo telomere addition. How this activity is suppressed remains unclear. Combining single-molecule imaging and deep sequencing, we show that the budding yeast telomerase RNA (TLC1 RNA) is spatially segregated to the nucleolus and excluded from sites of DNA repair in a cell cycle-dependent manner. Although TLC1 RNA accumulates in the nucleoplasm in G1/S, Pif1 activity promotes TLC1 RNA localization in the nucleolus in G2/M...
June 21, 2017: Journal of Cell Biology
https://www.readbyqxmd.com/read/28637694/dendritic-eph-organizes-dendrodendritic-segregation-in-discrete-olfactory-map-formation-in-drosophila
#7
Marie Anzo, Sayaka Sekine, Shirin Makihara, Kinhong Chao, Masayuki Miura, Takahiro Chihara
Proper function of the neural network results from the precise connections between axons and dendrites of presynaptic and postsynaptic neurons, respectively. In the Drosophila olfactory system, the dendrites of projection neurons (PNs) stereotypically target one of ∼50 glomeruli in the antennal lobe (AL), the primary olfactory center in the brain, and form synapses with the axons of olfactory receptor neurons (ORNs). Here, we show that Eph and Ephrin, the well-known axon guidance molecules, instruct the dendrodendritic segregation during the discrete olfactory map formation...
May 15, 2017: Genes & Development
https://www.readbyqxmd.com/read/28636661/robust-nonparametric-quantification-of-clustering-density-of-molecules-in-single-molecule-localization-microscopy
#8
Shenghang Jiang, Seongjin Park, Sai Divya Challapalli, Jingyi Fei, Yong Wang
We report a robust nonparametric descriptor, J'(r), for quantifying the density of clustering molecules in single-molecule localization microscopy. J'(r), based on nearest neighbor distribution functions, does not require any parameter as an input for analyzing point patterns. We show that J'(r) displays a valley shape in the presence of clusters of molecules, and the characteristics of the valley reliably report the clustering features in the data. Most importantly, the position of the J'(r) valley ([Formula: see text]) depends exclusively on the density of clustering molecules (ρc)...
2017: PloS One
https://www.readbyqxmd.com/read/28636363/distinct-protein-hydration-water-species-defined-by-spatially-resolved-spectra-of-intermolecular-vibrations
#9
Viren Sureshkumar Pattni, Tatiana Vasilevskaya, Walter Thiel, Matthias Heyden
In this molecular dynamics simulation study, we analyze intermolecular vibrations in the hydration shell of a solvated enyzme, the membrane type 1--matrix metalloproteinase, with high spatial resolution. Our approach allows us to characterize vibrational signatures of the local hydrogen bond network, the translational mobility of water molecules, as well as the molecular entropy, in specific local environments. Our study demonstrates the heterogeneity of water properties within the hydration shell of a complex biomolecule...
June 21, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28636351/heats-of-formation-of-medium-size-organic-compounds-from-contemporary-electronic-structure-methods
#10
Yury Minenkov, Heng Wang, Zhandong Wang, S Mani Sarathy, Luigi Cavallo
Computational electronic structure calculations are routinely undertaken to predict thermodynamic properties of the various species. However, the application of highly accurate wave function theory methods, such as the "gold standard" coupled cluster approach including single, double and partly triple excitations in perturbative fashion, CCSD(T), to large molecules is limited due to high computational cost. In this work, the promising domain based local pair natural orbital coupled cluster approach, DLPNO-CCSD(T), has been tested to reproduce 113 accurate formation enthalpies of medium-size molecules (few dozens heavy atoms) important for bio- and combustion chemistry via the reaction based Feller-Peterson-Dixon approach...
June 21, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28631377/state-of-the-art-technologies-to-explore-long-non-coding-rnas-in-cancer
#11
REVIEW
Saeede Salehi, Mohammad Naser Taheri, Negar Azarpira, Abdolhossein Zare, Abbas Behzad-Behbahani
Long non-coding RNAs (lncRNAs) comprise a vast repertoire of RNAs playing a wide variety of crucial roles in tissue physiology in a cell-specific manner. Despite being engaged in myriads of regulatory mechanisms, many lncRNAs have still remained to be assigned any functions. A constellation of experimental techniques including single-molecule RNA in situ hybridization (sm-RNA FISH), cross-linking and immunoprecipitation (CLIP), RNA interference (RNAi), Clustered regularly interspaced short palindromic repeats (CRISPR) and so forth has been employed to shed light on lncRNA cellular localization, structure, interaction networks and functions...
June 19, 2017: Journal of Cellular and Molecular Medicine
https://www.readbyqxmd.com/read/28630286/efficient-switching-of-mcherry-fluorescence-using-chemical-caging
#12
Bas M C Cloin, Elke De Zitter, Desiree Salas, Vincent Gielen, Gert E Folkers, Marina Mikhaylova, Maike Bergeler, Bartosz Krajnik, Jeremy Harvey, Casper C Hoogenraad, Luc Van Meervelt, Peter Dedecker, Lukas C Kapitein
Fluorophores with dynamic or controllable fluorescence emission have become essential tools for advanced imaging, such as superresolution imaging. These applications have driven the continuing development of photoactivatable or photoconvertible labels, including genetically encoded fluorescent proteins. These new probes work well but require the introduction of new labels that may interfere with the proper functioning of existing constructs and therefore require extensive functional characterization. In this work we show that the widely used red fluorescent protein mCherry can be brought to a purely chemically induced blue-fluorescent state by incubation with β-mercaptoethanol (βME)...
June 19, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28628737/analysis-of-structure-activity-relationships-based-on-the-hcv-sliib-ires-rna-targeting-gghyrfk-cu-complex
#13
Martin J Ross, Insiya Fidai, James Allan Cowan
New therapeutics for the targeting of the hepatitis C virus have been released in recent years. Although these therapies are less prone to resistance, they are still administered in cocktails as a combination of drugs targeting various aspects of the viral life cycle. Herein, we aim to contribute to an arsenal of new HCV therapeutics by targeting HCV internal ribosomal entry sequence (IRES) RNA via development of catalytic metallodrugs that function to degrade rather than inhibit the target molecule. Based on a previously characterized HCV IRES stem-loop IIb RNA-targeting metallopeptide Cu-GGHYrFK (1-Cu), an all L-analogue (3-Cu) and a series of additional complexes with single alanine substitutions in the targeting domain were prepared and screened to determine the influence each amino acid side-chain on RNA localization and recognition, and catalytic reactivity toward the RNA...
June 19, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/28623730/quantitative-microscopy-based-on-single-molecule-fluorescence
#14
REVIEW
Seung-Ryoung Jung, Bryant S Fujimoto, Daniel T Chiu
Quantitative microscopy is needed to understand reactions or phenomena carried out by biological molecules such as enzymes, receptors, and membrane-localized proteins. Counting the biomolecules of interest in single organelles or cellular compartments is critical in these approaches. In this brief perspective, we focus on the development of quantitative fluorescence microscopies that measure the precise copy numbers of proteins in cellular organelles or purified samples. We introduce recent improvements in quantitative microscopies to overcome undercounting or overcounting errors in certain conditions...
June 14, 2017: Current Opinion in Chemical Biology
https://www.readbyqxmd.com/read/28621967/mott-transition-in-a-metallic-liquid-gutzwiller-molecular-dynamics-simulations
#15
Gia-Wei Chern, Kipton Barros, Cristian D Batista, Joel D Kress, Gabriel Kotliar
We present a formulation of quantum molecular dynamics that includes electron correlation effects via the Gutzwiller method. Our new scheme enables the study of the dynamical behavior of atoms and molecules with strong electron interactions. The Gutzwiller approach goes beyond the conventional mean-field treatment of the intra-atomic electron repulsion and captures crucial correlation effects such as band narrowing and electron localization. We use Gutzwiller quantum molecular dynamics to investigate the Mott transition in the liquid phase of a single-band metal and uncover intriguing structural and transport properties of the atoms...
June 2, 2017: Physical Review Letters
https://www.readbyqxmd.com/read/28621371/does-z-equal-1-or-2-enhanced-powder-nmr-crystallography-verification-of-a-disordered-room-temperature-crystal-structure-of-a-p38-inhibitor-for-chronic-obstructive-pulmonary-disease
#16
Cory M Widdifield, Sten O Nilsson Lill, Anders Broo, Maria Lindkvist, Anna Pettersen, Anna Svensk Ankarberg, Peter Aldred, Staffan Schantz, Lyndon Emsley
The crystal structure of the Form A polymorph of N-cyclopropyl-3-fluoro-4-methyl-5-[3-[[1-[2-[2-(methylamino)ethoxy]phenyl]cyclopropyl]amino]-2-oxo-pyrazin-1-yl]benzamide (i.e., AZD7624), determined using single-crystal X-ray diffraction (scXRD) at 100 K, contains two molecules in the asymmetric unit (Z' = 2) and has regions of local static disorder. This substance has been in phase IIa drug development trials for the treatment of chronic obstructive pulmonary disease, a disease which affects over 300 million people and contributes to nearly 3 million deaths annually...
June 16, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28620384/measuring-leukocyte-adhesion-to-primary-endothelial-cells-after-photon-and-charged-particle-exposure-with-a-dedicated-laminar-flow-chamber
#17
Nadine Erbeldinger, Felicitas Rapp, Svetlana Ktitareva, Philipp Wendel, Anna S Bothe, Till Dettmering, Marco Durante, Thomas Friedrich, Bianca Bertulat, Stephanie Meyer, M C Cardoso, Stephanie Hehlgans, Franz Rödel, Claudia Fournier
The vascular endothelium interacts with all types of blood cells and is a key modulator of local and systemic inflammatory processes, for example, in the adhesion of blood leukocytes to endothelial cells (EC) and the following extravasation into the injured tissue. The endothelium is constantly exposed to mechanical forces caused by blood flow, and the resulting shear stress is essential for the maintenance of endothelial function. Changes in local hemodynamics are sensed by EC, leading to acute or persistent changes...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/28614668/cryptic-micro-heteroresistance-explains-m-tuberculosis-phenotypic-resistance
#18
John Z Metcalfe, Elizabeth Streicher, Grant Theron, Rebecca E Colman, Christopher Allender, Darrin Lemmer, Rob Warren, David M Engelthaler
BACKGROUND: Minority resistant M. tuberculosis subpopulations can be associated with phenotypic resistance, but are poorly detected by Sanger sequencing or commercial molecular diagnostic assays. The role of targeted next generation sequencing (NGS) in resolving these minor variant subpopulations is unclear. METHODS: We utilized Single Molecule-Overlapping Reads (SMOR), a targeted NGS approach that dramatically reduces sequencing error, to analyze primary cultured isolates phenotypically resistant to rifampin, fluoroquinolones, or aminoglycosides, but for which Sanger sequencing found no resistance-associated variants (RAVs) within respective resistance determining regions (RDRs) (Study Group)...
June 14, 2017: American Journal of Respiratory and Critical Care Medicine
https://www.readbyqxmd.com/read/28613879/generic-schemes-for-single-molecule-kinetics-2-information-content-of-the-poisson-indicator
#19
Thomas Avila, Daniel Evan Piephoff, Jianshu Cao
Recently, we described a pathway analysis technique (paper 1) for analyzing generic schemes for single-molecule kinetics based upon the first-passage time distribution. Here, we employ this method to derive expressions for the Poisson indicator, a normalized measure of stochastic variation (essentially equivalent to the Fano factor and Mandel's Q parameter), for various renewal (memoryless) enzymatic reactions. We examine its dependence on substrate concentration, without assuming all steps follow Poissonian kinetics...
June 14, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28608889/nanoscale-triplet-exciton-diffusion-via-imaging-of-up-conversion-emission-from-single-hybrid-nanoparticles-in-molecular-crystals
#20
Kaishi Narushima, Shuzo Hirata, Martin Vacha
Up-conversion materials composed of donor and acceptor molecules which convert low energy photons into higher energy ones by triplet-triplet annihilation can improve the sensitivity of photocatalysts or the efficiency of solar cells. The use of crystalline materials can lead to a decrease in the up-conversion threshold intensity due to increased diffusion length LT of triplet excitons. Here, we demonstrate direct microscopic imaging of triplet exciton diffusion in polycrystalline films. The generation of high local density of triplet states is achieved by functionalizing alumina nanospheres with donor molecules and dispersing them in the acceptor films...
June 13, 2017: Nanoscale
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