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Single molecule localization

Gil Henkin, Daniel Berard, Francis Stabile, Marjan Shayegan, Jason S Leith, Sabrina R Leslie
We present a dynamically adjustable nanofluidic platform for formatting the conformations of and visualizing the interaction kinetics between biomolecules in solution, offering new time resolution and control of the reaction processes. This platform extends Convex Lens-induced Confinement (CLiC), a technique for imaging molecules under confinement, by introducing a system for in-situ modification of the chemical environment; this system uses a deep microchannel to diffusively exchange reagents within the nanoscale imaging region, whose height is fixed by a nanopost array...
October 21, 2016: Analytical Chemistry
Carmine Di Rienzo, Paolo Annibale
The determination of the mode and rapidity of motion of individual molecules within a biological sample is becoming a more and more common analysis in biophysical investigations. Single molecule tracking (SMT) techniques allow reconstructing the trajectories of individual molecules within a movie, provided that the position from one frame to the other can be correctly linked. The outcomes, however, appear to depend on the specific method used, and most techniques display a limitation to capture fast modes of motion in a crowded environment...
October 1, 2016: Optics Letters
Jing Liu, Xiangyu Fu, Qiwei Chen, Yajie Zhang, Yongfeng Wang, Dahui Zhao, Wei Chen, Guo Qin Xu, Peilin Liao, Kai Wu
Ordered two-dimensional arrays of silver adatoms with tunable metal atom density stabilized by 1,4-diethynyl-2,5-dimethylbenzene, a terminal alkyne, were prepared on Ag(111) and scrutinized by scanning tunneling microscopy and density functional theory calculations. Stabilization of the adatom arrays was attributed to the substrate-mediated electron localizations of the Ag adatom and terminal alkynyl in the molecule.
October 17, 2016: Chemical Communications: Chem Comm
Tonika Lam, Dennis V Kulp, Rui Wang, Zheng Lou, Julia Taylor, Carlos E Rivera, Hui Yan, Qi Zhang, Zhonghua Wang, Hong Zan, Dmitri N Ivanov, Guangming Zhong, Paolo Casali, Zhenming Xu
IgG autoantibodies mediate pathology in systemic lupus patients and lupus-prone mice. In this study, we showed that the class-switched IgG autoantibody response in MRL/Fas(lpr/lpr) and C57/Sle1Sle2Sle2 mice was blocked by the CID 1067700 compound, which specifically targeted Ras-related in brain 7 (Rab7), an endosome-localized small GTPase that was upregulated in activated human and mouse lupus B cells, leading to prevention of disease development and extension of lifespan. These were associated with decreased IgG-expressing B cells and plasma cells, but unchanged numbers and functions of myeloid cells and T cells...
October 14, 2016: Journal of Immunology: Official Journal of the American Association of Immunologists
Amr S Abu Lila, Masakazu Fukushima, Cheng-Long Huang, Hiromi Wada, Tatsuhiro Ishida
Pemetrexed (PMX) is a key drug for the treatment of malignant pleural mesothelioma (MPM). However, its therapeutic efficacy is cruelly restricted in many clinical settings by the over-expression of thymidylate synthase (TS) gene. Recently, we emphasized the efficacy of locally administered shRNA designed against TS gene in enhancing the cytotoxic effect of PMX against orthotopically implanted MPM cells in tumor xenograft tumor model. In the present study, we investigated the efficacy of systemic, rather than local, delivery of TS RNAi molecule in sensitizing MPM cells to the cytotoxic effect of PMX...
October 14, 2016: Molecular Pharmaceutics
Artem K Efremov, Ricksen S Winardhi, Jie Yan
Recent development of single-molecule manipulation technologies has made it possible to exert constant force and torque on individual DNA biopolymers to probe their elastic characteristics and structural stability. It has been previously shown that depending on the nature of applied mechanical constraints, DNA can exist in several forms including B-, L-, and P-DNA. However, there is still a lack of understanding of how structural heterogeneity of DNA, which may naturally arise due to sequence-dependent DNA properties, protein binding, or DNA damage, influences local stability of the above DNA states...
September 2016: Physical Review. E
S K Adhikari
We consider the statics and dynamics of a stable, mobile three-dimensional (3D) spatiotemporal light bullet in a cubic-quintic nonlinear medium with a focusing cubic nonlinearity above a critical value and any defocusing quintic nonlinearity. The 3D light bullet can propagate with a constant velocity in any direction. Stability of the light bullet under a small perturbation is established numerically. We consider frontal collision between two light bullets with different relative velocities. At large velocities the collision is elastic with the bullets emerge after collision with practically no distortion...
September 2016: Physical Review. E
Wen-Liang Gong, Jie Yan, Ling-Xi Zhao, Chong Li, Zhen-Li Huang, Ben Zhong Tang, Ming-Qiang Zhu
Photoswitchable fluorophores are promising in single-molecule optical devices and super-resolution fluorescence imaging, especially in single-molecule photo-activated localization microscopy (PALM) or stochastic optical reconstruction microscopy (STORM). However, the scarcity of current photoswitchable fluorophores stimulates researchers to develop complicated optical systems and processing software, in accordance with the limited photoswitchable fluorescent proteins and organic fluorophores. Previous efforts to develop synthetic photoswitchable fluorophores have exhibited their promising potential in super-resolution fluorescence imaging...
October 14, 2016: Photochemical & Photobiological Sciences
Kenneth I Strauss, Kost V Elisevich
BACKGROUND: Epilepsy patients have distinct immune/inflammatory cell profiles and inflammatory mediator levels in the blood. Although the neural origin of inflammatory cells and mediators has been implied, few studies have measured these inflammatory components in the human brain itself. This study examines the brain levels of chemokines (8), cytokines (14), and vascular injury mediators (3) suspected of being altered in epilepsy. METHODS: Soluble protein extracts of fresh frozen resected hippocampus, entorhinal cortex, and temporal cortex from 58 medically refractory mesial temporal lobe epilepsy subjects and 4 nonepileptic neurosurgical subjects were assayed for 25 inflammation-related mediators using ultrasensitive low-density arrays...
October 13, 2016: Journal of Neuroinflammation
Georg Kastlunger, Robert Stadler
ABSTRACT: The paper provides a comprehensive theoretical description of electron transport through transition metal complexes in single molecule junctions, where the main focus is on an analysis of the structural parameters responsible for bias-induced conductance switching as found in recent experiments, where an interpretation was provided by our simulations. The switching could be theoretically explained by a two-channel model combining coherent electron transport and electron hopping, where the underlying mechanism could be identified as a charging of the molecule in the junction made possible by the presence of a localized electronic state on the transition metal center...
2016: Monatshefte Für Chemie
Erin Gemperline, Caitlin Keller, Dhileepkumar Jayaraman, Junko Maeda, Michael R Sussman, Jean-Michel Ané, Lingjun Li
Plant science is an important, rapidly developing area of study. Within plant science, one area of study that has grown tremendously with recent technological advances, such as mass spectrometry, is the field of plant-omics; however, plant peptidomics is relatively underdeveloped in comparison with proteomics and metabolomics. Endogenous plant peptides can act as signaling molecules and have been shown to affect cell division, development, nodulation, reproduction, symbiotic associations, and defense reactions...
October 11, 2016: Journal of Proteome Research
Soumya Mukherjee, Jingjing Lu, Gunasekaran Velmurugan, Shweta Singh, Gopalan Rajaraman, Jinkui Tang, Sujit K Ghosh
A coordination complex family comprising of six new dinuclear symmetric lanthanide complexes, namely, [Ln2(Lx)2(L')2(CH3OH)2]·yG (H2Lx: three related yet distinct Schiff-base linkers; x = 1-3, according to the nomenclature of the Schiff-base linker employed herein. HL': 2,6-dimethoxyphenol. yG refers to crystallographically assigned guest solvent species in the respective complexes; y = number of solvent molecules; Ln(III) = Dy/Gd) were isolated employing a mixed-ligand strategy stemming out of a strategic variation of the functionalities introduced among the constituent Schiff-base linkers...
October 11, 2016: Inorganic Chemistry
A J Wright, J L Richens, J P Bramble, N Cathcart, V Kitaev, P O'Shea, A J Hudson
We present a new technique for the study of model membranes on the length-scale of a single nano-sized liposome. Silver decahedral nanoparticles have been encapsulated by a model unilamellar lipid bilayer creating nano-sized lipid vesicles. The metal core has two roles (i) increasing the polarizability of vesicles, enabling a single vesicle to be isolated and confined in an optical trap, and (ii) enhancing Raman scattering from the bilayer, via the high surface-plasmon field at the sharp vertices of the decahedral particles...
September 15, 2016: Nanoscale
Adam S Backer, Maurice Y Lee, W E Moerner
Single-molecule orientation measurements provide unparalleled insight into a multitude of biological and polymeric systems. We report a simple, high-throughput technique for measuring the azimuthal orientation and rotational dynamics of single fluorescent molecules, which is compatible with localization microscopy. Our method involves modulating the polarization of an excitation laser, and analyzing the corresponding intensities emitted by single dye molecules and their modulation amplitudes. To demonstrate our approach, we use intercalating and groove-binding dyes to obtain super-resolved images of stretched DNA strands through binding-induced turn-on of fluorescence...
2016: Optica
Francisco F García-Prieto, Aurora Muñoz-Losa, M Luz Sánchez, M Elena Martín, Manuel A Aguilar
In an attempt to shed light on the environmental effects on the deactivation channels of the PYP chromophore, radiative and non-radiative deactivation mechanisms of the anionic p-coumaric acid methyl ester (pCE(-)) in the gas phase and water solution are compared at the CASPT2//CASSCF/cc-pVDZ level and, when necessary, at the CASPT2//CASPT2/cc-pVDZ level. We find that the solvent produces dramatic modifications on the free energy profile of the S1 state. Two twisted structures that are minima in the gas phase could not be localized in aqueous solution...
October 5, 2016: Physical Chemistry Chemical Physics: PCCP
Matteo Barborini, Sandro Sorella, Massimo Rontani, Stefano Corni
Scanning tunneling microscopy (STM) and spectroscopy probe the local density of states of single molecules electrically insulated from the substrate. The experimental images, although usually interpreted in terms of single-particle molecular orbitals, are associated with quasiparticle wave functions dressed by the whole electron-electron interaction. Here we propose an ab-initio approach based on quantum Monte Carlo to calculate the quasiparticle wave functions of molecules. Through the comparison between Monte Carlo wave functions and their uncorrelated Hartree-Fock counterparts we visualize the electronic correlation embedded in the simulated STM images, high-lighting the many-body features that might be observed...
October 6, 2016: Journal of Chemical Theory and Computation
Zoran Ristanović, Alexey V Kubarev, Johan Hofkens, Maarten B J Roeffaers, Bert M Weckhuysen
Visualizing proton-transfer processes at the nanoscale is essential for understanding the reactivity of zeolite-based catalyst materials. In this work, the Brønsted-acid-catalyzed oligomerization of styrene derivatives was used for the first time as a single molecule probe reaction to study the reactivity of individual zeolite H-ZSM-5 crystals in different zeolite framework, reactant and solvent environments. This was accomplished via the formation of distinct dimeric and trimeric fluorescent carbocations, characterized by their different photostability, as detected by single molecule fluorescence microscopy...
October 6, 2016: Journal of the American Chemical Society
Jason Yi, Asit Manna, Valarie A Barr, Jennifer Hong, Keir C Neuman, Lawrence E Samelson
Investigation of heterogeneous cellular structures using single molecule localization microscopy has been limited by poorly defined localization accuracy and inadequate multiplexing capacity. Utilizing fluorescent nano-diamonds as fiducial markers, we define and achieve localization precision required for single molecule accuracy in dSTORM images. Coupled with this advance, our new multiplexing strategy, madSTORM allows accurate targeting of multiple molecules using sequential binding and elution of fluorescent antibodies...
October 5, 2016: Molecular Biology of the Cell
Jeong-Sun Seo, Arang Rhie, Junsoo Kim, Sangjin Lee, Min-Hwan Sohn, Chang-Uk Kim, Alex Hastie, Han Cao, Ji-Young Yun, Jihye Kim, Junho Kuk, Gun Hwa Park, Juhyeok Kim, Hanna Ryu, Jongbum Kim, Mira Roh, Jeonghun Baek, Michael W Hunkapiller, Jonas Korlach, Jong-Yeon Shin, Changhoon Kim
Advances in genome assembly and phasing provide an opportunity to investigate the diploid architecture of the human genome and reveal the full range of structural variation across population groups. Here we report the de novo assembly and haplotype phasing of the Korean individual AK1 (ref. 1) using single-molecule real-time sequencing, next-generation mapping, microfluidics-based linked reads, and bacterial artificial chromosome (BAC) sequencing approaches. Single-molecule sequencing coupled with next-generation mapping generated a highly contiguous assembly, with a contig N50 size of 17...
October 5, 2016: Nature
Sebastian Malkusch, Mike Heilemann
Super-resolution fluorescence microscopy revolutionizes cell biology research and provides novel insights on how proteins are organized at the nanoscale and in the cellular context. In order to extract a maximum of information, specialized tools for image analysis are necessary. Here, we introduce the LocAlization Microscopy Analyzer (LAMA), a comprehensive software tool that extracts quantitative information from single-molecule super-resolution imaging data. LAMA allows characterizing cellular structures by their size, shape, intensity, distribution, as well as the degree of colocalization with other structures...
October 5, 2016: Scientific Reports
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