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Single molecule localization

Wenqing Shi, Yuhan Zeng, Cheng Zhu, Yucheng Xiao, Theodore R Cummins, Jianghui Hou, Lane A Baker
Integration of dual-barrel membrane patch-ion channel probes (MP-ICPs) to scanning ion conductance microscopy (SICM) holds promise of providing a revolutionized approach of spatially resolved chemical sensing. A series of experiments are performed to further the understanding of the system and to answer some fundamental questions, in preparation for future developments of this approach. First, MP-ICPs are constructed that contain different types of ion channels including transient receptor potential vanilloid 1 and large conductance Ca2+ -activated K+ channels to establish the generalizability of the methods...
December 11, 2017: Small
Manabu Koike, Yasutomo Yutoku, Aki Koike
Molecularly targeted therapies have high specificity and significant cancer-killing effect. However, their antitumor effect might be greatly diminished by variation in even a single amino acid in the target site, as it occurs, for example, as a consequence of SNPs. Increasing evidence suggests that the DNA repair protein Ku80 is an attractive target molecule for the development of next-generation radiosensitizers for human cancers. However, the localization, post-translational modifications (PTMs), and complex formation of Ku80 have not been elucidated in canines...
December 2017: FEBS Open Bio
Peeyush Sahay, Aditya Ganju, Huda M Almabadi, Hemendra M Ghimire, Murali M Yallapu, Omar Skalli, Meena Jaggi, Subhash C Chauhan, Prabhakar Pradhan
Light localization is a phenomenon which arises due to the interference effects of light waves inside a disordered optical medium. Quantification of degree light localization in optical media is widely used for characterizing degree of structural disorder in that media. Recently, this light localization approach was extended to analyze structural changes in biological cell like heterogeneous optical media, with potential application in cancer diagnostics. Confocal fluorescence microscopy was used to construct 'optical lattices', which represents 2D refractive index map corresponding to the spatial mass density distribution of a selected molecule inside the cell...
December 9, 2017: Journal of Biophotonics
Hong-Zhou Ye, Matthew Welborn, Nathan D Ricke, Troy Van Voorhis
The mean-field solutions of electronic excited states are much less accessible than ground state (e.g., Hartree-Fock) solutions. Energy-based optimization methods for excited states, like Δ-SCF (self-consistent field), tend to fall into the lowest solution consistent with a given symmetry-a problem known as "variational collapse." In this work, we combine the ideas of direct energy-targeting and variance-based optimization in order to describe excited states at the mean-field level. The resulting method, σ-SCF, has several advantages...
December 7, 2017: Journal of Chemical Physics
J Viljanen, T Sorvajärvi, J Toivonen
Combustion research requires detailed localized information on the dynamic combustion conditions to improve the accuracy of the simulations and, hence, improve the performance of the combustion processes. We have applied chemical reaction kinetics of potassium to measure the local temperature and O2 concentration in flue gas. An excess of free atomic potassium is created in the measurement volume by a photofragmenting precursor molecule such as potassium chloride or KOH which are widely released from solid fuels...
December 1, 2017: Optics Letters
Yilei Wu, Ji-Min Han, Michael Hong, Matthew D Krzyaniak, Anthea K Blackburn, Isurika R Fernando, Dennis D Cao, Michael R Wasielewski, J Fraser Stoddart
The synthesis of stable organic polyradicals is important for the development of magnetic materials. Herein, we report the synthesis, isolation, and characterization of a series of X-shaped pyromellitimide (PI) oligomers (Xn-R, n = 2-4, R = Hex or Ph) linked together by single C-C bonds between their benzenoid cores. We hypothesize that these oligomers might form high-spin states in their reduced forms because of the nearly orthogonal conformations adopted by their PI units. 1H and 13C nuclear magnetic resonance (NMR) spectroscopies confirmed the isolation of the dimeric, trimeric, and tetrameric homologues...
December 7, 2017: Journal of the American Chemical Society
M Ormaza, P Abufager, B Verlhac, N Bachellier, M-L Bocquet, N Lorente, L Limot
The active control of a molecular spin represents one of the main challenges in molecular spintronics. Up to now spin manipulation has been achieved through the modification of the molecular structure either by chemical doping or by external stimuli. However, the spin of a molecule adsorbed on a surface depends primarily on the interaction between its localized orbitals and the electronic states of the substrate. Here we change the effective spin of a single molecule by modifying the molecule/metal interface in a controlled way using a low-temperature scanning tunneling microscope...
December 7, 2017: Nature Communications
Shin-Nosuke Uno, Mako Kamiya, Akihiko Morozumi, Yasuteru Urano
We have developed the first green-light-emitting, spontaneously blinking fluorophore (SBF), HEtetTFER. In combination with our near-infrared-light-emitting SBF (HMSiR), HEtetTFER allows dual-colour single-molecule localization microscopy (SMLM) in buffer solution without any additive and without photoactivation.
December 7, 2017: Chemical Communications: Chem Comm
Nathan R Tucker, Micheal A McLellan, Dongjian Hu, Jiangchuan Ye, Victoria A Parsons, Robert W Mills, Sebastian Clauss, Elena Dolmatova, Marisa A Shea, David J Milan, Nandita S Scott, Mark Lindsay, Steven A Lubitz, Ibrahim J Domian, James R Stone, Honghuang Lin, Patrick T Ellinor
BACKGROUND: Restrictive cardiomyopathy (RCM) is a rare cardiomyopathy characterized by impaired diastolic ventricular function resulting in a poor clinical prognosis. Rarely, heritable forms of RCM have been reported, and mutations underlying RCM have been identified in genes that govern the contractile function of the cardiomyocytes. METHODS AND RESULTS: We evaluated 8 family members across 4 generations by history, physical examination, electrocardiography, and echocardiography...
December 2017: Circulation. Cardiovascular Genetics
Hendrik Deschout, Ilia Platzman, Daniel Sage, Lely Feletti, Joachim P Spatz, Aleksandra Radenovic
Cells rely on focal adhesions (FAs) to carry out a variety of important tasks, including motion, environmental sensing, and adhesion to the extracellular matrix. Although attaining a fundamental characterization of FAs is a compelling goal, their extensive complexity and small size, which can be below the diffraction limit, have hindered a full understanding. In this study we have used single-molecule localization microscopy (SMLM) to investigate integrin β3 and paxillin in rat embryonic fibroblasts growing on two different extracellular matrix-representing substrates (i...
December 5, 2017: Biophysical Journal
Marianne Renner, Lili Wang, Sabine Levi, Laetitia Hennekinne, Antoine Triller
In biological membranes, many factors such as cytoskeleton, lipid composition, crowding, and molecular interactions deviate lateral diffusion from the expected random walks. These factors have different effects on diffusion but act simultaneously, so the observed diffusion is a complex mixture of diffusive behaviors (directed, Brownian, anomalous, or confined). Therefore, commonly used approaches to quantify diffusion based on averaging of the displacements such as the mean square displacement, are not adapted to the analysis of this heterogeneity...
December 5, 2017: Biophysical Journal
Roger Oria, Tina Wiegand, Jorge Escribano, Alberto Elosegui-Artola, Juan Jose Uriarte, Cristian Moreno-Pulido, Ilia Platzman, Pietro Delcanale, Lorenzo Albertazzi, Daniel Navajas, Xavier Trepat, José Manuel García-Aznar, Elisabetta Ada Cavalcanti-Adam, Pere Roca-Cusachs
Cells can sense the density and distribution of extracellular matrix (ECM) molecules by means of individual integrin proteins and larger, integrin-containing adhesion complexes within the cell membrane. This spatial sensing drives cellular activity in a variety of normal and pathological contexts. Previous studies of cells on rigid glass surfaces have shown that spatial sensing of ECM ligands takes place at the nanometre scale, with integrin clustering and subsequent formation of focal adhesions impaired when single integrin-ligand bonds are separated by more than a few tens of nanometres...
December 6, 2017: Nature
Gengjing Zhao, Emma S Gleave, Meindert Hugo Lamers
High fidelity replicative DNA polymerases are unable to synthesize past DNA adducts that result from diverse chemicals, reactive oxygen species or UV light. To bypass these replication blocks, cells utilize specialized translesion DNA polymerases that are intrinsically error prone and associated with mutagenesis, drug resistance, and cancer. How untimely access of translesion polymerases to DNA is prevented is poorly understood. Here we use co-localization single-molecule spectroscopy (CoSMoS) to follow the exchange of the E...
December 6, 2017: ELife
Jean-Francois Nierengarten, Marie Steffenhagen, Alina Latus, Thi Minh Nguyet Trinh, Iwona Nierengarten, Ivan T Lucas, Suzanne Joiret, Jessem Landoulsi, Béatrice Delavaux-Nicot, Emmanuel Maisonhaute
A rotaxane scaffold incorporating two dithiolane anchoring units for the modification of gold surfaces has been functionalized with multiple copies of a redox unit, namely ferrocene. Surface modification has been first assessed at the single molecule level by atomic force microscopy (AFM) and scanning tunneling microscopy (STM) imaging, while tip enhanced Raman spectroscopy (TERS) provided the local vibrational signature of the ferrocenyl subunits of the rotaxanes grafted onto the gold surface. Finally, oxidation of the redox moieties within a rotaxane scaffold grafted onto gold microelectrodes has been investigated by ultrafast cyclic voltammetry...
December 5, 2017: Chemistry: a European Journal
Hyun-Hang Shin, Gyu Jin Yeon, Han-Kyu Choi, Sang-Min Park, Kang Sup Lee, Zee Hwan Kim
The existence of sub-nm plasmonic hot-spots and their relevance in spectroscopy and microscopy applications remain elusive despite a few recent theoretical and experimental evidences supporting this possibility. In this report, we present new spectroscopic evidence suggesting that angstrom-sized hot-spots exist on the surfaces of plasmon-excited nanostructures. Surface-enhanced Raman scattering (SERS) spectra of 4, 4'-biphenyl dithiols placed in metallic junctions show simultaneously blinking Stokes and anti-Stokes spectra, some of which exhibit only one prominent vibrational peak...
December 5, 2017: Nano Letters
Huseyin Atesci, Veerabhadrarao Kaliginedi, Jose A Celis Gil, Hiroaki Ozawa, Joseph M Thijssen, Peter Broekmann, Masa-Aki Haga, Sense Jan van der Molen
Although molecular rectifiers were proposed over four decades ago 1,2 , until recently reported rectification ratios (RR) were rather moderate 2-11 (RR ~ 101). This ceiling was convincingly broken using a eutectic GaIn top contact 12 to probe molecular monolayers of coupled ferrocene groups (RR ~ 105), as well as using scanning tunnelling microscopy-break junctions 13-16 and mechanically controlled break junctions 17 to probe single molecules (RR ~ 102-103). Here, we demonstrate a device based on a molecular monolayer in which the RR can be switched by more than three orders of magnitude (between RR ~ 100 and RR ≥ 103) in response to humidity...
December 4, 2017: Nature Nanotechnology
Domenica Spadaro, Shimin Le, Thierry Laroche, Isabelle Mean, Lionel Jond, Jie Yan, Sandra Citi
Tensile forces regulate epithelial homeostasis, but the molecular mechanisms behind this regulation are poorly understood. Using structured illumination microscopy and proximity ligation assays, we show that the tight junction protein ZO-1 exists in stretched and folded conformations within epithelial cells, depending on actomyosin-generated force. We also show that ZO-1 and ZO-2 regulate the localization of the transcription factor DbpA and the tight junction membrane protein occludin in a manner that depends on the organization of the actin cytoskeleton, myosin-II activity, and substrate stiffness, resulting in modulation of gene expression, cell proliferation, barrier function, and cyst morphogenesis...
November 30, 2017: Current Biology: CB
Yilai Li, Jeremy W Schroeder, Lyle A Simmons, Julie S Biteen
Although DNA replication and repair in bacteria have been extensively studied for many decades, in recent years the development of single-molecule microscopy has provided a new perspective on these fundamental processes. Because single-molecule imaging super-resolves the nanometer-scale dynamics of molecules, and because single-molecule imaging is sensitive to heterogeneities within a sample, this nanoscopic microscopy technique measures the motions, localizations, and interactions of proteins in real time without averaging ensemble observations, both in vitro and in vivo...
November 30, 2017: Current Opinion in Microbiology
Pooja Nath, Rahul Mangal, Ferdinand Friedrich Erich Kohle, Snehashis Choudhury, Suresh Narayanan, Ulrich B Wiesner, Lynden A Archer
The mean square displacement of nanoparticle probes dispersed in simple isotropic liquids and in polymer solutions is interrogated using Fluorescence Correlation Spectroscopy (FCS) and single particle tracking (SPT) experiments. Probe dynamics in different regimes of particle diameter (d) relative to characteristic polymer length scales, including the correlation length (ξ), the entanglement mesh size (a) and radius of gyration (Rg), are investigated. In simple fluids and for polymer solutions in which d > Rg, long-time particle dynamics obey random walk statistics , with the bulk zero-shear viscosity of the polymer solution determining the frictional resistance to particle motion...
December 1, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
Laura Mezquita, Melinda Charrier, Laura Faivre, Louise Dupraz, Béranger Lueza, Jordi Remon, David Planchard, Maria Virginia Bluthgen, Francesco Facchinetti, Arslane Rahal, Valentina Polo, Anas Gazzah, Caroline Caramella, Julien Adam, Jean Pierre Pignon, Jean-Charles Soria, Nathalie Chaput, Benjamin Besse
INTRODUCTION: The class I human leucocyte antigen (HLA) molecules play a critical role as an escape mechanism of antitumoral immunity. HLA-A2 status has been evaluated as a prognostic factor in lung cancer, mostly in localized disease and with inconsistent findings. We evaluated the role of HLA-A2 status as a prognostic factor in a large and homogeneus cohort of advanced NSCLC patients. METHODS: Advanced NSCLC patients eligible for platinum-based chemotherapy were consecutively included in a single center between October 2009 and July 2015 in the prospective MSN study (NCT02105168)...
October 2017: Lung Cancer: Journal of the International Association for the Study of Lung Cancer
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