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Single molecule localization

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https://www.readbyqxmd.com/read/28108449/quantification-of-fibrous-spatial-point-patterns-from-single-molecule-localization-microscopy-smlm-data
#1
Ruby Peters, Marta Benthem Muñiz, Juliette Griffié, David J Williamson, George W Ashdown, Christian D Lorenz, Dylan M Owen
MOTIVATION: Unlike conventional microscopy which produces pixelated images, SMLM produces data in the form of a list of localization coordinates - a spatial point pattern (SPP). Often, such SPPs are analyzed using cluster analysis algorithms to quantify molecular clustering within, for example, the plasma membrane. While SMLM cluster analysis is now well developed, techniques for analyzing fibrous structures remain poorly explored. RESULTS: Here, we demonstrate statistical methodology, based on Ripley's K-function to quantitatively assess fibrous structures in 2D SMLM data sets...
January 19, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28099801/highly-specific-and-sensitive-fluorescent-nanoprobes-for-image-guided-resection-of-sub-millimeter-peritoneal-tumors
#2
Aaron H Colby, Samantha Berry, Ann M Moran, Kristine Amber Pasion, Rong Liu, Yolonda L Colson, Nelson Ruiz-Opazo, Mark W Grinstaff, Victoria L M Herrera
A current challenge in the treatment of peritoneal carcinomatosis is the inability to detect, visualize, and resect small or microscopic tumors of pancreatic, ovarian or mesothelial origin. In these diseases, the completeness of primary tumor resection is directly correlated with patient survival, and, hence, identifying small sub-mm tumors (i.e., disseminated disease) is critical. Thus, new imaging techniques and probes are needed to improve cytoreductive surgery and patient outcomes. Highly-fluorescent rhodamine-labeled expansile nanoparticles (HFR-eNPs) are described for use as a visual aid during cytoreductive surgery of pancreatic carcinomatosis...
January 18, 2017: ACS Nano
https://www.readbyqxmd.com/read/28099017/absence-of-intramolecular-charge-transfer-with-4-fluoro-n-n-dimethylaniline-dma4f-contrary-to-an-experimental-report-supported-by-computations
#3
Klaas A Zachariasse, Attila Demeter, Sergey I Druzhinin
With 4-fluoro-N,N-dimethylaniline (DMA4F) only a single fluorescence from a locally excited (LE) state is observed, irrespective of solvent polarity, temperature, and excitation wavelength. The relatively small excited state dipole moment μe = 7.3 D confirms the identification as LE. The single exponential fluorescence decays in the nonpolar n-hexane (2.04 ns) and in the strongly polar acetonitrile (5.73 ns) are a further support. Similar results are obtained with 4-chloro-N,N-dimethylaniline (DMA4Cl), having a chlorobenzene subgroup, a somewhat better electron acceptor than the fluorobenzene moiety in DMA4F...
January 18, 2017: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/28098202/superresolution-imaging-of-clinical-formalin-fixed-paraffin-embedded-breast-cancer-with-single-molecule-localization-microscopy
#4
Matthew K Creech, Jing Wang, Xiaolin Nan, Summer L Gibbs
Millions of archived formalin-fixed, paraffin-embedded (FFPE) specimens contain valuable molecular insight into healthy and diseased states persevered in their native ultrastructure. To diagnose and treat diseases in tissue on the nanoscopic scale, pathology traditionally employs electron microscopy (EM), but this platform has significant limitations including cost and painstaking sample preparation. The invention of single molecule localization microscopy (SMLM) optically overcame the diffraction limit of light to resolve fluorescently labeled molecules on the nanoscale, leading to many exciting biological discoveries...
January 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28096443/stem-loop-rna-labeling-can-affect-nuclear-and-cytoplasmic-mrna-processing
#5
Stephanie Heinrich, Corinne L Sidler, Claus M Azzalin, Karsten Weis
The binding of sequence-specific RNA-interacting proteins, such as the bacteriophage MS2 or PP7 coat proteins, to their corresponding target sequences has been extremely useful and widely used to visualize single mRNAs in vivo. However, introduction of MS2 stem-loops into yeast mRNAs has recently been shown to lead to the accumulation of RNA fragments, suggesting that the loops impair mRNA decay. This result was questioned, because fragment occurrence was mainly assessed using ensemble methods, and their cellular localization and its implications had not been addressed on a single transcript level...
February 2017: RNA
https://www.readbyqxmd.com/read/28092441/local-mode-analysis-decoding-ir-spectra-by-visualizing-molecular-details
#6
Matthias Massarczyk, Till Rudack, Jürgen Schlitter, Jens Kuhne, Carsten Kötting, Klaus Gerwert
Integration of experimental and computational approaches to investigate chemical reactions in proteins has proven to be very successful. Experimentally, time-resolved FTIR difference-spectroscopy monitors chemical reactions at atomic detail. To decode detailed structural information encoded in IR spectra, QM/MM calculations are performed. Here, we present a novel method which we call Local Mode Analysis (LMA) for calculating IR spectra and assigning spectral IR bands on the basis of movements of nuclei and partial charges from just a single QM/MM trajectory...
January 16, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28088790/intraperitoneal-immunotherapy-with-t-cells-stably-and-transiently-expressing-anti-epcam-car-in-xenograft-models-of-peritoneal-carcinomatosis
#7
Wei Xia Ang, Zhendong Li, Zhixia Chi, Shou-Hui Du, Can Chen, Johan C K Tay, Han Chong Toh, John E Connolly, Xue Hu Xu, Shu Wang
The epithelial cell adhesion molecule (EpCAM) is overexpressed in a wide variety of tumor types, including peritoneal carcinomatosis (PC) from gastrointestinal and gynecological malignancies. To develop a chimeric antigen receptor T (CART) cell therapy approach to treat patients with end-stage PC, we constructed third generation CARs specific to EpCAM using the 4D5MOC-B single chain variable fragment. CART cells were generated with lentiviral transduction and exhibited specific in vitro killing activity against EpCAM-positive human ovarian and colorectal cancer cells...
January 10, 2017: Oncotarget
https://www.readbyqxmd.com/read/28079969/molecular-polygons-probe-the-role-of-intramolecular-strain-in-the-photophysics-of-%C3%AF-conjugated-chromophores
#8
Philipp Wilhelm, Jan Vogelsang, Georgiy Poluektov, Nina Schönfelder, Tristan J Keller, Stefan-Sven Jester, Sigurd Höger, John M Lupton
π-Conjugated segments, chromophores, are the electronically active units of polymer materials used in organic electronics. To elucidate the effect of the bending of these linear moieties on elementary electronic properties, such as luminescence color and radiative rate, we introduce a series of molecular polygons. The π-system in these molecules becomes so distorted in bichromophores (digons) that these absorb and emit light of arbitrary polarization: any part of the chain absorbs and emits radiation with equal probability...
January 12, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28079303/mononuclear-clusterfullerene-single-molecule-magnet-containing-strained-fused-pentagons-stabilized-by-a-nearly-linear-metal-cyanide-cluster
#9
Fupin Liu, Song Wang, Cong-Li Gao, Qingming Deng, Xianjun Zhu, Aram Kostanyan, Rasmus Westerström, Fei Jin, Su-Yuan Xie, Alexey A Popov, Thomas Greber, Shangfeng Yang
Fused-pentagons results in an increase of local steric strain according to the isolated pentagon rule (IPR), and for all reported non-IPR clusterfullerenes multiple (two or three) metals are required to stabilize the strained fused-pentagons, making it difficult to access the single-atom properties. Herein, we report the syntheses and isolations of novel non-IPR mononuclear clusterfullerenes MNC@C76 (M=Tb, Y), in which one pair of strained fused-pentagon is stabilized by a mononuclear cluster. The molecular structures of MNC@C76 (M=Tb, Y) were determined unambiguously by single-crystal X-ray diffraction, featuring a non-IPR C2v (19138)-C76 cage entrapping a nearly linear MNC cluster, which is remarkably different from the triangular MNC cluster within the reported analogous clusterfullerenes based on IPR-obeying C82 cages...
January 12, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28077434/transfer-of-allogeneic-cd4-t-cells-rescues-cd8-t-cells-in-anti-pd-l1-resistant-tumors-leading-to-tumor-eradication
#10
Ainhoa Arina, Theodore G Karrison, Eva Galka, Karin Schreiber, Ralph R Weichselbaum, Hans Schreiber
Adoptively transferred CD8(+) T cells can stabilize the size of solid tumors over long periods of time by exclusively recognizing antigen cross-presented on tumor stroma. However, these tumors eventually escape T cell-mediated growth control. The aim of this study was to eradicate such persistent cancers. In our model, the SIYRYYGL antigen is expressed by cancer cells that lack the MHC-I molecule K(b) needed for direct presentation, but the antigen is picked up and cross-presented by tumor stroma. A single injection of antigen-specific 2C CD8(+) T cells caused long-term inhibition of tumor growth, but without further intervention, tumors started to progress after approximately 3 months...
January 11, 2017: Cancer Immunology Research
https://www.readbyqxmd.com/read/28076349/mechanical-control-of-whole-body-shape-by-a-single-cuticular-protein-obstructor-e-in-drosophila-melanogaster
#11
Reiko Tajiri, Nobuhiro Ogawa, Haruhiko Fujiwara, Tetsuya Kojima
Body shapes are much more variable than body plans. One way to alter body shapes independently of body plans would be to mechanically deform bodies. To what extent body shapes are regulated physically, or molecules involved in physical control of morphogenesis, remain elusive. During fly metamorphosis, the cuticle (exoskeleton) covering the larval body contracts longitudinally and expands laterally to become the ellipsoidal pupal case (puparium). Here we show that Drosophila melanogaster Obstructor-E (Obst-E) is a protein constituent of the larval cuticle that confers the oriented contractility/expandability...
January 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28074833/shifting-molecular-localization-by-plasmonic-coupling-in-a-single-molecule-mirage
#12
Mario Raab, Carolin Vietz, Fernando Daniel Stefani, Guillermo Pedro Acuna, Philip Tinnefeld
Over the last decade, two fields have dominated the attention of sub-diffraction photonics research: plasmonics and fluorescence nanoscopy. Nanoscopy based on single-molecule localization offers a practical way to explore plasmonic interactions with nanometre resolution. However, this seemingly straightforward technique may retrieve false positional information. Here, we make use of the DNA origami technique to both control a nanometric separation between emitters and a gold nanoparticle, and as a platform for super-resolution imaging based on single-molecule localization...
January 11, 2017: Nature Communications
https://www.readbyqxmd.com/read/28073270/cooperative-molecular-behavior-enhances-the-thermal-conductance-of-binary-self-assembled-monolayer-junctions
#13
Shubhaditya Majumdar, Jonathan A Malen, Alan J H McGaughey
The effect of the local molecular environment on thermal transport through organic-inorganic heterojunctions is investigated using binary self-assembled monolayer (SAM) junctions built from a mixture of alkanethiol and alkanedithiol species sandwiched between gold leads. Thermoreflectance measurements and molecular dynamics simulations demonstrate that the thermal conductances of the binary SAM junctions vary with molecular composition and are greater than predictions of a parallel resistance model. The enhancement results from increased thermal transport through the alkanethiols, whose terminal methyl groups are confined by the anchored alkanedithiols...
January 11, 2017: Nano Letters
https://www.readbyqxmd.com/read/28072519/single-molecule-fluorescence-spectroscopy-of-photosynthetic-systems
#14
Toru Kondo, Wei Jia Chen, Gabriela S Schlau-Cohen
Photosynthesis begins when a network of pigment-protein complexes captures solar energy and transports it to the reaction center, where charge separation occurs. When necessary (under low light conditions), photosynthetic organisms perform this energy transport and charge separation with near unity quantum efficiency. Remarkably, this high efficiency is maintained under physiological conditions, which include thermal fluctuations of the pigment-protein complexes and changing local environments. These conditions introduce multiple types of heterogeneity in the pigment-protein complexes, including structural heterogeneity, energetic heterogeneity, and functional heterogeneity...
January 10, 2017: Chemical Reviews
https://www.readbyqxmd.com/read/28071978/nup82-functions-redundantly-with-nup136-in-a-salicylic-acid-dependent-defense-response-of-arabidopsis-thaliana
#15
Kentaro Tamura, Yoichiro Fukao, Noriyuki Hatsugai, Fumiaki Katagiri, Ikuko Hara-Nishimura
The nuclear pore complex (NPC) comprises more than 30 nucleoporins (Nups). NPC mediates macromolecular trafficking between the nucleoplasm and the cytoplasm, but specific roles of individual Nups are poorly understood in higher plants. Here, we show that the novel nucleoporin unique to angiosperm plants (designated as Nup82) functions in a salicylic acid-dependent defense in a redundant manner with Nup136, which is a component of the nuclear basket in the NPC. Arabidopsis thaliana Nup82 had a similar amino acid sequence to the N-terminal half of Nup136 and a Nup82-GFP fusion was localized on the nuclear envelope...
January 10, 2017: Nucleus
https://www.readbyqxmd.com/read/28068902/bacterial-microbiota-of-kazakhstan-cheese-revealed-by-single-molecule-real-time-smrt-sequencing-and-its-comparison-with-belgian-kalmykian-and-italian-artisanal-cheeses
#16
Jing Li, Yi Zheng, Haiyan Xu, Xiaoxia Xi, Qiangchuan Hou, Shuzhen Feng, Laga Wuri, Yanfei Bian, Zhongjie Yu, Lai-Yu Kwok, Zhihong Sun, Tiansong Sun
BACKGROUND: In Kazakhstan, traditional artisanal cheeses have a long history and are widely consumed. The unique characteristics of local artisanal cheeses are almost completely preserved. However, their microbial communities have rarely been reported. The current study firstly generated the Single Molecule, Real-Time (SMRT) sequencing bacterial diversity profiles of 6 traditional artisanal cheese samples of Kazakhstan origin, followed by comparatively analyzed the microbiota composition between the current dataset and those from cheeses originated from Belgium, Russian Republic of Kalmykia (Kalmykia) and Italy...
January 9, 2017: BMC Microbiology
https://www.readbyqxmd.com/read/28067372/selective-turn-on-and-modulation-of-resonant-energy-transfer-in-single-plasmonic-hybrid-nanostructures
#17
Łukasz Bujak, Tatsuya Ishii, Dharmendar Kumar Sharma, Shuzo Hirata, Martin Vacha
Förster resonant energy transfer (FRET) is a nonradiative process by which the energy of light absorbed by a donor molecule is transferred to an acceptor molecule over a distance of several nanometers. FRET plays a crucial role in photosynthesis and nature-inspired artificial light-harvesting systems that are being explored for use in energy conversion applications. Localized plasmons of metal nanoparticles can potentially lead to a significant increase of FRET efficiency and effective donor-acceptor distance...
January 9, 2017: Nanoscale
https://www.readbyqxmd.com/read/28065827/gastric-bypass-surgery-recruits-a-gut-ppar-%C3%AE-striatal-d1r-pathway-to-reduce-fat-appetite-in-obese-rats
#18
Mohammed K Hankir, Florian Seyfried, Constantin A Hintschich, Thi-Ai Diep, Karen Kleberg, Mathias Kranz, Winnie Deuther-Conrad, Luis A Tellez, Michael Rullmann, Marianne Patt, Jens Teichert, Swen Hesse, Osama Sabri, Peter Brust, Harald S Hansen, Ivan E de Araujo, Ute Krügel, Wiebke K Fenske
Bariatric surgery remains the single most effective long-term treatment modality for morbid obesity, achieved mainly by lowering caloric intake through as yet ill-defined mechanisms. Here we show in rats that Roux-en-Y gastric bypass (RYGB)-like rerouting of ingested fat mobilizes lower small intestine production of the fat-satiety molecule oleoylethanolamide (OEA). This was associated with vagus nerve-driven increases in dorsal striatal dopamine release. We also demonstrate that RYGB upregulates striatal dopamine 1 receptor (D1R) expression specifically under high-fat diet feeding conditions...
January 2, 2017: Cell Metabolism
https://www.readbyqxmd.com/read/28063491/fluorescence-based-in-situ-quantitative-imaging-for-cellular-lipids
#19
W Cho, Y Yoon, S-L Liu, K Baek, R Sheng
Membrane lipids are dynamic molecules and their local concentrations serve as regulatory signals for diverse biological processes. To achieve quantitative in situ imaging of various lipids, we developed a ratiometric analysis using fluorescence biosensors, each of which is composed of an engineered lipid-binding protein and a covalently attached solvatochromic fluorophore. To cover a wide range of lipid concentration, lipid-binding proteins are engineered to have variable dynamic ranges. These tunable sensors allow robust and sensitive in situ quantitative lipid imaging in mammalian cells, providing new insight into the spatiotemporal dynamics and fluctuation of key signaling lipids...
2017: Methods in Enzymology
https://www.readbyqxmd.com/read/28062046/recent-advances-in-biological-single-molecule-applications-of-optical-tweezers-and-fluorescence-microscopy
#20
M Hashemi Shabestari, A E C Meijering, W H Roos, G J L Wuite, E J G Peterman
Over the past two decades, single-molecule techniques have evolved into robust tools to study many fundamental biological processes. The combination of optical tweezers with fluorescence microscopy and microfluidics provides a powerful single-molecule manipulation and visualization technique that has found widespread application in biology. In this combined approach, the spatial (~nm) and temporal (~ms) resolution, as well as the force scale (~pN) accessible to optical tweezers is complemented with the power of fluorescence microscopy...
2017: Methods in Enzymology
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