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Single molecule localization

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https://www.readbyqxmd.com/read/29040675/fluctuation-localization-imaging-based-fluorescence-in-situ-hybridization-flifish-for-accurate-detection-and-counting-of-rna-copies-in-single-cells
#1
Yi Cui, Dehong Hu, Lye Meng Markillie, William B Chrisler, Matthew J Gaffrey, Charles Ansong, Lori Sussel, Galya Orr
Quantitative gene expression analysis in intact single cells can be achieved using single molecule-based fluorescence in situ hybridization (smFISH). This approach relies on fluorescence intensity to distinguish between true signals, emitted from an RNA copy hybridized with multiple oligonucleotide probes, and background noise. Thus, the precision in smFISH is often compromised by partial or nonspecific probe binding and tissue autofluorescence, especially when only a small number of probes can be fitted to the target transcript...
October 4, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29040309/targeted-pth4-expressing-cell-ablation-impairs-skeletal-mineralization-in-zebrafish
#2
Paula Suarez-Bregua, Ankur Saxena, Marianne E Bronner, Josep Rotllant
Skeletal development and mineralization are essential processes driven by the coordinated action of neural signals, circulating molecules and local factors. Our previous studies revealed that the novel neuropeptide Pth4, synthesized by hypothalamic cells, was involved in bone metabolism via phosphate regulation in adult zebrafish. Here, we investigate the role of pth4 during skeletal development using single-cell resolution, two-photon laser ablation of Pth4:eGFP-expressing cells and confocal imaging in vivo...
2017: PloS One
https://www.readbyqxmd.com/read/29040286/human-babesiosis-indication-of-a-molecular-mimicry-between-thrombospondin-domains-from-a-novel-babesia-microti-bmp53-protein-and-host-platelets-molecules
#3
Ahmed Abdelmoniem Mousa, Daniel Barry Roche, Mohamad Alaa Terkawi, Kyohko Kameyama, Ketsarin Kamyingkird, Patrick Vudriko, Akram Salama, Shinuo Cao, Sahar Orabi, Hanem Khalifa, Mohamed Ahmed, Mabrouk Attia, Ahmed Elkirdasy, Yoshifumi Nishikawa, Xuenan Xuan, Emmanuel Cornillot
Human babesiosis is caused by the apicomplexan parasite Babesia microti, which is of major public health concern in the United States and elsewhere, resulting in malaise and fatigue, followed by a fever and hemolytic anemia. In this paper we focus on the characterization of a novel B. microti thrombospondin domain (TSP1)-containing protein (BmP53) from the new annotation of the B. microti genome (locus 'BmR1_04g09041'). This novel protein (BmP53) had a single TSP1 and a transmembrane domain, with a short cytoplasmic tail containing a sub-terminal glutamine residue, but no signal peptide and Von Willebrand factor type A domains (VWA), which are found in classical thrombospondin-related adhesive proteins (TRAP)...
2017: PloS One
https://www.readbyqxmd.com/read/29036535/ploc-manimal-predict-subcellular-localization-of-animal-proteins-with-both-single-and-multiple-sites
#4
Xiang Cheng, Shu-Guang Zhao, Wei-Zhong Lin, Xuan Xiao, Kuo-Chen Chou
Motivation: Cells are deemed the basic unit of life. However, many important functions of cells as well as their growth and reproduction are performed via the protein molecules located at their different organelles or locations. Facing explosive growth of protein sequences, we are challenged to develop fast and effective method to annotate their subcellular localization. However, this is by no means an easy task. Particularly, mounting evidences have indicated proteins have multi-label feature meaning that they may simultaneously exist at, or move between, two or more different subcellular location sites...
July 24, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29036087/fast-and-accurate-three-dimensional-point-spread-function-computation-for-fluorescence-microscopy
#5
Jizhou Li, Feng Xue, Thierry Blu
The point spread function (PSF) plays a fundamental role in fluorescence microscopy. A realistic and accurately calculated PSF model can significantly improve the performance in 3D deconvolution microscopy and also the localization accuracy in single-molecule microscopy. In this work, we propose a fast and accurate approximation of the Gibson-Lanni model, which has been shown to represent the PSF suitably under a variety of imaging conditions. We express the Kirchhoff's integral in this model as a linear combination of rescaled Bessel functions, thus providing an integral-free way for the calculation...
June 1, 2017: Journal of the Optical Society of America. A, Optics, Image Science, and Vision
https://www.readbyqxmd.com/read/29032103/mast-cells-in-atherosclerotic-cardiovascular-disease-activators-and-actions
#6
Petri T Kovanen, Ilze Bot
Mast cells are potent actors involved in inflammatory reactions in various tissues, including both in the intimal and the adventitial layers of atherosclerotic arteries. In the arterial intima, the site of atherogenesis, mast cells are activated to degranulate, and thereby triggered to release an abundance of preformed inflammatory mediators, notably histamine, heparin, neutral proteases and cytokines stored in their cytoplasmic secretory granules. Depending on the stimulus, mast cell activation may also launch prolonged synthesis and secretion of single bioactive molecules, such as cytokines and derivatives of arachidonic acid...
October 12, 2017: European Journal of Pharmacology
https://www.readbyqxmd.com/read/29028767/prostate-specific-membrane-antigen-guided-salvage-lymph-node-dissection-in-recurrent-prostate-cancer-a-novel-technology-to-detect-lymph-node-metastases
#7
Tobias Maurer, Jürgen E Gschwend, Matthias Eiber
PURPOSE OF REVIEW: With Gallium (Ga)-prostate-specific membrane antigen (PSMA) PET/computed tomography (CT) as emerging imaging technique offering superior detection rates in biochemical recurrent prostate cancer, salvage lymph node dissection has gained increasing interest in localized oligometastatic prostate cancer. Currently, PSMA-targeting small molecules cannot only be linked to positron-emitting isotopes for imaging but also be labelled with γ-radiation emitting isotopes. These modified PSMA agents are evaluated for intraoperative guidance for resection of metastatic lymph nodes...
October 11, 2017: Current Opinion in Urology
https://www.readbyqxmd.com/read/29027556/effect-of-a-heavy-heteroatom-on-triplet-formation-and-interactions-in-single-conjugated-polymer-molecules-and-aggregates
#8
Benjamin D Datko, Alan K Thomas, Zhuping Fei, Martin Heeney, John K Grey
Triplet formation and interactions with emissive singlet excitons are investigated in poly(3-hexylselenophene) (P3HS) using single molecule spectroscopy. P3HS is a heavy atom analog of the more commonly studied poly(3-hexylthiophene) (P3HT), a benchmark polymer for solar cells. P3HS tends to aggregate strongly which necessitates dilution to ultra-low levels within a solid inert host in order to resolve photophysical responses of single chains. Fluorescence excitation intensity modulation is performed on isolated P3HS chains using a sequence of rectangular pulses of varying intensities to probe the presence of spin-forbidden triplet excitons...
October 13, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/29024122/guided-molecular-assembly-on-a-locally-reactive-2d-material
#9
Ben Warner, Tobias G Gill, Vasile Caciuc, Nicolae Atodiresei, Antoine Fleurence, Yasuo Yoshida, Yukio Hasegawa, Stefan Blügel, Yukiko Yamada-Takamura, Cyrus F Hirjibehedin
Atomically precise engineering of the position of molecular adsorbates on surfaces of 2D materials is key to their development in applications ranging from catalysis to single-molecule spintronics. Here, stable room-temperature templating of individual molecules with localized electronic states on the surface of a locally reactive 2D material, silicene grown on ZrB2 , is demonstrated. Using a combination of scanning tunneling microscopy and density functional theory, it is shown that the binding of iron phthalocyanine (FePc) molecules is mediated via the strong chemisorption of the central Fe atom to the sp(3) -like dangling bond of Si atoms in the linear silicene domain boundaries...
October 11, 2017: Advanced Materials
https://www.readbyqxmd.com/read/29023096/graphene-liquid-enclosure-for-single-molecule-analysis-of-membrane-proteins-in-whole-cells-using-electron-microscopy
#10
Indra N Dahmke, Andreas Verch, Justus Hermannsdörfer, Diana B Peckys, Robert S Weatherup, Stephan Hofmann, Niels de Jonge
Membrane proteins govern many important functions in cells via dynamic oligomerization into active complexes. However, analytical methods to study their distribution and functional state in relation to the cellular structure are currently limited. Here, we introduce a technique for studying single-membrane proteins within their native context of the intact plasma membrane. SKBR3 breast cancer cells were grown on silicon microchips with thin silicon nitride windows. The cells were fixed, and the epidermal growth factor receptor ErbB2 was specifically labeled with quantum dot (QD) nanoparticles...
October 16, 2017: ACS Nano
https://www.readbyqxmd.com/read/29022640/local-conformational-changes-in-the-8-17-deoxyribozyme-core-induced-by-activating-and-inactivating-divalent-metal-ions
#11
Alessio Peracchi, Maria Bonaccio, Alfredo Credali
The 8-17 deoxyribozyme (DNAzyme) is a catalytic DNA molecule capable of cleaving specific RNA substrates. The deoxyribozyme is activated by a wide variety of divalent metal ions, from Mg(2+) to Pb(2+), with just a few exceptions. It is not clear if metal ions are directly involved in catalysis, or are required to attain an active conformation, or both. In particular, the connection between metal-induced global structural rearrangements and catalysis is not straightforward. To gain more information on the local structural changes induced by metal ions, we introduced fluorescent 2-aminopurine (2-Ap) residues at different positions of the 8-17 'core'...
October 12, 2017: Organic & Biomolecular Chemistry
https://www.readbyqxmd.com/read/29021238/asy2-mer2-an-evolutionarily-conserved-mediator-of-meiotic-recombination-pairing-and-global-chromosome-compaction
#12
Sophie Tessé, Henri-Marc Bourbon, Robert Debuchy, Karine Budin, Emeline Dubois, Zhang Liangran, Romain Antoine, Tristan Piolot, Nancy Kleckner, Denise Zickler, Eric Espagne
Meiosis is the cellular program by which a diploid cell gives rise to haploid gametes for sexual reproduction. Meiotic progression depends on tight physical and functional coupling of recombination steps at the DNA level with specific organizational features of meiotic-prophase chromosomes. The present study reveals that every step of this coupling is mediated by a single molecule: Asy2/Mer2. We show that Mer2, identified so far only in budding and fission yeasts, is in fact evolutionarily conserved from fungi (Mer2/Rec15/Asy2/Bad42) to plants (PRD3/PAIR1) and mammals (IHO1)...
October 11, 2017: Genes & Development
https://www.readbyqxmd.com/read/28993619/enhanced-nanochannel-translocation-and-localization-of-genomic-dna-molecules-using-three-dimensional-nanofunnels
#13
Jinsheng Zhou, Yanqian Wang, Laurent D Menard, Sergey Panyukov, Michael Rubinstein, J Michael Ramsey
The ability to precisely control the transport of single DNA molecules through a nanoscale channel is critical to DNA sequencing and mapping technologies that are currently under development. Here we show how the electrokinetically driven introduction of DNA molecules into a nanochannel is facilitated by incorporating a three-dimensional nanofunnel at the nanochannel entrance. Individual DNA molecules are imaged as they attempt to overcome the entropic barrier to nanochannel entry through nanofunnels with various shapes...
October 9, 2017: Nature Communications
https://www.readbyqxmd.com/read/28991414/in-situ-spatial-complementation-of-aptamer-mediated-recognition-enables-live-cell-imaging-of-native-rna-transcripts-in-real-time
#14
Zejun Wang, Yao Luo, Xiaodong Xie, Xingjie Hu, Haiyun Song, Yun Zhao, Jiye Shi, Lihua Wang, Gennadi Glinsky, Nan Chen, Ratnesh Lal, Chunhai Fan
Direct cellular imaging of the localization and dynamics of biomolecules helps to understand their functions and reveals novel mechanisms at the single-cell resolution. Here, we report the development of an aptamer-initiated fluorescence complementation (AiFC) method for RNA imaging by engineering a green fluorescence protein (GFP)-mimicking turn-on RNA aptamer, Broccoli, into two split fragments that could tandemly bind to target mRNA. When genetically encoded in cells, nascent mRNA molecules recruited split Broccoli and brought the two fragments to the spatial proximity, which in-situ formed a fluorophore-binding site and turned on fluorescence...
October 9, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28989634/near-infrared-luminescent-metallacrowns-for-combined-in-vitro-cell-fixation-and-counter-staining
#15
Ivana Martinić, Svetlana V Eliseeva, Tu N Nguyen, Frédéric Foucher, David Gosset, Frances Westall, Vincent L Pecoraro, Stéphane Petoud
Cell fixation is an essential approach for preserving cell morphology, allowing the targeting and labelling of biomolecules with fluorescent probes. One of the key requirements for more efficient fluorescent labelling is the preservation of cell morphology, which usually requires a combination of several fixation techniques. In addition, the use of a counter stain is often essential to improve the contrast of the fluorescent probes. Current agents possess significant limitations, such as low resistance toward photobleaching and sensitivity to changes in the microenvironment...
September 1, 2017: Chemical Science
https://www.readbyqxmd.com/read/28987123/mixing-of-mnpc-electronic-states-at-the-mnpc-au-110-interface
#16
Pierluigi Gargiani, Simone Lisi, Giulia Avvisati, Pierluigi Mondelli, Sara Fatale, Maria Grazia Betti
Manganese-phthalocyanines form assembled chains with a variety of ordered super-structures, flat lying along the Au(110) reconstructed channels. The chains first give rise to a ×5 symmetry reconstruction, while further deposition of MnPc leads to a ×7 periodicity at the completion of the first single layer. A net polarization with the formation of an interface dipole is mainly due to the molecular π-states located on the macrocycles pyrrole rings, while the central metal ion induces a reduction in the polarization, whose amount is related to the Mn-Au interaction...
October 7, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28987089/spin-switch-in-iron-phthalocyanine-on-au-111-surface-by-hydrogen-adsorption
#17
Yu Wang, Xiaoguang Li, Xiao Zheng, Jinlong Yang
The manipulation of spin states at the molecular scale is of fundamental importance for the development of molecular spintronic devices. One of the feasible approaches for the modification of a molecular spin state is through the adsorption of certain specific atoms or molecules including H, NO, CO, NH3, and O2. In this paper, we demonstrate that the local spin state of an individual iron phthalocyanine (FePc) molecule adsorbed on an Au(111) surface exhibits controllable switching by hydrogen adsorption, as evidenced by using first-principles calculations based on density functional theory...
October 7, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28986512/cold-kit-psma-pet-imaging-phase-i-study-of-68-ga-thp-psma-pet-ct-in-patients-with-prostate-cancer
#18
Michael S Hofman, Peter Eu, Price Jackson, Emily Hong, David Binns, Amir Iravani, Declan Murphy, Catherine Mitchell, Shankar Siva, Rodney J Hicks, Jennifer D Young, Philip Blower, Gregory E Mullen
Objectives: Ga-68 labelled urea-based inhibitors of the prostate-specific membrane antigen (PSMA), such as (68)Ga-HBED-PSMA-11, are promising small molecules for targeting prostate cancer. A new radiopharmaceutical (68)Ga-THP-PSMA has a simplified design for one-step kit-based radiolabelling. It features the tris(hydroxypyridinone) (THP) ligand, which complexes (68)Ga3+ rapidly at low concentration, room temperature and over a wide pH range, enabling direct elution from a (68)Ge/(68)Ga generator into a lyophilized kit in one-step without manipulation...
October 6, 2017: Journal of Nuclear Medicine: Official Publication, Society of Nuclear Medicine
https://www.readbyqxmd.com/read/28986509/why-targeting-psma-is-a-game-changer-in-the-management-of-prostate-cancer-%C3%A2-a-urologist-s-point-of-view
#19
Nicholas M Donin, Robert Reiter
Prostate-specific membrane antigen (PSMA), is a transmembrane glycoprotein that is highly expressed on prostate adenocarcinomas, exhibits only limited expression in benign and extra-prostatic tissues, and thus represents an ideal target for the diagnosis and management of prostate cancer. Since its discovery over 30 years ago, significant effort has been made to develop clinical technology targeting PSMA. The last 5 years have seen an explosion of development of new agents targeting PSMA for diagnostic and therapeutic use...
October 6, 2017: Journal of Nuclear Medicine: Official Publication, Society of Nuclear Medicine
https://www.readbyqxmd.com/read/28985346/single-molecule-kinetic-analysis-of-hp1-chromatin-binding-reveals-a-dynamic-network-of-histone-modification-and-dna-interactions
#20
Louise C Bryan, Daniel R Weilandt, Andreas L Bachmann, Sinan Kilic, Carolin C Lechner, Pascal D Odermatt, Georg E Fantner, Sandrine Georgeon, Oliver Hantschel, Vassily Hatzimanikatis, Beat Fierz
Chromatin recruitment of effector proteins involved in gene regulation depends on multivalent interaction with histone post-translational modifications (PTMs) and structural features of the chromatin fiber. Due to the complex interactions involved, it is currently not understood how effectors dynamically sample the chromatin landscape. Here, we dissect the dynamic chromatin interactions of a family of multivalent effectors, heterochromatin protein 1 (HP1) proteins, using single-molecule fluorescence imaging and computational modeling...
August 3, 2017: Nucleic Acids Research
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