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Single molecule localization

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https://www.readbyqxmd.com/read/27932455/single-cell-profiling-reveals-that-erna-accumulation-at-enhancer-promoter-loops-is-not-required-to-sustain-transcription
#1
Samir Rahman, Cornelia E Zorca, Tatiana Traboulsi, Emmanuel Noutahi, Matthew R Krause, Sylvie Mader, Daniel Zenklusen
Enhancers are intergenic DNA elements that regulate the transcription of target genes in response to signaling pathways by interacting with promoters over large genomic distances. Recent studies have revealed that enhancers are bi-directionally transcribed into enhancer RNAs (eRNAs). Using single-molecule fluorescence in situ hybridization (smFISH), we investigated the eRNA-mediated regulation of transcription during estrogen induction in MCF-7 cells. We demonstrate that eRNAs are localized exclusively in the nucleus and are induced with similar kinetics as target mRNAs...
December 8, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27931835/management-of-patients-with-recurrent-advanced-cervical-cancer-beyond-first-line-platinum-regimens-where-do-we-stand-a-literature-review
#2
REVIEW
Stergios Boussios, Esmeralda Seraj, George Zarkavelis, Dimitrios Petrakis, Aristomenes Kollas, Aikaterini Kafantari, Abraam Assi, Konstantina Tatsi, Nicholas Pavlidis, George Pentheroudakis
BACKGROUND: Cervical cancer is the fourth most common cancer affecting women worldwide. Despite advances in screening and human papillomavirus (HPV) vaccination, a significant number of women present with or develop advanced disease. Palliative platinum-based chemotherapy (CT) is the standard first-line treatment for metastatic/recurrent cervical cancer. The prognosis remains poor and effective second line options are urgently needed. METHODS: We searched the English-language medical literature as well as relevant guideline databases, published from January 1981 to December 2015 and identified publications related to cervical cancer and its therapies...
December 2016: Critical Reviews in Oncology/hematology
https://www.readbyqxmd.com/read/27929472/three-dimensional-super-resolution-microscopy-of-f-actin-filaments-by-interferometric-photoactivated-localization-microscopy-ipalm
#3
Yilin Wang, Pakorn Kanchanawong
Fluorescence microscopy enables direct visualization of specific biomolecules within cells. However, for conventional fluorescence microscopy, the spatial resolution is restricted by diffraction to ~ 200 nm within the image plane and > 500 nm along the optical axis. As a result, fluorescence microscopy has long been severely limited in the observation of ultrastructural features within cells. The recent development of super resolution microscopy methods has overcome this limitation. In particular, the advent of photoswitchable fluorophores enables localization-based super resolution microscopy, which provides resolving power approaching the molecular-length scale...
December 1, 2016: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/27929085/multi-dimensional-super-resolution-imaging-enables-surface-hydrophobicity-mapping
#4
Marie N Bongiovanni, Julien Godet, Mathew H Horrocks, Laura Tosatto, Alexander R Carr, David C Wirthensohn, Rohan T Ranasinghe, Ji-Eun Lee, Aleks Ponjavic, Joelle V Fritz, Christopher M Dobson, David Klenerman, Steven F Lee
Super-resolution microscopy allows biological systems to be studied at the nanoscale, but has been restricted to providing only positional information. Here, we show that it is possible to perform multi-dimensional super-resolution imaging to determine both the position and the environmental properties of single-molecule fluorescent emitters. The method presented here exploits the solvatochromic and fluorogenic properties of nile red to extract both the emission spectrum and the position of each dye molecule simultaneously enabling mapping of the hydrophobicity of biological structures...
December 8, 2016: Nature Communications
https://www.readbyqxmd.com/read/27928514/a-microchip-for-high-throughput-axon-growth-drug-screening
#5
Hyun Soo Kim, Sehoon Jeong, Chiwan Koo, Arum Han, Jaewon Park
It has been recently known that not only the presence of inhibitory molecules associated with myelin but also the reduced growth capability of the axons limit mature central nervous system (CNS) axonal regeneration after injury. Conventional axon growth studies are typically conducted using multi-well cell culture plates that are very challenging to investigate localized effects of drugs and limited to low throughput. Unfortunately, there is currently no other in vitro tools that allow investigating localized axonal responses to biomolecules in high-throughput for screening potential drugs that might promote axonal growth...
July 2016: Micromachines
https://www.readbyqxmd.com/read/27924986/a-nasba-on-microgel-tethered-molecular-beacon-microarray-for-real-time-microbial-molecular-diagnostics
#6
Y Ma, X Dai, T Hong, G B Munk, M Libera
Despite their many advantages and successes, molecular beacon (MB) hybridization probes have not been extensively used in microarray formats because of the complicating probe-substrate interactions that increase the background intensity. We have previously shown that tethering to surface-patterned microgels is an effective means for localizing MB probes to specific surface locations in a microarray format while simultaneously maintaining them in as water-like an environment as possible and minimizing probe-surface interactions...
December 7, 2016: Analyst
https://www.readbyqxmd.com/read/27921323/the-application-of-strand-invasion-phenomenon-directed-by-peptide-nucleic-acid-pna-and-single-stranded-dna-binding-protein-ssb-for-the-recognition-of-specific-sequences-of-human-endogenous-retroviral-herv-w-family
#7
Grzegorz Machnik, Łukasz Bułdak, Jarosław Ruczyński, Tomasz Gąsior, Małgorzata Huzarska, Dariusz Belowski, Magdalena Alenowicz, Piotr Mucha, Piotr Rekowski, Bogusław Okopień
The HERV-W family of human endogenous retroviruses represents a group of numerous sequences that show close similarity in genetic composition. It has been documented that some members of HERV-W-derived expression products are supposed to play significant role in humans' pathology, such as multiple sclerosis or schizophrenia. Other members of the family are necessary to orchestrate physiological processes (eg, ERVWE1 coding syncytin-1 that is engaged in syncytiotrophoblast formation). Therefore, an assay that would allow the recognition of particular form of HERV-W members is highly desirable...
December 6, 2016: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/27918541/multidomain-structure-and-correlated-dynamics-determined-by-self-consistent-fret-networks
#8
Björn Hellenkamp, Philipp Wortmann, Florian Kandzia, Martin Zacharias, Thorsten Hugel
We present an approach that enables us to simultaneously access structure and dynamics of a multidomain protein in solution. Dynamic domain arrangements are experimentally determined by combining self-consistent networks of distance distributions with known domain structures. Local structural dynamics are correlated with the global arrangements by analyzing networks of time-resolved single-molecule fluorescence parameters. The strength of this hybrid approach is shown by an application to the flexible multidomain protein Hsp90...
December 5, 2016: Nature Methods
https://www.readbyqxmd.com/read/27914923/alloantigen-gene-transfer-to-hepatocytes-promotes-tolerance-to-pancreatic-islet-graft-by-inducing-cd8-regulatory-t-cells
#9
Valentin Le Guen, Jean-Paul Judor, Françoise Boeffard, Vanessa Gauttier, Nicolas Ferry, Jean-Paul Soulillou, Sophie Brouard, Sophie Conchon
BACKGROUND & AIM: Induction of donor-specific immune tolerance is a good alternative to chronic life-long immunosuppression for transplant patients. Donor major histocompatibility complex (MHC) molecules represent the main targets of the allogeneic immune response of transplant recipients. Liver-targeted gene transfer with viral vectors induces tolerance toward the encoded antigen. The aim of this work was to determine whether alloantigen gene transfer to hepatocytes induces tolerance and promotes graft acceptance...
November 30, 2016: Journal of Hepatology
https://www.readbyqxmd.com/read/27912755/establishment-of-high-reciprocal-connectivity-between-clonal-cortical-neurons-is-regulated-by-the-dnmt3b-dna-methyltransferase-and-clustered-protocadherins
#10
Etsuko Tarusawa, Makoto Sanbo, Atsushi Okayama, Toshio Miyashita, Takashi Kitsukawa, Teruyoshi Hirayama, Takahiro Hirabayashi, Sonoko Hasegawa, Ryosuke Kaneko, Shunsuke Toyoda, Toshihiro Kobayashi, Megumi Kato-Itoh, Hiromitsu Nakauchi, Masumi Hirabayashi, Takeshi Yagi, Yumiko Yoshimura
BACKGROUND: The specificity of synaptic connections is fundamental for proper neural circuit function. Specific neuronal connections that underlie information processing in the sensory cortex are initially established without sensory experiences to a considerable extent, and then the connections are individually refined through sensory experiences. Excitatory neurons arising from the same single progenitor cell are preferentially connected in the postnatal cortex, suggesting that cell lineage contributes to the initial wiring of neurons...
December 2, 2016: BMC Biology
https://www.readbyqxmd.com/read/27911791/a-functional-role-for-intrinsic-disorder-in-the-tau-tubulin-complex
#11
Ana M Melo, Juliana Coraor, Garrett Alpha-Cobb, Shana Elbaum-Garfinkle, Abhinav Nath, Elizabeth Rhoades
Tau is an intrinsically disordered protein with an important role in maintaining the dynamic instability of neuronal microtubules. Despite intensive study, a detailed understanding of the functional mechanism of tau is lacking. Here, we address this deficiency by using intramolecular single-molecule Förster Resonance Energy Transfer (smFRET) to characterize the conformational ensemble of tau bound to soluble tubulin heterodimers. Tau adopts an open conformation on binding tubulin, in which the long-range contacts between both termini and the microtubule binding region that characterize its compact solution structure are diminished...
November 23, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27908126/communication-multipole-approximations-of-distant-pair-energies-in-local-correlation-methods-with-pair-natural-orbitals
#12
Hans-Joachim Werner
The accuracy of multipole approximations for distant pair energies in local second-order Møller-Plesset perturbation theory (LMP2) as introduced by Hetzer et al. [Chem. Phys. Lett. 290, 143 (1998)] is investigated for three chemical reactions involving molecules with up to 92 atoms. Various iterative and non-iterative approaches are compared, using different energy thresholds for distant pair selection. It is demonstrated that the simple non-iterative dipole-dipole approximation, which has been used in several recent pair natural orbitals (PNO)-LMP2 and PNO-LCCSD (local coupled-cluster with singles and doubles) methods, may underestimate the distant pair energies by up to 50% and can lead to significant errors in relative energies, unless very tight thresholds are used...
November 28, 2016: Journal of Chemical Physics
https://www.readbyqxmd.com/read/27906373/efficient-homogeneous-illumination-and-optical-sectioning-for-quantitative-single-molecule-localization-microscopy
#13
Joran Deschamps, Andreas Rowald, Jonas Ries
Single-molecule localization microscopy (SMLM) relies on the switching of fluorescent molecules between a fluorescent and a dark state to achieve super resolution. This process is inherently dependent on the intensity distribution of the laser light used for both activation from the dark state and excitation of the bright state. Typically, laser light is coupled directly or via a single-mode fiber into the microscope, which leads to a Gaussian intensity profile in total internal reflection (TIR) or epi illumination...
November 28, 2016: Optics Express
https://www.readbyqxmd.com/read/27906033/the-role-of-the-backbone-torsion-in-protein-folding
#14
EDITORIAL
Irina Sorokina, Arcady Mushegian
BACKGROUND: The set of forces and sequence of events that govern the transition from an unfolded polypeptide chain to a functional protein with correct spatial structure remain incompletely known, despite the importance of the problem and decades of theory development, computer simulations, and laboratory experiments. Information about the correctly folded state of most proteins is likely to be present in their sequences, and yet many proteins fail to attain native structure after overexpression in a non-native environment or upon experimental denaturation and refolding...
December 1, 2016: Biology Direct
https://www.readbyqxmd.com/read/27905323/plasmonic-nano-protrusions-hierarchical-nanostructures-for-single-molecule-raman-spectroscopy
#15
Sagnik Basuray, Avinash Pathak, Sangho Bok, Biyan Chen, Steven C Hamm, Cherian J Mathai, Suchismita Guha, Keshab Gangopadhyay, Shubhra Gangopadhyay
Classical methods for enhancing the electromagnetic field from substrates for spectroscopic applications, such as surface-enhanced Raman spectroscopy (SERS), have involved the generation of hotspots through directed self-assembly of nanoparticles or by patterning nanoscale features using expensive nanolithography techniques. A novel large-area, cost-effective soft lithographic technique involving glancing angle deposition (GLAD) of silver on polymer gratings is reported here. This method produces hierarchical nanostructures with high enhancement factors capable of analyzing single-molecule SERS...
December 1, 2016: Nanotechnology
https://www.readbyqxmd.com/read/27897986/gold-nanoparticles-in-single-cell-analysis-for-surface-enhanced-raman-scattering
#16
REVIEW
Mine Altunbek, Gamze Kuku, Mustafa Culha
The need for new therapeutic approaches in the treatment of challenging diseases such as cancer, which often consists of a highly heterogeneous and complex population of cells, brought up the idea of analyzing single cells. The development of novel techniques to analyze single cells has been intensively studied to fully understand specific alternations inducing abnormalities in cellular function. One of the techniques used for single cell analysis is surface-enhanced Raman spectroscopy (SERS) in which a noble metal nanoparticle is used to enhance Raman scattering...
November 25, 2016: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/27892797/nek8-regulates-dna-damage-induced-rad51-foci-formation-and-replication-fork-protection
#17
Antonio Abeyta, Maria Castella, Celine Jacquemont, Toshiyasu Taniguchi
Proteins essential for homologous recombination play a pivotal role in the repair of DNA double strand breaks, DNA inter-strand crosslinks and replication fork stability. Defects in homologous recombination also play a critical role in the development of cancer and the sensitivity of these cancers to chemotherapy. RAD51, an essential factor for homologous recombination and replication fork protection, accumulates and forms immunocytochemically detectable nuclear foci at sites of DNA damage. To identify kinases that may regulate RAD51 localization to sites of DNA damage, we performed a human kinome siRNA library screen, using DNA damage-induced RAD51 foci formation as readout...
November 28, 2016: Cell Cycle
https://www.readbyqxmd.com/read/27885259/trackntrace-a-simple-and-extendable-open-source-framework-for-developing-single-molecule-localization-and-tracking-algorithms
#18
Simon Christoph Stein, Jan Thiart
Super-resolution localization microscopy and single particle tracking are important tools for fluorescence microscopy. Both rely on detecting, and tracking, a large number of fluorescent markers using increasingly sophisticated computer algorithms. However, this rise in complexity makes it difficult to fine-tune parameters and detect inconsistencies, improve existing routines, or develop new approaches founded on established principles. We present an open-source MATLAB framework for single molecule localization, tracking and super-resolution applications...
November 25, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27884621/photoantimicrobials-are-we-afraid-of-the-light
#19
REVIEW
Mark Wainwright, Tim Maisch, Santi Nonell, Kristjan Plaetzer, Adelaide Almeida, George P Tegos, Michael R Hamblin
Although conventional antimicrobial drugs have been viewed as miraculous cure-alls for the past 80 years, increasing antimicrobial drug resistance requires a major and rapid intervention. However, the development of novel but still conventional systemic antimicrobial agents, having only a single mode or site of action, will not alleviate the situation because it is probably only a matter of time until any such agents will also become ineffective. To continue to produce new agents based on this notion is unacceptable, and there is an increasing need for alternative approaches to the problem...
November 21, 2016: Lancet Infectious Diseases
https://www.readbyqxmd.com/read/27884103/amplimethprofiler-a-pipeline-for-the-analysis-of-cpg-methylation-profiles-of-targeted-deep-bisulfite-sequenced-amplicons
#20
Giovanni Scala, Ornella Affinito, Domenico Palumbo, Ermanno Florio, Antonella Monticelli, Gennaro Miele, Lorenzo Chiariotti, Sergio Cocozza
BACKGROUND: CpG sites in an individual molecule may exist in a binary state (methylated or unmethylated) and each individual DNA molecule, containing a certain number of CpGs, is a combination of these states defining an epihaplotype. Classic quantification based approaches to study DNA methylation are intrinsically unable to fully represent the complexity of the underlying methylation substrate. Epihaplotype based approaches, on the other hand, allow methylation profiles of cell populations to be studied at the single molecule level...
November 25, 2016: BMC Bioinformatics
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