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RNA Imaging

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https://www.readbyqxmd.com/read/28524836/effect-of-histone-deacetylase-inhibition-on-the-expression-of-multidrug-resistance-associated-protein-2-in-a-human-placental-trophoblast-cell-line
#1
Hong-Yu Duan, Dan Ma, Kai-Yu Zhou, Tao Wang, Yi Zhang, Yi-Fei Li, Jin-Lin Wu, Yi-Min Hua, Chuan Wang
BACKGROUND: Placental multidrug resistance-associated protein 2 (MRP2), encoded by ABCC2 gene in human, plays a significant role in regulating drugs' transplacental transfer rates. Studies on placental MRP2 regulation could provide more therapeutic targets for individualized and safe pharmacotherapy during pregnancy. Currently, the roles of epigenetic mechanisms in regulating placental drug transporters are still unclear. This study aimed to investigate the effect of histone deacetylases (HDACs) inhibition on MRP2 expression in the placental trophoblast cell line and to explore whether HDAC1/2/3 are preliminarily involved in this process...
June 5, 2017: Chinese Medical Journal
https://www.readbyqxmd.com/read/28524354/an-aggregating-amphiphilic-squaraine-a-light-up-probe-that-discriminates-parallel-g-quadruplexes
#2
Vincenzo Grande, Filippo Doria, Mauro Freccero, Frank Würthner
G-quadruplexes (G4s) are peculiar DNA or RNA tertiary structures that are involved in the regulation of many biological events within mammalian cells, bacteria, and viruses. Although their role as versatile therapeutic targets has been emphasized for 35 years, G4 selectivity over ubiquitous double-stranded DNA/RNA, as well as G4 differentiation by small molecules, still remains challenging. Here, a new amphiphilic dicyanovinyl-substituted squaraine, SQgl, is reported to act as an NIR fluorescent light-up probe discriminating an extensive panel of parallel G4s while it is non-fluorescent in the aggregated state...
May 19, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28523559/techniques-for-single-molecule-mrna-imaging-in-living-cells
#3
Kevin Czaplinski
Typical measurement of macromolecules in a biological sample typically averages the result over all the cells or molecules within the sample, and while these types of measurements provide very useful information, they completely miss heterogeneity among the components within the sample that could be a very important aspect of the sample's function. These techniques are also limited in their ability to examine intracellular spatial orientation of molecular activity, which is often a critical component to the regulation of biological processes, particularly in cells with unique spatial relationships, such as neurons...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28521463/endoplasmic-reticulum-protein-erp46-in-prostate-adenocarcinoma
#4
Wilhelmina C M Duivenvoorden, Sarah N Hopmans, Richard C Austin, Jehonathan H Pinthus
Endoplasmic reticulum (ER) protein ERp46 is a member of the protein disulfide isomerase family of oxidoreductases, which facilitates the reduction of disulfides in proteins and their folding. Accumulation of misfolded proteins has been implicated in cancer. The objectives of the present study were to investigate the role of ERp46 in prostate cancer, its expression and its effects on prostate cancer growth. A tissue microarray with human prostate cancer and normal prostate tissue samples was stained for ERp46 followed by image analysis...
May 2017: Oncology Letters
https://www.readbyqxmd.com/read/28516281/tof-sims-study-of-differentiation-of-human-bone-derived-stromal-cells-new-insights-into-osteoporosis
#5
Kaija Schaepe, Janina Werner, Kristina Glenske, Tessa Bartges, Anja Henss, Marcus Rohnke, Sabine Wenisch, Jürgen Janek
Lipids have numerous important functions in the human body, as they form the cells' plasma membranes and play a key role in many disease states, presumably also in osteoporosis. Here, the fatty acid composition of the outer plasma membranes of cells differentiated into the osteogenic and adipogenic direction is studied with surface-sensitive time-of-flight secondary ion mass spectrometry (ToF-SIMS). For data evaluation, principal component analysis (PCA) is applied. Human (bone-derived) mesenchymal stromal cells (hMSCs) from an osteoporotic donor and a control donor are compared to reveal differences in the fatty acid composition of the membranes...
May 18, 2017: Analytical and Bioanalytical Chemistry
https://www.readbyqxmd.com/read/28512712/post-translational-tubulin-modifications-in-human-astrocyte-cultures
#6
V Bleu Knight, Elba E Serrano
The cytoskeletal protein tubulin plays an integral role in the functional specialization of many cell types. In the central nervous system, post-translational modifications and the expression of specific tubulin isotypes in neurons have been analyzed in greater detail than in their astrocytic counterparts. In this study, we characterized post-translational specifications of tubulin in human astrocytes using the normal human astrocyte (NHA; Lonza) commercial cell line of fetal origin. Immunocytochemical techniques were implemented in conjunction with confocal microscopy to image class III β-tubulin (βIII-tubulin), acetylated tubulin, and polyglutamylated tubulin using fluorescent antibody probes...
May 17, 2017: Neurochemical Research
https://www.readbyqxmd.com/read/28511883/a-prostate-cancer-nimbosus-genomic-instability-and-schlap1-dysregulation-underpin-aggression-of-intraductal-and-cribriform-subpathologies
#7
Melvin L K Chua, Winnie Lo, Melania Pintilie, Jure Murgic, Emilie Lalonde, Vinayak Bhandari, Osman Mahamud, Anuradha Gopalan, Charlotte F Kweldam, Geert J L H van Leenders, Esther I Verhoef, Agnes Marije Hoogland, Julie Livingstone, Alejandro Berlin, Alan Dal Pra, Alice Meng, Junyan Zhang, Michèle Orain, Valérie Picard, Hélène Hovington, Alain Bergeron, Louis Lacombe, Yves Fradet, Bernard Têtu, Victor E Reuter, Neil Fleshner, Michael Fraser, Paul C Boutros, Theodorus H van der Kwast, Robert G Bristow
BACKGROUND: Intraductal carcinoma (IDC) and cribriform architecture (CA) represent unfavorable subpathologies in localized prostate cancer. We recently showed that IDC shares a clonal ancestry with the adjacent glandular adenocarcinoma. OBJECTIVE: We investigated for the co-occurrence of "aggression" factors, genomic instability and hypoxia, and performed gene expression profiling of these tumors. DESIGN, SETTING, AND PARTICIPANTS: A total of 1325 men were treated for localized prostate cancer from four academic institutions (University Health Network, CHU de Québec-Université Laval, Memorial Sloan Kettering Cancer Center [MSKCC], and Erasmus Medical Center)...
May 13, 2017: European Urology
https://www.readbyqxmd.com/read/28506802/stealth-magnetic-nanocarriers-of-sirna-as-platform-for-breast-cancer-theranostics
#8
J Bruniaux, S Ben Djemaa, K Hervé-Aubert, H Marchais, I Chourpa, S David
The endogenous mechanism of RNA interference is more and more used in research to obtain specific down-regulation of gene expression in diseases such as breast cancer. Currently, despite the new fields of study open up by RNA interference, the rapid degradation of siRNA by nucleases and their negative charges prevent them from crossing cell membranes. To overcome these limitations, superparamagnetic iron oxide nanoparticles (SPIONs) represent a promising alternative for nucleic acid delivery. Previously, we reported the magnetic siRNA nanovectors (MSN) formulation using electrostatic assembly of (1) SPIONs, also able to act as contrast agents for magnetic resonance imaging (MRI), (2) siRNA and (3) chitosan aiming at their protection and enhancing their transfection efficacy...
May 12, 2017: International Journal of Pharmaceutics
https://www.readbyqxmd.com/read/28506208/a-strategy-to-apply-quantitative-epistasis-analysis-on-developmental-traits
#9
Marta K Labocha, Wang Yuan, Boanerges Aleman-Meza, Weiwei Zhong
BACKGROUND: Genetic interactions are keys to understand complex traits and evolution. Epistasis analysis is an effective method to map genetic interactions. Large-scale quantitative epistasis analysis has been well established for single cells. However, there is a substantial lack of such studies in multicellular organisms and their complex phenotypes such as development. Here we present a method to extend quantitative epistasis analysis to developmental traits. METHODS: In the nematode Caenorhabditis elegans, we applied RNA interference on mutants to inactivate two genes, used an imaging system to quantitatively measure phenotypes, and developed a set of statistical methods to extract genetic interactions from phenotypic measurement...
May 15, 2017: BMC Genetics
https://www.readbyqxmd.com/read/28504723/cx3cr1-monocytes-modulate-learning-and-learning-dependent-dendritic-spine-remodeling-via-tnf-%C3%AE
#10
Juan Mauricio Garré, Hernandez Moura Silva, Juan J Lafaille, Guang Yang
Impaired learning and cognitive function often occurs during systemic infection or inflammation. Although activation of the innate immune system has been linked to the behavioral and cognitive effects that are associated with infection, the underlying mechanisms remain poorly understood. Here we mimicked viral immune activation with poly(I:C), a synthetic analog of double-stranded RNA, and longitudinally imaged postsynaptic dendritic spines of layer V pyramidal neurons in the mouse primary motor cortex using two-photon microscopy...
May 15, 2017: Nature Medicine
https://www.readbyqxmd.com/read/28501104/knockdown-of-cbp-p300-interacting-transactivator-with-glu-asp-rich-carboxy-terminal-domain-2-inhibits-cell-division-and-increases-apoptosis-in-gastric-cancer
#11
Ze Tang, Gan He, Jie Xu, Li Zhongfu
BACKGROUND: Cbp/P300-interacting transactivator with Glu/Asp-rich carboxy-terminal domain 2 (CITED2) is a pleiotropic protein associated with numerous cell functions, including transcription and differentiation. The role of CITED2 has been investigated in a number of malignancies; however, the roles of this protein in gastric cancers remain unclear. Therefore, we determined the role of CITED2 in gastric cancers. MATERIALS AND METHODS: Gastric cancer cell lines (MKN74, MKN28, 7901, and AGS) were used to assess CITED2 transcript levels...
May 1, 2017: Journal of Surgical Research
https://www.readbyqxmd.com/read/28496150/long-non-coding-rna-particle-bridges-histone-and-dna-methylation
#12
Valerie Bríd O'Leary, Sarah Hain, Doris Maugg, Jan Smida, Omid Azimzadeh, Soile Tapio, Saak Victor Ovsepian, Michael John Atkinson
PARTICLE (Gene PARTICL- 'Promoter of MAT2A-Antisense RadiaTion Induced Circulating LncRNA) expression is transiently elevated following low dose irradiation typically encountered in the workplace and from natural sources. This long non-coding RNA recruits epigenetic silencers for cis-acting repression of its neighbouring Methionine adenosyltransferase 2A gene. It now emerges that PARTICLE operates as a trans-acting mediator of DNA and histone lysine methylation. Chromatin immunoprecipitation sequencing (ChIP-seq) and immunological evidence established elevated PARTICLE expression linked to increased histone 3 lysine 27 trimethylation...
May 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28494275/synthetic-biological-approaches-for-rna-labelling-and-imaging-design-principles-and-future-opportunities
#13
REVIEW
Steven Pauff, Jamie M Withers, Iain Jw McKean, Simon P Mackay, Glenn A Burley
RNA is the most mercurial of all biomacromolecules. In contrast to DNA, where the predominant role is the storage of genetic information, the biological role of RNA varies; ranging from a template-based intermediary in gene expression to playing a direct role in catalysis. Their high turnover and metabolic lability makes the detection of specific sequences particularly challenging. This review describes the latest synthetic biological developments that enable the direct imaging of RNA both in vitro and in their native cellular environment...
May 8, 2017: Current Opinion in Biotechnology
https://www.readbyqxmd.com/read/28484218/a-molecular-beacon-based-approach-for-live-cell-imaging-of-rna-transcripts-with-minimal-target-engineering-at-the-single-molecule-level
#14
Mingming Chen, Zhao Ma, Xiaotian Wu, Shiqi Mao, Yantao Yang, Jie Tan, Christopher J Krueger, Antony K Chen
Analysis of RNA dynamics and localization at the single-molecule level in living cells has been predominantly achieved by engineering target RNAs with large insertions of tandem repeat sequences that are bound by protein-based or oligonucleotide-based fluorescent probes. Thus, individual RNAs are tagged by multiple fluorescent probes, making them detectable by fluorescence microscopy. Since large insertions may affect RNA processes including trafficking and localization, here we present a strategy to visualize single RNA transcripts in living cells using molecular beacons (MBs) - fluorogenic oligonucleotide probes - with minimal target engineering...
May 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28484023/coronavirus-nonstructural-protein-15-mediates-evasion-of-dsrna-sensors-and-limits-apoptosis-in-macrophages
#15
Xufang Deng, Matthew Hackbart, Robert C Mettelman, Amornrat O'Brien, Anna M Mielech, Guanghui Yi, C Cheng Kao, Susan C Baker
Coronaviruses are positive-sense RNA viruses that generate double-stranded RNA (dsRNA) intermediates during replication, yet evade detection by host innate immune sensors. Here we report that coronavirus nonstructural protein 15 (nsp15), an endoribonuclease, is required for evasion of dsRNA sensors. We evaluated two independent nsp15 mutant mouse coronaviruses, designated N15m1 and N15m3, and found that these viruses replicated poorly and induced rapid cell death in mouse bone marrow-derived macrophages. Infection of macrophages with N15m1, which expresses an unstable nsp15, or N15m3, which expresses a catalysis-deficient nsp15, activated MDA5, PKR, and the OAS/RNase L system, resulting in an early, robust induction of type I IFN, PKR-mediated apoptosis, and RNA degradation...
May 8, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28483922/quantitative-micro-spectroscopic-imaging-reveals-viral-and-cellular-rna-helicase-interactions-in-live-cells
#16
M J Corby, Michael R Stoneman, Gabriel Biener, Joel D Paprocki, Rajesh Kolli, Valerica Raicu, David N Frick
Human cells detect RNA viruses through a set of helicases called RIG-I like receptors (RLRs) that initiate the interferon response via a mitochondrial signaling complex. Many RNA viruses also encode helicases, which sometimes are covalently linked to proteases that cleave signaling proteins. One unresolved question is how RLRs interact with each other and with viral proteins in cells. This study examined the interactions among the hepatitis C virus (HCV) helicase and RLR helicases in live cells with quantitative micro-spectroscopic imaging (Q-MSI), a technique that determines Forster Resonance Energy Transfer (FRET) efficiency and sub-cellular donor and acceptor concentrations...
May 8, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28480997/nucleic-acid-templated-reactions-for-chemical-biology
#17
Margherita Di Pisa, Oliver Seitz
Nucleic acid directed bioorthogonal reactions offer the fascinating opportunity to potentially unveil and redirect a plethora of intracellular mechanisms. Nano- to picomolar amounts of specific RNA molecules serve as templates and catalyze the selective formation of molecules that i) exert biological effects or ii) provide measurable signals for RNA detection. Turnover of reactants on the template is a valuable asset when concentrations of RNA templates are low. The idea is to use RNA templated reactions to fully control biodistribution of drugs as well as pushing the detection limits of DNA or RNA analytes to extraordinary sensitivities...
May 8, 2017: ChemMedChem
https://www.readbyqxmd.com/read/28479380/crispr-groundbreaking-technology-for-rna-guided-genome-engineering
#18
EDITORIAL
Le Cong
Years of advances in high-throughput biotechnologies exemplified by nucleic acid sequencing and single-molecular imaging have led to our increasing capacity to interrogate genomes down to nucleotide accuracy with single-cell or even subcellular resolution, thereby gaining high-dimensional information on the genetic variants and epigenetic states associated with physiological and pathological processes. To achieve a causal understanding the exquisite biology encoded in our genome, researchers in the past decades have sought to develop companion genome engineering tools...
May 4, 2017: Analytical Biochemistry
https://www.readbyqxmd.com/read/28476570/expression-signatures-of-long-non-coding-rna-in-the-substantia-nigra-of-pre-symptomatic-mouse-model-of-parkinson-s-disease
#19
Fengjuan Jiao, Qingzhi Wang, Pei Zhang, Lulu Bu, Jianguo Yan, Bo Tian
Parkinson's disease (PD) is an age-dependent neurodegenerative disease that can be caused by a variety of factors. Growing evidence shows that prior to the motor phase of PD can express molecular or imaging markers. Many long non-coding RNAs (lncRNAs) have been identified in neurodegenerative disease. However, the biogenesis and function of lncRNAs in the pre-symptomatic stage of PD is poorly understood. Here, we profiled the expression of lncRNAs and mRNAs in the substantia nigra pars compacta (SNpc) of pre-symptomatic mice over-expressing human A30P*A53T α-synuclein by microarray analysis...
May 2, 2017: Behavioural Brain Research
https://www.readbyqxmd.com/read/28475895/slert-regulates-ddx21-rings-associated-with-pol-i-transcription
#20
Yu-Hang Xing, Run-Wen Yao, Yang Zhang, Chun-Jie Guo, Shan Jiang, Guang Xu, Rui Dong, Li Yang, Ling-Ling Chen
Dysregulated rRNA synthesis by RNA polymerase I (Pol I) is associated with uncontrolled cell proliferation. Here, we report a box H/ACA small nucleolar RNA (snoRNA)-ended long noncoding RNA (lncRNA) that enhances pre-rRNA transcription (SLERT). SLERT requires box H/ACA snoRNAs at both ends for its biogenesis and translocation to the nucleolus. Deletion of SLERT impairs pre-rRNA transcription and rRNA production, leading to decreased tumorigenesis. Mechanistically, SLERT interacts with DEAD-box RNA helicase DDX21 via a 143-nt non-snoRNA sequence...
May 4, 2017: Cell
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