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RNA Imaging

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https://www.readbyqxmd.com/read/29353086/ruthenium-dendrimers-as-carriers-for-anticancer-sirna
#1
Sylwia Michlewska, Maksim Ionov, Marta Maroto-Díaz, Aleksandra Szwed, Aliaksei Ihnatsyeu-Kachan, Svetlana Loznikova, Dzmitry Shcharbin, Marek Maly, Rafael Gomez Ramirez, Francisco Javier de la Mata, Maria Bryszewska
Dendrimers, which are considered as one of the most promising tools in the field of nanobiotechnology due to their structural organization, showed a great potential in gene therapy, drug delivery, medical imaging and as antimicrobial and antiviral agents. This article is devoted to study interactions between new carbosilane-based metallodendrimers containing ruthenium and anti-cancer small interfering RNA (siRNA). Formation of complexes between anti-cancer siRNAs and Ru-based carbosilane dendrimers was evaluated by transmission electron microscopy, circular dichroism and fluorescence...
January 12, 2018: Journal of Inorganic Biochemistry
https://www.readbyqxmd.com/read/29348171/a-cationic-c-terminal-patch-and-structural-rearrangements-in-ebola-virus-matrix-vp40-protein-control-its-interactions-with-phosphatidylserine
#2
Kathryn Del Vecchio, Cary T Frick, Jeevan B Gc, Shun-Ichiro Oda, Bernard S Gerstman, Erica Ollmann Saphire, Prem P Chapagain, Robert V Stahelin
Ebola virus (EBOV) is a filamentous lipid-enveloped virus that causes hemorrhagic fever with a high fatality rate. Viral protein 40 (VP40) is the major EBOV matrix protein and regulates viral budding from the plasma membrane. VP40 is a transformer/morpheein that can structurally rearrange its native homodimer into either a hexameric filament that facilitates viral budding or a RNA-binding octameric ring that regulates viral transcription. VP40 associates with plasma-membrane lipids such as phosphatidylserine (PS), and this association is critical to budding from the host cell...
January 18, 2018: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29346759/nf-%C3%AE%C2%BAb-chromatin-interactions-drive-diverse-phenotypes-by-modulating-transcriptional-noise
#3
Victor C Wong, Victor L Bass, M Elise Bullock, Arvind K Chavali, Robin E C Lee, Walther Mothes, Suzanne Gaudet, Kathryn Miller-Jensen
Noisy gene expression generates diverse phenotypes, but little is known about mechanisms that modulate noise. Combining experiments and modeling, we studied how tumor necrosis factor (TNF) initiates noisy expression of latent HIV via the transcription factor nuclear factor κB (NF-κB) and how the HIV genomic integration site modulates noise to generate divergent (low-versus-high) phenotypes of viral activation. We show that TNF-induced transcriptional noise varies more than mean transcript number and that amplification of this noise explains low-versus-high viral activation...
January 16, 2018: Cell Reports
https://www.readbyqxmd.com/read/29345990/imaging-mrna-in-vivo-from-birth-to-death
#4
Evelina Tutucci, Nathan M Livingston, Robert H Singer, Bin Wu
RNA is the fundamental information transfer system in the cell. The ability to follow single messenger RNAs (mRNAs) from transcription to degradation with fluorescent probes gives quantitative information about how the information is transferred fromDNAto proteins. This review focuses on the latest technological developments in the field of single-mRNA detection and their usage to study gene expression in both fixed and live cells. By describing the application of these imaging tools, we follow the journey of mRNA from transcription to decay in single cells, with single-molecule resolution...
January 18, 2018: Annual Review of Biophysics
https://www.readbyqxmd.com/read/29342213/circulating-neutrophil-transcriptome-may-reveal-intracranial-aneurysm-signature
#5
Vincent M Tutino, Kerry E Poppenberg, Kaiyu Jiang, James N Jarvis, Yijun Sun, Ashish Sonig, Adnan H Siddiqui, Kenneth V Snyder, Elad I Levy, John Kolega, Hui Meng
BACKGROUND: Unruptured intracranial aneurysms (IAs) are typically asymptomatic and undetected except for incidental discovery on imaging. Blood-based diagnostic biomarkers could lead to improvements in IA management. This exploratory study examined circulating neutrophils to determine whether they carry RNA expression signatures of IAs. METHODS: Blood samples were collected from patients receiving cerebral angiography. Eleven samples were collected from patients with IAs and 11 from patients without IAs as controls...
2018: PloS One
https://www.readbyqxmd.com/read/29338709/wormachine-machine-learning-based-phenotypic-analysis-tool-for-worms
#6
Adam Hakim, Yael Mor, Itai Antoine Toker, Amir Levine, Moran Neuhof, Yishai Markovitz, Oded Rechavi
BACKGROUND: Caenorhabditis elegans nematodes are powerful model organisms, yet quantification of visible phenotypes is still often labor-intensive, biased, and error-prone. We developed WorMachine, a three-step MATLAB-based image analysis software that allows (1) automated identification of C. elegans worms, (2) extraction of morphological features and quantification of fluorescent signals, and (3) machine learning techniques for high-level analysis. RESULTS: We examined the power of WorMachine using five separate representative assays: supervised classification of binary-sex phenotype, scoring continuous-sexual phenotypes, quantifying the effects of two different RNA interference treatments, and measuring intracellular protein aggregation...
January 16, 2018: BMC Biology
https://www.readbyqxmd.com/read/29338703/diagnostic-accuracy-and-prediction-increment-of-markers-of-epithelial-mesenchymal-transition-to-assess-cancer-cell-detachment-from-primary-tumors
#7
Evan L Busch, Prabhani Kuruppumullage Don, Haitao Chu, David B Richardson, Temitope O Keku, David A Eberhard, Christy L Avery, Robert S Sandler
BACKGROUND: Metastases play a role in about 90% of cancer deaths. Markers of epithelial-mesenchymal transition (EMT) measured in primary tumor cancer cells might provide diagnostic information about the likelihood that cancer cells have detached from the primary tumor. Used together with established diagnostic tests of detachment-lymph node evaluation and radiologic imaging-EMT marker measurements might improve the ability of clinicians to assess the patient's risk of metastatic disease...
January 16, 2018: BMC Cancer
https://www.readbyqxmd.com/read/29335794/effect-of-a-calcitonin-gene-related-peptide-binding-l-rna-aptamer-on-neuronal-activity-in-the-rat-spinal-trigeminal-nucleus
#8
Michael J M Fischer, Jakob Schmidt, Stanislav Koulchitsky, Sven Klussmann, Axel Vater, Karl Messlinger
BACKGROUND: Calcitonin gene-related peptide (CGRP) plays a major role in the pathogenesis of migraine and other primary headaches. Spinal trigeminal neurons integrate nociceptive afferent input from trigeminal tissues including intracranial afferents, and their activity is thought to reflect facial pain and headache in man. CGRP receptor inhibitors and anti-CGRP antibodies have been demonstrated to be therapeutically effective in migraine. In parallel, CGRP receptor inhibition has been shown to lower spinal trigeminal neuron activity in animal models of meningeal nociception...
January 15, 2018: Journal of Headache and Pain
https://www.readbyqxmd.com/read/29334988/epidermal-wnt-signalling-regulates-transcriptome-heterogeneity-and-proliferative-fate-in-neighbouring-cells
#9
Arsham Ghahramani, Giacomo Donati, Nicholas M Luscombe, Fiona M Watt
BACKGROUND: Canonical Wnt/beta-catenin signalling regulates self-renewal and lineage selection within the mammalian epidermis. Although the transcriptional response of keratinocytes that receive a Wnt signal is well characterized, little is known about the mechanism by which keratinocytes in proximity to the Wnt-receiving cell are co-opted to undergo a change in cell fate. RESULTS: To address this, we perform single-cell RNA-sequencing on mouse keratinocytes co-cultured with and without beta-catenin-activated neighbouring cells...
January 15, 2018: Genome Biology
https://www.readbyqxmd.com/read/29333465/in-vivo-exposure-effects-of-99mtc-methoxyisobutylisonitrile-on-the-fdxr-and-xpa-genes-expression-in-human-peripheral-blood-lymphocytes
#10
Mohammad Taghi Bahreyni-Toossi, Habibeh Vosoughi, Hosein Azimian, Abdul Rahim Rezaei, Mehdi Momennezhad
Objectives: In recent years, the application of radiopharmaceuticals in nuclear medicine has increased substantially. Following the diagnostic procedures performed in nuclear medicine departments, such as myocardial perfusion imaging, patients generally receive considerable doses of radiation. Normally, radiation-induced DNA damages are expected following exposure to a low-dose ionizing radiation. In order to detect molecular changes, high-sensitivity techniques must be utilized. The aim of this study was to assess the effect of a low-dose (below 10 mSv) gamma ray on gene expression using quantitative real-time polymerase chain reaction (qRT-PCR)...
2018: Asia Oceania Journal of Nuclear Medicine & Biology
https://www.readbyqxmd.com/read/29331264/altered-levels-of-the-splicing-factor-muscleblind-modifies-cerebral-cortical-function-in-mouse-models-of-myotonic-dystrophy
#11
Gang Chen, Russell E Carter, John D Cleary, Tammy S Reid, Laura P Ranum, Maurice S Swanson, Timothy J Ebner
Myotonic dystrophy (DM) is a progressive, multisystem disorder affecting skeletal muscle, heart, and central nervous system. In both DM1 and DM2, microsatellite expansions of CUG and CCUG RNA repeats, respectively, accumulate and disrupt functions of alternative splicing factors, including muscleblind (MBNL) proteins. Grey matter loss and white matter changes, including the corpus callosum, likely underlie cognitive and executive function deficits in DM patients. However, little is known how cerebral cortical circuitry changes in DM...
January 10, 2018: Neurobiology of Disease
https://www.readbyqxmd.com/read/29323386/highly-robust-uniform-and-ultra-sensitive-surface-enhanced-raman-scattering-substrates-for-microrna-detection-fabricated-by-using-silver-nanostructures-grown-in-gold-nanobowls
#12
Taeksu Lee, Jung-Sub Wi, Aram Oh, Hee-Kyung Na, JaeJong Lee, Kwangyeol Lee, Tae Geol Lee, Seungjoo Haam
Highly sensitive and reproducible surface enhanced Raman spectroscopy (SERS) requires not only a nanometer-level structural control, but also superb uniformity across the SERS substrate for practical imaging and sensing applications. However, in the past, increased reproducibility of the SERS signal was incompatible with increased SERS sensitivity. This work presents multiple silver nanocrystals inside periodically arrayed gold nanobowls (SGBs) via an electrochemical reaction at an overpotential of -3.0 V (vs...
January 11, 2018: Nanoscale
https://www.readbyqxmd.com/read/29323101/actin-filament-associated-protein-1-like-1-mediates-proliferation-and-survival-in-non-small-cell-lung-cancer-cells
#13
Meng Wang, Xingpeng Han, Wei Sun, Xin Li, Guohui Jing, Xun Zhang
BACKGROUND The actin filament-associated protein (AFAP) family consists of 3 novel adaptor proteins: AFAP1, AFAP1L1, and AFAP1L2/XB130. Although evidence shows that AFAP1 and AFAP1L2 play an oncogenic role, the effect of AFAP1L1 on tumor cell behavior has not been fully elucidated, and it remains unknown whether AFAP1L1 could be a prognostic marker and/or therapeutic target of lung cancer. MATERIAL AND METHODS Human A549 non-small cell lung cancer (NSCLC) cells were used in this study. AFAP1L1 gene was knocked down by AFAP1L1 short hairpin RNA (shRNA) transfection...
January 11, 2018: Medical Science Monitor: International Medical Journal of Experimental and Clinical Research
https://www.readbyqxmd.com/read/29322442/single-molecule-fluorescence-in-situ-hybridization-fish-of-circular-rna-cdr1as
#14
Christine Kocks, Anastasiya Boltengagen, Monika Piwecka, Agnieszka Rybak-Wolf, Nikolaus Rajewsky
Individual mRNA molecules can be imaged in fixed cells by hybridization with multiple, singly labeled oligonucleotide probes, followed by computational identification of fluorescent signals. This approach, called single-molecule RNA fluorescence in situ hybridization (smRNA FISH), allows subcellular localization and absolute quantification of RNA molecules in individual cells. Here, we describe a simple smRNA FISH protocol for two-color imaging of a circular RNA, CDR1as, simultaneously with an unrelated messenger RNA...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29321279/whole-mount-immunofluorescence-for-visualizing-endogenous-protein-and-injected-rna-in-xenopus-oocytes
#15
Samantha P Jeschonek, Kimberly L Mowry
Asymmetric distribution of mRNA and protein is a hallmark of cell polarity in many systems. The Xenopus laevis oocyte provides many technical advantages to studying such polarity. Thousands of oocytes at different stages of maturity can be harvested from a single ovary and, owing to their relatively large size, even the youngest oocytes can be manually microinjected. Microinjection of fluorescently labeled RNA combined with immunofluorescence of endogenous proteins can provide insight into the cytoplasmic interactions contributing to polarity...
January 10, 2018: Cold Spring Harbor Protocols
https://www.readbyqxmd.com/read/29321003/a-prototypical-non-malignant-epithelial-model-to-study-genome-dynamics-and-concurrently-monitor-micro-rnas-and-proteins-in-situ-during-oncogene-induced-senescence
#16
Eirini-Stavroula Komseli, Ioannis S Pateras, Thorbjørn Krejsgaard, Konrad Stawiski, Sophia V Rizou, Alexander Polyzos, Fani-Marlen Roumelioti, Maria Chiourea, Ioanna Mourkioti, Eleni Paparouna, Christos P Zampetidis, Sentiljana Gumeni, Ioannis P Trougakos, Dafni-Eleftheria Pefani, Eric O'Neill, Sarantis Gagos, Aristides G Eliopoulos, Wojciech Fendler, Dipanjan Chowdhury, Jiri Bartek, Vassilis G Gorgoulis
BACKGROUND: Senescence is a fundamental biological process implicated in various pathologies, including cancer. Regarding carcinogenesis, senescence signifies, at least in its initial phases, an anti-tumor response that needs to be circumvented for cancer to progress. Micro-RNAs, a subclass of regulatory, non-coding RNAs, participate in senescence regulation. At the subcellular level micro-RNAs, similar to proteins, have been shown to traffic between organelles influencing cellular behavior...
January 10, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29319504/automated-cell-type-classification-in-intact-tissues-by-single-cell-molecular-profiling
#17
Monica Nagendran, Daniel P Riordan, Pehr B Harbury, Tushar J Desai
A major challenge in biology is identifying distinct cell classes and mapping their interactions in vivo. Tissue-dissociative technologies enable deep single cell molecular profiling but do not provide spatial information. We developed a proximity ligation- in situ hybridization technology (PLISH) with exceptional signal strength, specificity, and sensitivity in tissue. Multiplexed data sets can be acquired using barcoded probes and rapid label-image-erase cycles, with automated calculation of single cell profiles, enabling clustering and anatomical re-mapping of cells...
January 10, 2018: ELife
https://www.readbyqxmd.com/read/29317592/gut-microbiome-populations-are-associated-with-structure-specific-changes-in-white-matter-architecture
#18
Irene M Ong, Jose G Gonzalez, Sean J McIlwain, Emily A Sawin, Andrew J Schoen, Nagesh Adluru, Andrew L Alexander, John-Paul J Yu
Altered gut microbiome populations are associated with a broad range of neurodevelopmental disorders including autism spectrum disorder and mood disorders. In animal models, modulation of gut microbiome populations via dietary manipulation influences brain function and behavior and has been shown to ameliorate behavioral symptoms. With striking differences in microbiome-driven behavior, we explored whether these behavioral changes are also accompanied by corresponding changes in neural tissue microstructure...
January 10, 2018: Translational Psychiatry
https://www.readbyqxmd.com/read/29314718/new-frontiers-in-rna-transport-and-local-translation-in-neurons
#19
REVIEW
S J Van Driesche, K C Martin
RNA localization to neuronal dendrites and axons is increasingly recognized as a significant and widespread mechanism of gene expression control in neurons. High-throughput RNA sequencing is rapidly expanding the universe of known localized mRNAs. Although there are inherent difficulties in preparing sequencing libraries from dendrites and axons in the context of intact brain, genetic labeling strategies have paved the way for improved studies of this type. As the list of localized mRNAs grows, there is increasing need for functional validation of localized transcripts - that is, do particular localized transcripts serve demonstrable physiologic functions in axons or dendrites? Finally, specific details about what localized mRNAs do once they reach distal processes have long been elusive...
January 5, 2018: Developmental Neurobiology
https://www.readbyqxmd.com/read/29311668/cliq-bid-a-method-to-quantify-bacteria-induced-damage-to-eukaryotic-cells-by-automated-live-imaging-of-bright-nuclei
#20
Yann Wallez, Stéphanie Bouillot, Emmanuelle Soleilhac, Philippe Huber, Ina Attrée, Eric Faudry
Pathogenic bacteria induce eukaryotic cell damage which range from discrete modifications of signalling pathways, to morphological alterations and even to cell death. Accurate quantitative detection of these events is necessary for studying host-pathogen interactions and for developing strategies to protect host organisms from bacterial infections. Investigation of morphological changes is cumbersome and not adapted to high-throughput and kinetics measurements. Here, we describe a simple and cost-effective method based on automated analysis of live cells with stained nuclei, which allows real-time quantification of bacteria-induced eukaryotic cell damage at single-cell resolution...
January 8, 2018: Scientific Reports
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