keyword
MENU ▼
Read by QxMD icon Read
search

RNA Imaging

keyword
https://www.readbyqxmd.com/read/28731408/defining-the-biological-basis-of-radiomic-phenotypes-in-lung-cancer
#1
Patrick Grossmann, Olya Stringfield, Nehme El-Hachem, Marilyn M Bui, Emmanuel Rios Velazquez, Chintan Parmar, Ralph Th Leijenaar, Benjamin Haibe-Kains, Philippe Lambin, Robert Gillies, Hugo Jwl Aerts
Medical imaging can visualize characteristics of human cancer noninvasively. Radiomics is an emerging field that translates these medical images into quantitative data to enable phenotypic profiling of tumors. While radiomics has been associated with several clinical endpoints, the complex relationships of radiomics, clinical factors, and tumor biology are largely unknown. To this end, we analyzed two independent cohorts of respectively 262 North American and 89 European patients with lung cancer, and consistently identified previously undescribed associations between radiomic imaging features, molecular pathways, and clinical factors...
July 21, 2017: ELife
https://www.readbyqxmd.com/read/28730478/high-content-imaging-and-rnai-screens-for-investigating-kinase-network-plasticity
#2
Simon R Stockwell, Sibylle Mittnacht
High-content imaging connects the information-rich method of microscopy with the systematic objective principles of software-driven analysis. Suited to automation and, therefore, considerable scale-up of study size, this approach can deliver multiparametric data over cell populations or at the level of the individual cell and has found considerable utility in reverse genetic and pharmacological screens. Here we present a method to screen small interfering RNA (siRNA) libraries allowing subsequent observation of the impact of each knockdown on two interlinked, high-content, G1-/S-phase cell cycle transition assays related to cyclin-dependent kinase (CDK) 2 activity...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28730451/using-planar-phi29-prna-three-way-junction-to-control-size-and-shape-of-rna-nanoparticles-for-biodistribution-profiling-in-mice
#3
Farzin Haque, Congcong Xu, Daniel L Jasinski, Hui Li, Peixuan Guo
RNA is rapidly emerging as a versatile building block for nanoparticle assembly due to its simplicity in base pairing, while exhibiting diversity in function such as enzymatic activity similar to some proteins. Recent advances in RNA nanotechnology have generated significant interests in applying RNA nanoparticles for various applications in nanotechnology and nanomedicine. In particular, assessing the effect of size and shape on cell entry and intracellular trafficking as well as in vivo biodistribution of nanoparticles is challenging due to the lack of nanoparticles rich in structure while varying in size and shape...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28730438/x-aptamer-selection-and-validation
#4
Ganesh L Lokesh, Hongyu Wang, Curtis H Lam, Varatharasa Thiviyanathan, Nancy Ward, David G Gorenstein, David E Volk
Aptamers and second generation analogs, such as X-Aptamers (XAs), SOMAmers, locked nucleic acids (LNAs), and others are increasingly being used for molecular pathway targeting, biomarker discovery, or disease diagnosis by interacting with protein targets on the surface of cells or in solution. Such targeting is being used for imaging, diagnostic evaluation, interference of protein function, or delivery of therapeutic agents. Selection of aptamers using the original SELEX method is cumbersome and time-consuming, often requiring 10-15 rounds of selection, and provides aptamers with a limited number of functional groups, namely four bases of DNA or RNA, although newer SELEX methods have increased this diversity...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28728963/structural-principles-of-fluorescent-rna-aptamers
#5
REVIEW
Robert J Trachman, Lynda Truong, Adrian R Ferré-D'Amaré
Several aptamer RNAs have been selected in vitro that bind to otherwise weakly fluorescent small molecules and enhance their fluorescence several thousand-fold. By genetically tagging cellular RNAs of interest with these aptamers and soaking cells in their cell-permeable cognate small-molecule fluorophores, it is possible to use them to study RNA localization and trafficking. These aptamers have also been fused to metabolite-binding RNAs to generate fluorescent biosensors. The 3D structures of three unrelated fluorogenic RNAs have been determined, and reveal a shared reliance on base quadruples (tetrads) to constrain the photo-excited chromophore...
July 17, 2017: Trends in Pharmacological Sciences
https://www.readbyqxmd.com/read/28727543/non-small-cell-lung-cancer-radiogenomics-map-identifies-relationships-between-molecular-and-imaging-phenotypes-with-prognostic-implications
#6
Mu Zhou, Ann Leung, Sebastian Echegaray, Andrew Gentles, Joseph B Shrager, Kristin C Jensen, Gerald J Berry, Sylvia K Plevritis, Daniel L Rubin, Sandy Napel, Olivier Gevaert
Purpose To create a radiogenomic map linking computed tomographic (CT) image features and gene expression profiles generated by RNA sequencing for patients with non-small cell lung cancer (NSCLC). Materials and Methods A cohort of 113 patients with NSCLC diagnosed between April 2008 and September 2014 who had preoperative CT data and tumor tissue available was studied. For each tumor, a thoracic radiologist recorded 87 semantic image features, selected to reflect radiologic characteristics of nodule shape, margin, texture, tumor environment, and overall lung characteristics...
July 20, 2017: Radiology
https://www.readbyqxmd.com/read/28724529/coactivators-and-general-transcription-factors-have-two-distinct-dynamic-populations-dependent-on%C3%A2-transcription
#7
Nikolaos Vosnakis, Marc Koch, Elisabeth Scheer, Pascal Kessler, Yves Mély, Pascal Didier, László Tora
SAGA and ATAC are two distinct chromatin modifying co-activator complexes with distinct enzymatic activities involved in RNA polymerase II (Pol II) transcription regulation. To investigate the mobility of co-activator complexes and general transcription factors in live-cell nuclei, we performed imaging experiments based on photobleaching. SAGA and ATAC, but also two general transcription factors (TFIID and TFIIB), were highly dynamic, exhibiting mainly transient associations with chromatin, contrary to Pol II, which formed more stable chromatin interactions...
July 19, 2017: EMBO Journal
https://www.readbyqxmd.com/read/28724075/a-comprehensive-image-based-phenomic-analysis-reveals-the-complex-genetic-architecture-of-shoot-growth-dynamics-in-rice-oryza-sativa
#8
Malachy T Campbell, Qian Du, Kan Liu, Chris J Brien, Bettina Berger, Chi Zhang, Harkamal Walia
Early vigor is an important trait for many rice ( L.)-growing environments. However, genetic characterization and improvement for early vigor is hindered by the temporal nature of the trait and strong genotype × environment effects. We explored the genetic architecture of shoot growth dynamics during the early and active tillering stages by applying a functional modeling and genomewide association (GWAS) mapping approach on a diversity panel of ∼360 rice accessions. Multiple loci with small effects on shoot growth trajectory were identified, indicating a complex polygenic architecture...
July 2017: Plant Genome
https://www.readbyqxmd.com/read/28714696/genetically-encoded-fluorescent-rna-sensor-for-ratiometric-imag-ing-of-microrna-in-living-tumor-cells
#9
Zhan-Ming Ying, Zhan Wu, Bin Tu, Weihong Tan, Jian-Hui Jiang
Light-up RNA aptamers are valuable tools for fluorescence imaging of RNA in living cells and thus for elucidating RNA functions and dynamics. However, no light-up RNA sensor has been reported for imaging of microRNAs (miRs) in mammalian cells. We herein report a novel genetically-encoded RNA sensor for fluorescent imaging of miRs in liv-ing tumor cells using a light-up RNA aptamer which binds to sulforhodamine and separates it from a conjugated contact quencher. Based on the structural switching mechanism characteristic for molecular beacon, we show that the RNA sensor activates high-contrast fluorescence from the sulfor-hodamine-quencher conjugate when its stem-loop respon-sive motif hybridizes with target miR...
July 17, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28712653/neural-circuit-specialized-astrocytes-transcriptomic-proteomic-morphological-and-functional-evidence
#10
Hua Chai, Blanca Diaz-Castro, Eiji Shigetomi, Emma Monte, J Christopher Octeau, Xinzhu Yu, Whitaker Cohn, Pradeep S Rajendran, Thomas M Vondriska, Julian P Whitelegge, Giovanni Coppola, Baljit S Khakh
Astrocytes are ubiquitous in the brain and are widely held to be largely identical. However, this view has not been fully tested, and the possibility that astrocytes are neural circuit specialized remains largely unexplored. Here, we used multiple integrated approaches, including RNA sequencing (RNA-seq), mass spectrometry, electrophysiology, immunohistochemistry, serial block-face-scanning electron microscopy, morphological reconstructions, pharmacogenetics, and diffusible dye, calcium, and glutamate imaging, to directly compare adult striatal and hippocampal astrocytes under identical conditions...
July 11, 2017: Neuron
https://www.readbyqxmd.com/read/28705612/cardiac-mitochondrial-dynamics-mir-mediated-regulation-during-cardiac-injury
#11
Anusha Sivakumar, Ramasamy Subbiah, Rekha Balakrishnan, Jeyaprakash Rajendhran
Mitochondrial integrity is indispensable for cardiac health. With the advent of modern imaging technologies, mitochondrial motility and dynamics within the cell are extensively studied. Terminally differentiated and well-structured cardiomyocytes depict little mitochondrial division and fusion, questioning the contribution of mitochondrial fusion proteins (Mitofusin 1/2 and Optic Atrophy 1 protein) and fission factors (Dynamin-like protein 1 and mitochondrial fission 1 protein) in cardiomyocyte homeostasis...
July 10, 2017: Journal of Molecular and Cellular Cardiology
https://www.readbyqxmd.com/read/28698494/fluorogenic-labeling-strategies-for-biological-imaging
#12
REVIEW
Chenge Li, Alison G Tebo, Arnaud Gautier
The spatiotemporal fluorescence imaging of biological processes requires effective tools to label intracellular biomolecules in living systems. This review presents a brief overview of recent labeling strategies that permits one to make protein and RNA strongly fluorescent using synthetic fluorogenic probes. Genetically encoded tags selectively binding the exogenously applied molecules ensure high labeling selectivity, while high imaging contrast is achieved using fluorogenic chromophores that are fluorescent only when bound to their cognate tag, and are otherwise dark...
July 9, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28696509/an-l-rna-aptamer-with-expanded-chemical-functionality-that-inhibits-microrna-biogenesis
#13
Adam Michael Kabza, Jonathan Thomas Sczepanski
In order to facilitate isolation of L-aptamers with novel RNA-binding properties, we have employed a cationic nucleotide, 5-aminoallyl-uridine, during the mirror image in vitro selection process. In this effort, we identified a modified L-RNA aptamer (MLRA) capable of binding oncogenic pre-miR-19a with exceptional affinity, and we show that the cationic modification is absolutely critical for binding. Furthermore, formation of the MLRA-pre-miR-19a complex inhibits Dicer-mediated cleavage of the pre-miR, thus blocking formation of the mature functional microRNA...
July 11, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/28696436/reduced-trpc6-mrna-levels-in-the-blood-cells-of-patients-with-alzheimer-s-disease-and-mild-cognitive-impairment
#14
R Lu, J Wang, R Tao, J Wang, T Zhu, W Guo, Y Sun, H Li, Y Gao, W Zhang, C J Fowler, Q Li, S Chen, Z Wu, C L Masters, C Zhong, N Jing, Y Wang, Y Wang
Transient receptor potential canonical 6 (TRPC6) inhibits β-amyloid (Aβ) production. Hyperforin, the TRPC6 agonist, reduces Aβ levels and improves cognitive performance in Alzheimer's disease (AD) models. However, it's unknown whether TRPC6 expression is changed in AD patients. In this case-control study, we measured TRPC6 expression levels in the peripheral blood cells of four independent AD sets from five hospitals and one mild cognitive impairment (MCI) set from a local community (229 AD, 70 MCI, 40 Parkinson disease and 359 controls from China, total n=698) using quantitative real-time PCR assay...
July 11, 2017: Molecular Psychiatry
https://www.readbyqxmd.com/read/28694064/rna-fluorescence-in-situ-hybridization-for-high-content-screening
#15
Emmanuelle Querido, Lynda Dekakra-Bellili, Pascal Chartrand
Single molecule RNA imaging using fluorescent in situ hybridization (FISH) can provide quantitative information on mRNA abundance and localization in a single cell. There is now a growing interest in screening for modifiers of RNA abundance and/or localization. For instance, microsatellite expansion within RNA can lead to toxic gain-of-function via mislocalization of these transcripts into RNA aggregate and sequestration of RNA-binding proteins. Screening for inhibitors of these RNA aggregate can be performed by high-throughput RNA FISH...
July 7, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28690601/illuminating-messengers-an-update-and-outlook-on-rna-visualization-in-bacteria
#16
REVIEW
Lieke A van Gijtenbeek, Jan Kok
To be able to visualize the abundance and spatiotemporal features of RNAs in bacterial cells would permit obtaining a pivotal understanding of many mechanisms underlying bacterial cell biology. The first methods that allowed observing single mRNA molecules in individual cells were introduced by Bertrand et al. (1998) and Femino et al. (1998). Since then, a plethora of techniques to image RNA molecules with the aid of fluorescence microscopy has emerged. Many of these approaches are useful for the large eukaryotic cells but their adaptation to study RNA, specifically mRNA molecules, in bacterial cells progressed relatively slow...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28687335/a-genome-wide-transcriptomic-analysis-of-articular-cartilage-during-normal-maturation-in-pigs
#17
Naga Suresh Adapala, Harry K W Kim
OBJECTIVE: The articular cartilage undergoes dramatic changes in structure and composition during post-natal maturation, but the associated transcriptional changes are not well characterized. Compared to a mature stage, the immature articular cartilage shows developmental features such as increased thickness, presence of blood vessels, and the presence of a deep layer of growth cartilage which undergoes endochondral ossification. These features decrease during normal development. Following maturation, the articular cartilage is known to undergo few minor modifications...
July 4, 2017: Gene
https://www.readbyqxmd.com/read/28687070/massively-parallel-nanowell-based-single-cell-gene-expression-profiling
#18
Leonard D Goldstein, Ying-Jiun Jasmine Chen, Jude Dunne, Alain Mir, Hermann Hubschle, Joseph Guillory, Wenlin Yuan, Jingli Zhang, Jeremy Stinson, Bijay Jaiswal, Kanika Bajaj Pahuja, Ishminder Mann, Thomas Schaal, Leo Chan, Sangeetha Anandakrishnan, Chun-Wah Lin, Patricio Espinoza, Syed Husain, Harris Shapiro, Karthikeyan Swaminathan, Sherry Wei, Maithreyan Srinivasan, Somasekar Seshagiri, Zora Modrusan
BACKGROUND: Technological advances have enabled transcriptome characterization of cell types at the single-cell level providing new biological insights. New methods that enable simple yet high-throughput single-cell expression profiling are highly desirable. RESULTS: Here we report a novel nanowell-based single-cell RNA sequencing system, ICELL8, which enables processing of thousands of cells per sample. The system employs a 5,184-nanowell-containing microchip to capture ~1,300 single cells and process them...
July 7, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28685184/morphological-and-molecular-characterisation-of-aporocotyle-margolisi-smith-1967-digenea-aporocotylidae-from-the-north-pacific-hake-merluccius-productus-ayres-gadiformes-merlucciidae-off-oregon-usa
#19
Jesus S Hernández-Orts, David I Hernández-Mena, Gema Alama-Bermejo, Roman Kuchta, Kym C Jacobson
Aporocotylid blood flukes conspecific with Aporocotyle margolisi Smith, 1967 were collected from the bulbus arteriosus of the North Pacific hake Merluccius productus (Ayres). This study revisits the morphology of A. margolisi, including drawings, measurements and scanning electron microscopy images, and provides for the first time molecular data for the large subunit of the ribosomal RNA (28S rDNA) and the mitochondrial cytochrome c oxidase subunit 1 (cox1) genes for this species. A 28S rDNA phylogenetic study of A...
July 6, 2017: Systematic Parasitology
https://www.readbyqxmd.com/read/28682593/selective-and-high-dynamic-range-assay-format-for-multiplex-detection-of-pathogenic-pseudomonas-aeruginosa-salmonella-typhimurium-and-legionella-pneumophila-rnas-using-surface-plasmon-resonance-imaging
#20
F Melaine, M Saad, S Faucher, M Tabrizian
Due to its well-characterized and highly conserved structure, as well as its relative abundance in metabolically active cells, bacterial 16S rRNA sequence plays an important role in microbial identification. In this work, a biosensing strategy has been developed for simultaneous detection of 16S rRNA analytes of three pathogenic bacterial strains: Legionella pneumophila, Pseudomonas aeruginosa, and Salmonella typhimurium. Surface plasmon resonance imaging (SPRi) was used as a detection technique coupled with DNA probe sandwich assemblies and gold nanoparticles (GNPs) for signal amplification...
July 18, 2017: Analytical Chemistry
keyword
keyword
40843
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"