keyword
MENU ▼
Read by QxMD icon Read
search

RNA Imaging

keyword
https://www.readbyqxmd.com/read/27906860/liquid-biopsy-for-early-detection-of-lung-cancer
#1
Paul Hofman
PURPOSE OF REVIEW: The possibility of complete recovery for a lung cancer patient depends on very early diagnosis, as it allows total surgical resection. Screening for this cancer in a high-risk population can be performed using a radiological approach, but this holds a certain number of limitations. Liquid biopsy could become an alternative and complementary screening approach to chest imaging for early diagnosis of lung cancer. RECENT FINDINGS: Several circulating biomarkers indicative of lung cancer can be investigated in blood, such as circulating tumor cells, circulating free nucleic acids (RNA and DNA) and proteins...
January 2017: Current Opinion in Oncology
https://www.readbyqxmd.com/read/27903772/diverse-activities-of-viral-cis-acting-rna-regulatory-elements-revealed-using-multi-color-long-term-single-cell-imaging
#2
Ginger M Pocock, Laraine L Zimdars, Ming Yuan, Kevin W Eliceiri, Paul Ahlquist, Nathan M Sherer
Cis-acting RNA structural elements govern crucial aspects of viral gene expression. How these structures and other post-transcriptional signals affect RNA trafficking and translation in the context of single cells is poorly understood. Herein we describe a multi-color, long-term (>24 h) imaging strategy for measuring integrated aspects of viral RNA regulatory control in individual cells. We apply this strategy to demonstrate differential mRNA trafficking behaviors governed by RNA elements derived from three retroviruses (HIV-1, murine leukemia virus, and Mason-Pfizer monkey virus), two hepadnaviruses (hepatitis B virus and woodchuck hepatitis virus) and an intron-retaining transcript encoded by the cellular NXF1 gene...
November 30, 2016: Molecular Biology of the Cell
https://www.readbyqxmd.com/read/27902397/vesivirus-2117-capsids-more-closely-resemble-sapovirus-and-lagovirus-particles-than-other-known-vesivirus-structures
#3
Michaela Conley, Edward Emmott, Richard Orton, David Taylor, Daniel Carneiro, Kazuyoshi Murata, Ian Goodfellow, Grant Hansman, David Bhella
Vesivirus 2117 is an adventitious agent that in 2009, was identified as a contaminant of CHO cells propagated in bioreactors at a pharmaceutical manufacturing plant belonging to Genzyme. The consequent interruption in supply of Fabrazyme and Cerezyme (drugs used to treat Fabry and Gaucher disease respectively), caused significant economic losses. Vesivirus 2117 is a member of the Caliciviridae; a family of small icosahedral viruses encoding a positive sense RNA genome. We have used cryo-electron microscopy and three dimensional image reconstruction to calculate a structure of vesivirus 2117 virus like particles as well as feline calicivirus and a chimeric sapovirus...
November 14, 2016: Journal of General Virology
https://www.readbyqxmd.com/read/27901317/dendrimer-stabilized-gold-nanostars-as-a-multifunctional-theranostic-nanoplatform-for-ct-imaging-photothermal-therapy-and-gene-silencing-of-tumors
#4
Ping Wei, Jingwen Chen, Yong Hu, Xin Li, Han Wang, Mingwu Shen, Xiangyang Shi
Development of versatile nanomaterials combining diagnostic and therapeutic functionalities within one single nanoplatform is extremely important for tumor theranostics. In this work, the authors report the synthesis of a gold nanostar (Au NS)-based theranostic platform stabilized with cyclic arginine-glycine-aspartic (Arg-Gly-Asp, RGD) peptide-modified amine-terminated generation 3 poly(amidoamine) dendrimers. The formed RGD-modified dendrimer-stabilized Au NSs (RGD-Au DSNSs) are used as a gene delivery vector to complex small interfering RNA (siRNA) for computed tomography (CT) imaging, thermal imaging, photothermal therapy (PTT), and gene therapy of tumors...
November 30, 2016: Advanced Healthcare Materials
https://www.readbyqxmd.com/read/27899677/the-mouse-gene-expression-database-gxd-2017-update
#5
Jacqueline H Finger, Constance M Smith, Terry F Hayamizu, Ingeborg J McCright, Jingxia Xu, Meiyee Law, David R Shaw, Richard M Baldarelli, Jon S Beal, Olin Blodgett, Jeff W Campbell, Lori E Corbani, Jill R Lewis, Kim L Forthofer, Pete J Frost, Sharon C Giannatto, Lucie N Hutchins, Dave B Miers, Howie Motenko, Kevin R Stone, Janan T Eppig, James A Kadin, Joel E Richardson, Martin Ringwald
The Gene Expression Database (GXD; www.informatics.jax.org/expression.shtml) is an extensive and well-curated community resource of mouse developmental expression information. Through curation of the scientific literature and by collaborations with large-scale expression projects, GXD collects and integrates data from RNA in situ hybridization, immunohistochemistry, RT-PCR, northern blot and western blot experiments. Expression data from both wild-type and mutant mice are included. The expression data are combined with genetic and phenotypic data in Mouse Genome Informatics (MGI) and made readily accessible to many types of database searches...
November 28, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27883889/inferring-cell-state-transition-dynamics-from-lineage-trees-and-endpoint-single-cell-measurements
#6
Sahand Hormoz, Zakary S Singer, James M Linton, Yaron E Antebi, Boris I Shraiman, Michael B Elowitz
As they proliferate, living cells undergo transitions between specific molecularly and developmentally distinct states. Despite the functional centrality of these transitions in multicellular organisms, it has remained challenging to determine which transitions occur and at what rates without perturbations and cell engineering. Here, we introduce kin correlation analysis (KCA) and show that quantitative cell-state transition dynamics can be inferred, without direct observation, from the clustering of cell states on pedigrees (lineage trees)...
November 23, 2016: Cell Systems
https://www.readbyqxmd.com/read/27883258/bivalent-display-of-dicysteine-on-pna-for-homogenous-dna-rna-detection-via-in-situ-fluorescence-labelling
#7
Gemin Fang, Oliver Seitz
Fluorogenic probes that signal the presence of specific DNA or RNA sequences are key enabling tools for molecular disease diagnosis and imaging studies. Usually, at least one fluorophore is attached via covalent bonds to an oligonucleotide probe. However, the additional conjugation step increases costs. Herein we introduce a method that avoids the requirement for the preparation of fluorescence labeled oligonucleotides and provides the opportunity to alter the fluorogenic reporter dye without resynthesis. The method is based on adjacent hybridization of two dicysteine-containing peptide nucleic acid probes to form a bipartite tetracysteine motif which binds profluorescent bisarsenical dyes such as FIAsH, ReAsH or CrAsH...
November 24, 2016: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/27882487/delivery-of-small-interfering-rna-to-inhibit-vascular-endothelial-growth-factor-in-zebrafish-using-natural-brain-endothelia-cell-secreted-exosome-nanovesicles-for-the-treatment-of-brain-cancer
#8
Tianzhi Yang, Brittany Fogarty, Bret LaForge, Salma Aziz, Thuy Pham, Leanne Lai, Shuhua Bai
Although small interfering RNA (siRNA) holds great therapeutic promise, its delivery to the disease site remains a paramount obstacle. In this study, we tested whether brain endothelial cell-derived exosomes could deliver siRNA across the blood-brain barrier (BBB) in zebrafish. Natural exosomes were isolated from brain endothelial bEND.3 cell culture media and vascular endothelial growth factor (VEGF) siRNA was loaded in exosomes with the assistance of a transfection reagent. While fluorescence-activated cell flow cytometry and immunocytochemistry staining studies indicated that wild-type exosomes significantly increased the uptake of fluorescence-labeled siRNA in the autologous brain endothelial cells, decreased fluorescence intensity was observed in the cells treated with the tetraspanin CD63 antibody-blocked exosome-delivered formulation (p < 0...
November 23, 2016: AAPS Journal
https://www.readbyqxmd.com/read/27874027/circulating-long-non-coding-rnas-as-biomarkers-of-left-ventricular-diastolic-function-and-remodelling-in-patients-with-well-controlled-type-2-diabetes
#9
D de Gonzalo-Calvo, F Kenneweg, C Bang, R Toro, R W van der Meer, L J Rijzewijk, J W Smit, H J Lamb, V Llorente-Cortes, T Thum
Contractile dysfunction is underdiagnosed in early stages of diabetic cardiomyopathy. We evaluated the potential of circulating long non-coding RNAs (lncRNAs) as biomarkers of subclinical cardiac abnormalities in type 2 diabetes. Forty-eight men with well-controlled type 2 diabetes and 12 healthy age-matched volunteers were enrolled in the study. Left ventricular (LV) parameters were measured by magnetic resonance imaging. A panel of lncRNAs was quantified in serum by RT-qPCR. No differences in expression levels of lncRNAs were observed between type 2 diabetes patients and healthy volunteers...
November 22, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27873472/perfect-timing-splicing-and-transcription-rates-in-living-cells
#10
REVIEW
Tara Alpert, Lydia Herzel, Karla M Neugebauer
An important step toward understanding gene regulation is the elucidation of the time necessary for the completion of individual steps. Measurement of reaction rates can reveal potential nodes for regulation. For example, measurements of in vivo transcription elongation rates reveal regulation by DNA sequence, gene architecture, and chromatin. Pre-mRNA splicing is regulated by transcription elongation rates and vice versa, yet the rates of RNA processing reactions remain largely elusive. Since the 1980s, numerous model systems and approaches have been used to determine the precise timing of splicing in vivo...
November 21, 2016: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/27873206/discovery-of-rna-binding-small-molecules-using-small-molecule-microarrays
#11
Colleen M Connelly, Fardokht A Abulwerdi, John S Schneekloth
New methods to identify RNA-binding small molecules open yet unexplored opportunities for the pharmacological modulation of RNA-driven biology and disease states. One such approach is the use of small molecule microarrays (SMMs). Typically, SMMs are generated by spatially arraying and covalently linking a library of small molecules to a glass surface. Next, incubation of the arrays with a fluorescently labeled RNA reveals binding interactions that are detected upon slide imaging. The relative ease with which SMMs are manufactured enables the screening of multiple oligonucleotides in parallel against tens of thousands of small molecules, providing information about both binding and selectivity of identified RNA-small molecule interactions...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27869821/synthetic-recording-and-in-situ-readout-of-lineage-information-in-single-cells
#12
Kirsten L Frieda, James M Linton, Sahand Hormoz, Joonhyuk Choi, Ke-Huan K Chow, Zakary S Singer, Mark W Budde, Michael B Elowitz, Long Cai
Reconstructing the lineage relationships and dynamic event histories of individual cells within their native spatial context is a long-standing challenge in biology. Many biological processes of interest occur in optically opaque or physically inaccessible contexts, necessitating approaches other than direct imaging. Here, we describe a new synthetic system that enables cells to record lineage information and event histories in the genome in a format that can be subsequently read out in single cells in situ...
November 21, 2016: Nature
https://www.readbyqxmd.com/read/27866274/ryanodine-receptor-type-3-does-not-contribute-to-contractions-in-the-mouse-myometrium-regardless-of-pregnancy
#13
Katsuhito Matsuki, Masashi Takemoto, Yoshiaki Suzuki, Hisao Yamamura, Susumu Ohya, Hiroshi Takeshima, Yuji Imaizumi
Ryanodine receptor type 3 (RyR3) is expressed in myometrial smooth muscle cells (MSMCs). The short isoform of RyR3 is a dominant negative variant (DN-RyR3) and negatively regulates the functions of RyR2 and full-length (FL)-RyR3. DN-RyR3 has been suggested to function as a major RyR3 isoform in non-pregnant (NP) mouse MSMCs, and FL-RyR3 may also be upregulated during pregnancy (P). This increase in the FL-RyR3/DN-RyR3 ratio may contribute to the strong contractions by MSMCs for parturition. In the present study, spontaneous contractions by the myometrium in NP and P mice were highly susceptible to nifedipine but were not affected by ryanodine...
November 20, 2016: Pflügers Archiv: European Journal of Physiology
https://www.readbyqxmd.com/read/27864646/low-level-laser-irradiation-modulates-brain-derived-neurotrophic-factor-mrna-transcription-through-calcium-dependent-activation-of-the-erk-creb-pathway
#14
Xiaodong Yan, Juanfang Liu, Zhengping Zhang, Wenhao Li, Siguo Sun, Jian Zhao, Xin Dong, Jixian Qian, Honghui Sun
Low-level laser (LLL) irradiation has been reported to promote neuronal differentiation, but the mechanism remains unclear. Brain-derived neurotrophic factor (BDNF) has been confirmed to be one of the most important neurotrophic factors because it is critical for the differentiation and survival of neurons during development. Thus, this study aimed to investigate the effects of LLL irradiation on Bdnf messenger RNA (mRNA) transcription and the molecular pathway involved in LLL-induced Bdnf mRNA transcription in cultured dorsal root ganglion neurons (DRGNs) using Ca(2+) imaging, pharmacological detections, RNA interference, immunocytochemistry assay, Western blot, and qPCR analysis...
November 19, 2016: Lasers in Medical Science
https://www.readbyqxmd.com/read/27860833/a-critical-and-comparative-review-of-fluorescent-tools-for-live-cell-imaging
#15
Elizabeth A Specht, Esther Braselmann, Amy E Palmer
Fluorescent tools have revolutionized our ability to probe biological dynamics, particularly at the cellular level. Fluorescent sensors have been developed on several platforms, utilizing either small molecule dyes or fluorescent proteins, to monitor proteins, RNA, DNA, small molecules, and even cellular properties, such as pH and membrane potential. We briefly summarize the impressive history of tool development for these various applications and then discuss the most recent noteworthy developments in more detail...
November 16, 2016: Annual Review of Physiology
https://www.readbyqxmd.com/read/27852929/eliminating-blurry-bands-in-gels-with-a-simple-cost-effective-repair-to-the-gel-cassette
#16
Jamie L Bingaman, Erica A Frankel, Chelsea M Hull, Kathleen A Leamy, Kyle J Messina, David Mitchell, Hongmarn Park, Laura E Ritchey, Paul Babitzke, Philip C Bevilacqua
Gel electrophoresis and subsequent imaging using phosphorimagers is one of the most important and widely used techniques in RNA and DNA analysis. Radiolabeling nucleic acids with (32)P and detecting bands using a phoshorimager are useful both in a qualitative sense for nucleic acid detection and in a quantitative sense for structural, kinetic, or binding-based assays. Because of this, good resolution of gel bands based on molecular weight and size of RNA or DNA is essential for analysis. The appearance of blurry gel bands of (32)P-labeled RNA and DNA thus represents a serious problem in the laboratory...
December 2016: RNA
https://www.readbyqxmd.com/read/27852860/nes-masking-regulates-hiv-1-rev-trafficking-and-viral-rna-nuclear-export
#17
Ryan T Behrens, Mounavya Aligeti, Ginger M Pocock, Christina A Higgins, Nathan M Sherer
: HIV-1's Rev protein forms a homooligomeric adaptor complex linking viral RNAs to the cellular CRM1/Ran-GTP nuclear export machinery through the activity of Rev's prototypical leucine-rich nuclear export signal (NES). In this study we used a functional fluorescently-tagged Rev fusion protein as a platform to study the effects of modulating Rev NES identity, number, position, or strength on Rev subcellular trafficking, viral RNA nuclear export, and infectious virion production. We found Rev activity to be remarkably tolerant of diverse NES sequences including supraphysiological NES (SNES) peptides that otherwise arrest CRM1 transport complexes at nuclear pores...
November 16, 2016: Journal of Virology
https://www.readbyqxmd.com/read/27851973/soft-x-ray-tomography-reveals-gradual-chromatin-compaction-and-reorganization-during-neurogenesis-in%C3%A2-vivo
#18
Mark A Le Gros, E Josephine Clowney, Angeliki Magklara, Angela Yen, Eirene Markenscoff-Papadimitriou, Bradley Colquitt, Markko Myllys, Manolis Kellis, Stavros Lomvardas, Carolyn A Larabell
The realization that nuclear distribution of DNA, RNA, and proteins differs between cell types and developmental stages suggests that nuclear organization serves regulatory functions. Understanding the logic of nuclear architecture and how it contributes to differentiation and cell fate commitment remains challenging. Here, we use soft X-ray tomography (SXT) to image chromatin organization, distribution, and biophysical properties during neurogenesis in vivo. Our analyses reveal that chromatin with similar biophysical properties forms an elaborate connected network throughout the entire nucleus...
November 15, 2016: Cell Reports
https://www.readbyqxmd.com/read/27849558/identification-of-a-fluorescent-small-molecule-enhancer-for-therapeutic-autophagy-in-colorectal-cancer-by-targeting-mitochondrial-protein-translocase-tim44
#19
Yinghui Huang, Jie Zhou, Shenglin Luo, Yang Wang, Jintao He, Peng Luo, Zelin Chen, Tao Liu, Xu Tan, Juanjuan Ou, Hongming Miao, Houjie Liang, Chunmeng Shi
OBJECTIVE: As the modulation of autophagic processes can be therapeutically beneficial to cancer treatment, the identification of novel autophagic enhancers is highly anticipated. However, current autophagy-inducing anticancer agents exert undesired side effects owing to their non-specific biodistribution in off-target tissues. This study aims to develop a multifunctional agent to integrate cancer targeting, imaging and therapy and to investigate its mechanism. DESIGN: A series of mitochondria-targeting near-infrared (NIR) fluorophores were synthesised, screened and identified for their autophagy-enhancing activity...
November 14, 2016: Gut
https://www.readbyqxmd.com/read/27836667/exploring-the-potential-of-genome-editing-crispr-cas9-technology
#20
REVIEW
Vijai Singh, Darren Braddick, Pawan Kumar Dhar
CRISPR-Cas9 is an RNA-mediated adaptive immune system that protects bacteria and archaea from viruses or plasmids. Herein we discuss the recent development of CRISPR-Cas9 into a key technology for genome editing, targeting, and regulation in a wide range of organisms and cell types. It requires a custom designed single guide-RNA (sgRNA), a Cas9 endonuclease, and PAM sequences in the target region. The sgRNA-Cas9 complex binds to its target and creates a double-strand break (DSB) that can be repaired by non-homologous end joining (NHEJ) or by the homology-directed repair (HDR) pathway, modifying or permanently replacing the genomic target sequence...
November 9, 2016: Gene
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"