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RNA Imaging

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https://www.readbyqxmd.com/read/29166707/-establishment-of-myocardial-targeted-nanoparticles-and-preliminary-evaluation-of-its-effects-on-prevention-and-treatment-of-myocardial-injury
#1
Y Y Liu, C Wang, P F Luo, Z F Xia
Objective: To establish 3-{4-[2-hydroxyl-(1-methylethylamino) propoxy] phenyl} propionic acid cetylesters (PAC) modified nanoparticles, and preliminarily explore its cardiomyocyte-targeting function and protection effects on myocardium. Methods: (1) HL-1 myocardial cells were divided into cyanidin-3 (Cy3) marked non-targeted small interference RNA (Cy3-siNC) group and Cy3 marked small interference RNA designed for the nuclear factor kappa B (NF-κB)-p65 gene (Cy3-si435) group according to the random number table, with 3 wells in each group...
November 20, 2017: Zhonghua Shao Shang za Zhi, Zhonghua Shaoshang Zazhi, Chinese Journal of Burns
https://www.readbyqxmd.com/read/29164876/live-cell-imaging-of-endogenous-rnas-using-pumilio-homology-domain-mutants-principles-and-applications
#2
Hideaki Yoshimura
Recently, dynamic changes in RNA location in space and time in living cells have become a target of interest in biology because of their essential roles in controlling physiological phenomena. To visualize RNA, methods for the fluorescence labeling of RNA in living cells have been developed. For RNA labeling, oligonucleotide-based RNA probes have mainly been used because of their high selectivity for target RNAs. By contrast, protein-based RNA probes have not been used widely because of their lack of design flexibility, although they have various potential advantages compared with nucleotide-based probes, such as controllability of intracellular localization, high detectability, and ease of introduction to cells and transgenic organisms in cell type and tissue specific manner by genetic engineering techniques...
November 22, 2017: Biochemistry
https://www.readbyqxmd.com/read/29164052/development-of-novel-patient-derived-xenografts-from-breast-cancer-brain-metastases
#3
María J Contreras-Zárate, D Ryan Ormond, Austin E Gillen, Colton Hanna, Nicole L Day, Natalie J Serkova, Britta M Jacobsen, Susan M Edgerton, Ann D Thor, Virginia F Borges, Kevin O Lillehei, Michael W Graner, Peter Kabos, Diana M Cittelly
Brain metastases are an increasing burden among breast cancer patients, particularly for those with HER2(+) and triple negative (TN) subtypes. Mechanistic insight into the pathophysiology of brain metastases and preclinical validation of therapies has relied almost exclusively on intracardiac injection of brain-homing cells derived from highly aggressive TN MDA-MB-231 and HER2(+) BT474 breast cancer cell lines. Yet, these well characterized models are far from representing the tumor heterogeneity observed clinically and, due to their fast progression in vivo, their suitability to validate therapies for established brain metastasis remains limited...
2017: Frontiers in Oncology
https://www.readbyqxmd.com/read/29157313/calpain-5-gene-expression-in-the-mouse-eye-and-brain
#4
Kellie Schaefer, MaryAnn Mahajan, Anuradha Gore, Stephen H Tsang, Alexander G Bassuk, Vinit B Mahajan
OBJECTIVE: Our objective was to characterize CAPN5 gene expression in the mouse central nervous system. Mouse brain and eye sections were probed with two high-affinity RNA oligonucleotide analogs designed to bind CAPN5 RNA and one scramble, control oligonucleotide. Images were captured in brightfield. RESULTS: CAPN5 RNA probes were validated on mouse breast cancer tumor tissue. In the eye, CAPN5 was expressed in the ganglion cell, inner nuclear and outer nuclear layers of the retina...
November 21, 2017: BMC Research Notes
https://www.readbyqxmd.com/read/29156758/development-of-novel-long-noncoding-rna-malat1-near-infrared-optical-probes-for-in-vivo-tumour-imaging
#5
Meng-Jie Dong, Cai-Qin Wang, Guo-Lin Wang, Yue-Hong Wang, Zhen-Feng Liu
With the advent of next-generation sequencing technology, there is rapidly increasing interest in long noncoding RNAs (lncRNAs). The objectives of this study were to develop a novel lncRNA MALAT1 near-infrared optical probe, to evaluate the characteristics of this optical imaging probe in vitro and to determine whether it can be used for imaging MALAT1 expression in malignant tumours in vivo. Conjugation of Cy5.5 to MALAT1 ASO was accomplished using standard NHS (N-hydroxysuccinimide) ester procedures, and the labelled MALAT1 ASO was purified with a Glen-Pak DNA Purification Cartridge and reversed-phase high performance liquid chromatography (HPLC)...
October 17, 2017: Oncotarget
https://www.readbyqxmd.com/read/29156720/novel-strategies-of-raman-imaging-for-brain-tumor-research
#6
Imiela Anna, Polis Bartosz, Polis Lech, Abramczyk Halina
Raman diagnostics and imaging have been shown to be an effective tool for the analysis and discrimination of human brain tumors from normal structures. Raman spectroscopic methods have potential to be applied in clinical practice as they allow for identification of tumor margins during surgery. In this study, we investigate medulloblastoma (grade IV WHO) (n= 5), low-grade astrocytoma (grades I-II WHO) (n =4), ependymoma (n=3) and metastatic brain tumors (n= 1) and the tissue from the negative margins used as normal controls...
October 17, 2017: Oncotarget
https://www.readbyqxmd.com/read/29153840/association-of-omics-features-with-histopathology-patterns-in-lung-adenocarcinoma
#7
Kun-Hsing Yu, Gerald J Berry, Daniel L Rubin, Christopher Ré, Russ B Altman, Michael Snyder
Adenocarcinoma accounts for more than 40% of lung malignancy, and microscopic pathology evaluation is indispensable for its diagnosis. However, how histopathology findings relate to molecular abnormalities remains largely unknown. Here, we obtained H&E-stained whole-slide histopathology images, pathology reports, RNA sequencing, and proteomics data of 538 lung adenocarcinoma patients from The Cancer Genome Atlas and used these to identify molecular pathways associated with histopathology patterns. We report cell-cycle regulation and nucleotide binding pathways underpinning tumor cell dedifferentiation, and we predicted histology grade using transcriptomics and proteomics signatures (area under curve >0...
November 13, 2017: Cell Systems
https://www.readbyqxmd.com/read/29153838/unsupervised-trajectory-analysis-of-single-cell-rna-seq-and-imaging-data-reveals-alternative-tuft-cell-origins-in-the-gut
#8
Charles A Herring, Amrita Banerjee, Eliot T McKinley, Alan J Simmons, Jie Ping, Joseph T Roland, Jeffrey L Franklin, Qi Liu, Michael J Gerdes, Robert J Coffey, Ken S Lau
Modern single-cell technologies allow multiplexed sampling of cellular states within a tissue. However, computational tools that can infer developmental cell-state transitions reproducibly from such single-cell data are lacking. Here, we introduce p-Creode, an unsupervised algorithm that produces multi-branching graphs from single-cell data, compares graphs with differing topologies, and infers a statistically robust hierarchy of cell-state transitions that define developmental trajectories. We have applied p-Creode to mass cytometry, multiplex immunofluorescence, and single-cell RNA-seq data...
November 7, 2017: Cell Systems
https://www.readbyqxmd.com/read/29150003/crispr-cas9-technology-applications-and-human-disease-modeling
#9
Marta Martinez-Lage, Raúl Torres-Ruiz, Sandra Rodriguez-Perales
The CRISPR/Cas9 system development has revolutionized the field of genome engineering through the efficient creation of targeted breaks in the DNA of almost any organism and cell type, opening an avenue for a wide range of applications in biomedical research and medicine. Apart from gene edition through knock-in or knock-out approaches, CRISPR/Cas9 technology has been used for many other purposes, including regulation of endogenous gene expression, epigenome editing, live-cell imaging of chromosomal loci, edition of RNA and high-throughput screening...
2017: Progress in Molecular Biology and Translational Science
https://www.readbyqxmd.com/read/29148777/programmable-rna-binding-proteins-for-imaging-and-therapeutics
#10
Simone Rauch, Bryan C Dickinson
No abstract text is available yet for this article.
November 17, 2017: Biochemistry
https://www.readbyqxmd.com/read/29144820/pheochromocytoma-a-genetic-and-diagnostic-update
#11
Leilani B Mercado-Asis, Katherine I Wolf, Ivana Jochmanova, David Taïeb
OBJECTIVE: Pheochromocytomas and paragangliomas (PPGLs) are neuroendocrine tumors derived from adrenal or extra-adrenal locations, respectively. Upon suspicion of PPGL, specific metabolomic, molecular, biochemical, imaging, and histopathological studies are performed to prove, localize, treat, and monitor disease progression. Recently, improved diagnostic tools allow physicians to accurately diagnose PPGL, even in patients presenting with small (less than 1 cm) or biochemically silent tumors, which previously delayed proper detection and treatment...
November 16, 2017: Endocrine Practice
https://www.readbyqxmd.com/read/29144411/nucleic-acid-aptamers-emerging-applications-in-medical-imaging-nanotechnology-neurosciences-and-drug-delivery
#12
REVIEW
Pascal Röthlisberger, Cécile Gasse, Marcel Hollenstein
Recent progresses in organic chemistry and molecular biology have allowed the emergence of numerous new applications of nucleic acids that markedly deviate from their natural functions. Particularly, DNA and RNA molecules-coined aptamers-can be brought to bind to specific targets with high affinity and selectivity. While aptamers are mainly applied as biosensors, diagnostic agents, tools in proteomics and biotechnology, and as targeted therapeutics, these chemical antibodies slowly begin to be used in other fields...
November 16, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29143844/charged-probes-turn-on-selective-fluorescence-for-rna
#13
Bahareh Shirinfar, Humaira Seema, Nisar Ahmed
RNA controls many biological processes. The selective detection and imaging of RNA molecules can provide information about their location, kinetics, and functions at the cellular level. The imidazolium-based positively charged probes would play a significant role in the deep investigation of RNA biomolecules to check their therapeutic potential and aid in the future rational molecular and drug design.
November 16, 2017: Organic & Biomolecular Chemistry
https://www.readbyqxmd.com/read/29138205/long-term-prognosis-of-young-breast-cancer-patients-%C3%A2-40-years-who-did-not-receive-adjuvant-systemic-treatment-protocol-for-the-paradigm-initiative-cohort-study
#14
Gwen Mhe Dackus, Natalie D Ter Hoeve, Mark Opdam, Willem Vreuls, Zsuzsanna Varga, Esther Koop, Stefan M Willems, Carolien Hm Van Deurzen, Emilie J Groen, Alicia Cordoba, Jos Bart, Antien L Mooyaart, Jan G van den Tweel, Vicky Zolota, Jelle Wesseling, Anna Sapino, Ewa Chmielik, Ales Ryska, Frederic Amant, Annegien Broeks, Ron Kerkhoven, Nikolas Stathonikos, Mitko Veta, Adri Voogd, Katarzyna Jozwiak, Michael Hauptmann, Marlous Hoogstraat, Marjanka K Schmidt, Gabe Sonke, Elsken van der Wall, Sabine Siesling, Paul J van Diest, Sabine C Linn
INTRODUCTION: Currently used tools for breast cancer prognostication and prediction may not adequately reflect a young patient's prognosis or likely treatment benefit because they were not adequately validated in young patients. Since breast cancers diagnosed at a young age are considered prognostically unfavourable, many treatment guidelines recommend adjuvant systemic treatment for all young patients. Patients cured by locoregional treatment alone are, therefore, overtreated. Lack of prognosticators for young breast cancer patients represents an unmet medical need and has led to the initiation of the PAtients with bReAst cancer DIaGnosed preMenopausally (PARADIGM) initiative...
November 14, 2017: BMJ Open
https://www.readbyqxmd.com/read/29136454/immediate-label-free-ex-vivo-evaluation-of-human-brain-tumor-biopsies-with-confocal-reflectance-microscopy
#15
Jennifer M Eschbacher, Joseph F Georges, Evgenii Belykh, Mohammedhassan Izady Yazdanabadi, Nikolay L Martirosyan, Emily Szeto, Catherine Y Seiler, Michael A Mooney, Jessica K Daniels, Katherine Y Goehring, Kendall R Van Keuren-Jensen, Mark C Preul, Stephen W Coons, Shwetal Mehta, Peter Nakaji
Confocal microscopy utilizing fluorescent dyes is widely gaining use in the clinical setting as a diagnostic tool. Reflectance confocal microscopy is a method of visualizing tissue specimens without fluorescent dyes while relying on the natural refractile properties of cellular and subcellular structures. We prospectively evaluated 76 CNS lesions with confocal reflectance microscopy (CRM) to determine cellularity, architecture, and morphological characteristics. A neuropathologist found that all cases showed similar histopathological features when compared to matched hematoxylin and eosin-stained sections...
December 1, 2017: Journal of Neuropathology and Experimental Neurology
https://www.readbyqxmd.com/read/29135031/comparative-proteomics-illustrates-the-molecular-mechanism-of-potato-solanum-tuberosum-l-tuberization-inhibited-by-exogenous-gibberellins-in-vitro
#16
Lixiang Cheng, Yuping Wang, Yueshan Liu, Qingquan Zhang, Huihui Gao, Zhang Feng
Among the multiple environmental signals and hormonal factors regulating potato tuberization, gibberellins (GAs) are important components of the signaling pathways in these processes. To understand the GAs-signaling response mechanism of potato tuberization, a comparative proteomics approach was applied to analyze proteome change of potato tuberization in vitro subjected to a range of exogenous GA3 treatments (0, 0.01, 0.1 and 1.0 μΜ) using two-dimensional gel electrophoresis. Quantitative image analyses showed that a total of 37 protein spots have their abundance significantly altered more than 2-fold...
November 14, 2017: Physiologia Plantarum
https://www.readbyqxmd.com/read/29131211/pharmaco-genomic-investigations-of-organo-iridium-anticancer-complexes-reveal-novel-mechanism-of-action
#17
Jessica M Hearn, George M Hughes, Isolda Romero-Canelón, Alison F Munro, Belén Rubio-Ruiz, Zhe Liu, Neil O Carragher, Peter J Sadler
Resistance to platinum drugs (used in >50% of cancer chemotherapies) is a clinical problem. Other precious metal complexes with distinct mechanisms of action might overcome this. Half-sandwich organometallic complexes containing arene or cyclopentadienyl (Cp) ligands show promise. We screened two iridium(iii) complexes [Ir(Cp(Xbiph))(ppy)Cl] (ZL49, 1, ppy = phenylpyridine) and [Ir(Cp(Xph))(azpyNMe2)Cl]PF6 (ZL109, 2, azpyNMe2 = N,N-dimethylphenylazopyridine) in 916 cancer cell lines from 28 tissue types. On average, complex 2 was 78× more potent than 1, 36× more active than cisplatin (CDDP), and strongly active (nanomolar) in patient-derived ovarian cancer cell lines...
November 13, 2017: Metallomics: Integrated Biometal Science
https://www.readbyqxmd.com/read/29131164/an-improved-ms2-system-for-accurate-reporting-of-the-mrna-life-cycle
#18
Evelina Tutucci, Maria Vera, Jeetayu Biswas, Jennifer Garcia, Roy Parker, Robert H Singer
The MS2-MCP system enables researchers to image multiple steps of the mRNA life cycle with high temporal and spatial resolution. However, for short-lived mRNAs, the tight binding of the MS2 coat protein (MCP) to the MS2 binding sites (MBS) protects the RNA from being efficiently degraded, and this confounds the study of mRNA regulation. Here, we describe a reporter system (MBSV6) with reduced affinity for the MCP, which allows mRNA degradation while preserving single-molecule detection determined by single-molecule FISH (smFISH) or live imaging...
November 13, 2017: Nature Methods
https://www.readbyqxmd.com/read/29130211/detection-of-the-first-round-of-translation-the-trick-assay
#19
Franka Voigt, Jan Eglinger, Jeffrey A Chao
Quantitative fluorescence microscopy techniques are frequently applied to answer fundamental biological questions. Single-molecule RNA imaging methods have enabled the direct observation of the initial steps of the mRNA life cycle in living cells, however, the dynamic mechanisms that regulate mRNA translation are still poorly understood. We have developed an RNA biosensor that can assess the translational state of individual mRNA transcripts with spatiotemporal resolution in living cells. In this chapter, we describe how to perform a TRICK (translating RNA imaging by coat protein knock-off) experiment and specifically focus on a detailed description of our image processing and data analysis procedure...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29130210/imaging-newly-transcribed-rna-in-cells-by-using-a-clickable-azide-modified-utp-analog
#20
Anupam A Sawant, Sanjeev Galande, Seergazhi G Srivatsan
Robust RNA labeling and imaging methods that enable the understanding of cellular RNA biogenesis and function are highly desired. In this context, we describe a practical chemical labeling method based on a bioorthogonal reaction, namely, azide-alkyne cycloaddition reaction, which facilitates the fluorescence imaging of newly transcribed RNA in both fixed and live cells. This strategy involves the transfection of an azide-modified UTP analog (AMUTP) into mammalian cells, which gets specifically incorporated into RNA transcripts by RNA polymerases present inside the cells...
2018: Methods in Molecular Biology
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