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RNA Imaging

Juliane Mundorf, Mirka Uhlirova
Drosophila melanogaster has emerged as a powerful experimental system for functional and mechanistic studies of tumor development and progression in the context of a whole organism. Sophisticated techniques to generate genetic mosaics facilitate induction of visually marked, genetically defined clones surrounded by normal tissue. The clones can be analyzed through diverse molecular, cellular and omics approaches. This study describes how to generate fluorescently labeled clonal tumors of varying malignancy in the eye/antennal imaginal discs (EAD) of Drosophila larvae using the Mosaic Analysis with a Repressible Cell Marker (MARCM) technique...
October 6, 2016: Journal of Visualized Experiments: JoVE
Irina Trofimova, Alla Krasikova
Tandemly organized highly repetitive DNA sequences are crucial structural and functional elements of eukaryotic genomes. Despite extensive evidence, satellite DNA remains an enigmatic part of the eukaryotic genome, with biological role and significance of tandem repeat transcripts remaining rather obscure. Data on tandem repeats transcription in amphibian and avian model organisms is fragmentary despite their genomes being thoroughly characterized. Review systematically covers historical and modern data on transcription of amphibian and avian satellite DNA in somatic cells and during meiosis when chromosomes acquire special lampbrush form...
October 20, 2016: RNA Biology
Nynke Oosterhof, Inge R Holtman, Laura E Kuil, Herma C van der Linde, Erik W G M Boddeke, Bart J L Eggen, Tjakko J van Ham
Microglia are brain resident macrophages important for brain development, connectivity, homeostasis and disease. However, it is still largely unclear how microglia functions and their identity are regulated at the molecular level. Although recent transcriptomic studies have identified genes specifically expressed in microglia, the function of most of these genes in microglia is still unknown. Here, we performed RNA sequencing on microglia acutely isolated from healthy and neurodegenerative zebrafish brains...
October 19, 2016: Glia
Neema Jamshidi, Danshan Huang, Fereidoun G Abtin, Christopher T Loh, Stephen T Kee, Robert D Suh, Shota Yamamoto, Kingshuk Das, Sarah Dry, Scott Binder, Dieter R Enzmann, Michael D Kuo
Purpose To identify the variables and factors that affect the quantity and quality of nucleic acid yields from imaging-guided core needle biopsy. Materials and Methods This study was approved by the institutional review board and compliant with HIPAA. The authors prospectively obtained 232 biopsy specimens from 74 patients (177 ex vivo biopsy samples from surgically resected masses were obtained from 49 patients and 55 in vivo lung biopsy samples from computed tomographic [CT]-guided lung biopsies were obtained from 25 patients) and quantitatively measured DNA and RNA yields with respect to needle gauge, number of needle passes, and percentage of the needle core...
October 18, 2016: Radiology
David S Lynch, Wei Jia Zhang, Rahul Lakshmanan, Justin A Kinsella, Günes Altiokka Uzun, Merih Karbay, Zeynep Tüfekçioglu, Hasmet Hanagasi, Georgina Burke, Nicola Foulds, Simon R Hammans, Anupam Bhattacharjee, Heather Wilson, Matthew Adams, Mark Walker, James A R Nicoll, Jeremy Chataway, Nick Fox, Indran Davagnanam, Rahul Phadke, Henry Houlden
Importance: Adult-onset leukoencephalopathy with axonal spheroids and pigmented glia (ALSP) is a frequent cause of adult-onset leukodystrophy known to be caused by autosomal dominant mutations in the CSF1R (colony-stimulating factor 1) gene. The discovery that CSF1R mutations cause ALSP led to more accurate prognosis and genetic counseling for these patients in addition to increased interest in microglia as a target in neurodegeneration. However, it has been known since the discovery of the CSF1R gene that there are patients with typical clinical and radiologic evidence of ALSP who do not carry pathogenic CSF1R mutations...
October 17, 2016: JAMA Neurology
Jovan Nikolic, Ahmet Civas, Zoé Lama, Cécile Lagaudrière-Gesbert, Danielle Blondel
Stress granules (SGs) are membrane-less dynamic structures consisting of mRNA and protein aggregates that form rapidly in response to a wide range of environmental cellular stresses and viral infections. They act as storage sites for translationally silenced mRNAs under stress conditions. During viral infection, SG formation results in the modulation of innate antiviral immune responses, and several viruses have the ability to either promote or prevent SG assembly. Here, we show that rabies virus (RABV) induces SG formation in infected cells, as revealed by the detection of SG-marker proteins Ras GTPase-activating protein-binding protein 1 (G3BP1), T-cell intracellular antigen 1 (TIA-1) and poly(A)-binding protein (PABP) in the RNA granules formed during viral infection...
October 2016: PLoS Pathogens
Jing Xu, Yanjun Wang, Luzhu Yang, Yanfang Gao, Baoxin Li, Yan Jin
Human telomerase RNA (hTR), works as a template for synthesis of telomeric DNA repeats at the ends of linear eukaryotic chromosomes, is overexpressed in tumor cells and its concentration has a positive correlation with telomerase activity. The lack of facile and reliable method for detection of hTR in complex matric limited its application for clinical diagnosis. To address the limitation, herein, we proposed a facile and reliable flow cytometric assay for sensitive and specific detection of hTR by combing magnetic enrichment with signal amplification of DNA toehold strand displacement reaction (TSDR)...
August 13, 2016: Biosensors & Bioelectronics
M P Economides, P Mahale, A Kyvernitakis, F Turturo, H Kantarjian, A Naing, J Hosry, T L Shigle, A Kaseb, H A Torres
BACKGROUND: Antiviral therapy improves hepatic outcomes in hepatitis C virus (HCV)-infected cancer patients. However, such patients are not treated simultaneously with antivirals and chemotherapy, owing to overlapping toxicities with previous standard of care treatment of pegylated interferon and ribavirin. AIM: To examine the safety and clinically-significant drug-drug interactions observed in patients who received simultaneous treatment with direct-acting antivirals (DAAs) and chemotherapy...
October 11, 2016: Alimentary Pharmacology & Therapeutics
Eric Piver, Audrey Boyer, Julien Gaillard, Anne Bull, Elodie Beaumont, Philippe Roingeard, Jean-Christophe Meunier
OBJECTIVE: HCV particles are associated with very low-density lipoprotein components in chronically infected patients. These hybrid particles, or 'lipo-viro particles' (LVPs), are rich in triglycerides, and contain the viral RNA, the capsid protein, E1E2 envelope glycoproteins and apolipoproteins B and E. However, their specific ultrastructural organisation has yet to be determined. We developed a strategy for the preparation of any viral sample that preserves the native structure of the LVPs, facilitating their precise morphological characterisation...
October 11, 2016: Gut
Yi Li, Chi Zhang, Danmeng Shuai, Saraschandra Naraginti, Dawei Wang, Wenlong Zhang
The challenge to achieve effective water disinfection of pathogens, especially viruses, with minimized harmful disinfection byproducts calls for a cost-effective and environmentally benign technology. Here, polymeric graphitic carbon nitride (g-C3N4), as a metal-free robust photocatalyst, was explored for the first time for its ability to inactivate viruses under visible light irradiation. MS2 with an initial concentration of 1 × 10(8) PFU/mL was completely inactivated by g-C3N4 with a loading of 150 mg/L under visible light irradiation of 360 min...
October 5, 2016: Water Research
Lan V Pham, Jerry L Bryant, Richard Mendez, Juan Chen, Archito T Tamayo, Zijun Y Xu-Monette, Ken H Young, Ganiraju C Manyam, David Yang, L Jeffrey Medeiros, Richard J Ford
The hexosamine biosynthetic pathway (HBP) requires two key nutrients glucose and glutamine for O-linked N-acetylglucosamine (O-GlcNAc) cycling, a post-translational protein modification that adds GlcNAc to nuclear and cytoplasmic proteins. Increased GlcNAc has been linked to regulatory factors involved in cancer cell growth and survival. However, the biological significance of GlcNAc in diffuse large B-cell lymphoma (DLBCL) is not well defined. This study is the first to show that both the substrate and the endpoint O-GlcNAc transferase (OGT) enzyme of the HBP were highly expressed in DLBCL cell lines and in patient tumors compared with normal B-lymphocytes...
October 3, 2016: Oncotarget
Feriel Melaine, Clothilde Coilhac, Yoann Roupioz, Arnaud Buhot
Small molecules (MW < 1000 Da) represent a large class of biomarkers of interest. Recently, a new class of biosensors has been emerging thanks to the recognition properties of aptamers, short DNA or RNA single strands, selected against such small molecular targets. Among them, an adenosine-specific aptamer has been largely described and used due to its remarkable affinity to this small target (KD = 6 μM). In this paper, we achieved the proof-of-principle of an aptasensor based on the thermodynamic follow-up of adenosine binding with engineered split-aptamer sequences...
September 29, 2016: Nanoscale
Zhengyi Zhao, Hui Zhang, Dan Shu, Carlo Montemagno, Baoquan Ding, Jingyuan Li, Peixuan Guo
The significance of bionanomotors in nanotechnology is analogous to mechanical motors in daily life. Here the principle and approach for designing and constructing biomimetic nanomotors with continuous single-directional motion are reported. This bionanomotor is composed of a dodecameric protein channel, a six-pRNA ring, and an ATPase hexamer. Based on recent elucidations of the one-way revolving mechanisms of the phi29 double-stranded DNA (dsDNA) motor, various RNA and protein elements are designed and tested by single-molecule imaging and biochemical assays, with which the motor with active components has been constructed...
October 6, 2016: Small
Daseul Park, Hafiz Muhammad Shahbaz, Sun-Hyoung Kim, Mijin Lee, Wooseong Lee, Jong-Won Oh, Dong-Un Lee, Jiyong Park
Human norovirus (HuNoV) is the primary cause of viral gastroenteritis worldwide. Fresh blueberries are among high risk foods associated with norovirus related outbreaks. Therefore, it is important to assess intervention strategies to reduce the risk of foodborne illness. The disinfection efficiency of decontamination methods is difficult to evaluate for fruits and vegetables due to an inconsistent degree of contamination and irregular surface characteristics. The inactivation efficiency and mechanism of murine norovirus 1 (MNV-1, a surrogate for HuNoV) was studied on an experimentally prepared solidified agar matrix (SAM) to simulate blueberries using different wavelengths (A, B, C) of UV light both with and without TiO2 photocatalysis (TP)...
December 5, 2016: International Journal of Food Microbiology
Hua He, Zhencai Wang, Tiantian Cheng, Xu Liu, Xiaojuan Wang, Junying Wang, Hao Ren, Yawei Sun, Yanzhuo Song, Jiang Yang, Yongqing Xia, Shengjie Wang, Xiao-Dong Zhang, Fang Huang
Fluorescence imaging requires bio-selective, sensitive, nontoxic molecular probes to detect precise location of lesions for fundamental research and clinical applications. Typical inorganic semiconductor nanomaterials with large sizes (> 10 nm) can offer high-quality fluorescence imaging due to their fascinating optical properties, but are limited to low selectivity as well as slow clearance pathway. We here report an N- and O-rich carbogenic small molecular complex (SMC, MW < 1000 Da) that exhibit high quantum yield (up to 80%), nucleic acid-binding enhanced excitation-dependent fluorescence (EDF) and a near infrared (NIR) emission peaked at 850 nm with an ultra-large Stokes shift (~ 500 nm)...
October 5, 2016: ACS Applied Materials & Interfaces
Katherine E Bujold, John Chu Chia Hsu, Hanadi F Sleiman
We set out to design, synthesize and optimize a DNA-minimal cage capable of encapsulating oligonucleotide drugs to facilitate their delivery. Through rational design and optimization using in vitro assays, we have assembled the first DNA "nanosuitcase" that can encapsulate a siRNA construct and release it upon recognition of an oligonucleotide trigger. The latter may be a messenger RNA (mRNA) or a microRNA (miRNA) which offers potential for dual or synergistic therapy. This construct assembles in near 100% yield, releases its cargo on demand and can sustain biological conditions...
October 4, 2016: Journal of the American Chemical Society
Naseem Akhtar, Riaz A Khan
Skin cancer is among one of the most common human malignancies wide-spread world-over with mortality statistics rising continuously at an alarming rate. The increasing frequency of these malignancies has marked the need for adopting effective treatment plan coupled with better and site-specific delivery options for the desired therapeutic agent's availability at the affected site. The concurrent delivery approaches to cancerous tissues are under constant challenge and, as a result, are evolving and gaining advancements in terms of delivery modes, therapeutic agents and site-specificity of the therapeutics delivery...
September 30, 2016: Progress in Lipid Research
Jinming Li, Yuanyuan Wang, Shanshan Xue, Jinghua Sun, Wei Zhang, Ping Hu, Liangnian Ji, Zongwan Mao
In recent years, lung cancer has become one of the fastest growing cancers in the world. Thus, the development of efficient combination therapy to treat lung cancer has attracted significant attention in the cancer therapy field. In this article, we developed a single vehicle drug delivery system, based on quantum dot (QD) nanoparticles, to deliver small interfering RNA (siRNA; target Bcl-2) and different anticancer drugs (carboplatin, paclitaxel, and doxorubicin) simultaneously for treating A549 lung cancer cells efficiently by combination therapy...
2016: International Journal of Nanomedicine
Steffen Zopf, Lara Rösch, Peter C Konturek, Ruediger S Goertz, Markus F Neurath, Deike Strobel
BACKGROUND Non-invasive procedures such as acoustic radiation force impulse imaging (ARFI) shear-wave elastography are currently used for the assessment of liver fibrosis. In the course of chronic hepatitis C, significant liver fibrosis or cirrhosis develops in approximately 25% of patients, which is a negative predictor of antiviral treatment response. Cirrhosis can be prevented by successful virus elimination. In this prospective study, a pretreatment ARFI cutoff value of 1.5 m/s was evaluated in relation to sustained virological response to anti-HCV therapy...
2016: Medical Science Monitor: International Medical Journal of Experimental and Clinical Research
Matthew J Hill, Richard Killick, Katherinne Navarrete, Aleksandra Maruszak, Gemma M McLaughlin, Brenda P Williams, Nicholas J Bray
BACKGROUND: Common variants in the TCF4 gene are among the most robustly supported genetic risk factors for schizophrenia. Rare TCF4 deletions and loss-of-function point mutations cause Pitt-Hopkins syndrome, a developmental disorder associated with severe intellectual disability. METHODS: To explore molecular and cellular mechanisms by which TCF4 perturbation could interfere with human cortical development, we experimentally reduced the endogenous expression of TCF4 in a neural progenitor cell line derived from the developing human cerebral cortex using RNA interference...
September 29, 2016: Journal of Psychiatry & Neuroscience: JPN
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