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RNA Imaging

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https://www.readbyqxmd.com/read/28429532/neu1-sialidase-interacts-with-perilipin-1-on-lipid-droplets-and-inhibits-lipolysis-in-3t3-l1-adipocytes
#1
Yujin Natori, Miwako Nasui, Fumiko Kihara-Negishi
Fatty acids are stored within adipocytes in lipid droplets (LDs) as triacylglycerol (TG), which is converted to free fatty acid (FFA) and glycerol via lipolysis. Increased plasma FFA levels in obesity are associated with several clinical conditions. We previously found that Neu1 activity is aberrant in the epididymal fat and liver of obese and diabetic mice. Here, we examined involvement of Neu1 in lipolysis in 3T3-L1 adipocytes. Small interfering RNA against Neu1 was introduced into adipocytes, and glycerol concentrations were measured in the culture medium...
April 21, 2017: Genes to Cells: Devoted to Molecular & Cellular Mechanisms
https://www.readbyqxmd.com/read/28428090/preparation-and-characterization-of-lipid-nanoparticle-pdna-complexes-for-stat3-downregulation-and-overcoming-chemotherapy-resistance-in-lung-cancer-cells
#2
Mustafa Kotmakçı, Vildan Bozok Çetintaş, A Gülten Kantarcı
Developments in the field of molecular oncology have revealed that resistance to chemotherapeutics is acqured through several mechanisms including overexpression of common oncogenic proteins. Signal Transducer and Activator of Transcription 3 (STAT3) is one of these oncogenes that is overexpressed in many cancer types. RNA interference (RNAi) is proven powerful tool for downregulating STAT3, allowing re-sensitization of resistant cancer cells. However, delivery of RNA interference-mediating molecules for STAT3 downregulation in lung cancer cells is limited to a small number of studies most of which employ commercially available transfection kits...
April 17, 2017: International Journal of Pharmaceutics
https://www.readbyqxmd.com/read/28428068/comparative-analysis-of-gene-expression-profiles-for-several-migrating-cell-types-identifies-cell-migration-regulators
#3
Young-Kyung Bae, Frank Macabenta, Heather Leigh Curtis, Angelike Stathopoulos
Cell migration is an instrumental process that ensures cells are properly positioned to support the specification of distinct tissue types during development. To provide insight, we used fluorescence activated cell sorting (FACS) to isolate two migrating cell types from the Drosophila embryo: caudal visceral mesoderm (CVM) cells, precursors of longitudinal muscles of the gut, and hemocytes (HCs), the Drosophila equivalent of blood cells. ~350 genes were identified from each of the sorted samples using RNA-seq, and in situ hybridization was used to confirm expression within each cell type or, alternatively, within other interacting, co-sorted cell types...
April 17, 2017: Mechanisms of Development
https://www.readbyqxmd.com/read/28426722/interactions-between-mitoneet-and-naf-1-in-cells
#4
Ola Karmi, Sarah H Holt, Luhua Song, Sagi Tamir, Yuting Luo, Fang Bai, Ammar Adenwalla, Merav Darash-Yahana, Yang-Sung Sohn, Patricia A Jennings, Rajeev K Azad, Jose' N Onuchic, Faruck Morcos, Rachel Nechushtai, Ron Mittler
The NEET proteins mitoNEET (mNT) and nutrient-deprivation autophagy factor-1 (NAF-1) are required for cancer cell proliferation and resistance to oxidative stress. NAF-1 and mNT are also implicated in a number of other human pathologies including diabetes, neurodegeneration and cardiovascular disease, as well as in development, differentiation and aging. Previous studies suggested that mNT and NAF-1 could function in the same pathway in mammalian cells, preventing the over-accumulation of iron and reactive oxygen species (ROS) in mitochondria...
2017: PloS One
https://www.readbyqxmd.com/read/28424513/super-multiplex-vibrational-imaging
#5
Lu Wei, Zhixing Chen, Lixue Shi, Rong Long, Andrew V Anzalone, Luyuan Zhang, Fanghao Hu, Rafael Yuste, Virginia W Cornish, Wei Min
The ability to visualize directly a large number of distinct molecular species inside cells is increasingly essential for understanding complex systems and processes. Even though existing methods have successfully been used to explore structure-function relationships in nervous systems, to profile RNA in situ, to reveal the heterogeneity of tumour microenvironments and to study dynamic macromolecular assembly, it remains challenging to image many species with high selectivity and sensitivity under biological conditions...
April 19, 2017: Nature
https://www.readbyqxmd.com/read/28420169/ultrasensitive-label-free-sensing-of-il-6-based-on-pase-functionalized-carbon-nanotube-micro-arrays-with-rna-aptamers-as-molecular-recognition-elements
#6
Farhad Khosravi, Seyed Masoud Loeian, Balaji Panchapakesan
This study demonstrates the rapid and label-free detection of Interleukin-6 (IL-6) using carbon nanotube micro-arrays with aptamer as the molecular recognition element. Single wall carbon nanotubes micro-arrays biosensors were manufactured using photo-lithography, metal deposition, and etching techniques. Nanotube biosensors were functionalized with 1-Pyrenebutanoic Acid Succinimidyl Ester (PASE) conjugated IL-6 aptamers. Real time response of the sensor conductance was monitored with increasing concentration of IL-6 (1 pg/mL to 10 ng/mL), exposure to the sensing surface in buffer solution, and clinically relevant spiked blood samples...
April 17, 2017: Biosensors
https://www.readbyqxmd.com/read/28418268/the-folding-competence-of-hiv-1-tat-mediated-by-interaction-with-tar-rna
#7
Jung Min Kim, Hee Sun Choi, Baik Lin Seong
The trans-activator Tat protein of HIV-1 belongs to the large family of intrinsically disordered proteins (IDPs), and is known to recruit various host proteins for the transactivation of viral RNA synthesis. Tat protein interacts with the transactivator response RNA (TAR RNA), exhibiting RNA chaperone activities for structural rearrangement of interacting RNAs. Here, considering that Tat-TAR RNA interaction is mutually cooperative, we examined the potential role of TAR RNA as Chaperna - RNA that provides chaperone function to proteins - for the folding of HIV-1 Tat...
April 18, 2017: RNA Biology
https://www.readbyqxmd.com/read/28416600/induction-of-an-ifn-mediated-antiviral-response-by-a-self-amplifying-rna-vaccine-implications-for-vaccine-design
#8
Timothy Pepini, Anne-Marie Pulichino, Thomas Carsillo, Alicia L Carlson, Farid Sari-Sarraf, Katrin Ramsauer, Jason C Debasitis, Giulietta Maruggi, Gillis R Otten, Andrew J Geall, Dong Yu, Jeffrey B Ulmer, Carlo Iavarone
RNA-based vaccines have recently emerged as a promising alternative to the use of DNA-based and viral vector vaccines, in part because of the potential to simplify how vaccines are made and facilitate a rapid response to newly emerging infections. SAM vaccines are based on engineered self-amplifying mRNA (SAM) replicons encoding an Ag, and formulated with a synthetic delivery system, and they induce broad-based immune responses in preclinical animal models. In our study, in vivo imaging shows that after the immunization, SAM Ag expression has an initial gradual increase...
April 17, 2017: Journal of Immunology: Official Journal of the American Association of Immunologists
https://www.readbyqxmd.com/read/28411393/global-exosome-transcriptome-profiling-reveals-biomarkers-for-multiple-sclerosis
#9
Igor Selmaj, Maria Cichalewska, Magdalena Namiecinska, Grazyna Galazka, Wojciech Horzelski, Krzysztof W Selmaj, Marcin P Mycko
OBJECTIVE: Accumulating evidence supports a role for exosomes in immune regulation. In this study, we investigated the total circulating exosome transcriptome in relapsing-remitting multiple sclerosis patients (RRMS) and healthy controls (HC). METHODS: Next generation sequencing (NGS) was used to define the global RNA profile of serum exosomes in 19 RRMS patients (9 in relapse, 10 in remission) and 10 HC. We analyzed 5 million reads and over 50,000 transcripts per sample, including a detailed analysis of microRNA (miRNA) differentially expressed in RRMS...
April 15, 2017: Annals of Neurology
https://www.readbyqxmd.com/read/28405197/mass-spectrometry-based-molecular-3d-cartography-of-plant-metabolites
#10
Dimitrios J Floros, Daniel Petras, Clifford A Kapono, Alexey V Melnik, Tie-Jun Ling, Rob Knight, Pieter C Dorrestein
Plants play an essential part in global carbon fixing through photosynthesis and are the primary food and energy source for humans. Understanding them thoroughly is therefore of highest interest for humanity. Advances in DNA and RNA sequencing and in protein and metabolite analysis allow the systematic description of plant composition at the molecular level. With imaging mass spectrometry, we can now add a spatial level, typically in the micrometer-to-centimeter range, to their compositions, essential for a detailed molecular understanding...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28404480/2d-and-3d-fish-of-expanded-repeat-rnas-in-human-lymphoblasts
#11
Martyna O Urbanek, Michał Michalak, Wlodzimierz J Krzyzosiak
The first methods for visualizing RNAs within cells were designed for simple imaging of specific transcripts in cells or tissues and since then significant technical advances have been made in this field. Today, high-resolution images can be obtained, enabling visualization of single transcript molecules, quantitative analyses of images, and precise localization of RNAs within cells as well as co-localization of transcripts with specific proteins or other molecules. In addition, tracking of RNA dynamics within single cell has become possible...
April 9, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28399446/enzyme-mediated-tagging-of-rna
#12
REVIEW
Lea Anhäuser, Andrea Rentmeister
RNA molecules can play diverse roles in the cell owing to their secondary structure dynamics and various binding modes. Studying localization and dynamics of RNA in vitro or in cells requires tagging with suitable reporter molecules-fluorophores being the most prominent ones. Enzymatic RNA labeling approaches are currently emerging as valuable alternatives to purely chemical synthesis and to binding- or hybridization-based RNA-imaging approaches. Different classes of enzymes allow for cotranscriptional or posttranscriptional installation of small functional groups in RNA...
April 8, 2017: Current Opinion in Biotechnology
https://www.readbyqxmd.com/read/28396000/measuring-signaling-and-rna-seq-in-the-same-cell-links-gene-expression-to-dynamic-patterns-of-nf-%C3%AE%C2%BAb-activation
#13
Keara Lane, David Van Valen, Mialy M DeFelice, Derek N Macklin, Takamasa Kudo, Ariel Jaimovich, Ambrose Carr, Tobias Meyer, Dana Pe'er, Stéphane C Boutet, Markus W Covert
Signaling proteins display remarkable cell-to-cell heterogeneity in their dynamic responses to stimuli, but the consequences of this heterogeneity remain largely unknown. For instance, the contribution of the dynamics of the innate immune transcription factor nuclear factor κB (NF-κB) to gene expression output is disputed. Here we explore these questions by integrating live-cell imaging approaches with single-cell sequencing technologies. We used this approach to measure both the dynamics of lipopolysaccharide-induced NF-κB activation and the global transcriptional response in the same individual cell...
April 4, 2017: Cell Systems
https://www.readbyqxmd.com/read/28390866/activation-of-transforming-growth-factor-beta-1-signaling-in-gastric-cancer-associated-fibroblasts-increases-their-motility-via-expression-of-rhomboid-5-homolog-2-and-ability-to-induce-invasiveness-of-gastric-cancer-cells
#14
Takatsugu Ishimoto, Keisuke Miyake, Tannistha Nandi, Masakazu Yashiro, Nobuyuki Onishi, Kie Kyon Huang, Suling Joyce Lin, Ramnarayanan Kalpana, Su Ting Tay, Yuka Suzuki, Byoung Chul Cho, Daisuke Kuroda, Kota Arima, Daisuke Izumi, Masaaki Iwatsuki, Yoshifumi Baba, Eiji Oki, Masayuki Watanabe, Hideyuki Saya, Kosei Hirakawa, Hideo Baba, Patrick Tan
BACKGROUND & AIMS: Fibroblasts that interact with cancer cells are called cancer-associated fibroblasts (CAFs)-they promote progression of different tumor types. We investigated the characteristics and functions of CAFs in diffuse-type gastric cancers (DGCs) by analyzing features of their genome and gene expression patterns. METHODS: We isolated CAFs and adjacent non-cancer fibroblasts (NFs) from 110 GC tissues from patients who underwent gastrectomy in Japan from 2008 through 2016...
April 5, 2017: Gastroenterology
https://www.readbyqxmd.com/read/28387814/grey-and-white-matter-abnormalities-in-treated-hiv-disease-and-their-relationship-to-cognitive-function
#15
Jonathan Underwood, James H Cole, Matthan Caan, Davide De Francesco, Robert Leech, Rosan A van Zoest, Tanja Su, Gert J Geurtsen, Ben A Schmand, Peter Portegies, Maria Prins, Ferdinand W N M Wit, Caroline A Sabin, Charles Majoie, Peter Reiss, Alan Winston, David J Sharp
Background: Long-term comorbidities such as cognitive impairment remain prevalent in otherwise effectively treated people-living-with-HIV. We investigate the relationship between cognitive impairment and brain structure in successfully treated patients using multi-modal neuroimaging from the Co-morBidity in Relation to AIDS (COBRA) cohort. Methods: Cognitive function, brain tissue volumes and white matter microstructure were assessed in 134 HIV-positive patients and 79 controls...
April 6, 2017: Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America
https://www.readbyqxmd.com/read/28382156/theranostic-nucleic-acid-binding-nanoprobe-exerts-anti-inflammatory-and-cytoprotective-effects-in-ischemic-injury
#16
Howard H Chen, Hushan Yuan, Hoonsung Cho, Yan Feng, Soeun Ngoy, Anand T N Kumar, Ronglih Liao, Wei Chao, Lee Josephson, David E Sosnovik
Extracellular nucleic acids are proinflammatory molecules that have been implicated in a diverse range of diseases. We report here the development of a multivalent nucleic acid scavenging nanoprobe, where the fluorochrome thiazole orange (TO) is conjugated to a polymeric 40 kDa dextran carrier. Dextran-TO (Dex-TO) has nanomolar affinity for mammalian and bacterial nucleic acids and attenuates the production of inflammatory cytokines from activated macrophages exposed to DNA and RNA. Mice with myocardial ischemia reperfusion that were treated with Dex-TO showed a decrease in myocardial macrophage infiltration at 24 hours (p<0...
2017: Theranostics
https://www.readbyqxmd.com/read/28379574/the-role-of-angiogenesis-in-group-3-medulloblastoma-pathogenesis-and-survival
#17
Eric M Thompson, Stephen T Keir, Talaignair Venkatraman, Christopher Lascola, Kristen W Yeom, Andrew B Nixon, Yingmiao Liu, Daniel Picard, Marc Remke, Darell D Bigner, Vijay Ramaswamy, Michael D Taylor
Background: Of the 4 medulloblastoma subgroups, Group 3 is the most aggressive but the importance of angiogenesis is unknown. This study sought to determine the role of angiogenesis and identify clinically relevant biomarkers of tumor vascularity and survival in Group 3 medulloblastoma. Methods: VEGFA mRNA expression and survival from several patient cohorts were analyzed. Group 3 xenografts were implanted intracranially in nude rats. Dynamic susceptibility weighted (DSC) MRI and susceptibility weighted imaging (SWI) were obtained...
April 3, 2017: Neuro-oncology
https://www.readbyqxmd.com/read/28375743/engineering-and-in-vivo-applications-of-riboswitches
#18
Zachary F Hallberg, Yichi Su, Rebekah Z Kitto, Ming C Hammond
Riboswitches are common gene regulatory units mostly found in bacteria that are capable of altering gene expression in response to a small molecule. These structured RNA elements consist of two modular subunits: an aptamer domain that binds with high specificity and affinity to a target ligand and an expression platform that transduces ligand binding to a gene expression output. Significant progress has been made in engineering novel aptamer domains for new small molecule inducers of gene expression. Modified expression platforms have also been optimized to function when fused with both natural and synthetic aptamer domains...
March 30, 2017: Annual Review of Biochemistry
https://www.readbyqxmd.com/read/28375678/intracellular-distribution-and-nuclear-activity-of-antisense-oligonucleotides-after-unassisted-uptake-in-myoblasts-and-differentiated-myotubes-in-vitro
#19
Anchel González-Barriga, Bram Nillessen, Julia Kranzen, Ingeborg D G van Kessel, Huib J E Croes, Begoña Aguilera, Peter C de Visser, Nicole A Datson, Susan A M Mulders, Judith C T van Deutekom, Bé Wieringa, Derick G Wansink
Clinical efficacy of antisense oligonucleotides (AONs) for the treatment of neuromuscular disorders depends on efficient cellular uptake and proper intracellular routing to the target. Selection of AONs with highest in vitro efficiencies is usually based on chemical or physical methods for forced cellular delivery. Since these methods largely bypass existing natural mechanisms for membrane passage and intracellular trafficking, spontaneous uptake and distribution of AONs in cells are still poorly understood...
April 4, 2017: Nucleic Acid Therapeutics
https://www.readbyqxmd.com/read/28373576/dual-bioluminescence-and-near-infrared-fluorescence-monitoring-to-evaluate-spherical-nucleic-acid-nanoconjugate-activity-in-vivo
#20
Timothy L Sita, Fotini M Kouri, Lisa A Hurley, Timothy J Merkel, Alexandra Chalastanis, Jasmine L May, Serena T Ghelfi, Lisa E Cole, Thomas C Cayton, Stacey N Barnaby, Anthony J Sprangers, Nikunjkumar Savalia, Charles David James, Andrew Lee, Chad A Mirkin, Alexander H Stegh
RNA interference (RNAi)-based gene regulation platforms have shown promise as a novel class of therapeutics for the precision treatment of cancer. Techniques in preclinical evaluation of RNAi-based nanoconjugates have yet to allow for optimization of their gene regulatory activity. We have developed spherical nucleic acids (SNAs) as a blood-brain barrier-/blood-tumor barrier-penetrating nanoconjugate to deliver small interfering (si) and micro (mi)RNAs to intracranial glioblastoma (GBM) tumor sites. To identify high-activity SNA conjugates and to determine optimal SNA treatment regimens, we developed a reporter xenograft model to evaluate SNA efficacy in vivo...
April 3, 2017: Proceedings of the National Academy of Sciences of the United States of America
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