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https://www.readbyqxmd.com/read/29140259/ramanomics-new-omics-disciplines-using-micro-raman-spectrometry-with-biomolecular-component-analysis-for-molecular-profiling-of-biological-structures
#1
REVIEW
Andrey N Kuzmin, Artem Pliss, Paras N Prasad
Modern instrumentation for Raman microspectroscopy and current techniques in analysis of spectral data provide new opportunities to study molecular interactions and dynamics at subcellular levels in biological systems. Implementation of biomolecular component analysis (BCA) to microRaman spectrometry provides basis for the emergence of Ramanomics, a new biosensing discipline with unprecedented capabilities to measure concentrations of distinct biomolecular groups in live cells and organelles. Here we review the combined use of microRaman-BCA techniques to probe absolute concentrations of proteins, DNA, RNA and lipids in single organelles of live cells...
November 15, 2017: Biosensors
https://www.readbyqxmd.com/read/29136454/immediate-label-free-ex-vivo-evaluation-of-human-brain-tumor-biopsies-with-confocal-reflectance-microscopy
#2
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/29133129/hbsag-mrna-degradation-induced-by-dihydroquinolizinone-molecule-depends-on-hbv-posttranscriptional-regulatory-element
#3
Tianlun Zhou, Timothy Block, Fei Liu, Andrew S Kondratowicz, Liren Sun, Siddhartha Rawat, Jeffrey Branson, Fang Guo, Hongyan Liang, Lauren Bailey, Chris Moore, Xiaohe Wang, Andy Cuconatti, Min Gao, Amy C H Lee, Troy Harasym, Tim Chiu, Dimitar Gotchev, Bruce Dorsey, Rene Rijnbrand, Michael J Sofia
In pursuit of novel therapeutics targeting the hepatitis B virus (HBV) infection, we evaluated a dihydroquinolizinone compound (DHQ-1) that possessed nanomolar activities against the production of virion and surface protein (HBsAg) in tissue culture. This compound also showed broad HBV genotype coverage and was inactive against a panel of DNA and RNA viruses of other species. Oral administration of DHQ-1 in the AAV-HBV mouse model resulted in a strong reduction of serum HBsAg as soon as 4 days following the commencement of treatment...
November 10, 2017: Antiviral Research
https://www.readbyqxmd.com/read/29130207/rna-live-imaging-in-the-model-microorganism-ustilago-maydis
#4
Sabrina Zander, Kira Müntjes, Michael Feldbrügge
An essential feature of protein expression is the tight regulation of when and where a protein is translated from its cognate mRNA. This spatiotemporal expression is particularly important in guaranteeing the correct and efficient targeting of proteins to defined subcellular sites. In order to achieve local translation, mRNAs must be deposited at specific locations. A common mechanism is the active transport of mRNAs along the actin or microtubule cytoskeleton. To study such dynamic transport processes in vivo RNA live imaging is the method of choice...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29130187/the-secret-life-of-rna-lessons-from-emerging-methodologies
#5
Caroline Medioni, Florence Besse
The last past decade has witnessed a revolution in our appreciation of transcriptome complexity and regulation. This remarkable expansion in our knowledge largely originates from the advent of high-throughput methodologies, and the consecutive discovery that up to 90% of eukaryotic genomes are transcribed, thus generating an unanticipated large range of noncoding RNAs (Hangauer et al., 15(4):112, 2014). Besides leading to the identification of new noncoding RNA species, transcriptome-wide studies have uncovered novel layers of posttranscriptional regulatory mechanisms controlling RNA processing, maturation or translation, and each contributing to the precise and dynamic regulation of gene expression...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29116221/establishment-of-a-fluorescent-in-situ-hybridization-assay-for-imaging-hepatitis-b-virus-nucleic-acids-in-cell-culture-models
#6
Xiaonan Zhang, Lei Yue, Zhanqing Zhang, Zhenghong Yuan
While chronic hepatitis B remains a global public health problem, the detailed spatiotemporal dynamics of the key molecular events leading to the multiplication and egress of hepatitis B virus (HBV) are still largely unclear. Previously, we developed a chromogenic in situ hybridization assay for detection of HBV RNA, DNA and covalently closed circular DNA in clinical liver biopsies. Here, we report the establishment of a fluorescent in situ hybridization method for the visualization of HBV RNA, HBV core particle DNA and intranuclear DNA in a tetracycline-inducible HBV replication system (HepAD38) and a de novo infection system (HepG2-NTCP)...
November 8, 2017: Emerging Microbes & Infections
https://www.readbyqxmd.com/read/29112323/identification-of-gbf1-as-a-cellular-factor-required-for-hepatitis-e-virus-rna-replication
#7
Rayan Farhat, Maliki Ankavay, Nadjet Lebsir, Jérôme Gouttenoire, Catherine L Jackson, Czeslaw Wychowski, Darius Moradpour, Jean Dubuisson, Yves Rouille, Laurence Cocquerel
The hepatitis E virus (HEV) genome is a single-stranded, positive-sense RNA that encodes three proteins including the ORF1 replicase. Mechanisms of HEV replication in host cells are unclear and only a few cellular factors involved in this step have been identified so far. Here, we used brefeldin A (BFA) that blocks the activity of the cellular Arf guanine nucleotide exchange factors GBF1, BIG1 and BIG2, which play a major role in reshuffling of cellular membranes. We showed that BFA inhibits HEV replication in a dose-dependent manner...
November 7, 2017: Cellular Microbiology
https://www.readbyqxmd.com/read/29109780/metabolomic-profiling-of-extracellular-vesicles-and-alternative-normalization-methods-reveal-enriched-metabolites-and-strategies-to-study-prostate-cancer-related-changes
#8
Maija Puhka, Maarit Takatalo, Maria-Elisa Nordberg, Sami Valkonen, Jatin Nandania, Maria Aatonen, Marjo Yliperttula, Saara Laitinen, Vidya Velagapudi, Tuomas Mirtti, Olli Kallioniemi, Antti Rannikko, Pia R-M Siljander, Taija Maria Af Hällström
Body fluids are a rich source of extracellular vesicles (EVs), which carry cargo derived from the secreting cells. So far, biomarkers for pathological conditions have been mainly searched from their protein, (mi)RNA, DNA and lipid cargo. Here, we explored the small molecule metabolites from urinary and platelet EVs relative to their matched source samples. As a proof-of-concept study of intra-EV metabolites, we compared alternative normalization methods to profile urinary EVs from prostate cancer patients before and after prostatectomy and from healthy controls...
2017: Theranostics
https://www.readbyqxmd.com/read/29100074/plexin-b2-mediates-physiologic-and-pathologic-functions-of-angiogenin
#9
Wenhao Yu, Kevin A Goncalves, Shuping Li, Hiroko Kishikawa, Guangjie Sun, Hailing Yang, Nil Vanli, Yunxia Wu, Yuxiang Jiang, Miaofen G Hu, Roland H Friedel, Guo-Fu Hu
Angiogenin (ANG) is a secreted ribonuclease (RNase) with cell-type- and context-specific roles in growth, survival, and regeneration. Although these functions require receptor-mediated endocytosis and appropriate subcellular localization, the identity of the cell surface receptor remains undefined. Here, we show that plexin-B2 (PLXNB2) is the functional receptor for ANG in endothelial, cancer, neuronal, and normal hematopoietic and leukemic stem and progenitor cells. Mechanistically, PLXNB2 mediates intracellular RNA processing that contribute to cell growth, survival, and regenerative capabilities of ANG...
November 2, 2017: Cell
https://www.readbyqxmd.com/read/29095923/pofut1-point-mutations-that-disrupt-o-fucosyltransferase-activity-destabilize-the-protein-and-abolish-notch1-signaling-during-mouse-somitogenesis
#10
Rieko Ajima, Emiko Suzuki, Yumiko Saga
The segmental pattern of the vertebrate body is established via the periodic formation of somites from the presomitic mesoderm (PSM). This periodical process is controlled by the cyclic and synchronized activation of Notch signaling in the PSM. Protein O-fucosyltransferase1 (Pofut1), which transfers O-fucose to the EGF domains of the Notch1 receptor, is indispensable for Notch signaling activation. The Drosophila homologue Ofut1 was reported to control Notch localization via two different mechanisms, working as a chaperone for Notch or as a regulator of Notch endocytosis...
2017: PloS One
https://www.readbyqxmd.com/read/29093729/an-update-on-the-intracellular-and-intercellular-trafficking-of-carmoviruses
#11
REVIEW
José A Navarro, Vicente Pallás
Despite harboring the smallest genomes among plant RNA viruses, carmoviruses have emerged as an ideal model system for studying essential steps of the viral cycle including intracellular and intercellular trafficking. Two small movement proteins, formerly known as double gene block proteins (DGBp1 and DGBp2), have been involved in the movement throughout the plant of some members of carmovirus genera. DGBp1 RNA-binding capability was indispensable for cell-to-cell movement indicating that viral genomes must interact with DGBp1 to be transported...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29079635/cefra-seq-reveals-broad-asymmetric-mrna-and-non-coding-rna-distribution-profiles-in-drosophila-and-human-cells
#12
Louis Philip Benoit Bouvrette, Neal A L Cody, Julie Bergalet, Fabio Alexis Lefebvre, Cédric Diot, Xiaofeng Wang, Mathieu Blanchette, Eric Lécuyer
Cells are highly asymmetrical, a feature that relies on the sorting of molecular constituents, including proteins, lipids and nucleic acids, to distinct subcellular locales. The localization of RNA molecules is an important layer of gene regulation required to modulate localized cellular activities, although its global prevalence remains unclear. We combine biochemical cell fractionation with RNA sequencing (CeFra-seq) analysis to assess the prevalence and conservation of RNA asymmetric distribution on a transcriptome-wide scale in Drosophila and human cells...
October 27, 2017: RNA
https://www.readbyqxmd.com/read/29073276/riboproteomics-a-versatile-approach-for-the-identification-of-host-protein-interaction-network-in-plant-pathogenic-noncoding-rnas
#13
Sonali Chaturvedi, A L N Rao
Pathogenic or non-pathogenic small (17 to 30 nt) and long (>200 nt) non-coding RNAs (ncRNAs) have been implicated in the regulation of gene expression at transcriptional, post-transcriptional and epigenetic level by interacting with host proteins. However, lack of suitable experimental system precludes the identification and evaluation of the functional significance of host proteins interacting with ncRNAs. In this study, we present a first report on the application of riboproteomics to identify host proteins interacting with small, highly pathogenic, noncoding satellite RNA (sat-RNA) associated with Cucumber mosaic virus, the helper virus (HV)...
2017: PloS One
https://www.readbyqxmd.com/read/29071687/nuclear-cytometry-analysis-of-the-patterns-of-dna-synthesis-and-transcription-using-flow-cytometry-confocal-microscopy-and-rna-sequencing
#14
David W Galbraith, Elwira Sliwinska, Partha Samadder
Eukaryotes are defined by cells that contain a nucleus and other membrane-bound organelles. Cytometric analysis in situ, utilizing imaging, provides a useful understanding of the structure and function of the various subcellular components, particularly when combined with methods that preserve the living state. In terms of information provided by the observation of eukaryotic nuclei, imaging has provided a wealth of information about cellular multiplication. When organisms are present in multicellular form (tissues and organs), this property does not generally confound imaging cytometry...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29069457/nol12-is-a-multifunctional-rna-binding-protein-at-the-nexus-of-rna-and-dna-metabolism
#15
Daniel D Scott, Christian Trahan, Pierre J Zindy, Lisbeth C Aguilar, Marc Y Delubac, Eric L Van Nostrand, Srivathsan Adivarahan, Karen E Wei, Gene W Yeo, Daniel Zenklusen, Marlene Oeffinger
To counteract the breakdown of genome integrity, eukaryotic cells have developed a network of surveillance pathways to prevent and resolve DNA damage. Recent data has recognized the importance of RNA binding proteins (RBPs) in DNA damage repair (DDR) pathways. Here, we describe Nol12 as a multifunctional RBP with roles in RNA metabolism and genome maintenance. Nol12 is found in different subcellular compartments-nucleoli, where it associates with ribosomal RNA and is required for efficient separation of large and small subunit precursors at site 2; the nucleoplasm, where it co-localizes with the RNA/DNA helicase Dhx9 and paraspeckles; as well as GW/P-bodies in the cytoplasm...
October 23, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29062908/megamitochondria-formation-in-hepatocytes-of-patient-with-chronic-hepatitis-c-a-case-report
#16
Anna Wieczorek, Piotr M Stępień, Dorota Zarębska-Michaluk, Wiesław Kryczka, Paweł Pabjan, Teodora Król
Although chronic hepatitis C virus (HCV) infection affect 185 million people world-wide, pathomechanism of liver damage is still unclear. Electron microscopy can reveal liver injury in very early stage and help understanding the mechanisms that is crucial in the pathogenesis of chronic hepatitis C. We present the morphological changes in the liver of HCV infected 24-year-old female patient, using light and transmission electron microscopy. Examination by TEM revealed wide range of specific subcellular abnormalities in hepatocellular ultrastructure...
September 2017: Clin Exp Hepatol
https://www.readbyqxmd.com/read/29059327/evaluation-of-fluorescence-in-situ-hybridization-techniques-to-study-long-non-coding-rna-expression-in-cultured-cells
#17
Ricardo J Soares, Giulia Maglieri, Tony Gutschner, Sven Diederichs, Anders H Lund, Boye S Nielsen, Kim Holmstrøm
Deciphering the functions of long non-coding RNAs (lncRNAs) is facilitated by visualization of their subcellular localization using in situ hybridization (ISH) techniques. We evaluated four different ISH methods for detection of MALAT1 and CYTOR in cultured cells: a multiple probe detection approach with or without enzymatic signal amplification, a branched-DNA (bDNA) probe and an LNA-modified probe with enzymatic signal amplification. All four methods adequately stained MALAT1 in the nucleus in all of three cell lines investigated, HeLa, NHDF and T47D, and three of the methods detected the less expressed CYTOR...
October 20, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29046345/endoplasmic-reticulum-transmembrane-proteins-zdhhc1-and-sting-both-act-as-direct-adaptors-for-irf3-activation-in-teleost
#18
Xiaowen Xu, Meifeng Li, Zhen Wu, Haizhou Wang, Liqiang Wang, Keyi Huang, Xiancheng Liu, Qunhao Hou, Gang Lin, Chengyu Hu
IFN regulatory factor (IRF)3 is a central regulator for IFN-β expression in different types of pathogenic infections. Mammals have various pathogenic sensors that are involved in monitoring pathogen intrusions. These sensors can trigger IRF3-mediated antiviral responses through different pathways. Endoplasmic reticulum-associated proteins stimulator of IFN gene (STING) and zinc finger DHHC-type containing 1 (ZDHHC1) are critical mediators of IRF3 activation in response to viral DNA infections. In this study, grass carp STING and ZDHHC1 were found to have some similar molecular features and subcellular localization, and both were upregulated upon stimulation with polyinosinic:polycytidylic acid, B-DNA, or Z-DNA...
October 18, 2017: Journal of Immunology: Official Journal of the American Association of Immunologists
https://www.readbyqxmd.com/read/29044170/phosphorylation-regulates-the-subcellular-localization-of-cucumber-mosaic-virus-2b-protein
#19
Katalin Nemes, Ákos Gellért, Asztéria Almási, Pál Vági, Réka Sáray, Katalin Kádár, Katalin Salánki
The 2b protein of Cucumber mosaic virus has a role in nearly all steps of the viral cycle including cell-to-cell movement, symptom induction and suppression of antiviral RNA silencing. Previous studies demonstrated the presence of 2b protein in the nucleus and in cytoplasm as well. Phosphorylation site of 2b protein is conserved in all CMV isolates, including proposed constitute motifs for casein kinase II and cyclin-dependent kinase 2. To discern the impact of 2b protein phosphorylation, we created eight different mutants to mimic the non-phosporylated (serine to alanine) as well as the phosphorylated state (serine to aspartic acid) of the protein...
October 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29036633/rna-sequencing-of-brassica-napus-reveals-cellular-redox-control-of-sclerotinia-infection
#20
Ian J Girard, Chaobo Tong, Michael G Becker, Xingyu Mao, Junyan Huang, Teresa de Kievit, W G Dilantha Fernando, Shengyi Liu, Mark F Belmonte
Brassica napus is one of the world's most valuable oilseeds and is under constant pressure by the necrotrophic fungal pathogen, Sclerotinia sclerotiorum, the causal agent of white stem rot. Despite our growing understanding of host pathogen interactions at the molecular level, we have yet to fully understand the biological processes and underlying gene regulatory networks responsible for determining disease outcomes. Using global RNA sequencing, we profiled gene activity at the first point of infection on the leaf surface 24 hours after pathogen exposure in susceptible (B...
September 27, 2017: Journal of Experimental Botany
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