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Judith Grau-Expósito, Carla Serra-Peinado, Lucia Miguel, Jordi Navarro, Adrià Curran, Joaquin Burgos, Imma Ocaña, Esteban Ribera, Ariadna Torrella, Bibiana Planas, Rosa Badía, Josep Castellví, Vicenç Falcó, Manuel Crespo, Maria J Buzon
Cells that actively transcribe HIV-1 have been defined as the "active viral reservoir" in HIV-infected individuals. However, important technical limitations have precluded the characterization of this specific viral reservoir during both treated and untreated HIV-1 infections. Here, we used a novel single-cell RNA fluorescence in situ hybridization-flow cytometry (FISH-flow) assay that requires only 15 million unfractionated peripheral blood mononuclear cells (PBMCs) to characterize the specific cell subpopulations that transcribe HIV RNA in different subsets of CD4+ T cells...
July 11, 2017: MBio
Riccardo Arrigucci, Yuri Bushkin, Felix Radford, Karim Lakehal, Pooja Vir, Richard Pine, December Martin, Jeffrey Sugarman, Yanlin Zhao, George S Yap, Alfred A Lardizabal, Sanjay Tyagi, Maria Laura Gennaro
We describe a flow-cytometry-based protocol for intracellular mRNA measurements in nonadherent mammalian cells using fluorescence in situ hybridization (FISH) probes. The method, which we call FISH-Flow, allows for high-throughput multiparametric measurements of gene expression, a task that was not feasible with earlier, microscopy-based approaches. The FISH-Flow protocol involves cell fixation, permeabilization and hybridization with a set of fluorescently labeled oligonucleotide probes. In this protocol, surface and intracellular protein markers can also be stained with fluorescently labeled antibodies for simultaneous protein and mRNA measurement...
June 2017: Nature Protocols
Kaley M Wilburn, Henry C Mwandumba, Kondwani C Jambo, Saikat Boliar, Sabrina Solouki, David G Russell, David W Gludish
8E5/LAV cells harbor a single HIV provirus, and are used frequently to generate standards for HIV genome quantification. Using flow cytometry-based in situ mRNA hybridization validated by qPCR, we find that different batches of 8E5 cells contain varying numbers of cells lacking viral mRNA and/or viral genomes. These findings raise concerns for studies employing 8E5 cells for quantitation, and highlight the value of mRNA FISH and flow cytometry in the detection and enumeration of HIV-positive cells.
August 11, 2016: Retrovirology
Mei Jiang, Zhang-Lin Zhang, Yan-Hong Xin, Shu-Yuan Liu, Xin Li, La-Gen Wan
OBJECTIVE: To study the signal patterns of dual color dual fusion fluorescence in situ hybridization (DCDF-FISH) for detection of genetic abnormality in adult acute lymphoblastic leukemia (ALL) patients and their diagnostic value and clinical application. METHODS: The clinical data of 68 ALL patients confirmed in our hospital were analyzed retrospectively; The bone marrow samples were detected by DCDF-FISH, flow cytometry, conventional cytogenetics (CCG), reverse transcriptase polymerase chain reaction (RT-PCR), and the correlation of these results was compared...
April 2016: Zhongguo Shi Yan Xue Ye Xue za Zhi
Kathryn A Fuller, Sophia Bennett, Henry Hui, Aron Chakera, Wendy N Erber
Fluorescence in situ hybridization (FISH) is a microscopy technique which uses a fluorescent probe to detect DNA sequences and is generally performed on metaphase spreads or interphase nuclei of intact cells on a slide. In a diagnostic laboratory, cells are hybridized with fluorescent probes and up to 200 cells counted for the number of cells with probe "spots." Recent modifications to standard FISH include immuno-FISH, where chromosomal abnormalities are detected only in cells by their phenotype, and S-FISH where probe hybridization is performed on whole cells in suspension...
August 2016: Cytometry. Part A: the Journal of the International Society for Analytical Cytology
Pooja Vir, Riccardo Arrigucci, Karim Lakehal, Amy L Davidow, Richard Pine, Sanjay Tyagi, Yuri Bushkin, Alfred Lardizabal, Maria Laura Gennaro
RNA flow cytometry (FISH-Flow) achieves high-throughput measurement of single-cell gene expression by combining in-situ nucleic acid hybridization with flow cytometry. We tested whether antigen-specific T-cell responses detected by FISH-Flow correlated with latent tuberculosis infection (LTBI), a condition affecting one-third of the world population. Peripheral-blood mononuclear cells from donors, identified as positive or negative for LTBI by current medical practice, were stimulated ex vivo with mycobacterial antigen...
2015: PloS One
Fabíola Carvalho Santos, Romain Guyot, Cacilda Borges do Valle, Lucimara Chiari, Vânia Helena Techio, Pat Heslop-Harrison, André Luís Laforga Vanzela
Like other eukaryotes, the nuclear genome of plants consists of DNA with a small proportion of low-copy DNA (genes and regulatory sequences) and very abundant DNA sequence motifs that are repeated thousands up to millions of times in the genomes including transposable elements (TEs) and satellite DNA. Retrotransposons, one class of TEs, are sequences that amplify via an RNA intermediate and reinsert into the genome, are often the major fraction of a genome. Here, we put research on retrotransposons into the larger context of plant repetitive DNA and genome behaviour, showing features of genome evolution in a grass genus, Brachiaria, in relation to other plant species...
September 2015: Chromosome Research
Juliette Gaillard, Marielle Thomas, Angélique Lazartigues, Bénilde Bonnefille, Christelle Pallez, Xavier Dauchy, Cyril Feidt, Damien Banas
Barrage fishponds may represent a significant surface water area in some French regions. Knowledge on their effect on water resources is therefore necessary for the development of appropriate water quality management plans at the regional scale. Although there is much information on the nutrient removal capacity of these water bodies, little attention has been paid to other agricultural contaminants such as pesticides. The present paper reports the results of a 1-year field monitoring of pesticide concentrations and water flows measured upstream and downstream from a fishpond in North East France to evaluate its capacity in reducing pesticide loads...
January 2016: Environmental Science and Pollution Research International
Knut Marius Myrvold, Brian P Kennedy
Self-thinning patterns are frequently used to describe density dependence in populations on timescales shorter than the organism's life span and have been used to infer carrying capacity of the environment. Among mobile animals, this concept has been used to document density dependence in stream salmonids, which compete over access to food and space. The carrying capacity, growth conditions, and initial cohort sizes often vary between streams and stream sections, which would influence the onset and strength of the density dependence...
August 2015: Ecology and Evolution
M E Barnes, C R Hewitt, T M Parker
This study examined occupational noise within two rearing facilities at a production fish hatchery and evaluated two simple noise reduction techniques. Ambient noise levels in the hatchery tank room ranged from 50 dB in the absence of flowing water to over 73 dB when water was flowing to all 35 tanks under typical hatchery operating procedures. Covering the open standpipes did not significantly reduce noise levels. However, placing partial tank covers over the top of the tanks above the water inlet significantly reduced noise levels, both with and without the use of standpipe covers...
July 2015: Journal of Agricultural Safety and Health
Lidia Marszał, Dagmara Błońska
The aim of the current study was to examine whether environmental conditions may explain interpopulation variation in fecundity and egg size of the spirlin from two rivers of the Vistula River basin. The obtained results indicated that the reproductive performance, including the gonadosomatic index, was similar in both rivers and fecundity increased with total length of females. The observed differences in water temperatures and flow speed between the rivers were too small to cause discernible differences in the reproductive performance of fish...
September 2015: Reproductive Biology
Khaled A Abdel-Moein, Hossam Saeed, Ahmed Samir
Helicobacter pylori is one of the most common human pathogens worldwide with serious clinical outcomes. Although, H. pylori is a major water-borne pathogen, its occurrence in fish is still unknown. This leads us to conduct the current study in order to clarify this point and to investigate the potential role of fish in the epidemiology of H. pylori. For this purpose, fecal samples were obtained from 315 fish from different species and were caught from various aquatic environments at different localities in Egypt...
December 2015: Acta Tropica
Ghaleb Elyamany, Ali Matar Alzahrani, Eman Al Mussaed, Hassan Aljasem, Sultan Alotaibi, Hatem Elghezal
The recent World Health Organization (WHO) classification defines mantle cell lymphoma (MCL) as a distinct entity characterized by a unique immunophenotype and a molecular hallmark of chromosomal translocation t(11;14)(q13;q32). We report an unusual case of an advanced stage of CD5 negative MCL with a blastoid variant with a massive bone marrow (BM) necrosis as an initial presenting feature, with no adenopathy or hepatosplenomegaly. The pathologic features showed blastoid variant of MCL and flow cytometry showed that the tumor cells were CD5-, CD19+, CD20+, FMC-7+, CD23-, and lambda light chain restricted...
2015: Case Reports in Hematology
Elina Laanto, Jaana K H Bamford, Janne J Ravantti, Lotta-Riina Sundberg
Flavobacterium columnare, the causative agent of columnaris disease in fish, causes millions of dollars of losses in the US channel catfish industry alone, not to mention aquaculture industry worldwide. Novel methods are needed for the control and treatment of bacterial diseases in aquaculture to replace traditionally used chemotherapies. A potential solution could be the use of phages, i.e., bacterial viruses, host-specific and self-enriching particles that can be can easily distributed via water flow. We examined the efficacy of phages to combat columnaris disease...
2015: Frontiers in Microbiology
M I Ríos-Pulgarín, M Barletta, N J Mancera-Rodríguez
The seasonal and interannual changes of the fish assemblage in the main channel and littoral zone of the Guarinó River, a torrential system located in the Colombian Andean foothills, were examined in relation to the physical and chemical environmental changes associated with the hydrological cycle and the El Niño-La Niña-Southern Oscillation (ENSO) between 2007 and 2010. Four samplings per year (in dry season and high water) were performed. Environmental variables (temperature, pH, conductivity, turbidity, oxygen, total nitrogen, orthophosphate, depth and flow rate) were contrasted with ANOVAs and a discriminant analysis to establish temporal patterns...
July 2016: Journal of Fish Biology
Jenna E Cavallin, Kathleen M Jensen, Michael D Kahl, Daniel L Villeneuve, Kathy E Lee, Anthony L Schroeder, Joe Mayasich, Evan P Eid, Krysta R Nelson, Rebecca Y Milsk, Brett R Blackwell, Jason P Berninger, Carlie A LaLone, Chad Blanksma, Terri Jicha, Colleen Elonen, Rodney Johnson, Gerald T Ankley
Wastewater treatment plant (WWTP) effluents are known contributors of chemical mixtures into the environment. Of particular concern are endocrine-disrupting compounds, such as estrogens, which can affect the hypothalamic-pituitary-gonadal axis function in exposed organisms. The present study examined reproductive effects in fathead minnows exposed for 21 d to a historically estrogenic WWTP effluent. Fathead minnow breeding pairs were held in control water or 1 of 3 effluent concentrations (5%, 20%, and 100%) in a novel onsite, flow-through system providing real-time exposure...
March 2016: Environmental Toxicology and Chemistry
F Huhn, W M van Rees, M Gazzola, D Rossinelli, G Haller, P Koumoutsakos
Undulatory swimmers flex their bodies to displace water, and in turn, the flow feeds back into the dynamics of the swimmer. At moderate Reynolds number, the resulting flow structures are characterized by unsteady separation and alternating vortices in the wake. We use the flow field from simulations of a two-dimensional, incompressible viscous flow of an undulatory, self-propelled swimmer and detect the coherent Lagrangian vortices in the wake to dissect the driving momentum transfer mechanisms. The detected material vortex boundary encloses a Lagrangian control volume that serves to track back the vortex fluid and record its circulation and momentum history...
August 2015: Chaos
Li Tan, Xiaoping Wei, Lixia Zheng, Jincai Zeng, Haibo Liu, Shaojiang Yang, Huo Tan
PURPOSE: The aim of this study was to investigate how the amplification of HMGA2 contributes to acute myeloid leukemia (AML) cell proliferation. METHODS: The amplification and expression of HMGA2 were examined by FISH, qRT-PCR and Western blot in AML cases. The effect of HMGA2 knockdown on cell proliferation was analyzed with XTT, colony-forming assays and BrdUrd incorporation assays. The effects of HMGA2 knockdown on cell cycle were studied by flow cytometry analysis...
February 2016: Journal of Cancer Research and Clinical Oncology
Aryane Campos Reis, Lyderson Facio Viccini, Saulo Marçal de Sousa
Accessions of Plectranthusbarbatus (Lamiaceae), a medicinal plant, were investigated using a cytogenetic approach and flow cytometry (FCM). Here, we describe for the first time details of the karyotype including chromosome morphology, physical mapping of GC rich bands (CMA3 banding), as well as the mapping of 45S and 5S rDNA sites. All accessions studied showed karyotypes with 2n = 30 small metacentric and submetacentric chromosomes. The CMA3 banding and fluorescent in situ hybridization techniques revealed coincidence between CMA3 bands and 45S rDNA sites (6 terminal marks) while for the 5S rDNA were observed 4 subterminal marks no coincident with CMA3 marks...
2015: Comparative Cytogenetics
Pengfei Li, Shina Wei, Lingli Zhou, Min Yang, Yepin Yu, Jingguang Wei, Guohua Jiang, Qiwei Qin
Singapore grouper iridovirus (SGIV) is a major viral pathogen of grouper aquaculture, and has caused heavy economic losses in China and South-east Asia. In this study, we generated four ssDNA aptamers against SGIV-infected grouper spleen (GS) cells using SELEX (systematic evolution of ligands by exponential enrichment) technology. Four aptamers exhibited high affinity to SGIV-infected GS cells, in particular the Q2 aptamer. Q2 had a binding affinity of 12.09 nM, the highest of the four aptamers. These aptamers also recognized SGIV-infected tissues with high levels of specificity...
November 2015: Journal of General Virology
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