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https://www.readbyqxmd.com/read/28109146/-cloning-expression-and-activity-identification-of-human-innate-immune-protein-apolipoprotein-b-mrna-editing-enzyme-catalytic-subunit-3a-apobec3a
#1
Shan Cheng, Liyan Cao, Juan Du, Wenyong Wang, Yanhai Guo
Objective To construct the expression vector of apolipoprotein B mRNA editing enzyme catalytic subunit 3A (APOBEC3A), express APOBEC3A in eukaryotic cells and identify its cytosine deaminase activity. Methods The APOBEC3A gene was obtained by PCR and inserted into the eukaryotic expression vector pcDNA3.0(+). The recombinant vector pcDNA3.0-APOBEC3A was then transfected into HEK293T and HepG2 cells after confirmed by DNA sequencing. The recombinant protein was purified by Ni-NTA HisBind affinity column. Western blot analysis was used to detect the expression of APOBEC3A protein...
February 2017: Xi Bao Yu Fen Zi Mian Yi Xue za Zhi, Chinese Journal of Cellular and Molecular Immunology
https://www.readbyqxmd.com/read/28108447/mirmine-a-database-of-human-mirna-expression-profiles
#2
Bharat Panwar, Gilbert S Omenn, Yuanfang Guan
MOTIVATION: MicroRNAs (miRNAs) are small non-coding RNAs that are involved in post-transcriptional regulation of gene expression. In this high-throughput sequencing era, a tremendous amount of RNA-seq data is accumulating, and full utilization of publicly available miRNA data is an important challenge. These data are useful to determine expression values for each miRNA, but quantification pipelines are in a primitive stage and still evolving; there are many factors that affect expression values significantly...
January 19, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28108401/constitutive-expression-and-characterization-of-a-surface-srs-ncsrs67-protein-of-neospora-caninum-with-no-orthologue-in-toxoplasma-gondii
#3
Marcos Alexandre Bezerra, Luiz Miguel Pereira, Aline Bononi, Carla Agostino Biella, Luciana Baroni, Leticia Pollo-Oliveira, Ana Patrícia Yatsuda
Neospora caninum is a parasite of the Apicomplexa phylum responsible for abortion and losses of fertility in cattle. As part of its intracellular cycle, the first interaction of the parasite with the target cell is performed with the surface proteins known as the SRS superfamily (Surface Antigen Glycoprotein - Related Sequences). SAG related or SRS proteins have been a target of intense research due to its immunodominant pattern, exhibiting potential as diagnostic and/or vaccine candidates. The aim of this study was the cloning, expression and characterization of the gene NcSRS67 of N...
January 17, 2017: Parasitology International
https://www.readbyqxmd.com/read/28107752/genome-nuclear-lamina-interactions-from-cell-populations-to-single-cells
#4
REVIEW
J Omar Yáñez-Cuna, Bas van Steensel
Lamina-associated domains (LADs) are large genomic regions that interact with the nuclear lamina (NL) and help to guide the spatial folding of chromosomes in the interphase nucleus. LADs have been linked to gene repression and other functions. Recent studies have begun to uncover some of the molecular players that drive LAD-NL interactions. A picture emerges in which DNA sequence, chromatin components and nuclear lamina proteins play an important role. Complementary to this, imaging and single-cell genomics approaches have revealed that some LAD-NL interactions are variable from cell to cell, while others are very stable...
January 17, 2017: Current Opinion in Genetics & Development
https://www.readbyqxmd.com/read/28107386/regulation-of-pi-2b-pilus-expression-in-hypervirulent-streptococcus-agalactiae-st-17-bm110
#5
Bruno Périchon, Noémi Szili, Laurence du Merle, Isabelle Rosinski-Chupin, Myriam Gominet, Samuel Bellais, Claire Poyart, Patrick Trieu-Cuot, Shaynoor Dramsi
The widely spread Streptococcus agalactiae (also known as Group B Streptococcus, GBS) "hypervirulent" ST17 clone is strongly associated with neonatal meningitis. The PI-2b locus is mainly found in ST17 strains but is also present in a few non ST17 human isolates such as the ST-7 prototype strain A909. Here, we analysed the expression of the PI-2b pilus in the ST17 strain BM110 as compared to the non ST17 A909. Comparative genome analyses revealed the presence of a 43-base pair (bp) hairpin-like structure in the upstream region of PI-2b operon in all 26 ST17 genomes, which was absent in the 8 non-ST17 strains carrying the PI-2b locus...
2017: PloS One
https://www.readbyqxmd.com/read/28107222/romidepsin-induced-hiv-1-viremia-during-effective-art-contains-identical-viral-sequences-with-few-deleterious-mutations
#6
Anni Winckelmann, Kirston Barton, Bonnie Hiener, Timothy E Schlub, Wei Shao, Thomas A Rasmussen, Lars Østergaard, Ole S Søgaard, Martin Tolstrup, Sarah Palmer
OBJECTIVE: To investigate the origin of the HIV-1 viremia induced by the latency-reversing agent romidepsin. DESIGN: Six individuals on suppressive antiretroviral therapy received romidepsin administered intravenously once weekly for three consecutive weeks. CD4+ T-cells were obtained at baseline, following the second and third romidepsin infusion, and 10 weeks after the final romidepsin treatment. METHODS: Single-genome sequencing of the env region was used to genetically characterize the virus from proviral DNA, the transcribed cell-associated RNA and the plasma RNA pool...
January 19, 2017: AIDS
https://www.readbyqxmd.com/read/28106924/incidence-clinicopathologic-features-and-fusion-transcript-landscape-of-translocation-renal-cell-carcinomas
#7
Marion Classe, Gabriel G Malouf, Xiaoping Su, Hui Yao, Erika J Thompson, Denaha J Doss, Valérie Grégoire, Julien Lenobin, Jean-Christophe Fantoni, Hélène Sudour-Bonnange, David Khayat, Sébastien Aubert, Nizar M Tannir, Xavier Leroy
AIMS: Translocation renal cell carcinoma (tRCC) is a rare subtype of kidney tumour characterized by translocations involving the transcription factor TFE3 or TFEB. tRCC was introduced into the World Health Organization classification in 2004, but much is still unknown about the natural history, clinicopathologic features, and outcomes of the disease. The aim of this study was to describe the landscape of fusion transcript in a large single-institution series of FISH confirmed tRCCs and then to confront it to morphological and clinical data...
January 20, 2017: Histopathology
https://www.readbyqxmd.com/read/28106558/validation-of-suspected-somatic-single-nucleotide-variations-in-the-brain-of-alzheimer-s-disease-patients
#8
Alberto Gomez-Ramos, Angel J Picher, Esther García, Patricia Garrido, Felix Hernandez, Eduardo Soriano, Jesús Avila
Next-generation sequencing techniques and genome-wide association study analyses have provided a huge amount of data, thereby enabling the identification of DNA variations and mutations related to disease pathogenesis. New techniques and software tools have been developed to improve the accuracy and reliability of this identification. Most of these tools have been designed to discover and validate single nucleotide variants (SNVs). However, in addition to germ-line mutations, human tissues bear genomic mosaicism, which implies that somatic events are present only in low percentages of cells within a given tissue, thereby hindering the validation of these variations using standard genetic tools...
January 19, 2017: Journal of Alzheimer's Disease: JAD
https://www.readbyqxmd.com/read/28106276/crispr-cas9-mediated-deletion-of-c1eis-inhibits-chicken-embryonic-stem-cell-differentiation-into-male-germ-cells-gallus-gallus
#9
Qisheng Zuo, Kai Jin, Yingjie Wang, Jiuzhou Song, Yani Zhang, Bichun Li
We previously found that C1EIS is preferentially expressed in Chicken spermatogonial stem cells (SSCs) by RNA sequencing (RNA-seq), so our current study focused on C1EIS's role in Chicken embryonic stem cells (ESCs) differentiation into male germ cells. We constructed a CRISPR/Cas9 vector targeting C1EIS. T7 endonuclease I (T7EI) digestion method and sequencing of TA cloning were used to detect the knock-out efficiency of the Single guide RNA (sgRNA) after the cas9/gRNA vector transfected into D fibroblasts 1(DF-1), ESCs and Chicken embryos...
January 20, 2017: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/28106114/multiplexing-pka-and-erk1-2-kinases-fret-biosensors-in-living-cells-using-single-excitation-wavelength-dual-colour-flim
#10
Claire Demeautis, François Sipieter, Julien Roul, Catherine Chapuis, Sergi Padilla-Parra, Franck B Riquet, Marc Tramier
Monitoring of different signalling enzymes in a single assay using multiplex biosensing provides a multidimensional workspace to elucidate biological processes, signalling pathway crosstalk, and determine precise sequence of events at the single living cell level. In this study, we interrogate the complexity in cAMP/PKA-MAPK/ERK1&2 crosstalk by using multi-parameter biosensing experiments to correlate biochemical activities simultaneously in time and space. Using a single excitation wavelength dual colour FLIM method we are able to detect fluorescence lifetime images of two donors to simultaneously measure PKA and ERK1&2 kinase activities in the same cellular localization by using FRET biosensors...
January 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28105940/integrated-single-cell-data-analysis-reveals-cell-specific-networks-and-novel-coactivation-markers
#11
Shila Ghazanfar, Adam J Bisogni, John T Ormerod, David M Lin, Jean Y H Yang
BACKGROUND: Large scale single cell transcriptome profiling has exploded in recent years and has enabled unprecedented insight into the behavior of individual cells. Identifying genes with high levels of expression using data from single cell RNA sequencing can be useful to characterize very active genes and cells in which this occurs. In particular single cell RNA-Seq allows for cell-specific characterization of high gene expression, as well as gene coexpression. RESULTS: We offer a versatile modeling framework to identify transcriptional states as well as structures of coactivation for different neuronal cell types across multiple datasets...
December 5, 2016: BMC Systems Biology
https://www.readbyqxmd.com/read/28105931/regulatory-single-nucleotide-polymorphisms-rsnps-at-the-promoters-1a-and-1b-of-the-human-apc-gene
#12
Marina Yu Matveeva, Elena V Kashina, Vasily V Reshetnikov, Leonid O Bryzgalov, Elena V Antontseva, Natalia P Bondar, Tatiana I Merkulova
BACKGROUND: Germline mutations in the coding sequence of the tumour suppressor APC gene give rise to familial adenomatous polyposis (which leads to colorectal cancer) and are associated with many other oncopathologies. The loss of APC function because of deletion of putative promoter 1A or 1B also results in the development of colorectal cancer. Since the regions of promoters 1A and 1B contain many single nucleotide polymorphisms (SNPs), the aim of this study was to perform functional analysis of some of these SNPs by means of an electrophoretic mobility shift assay (EMSA) and a luciferase reporter assay...
December 22, 2016: BMC Genetics
https://www.readbyqxmd.com/read/28105835/silver-nanoclusters-beacon-as-stimuli-responsive-versatile-platform-for-multiplex-dnas-detection-and-aptamer-substrate-complexes-sensing
#13
Guoliang Liu, Jingjing Li, Da-Qian Feng, Jun-Jie Zhu, Wei Wang
An activatable silver nanoclusters beacon (ASNCB) was synthesized through a facile one-pot approach and applied for multiplex DNAs, small molecule, and protein sensing. Multifunctional single-stranded DNA sequences are rationally designed and used for ASNCB in situ synthesis. Via target-responsive structure transformation of ASNCB, target recognition induced ASNCB conformational transition and lit up the fluorescent signal of silver nanoclusters. By further implementing two different color ASNCBs (520 and 600 nm), the parallel multiplexed analysis of two target genes (Influenza A virus genes H1N1 and H5N1) is achieved...
January 3, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28104713/multimerization-properties-of-piggymac-a-domesticated-piggybac-transposase-involved-in-programmed-genome-rearrangements
#14
Emeline Dubois, Nathalie Mathy, Vinciane Régnier, Julien Bischerour, Céline Baudry, Raphaëlle Trouslard, Mireille Bétermier
During sexual processes, the ciliate Paramecium eliminates 25-30% of germline DNA from its somatic genome. DNA elimination includes excision of ∼45 000 short, single-copy internal eliminated sequences (IESs) and depends upon PiggyMac (Pgm), a domesticated piggyBac transposase that is essential for DNA cleavage at IES ends. Pgm carries a core transposase region with a putative catalytic domain containing three conserved aspartic acids, and a downstream cysteine-rich (CR) domain. A C-terminal extension of unknown function is predicted to adopt a coiled-coil (CC) structure...
January 18, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28103803/variational-inference-for-rare-variant-detection-in-deep-heterogeneous-next-generation-sequencing-data
#15
Fan Zhang, Patrick Flaherty
BACKGROUND: The detection of rare single nucleotide variants (SNVs) is important for understanding genetic heterogeneity using next-generation sequencing (NGS) data. Various computational algorithms have been proposed to detect variants at the single nucleotide level in mixed samples. Yet, the noise inherent in the biological processes involved in NGS technology necessitates the development of statistically accurate methods to identify true rare variants. RESULTS: We propose a Bayesian statistical model and a variational expectation maximization (EM) algorithm to estimate non-reference allele frequency (NRAF) and identify SNVs in heterogeneous cell populations...
January 19, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28103286/mirnas-do-not-regulate-circadian-protein-synthesis-in-the-dinoflagellate-lingulodinium-polyedrum
#16
Steve Dagenais-Bellefeuille, Mathieu Beauchemin, David Morse
Dinoflagellates have been shown to express miRNA by bioinformatics and RNA blot (Northern) analyses. However, it is not yet known if miRNAs are able to alter gene expression in this class of organisms. We have assessed the possibility that miRNA may mediate circadian regulation of gene expression in the dinoflagellate Lingulodinium polyedrum using the Luciferin Binding Protein (LBP) as a specific example. LBP is a good candidate for regulation by miRNA since mRNA levels are constant over the daily cycle while protein synthesis is restricted by the circadian clock to a period of several hours at the start of the night phase...
2017: PloS One
https://www.readbyqxmd.com/read/28103239/identifying-t-cell-receptors-from-high-throughput-sequencing-dealing-with-promiscuity-in-tcr%C3%AE-and-tcr%C3%AE-pairing
#17
Edward S Lee, Paul G Thomas, Jeff E Mold, Andrew J Yates
Characterisation of the T cell receptors (TCR) involved in immune responses is important for the design of vaccines and immunotherapies for cancer and autoimmune disease. The specificity of the interaction between the TCR heterodimer and its peptide-MHC ligand derives largely from the juxtaposed hypervariable CDR3 regions on the TCRα and TCRβ chains, and obtaining the paired sequences of these regions is a standard for functionally defining the TCR. A brute force approach to identifying the TCRs in a population of T cells is to use high-throughput single-cell sequencing, but currently this process remains costly and risks missing small clones...
January 19, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28103133/role-of-choline-in-the-modulation-of-degenerative-processes-in-vivo-and-in-vitro-studies
#18
Tania Merinas-Amo, Inmaculada Tasset-Cuevas, Antonio M Díaz-Carretero, Ángeles Alonso-Moraga, Fernando Calahorro
The purpose of the present study was to examine the nutraceutical potential of choline as an added value to its well-known brain nutrient role. Several toxicity, antitoxicity, genotoxicity, antigenotoxicity, and longevity endpoints were checked in the somatic mutation and recombination test in in vivo Drosophila animal model. Cytotoxicity in human leukemia-60 cell line (HL-60) promyelocytic and NIH3T3 mouse fibroblast cells, proapoptotic DNA fragmentation, comet assay, methylation status, and macroautophagy (MA) activity were tested in in vitro assays...
January 19, 2017: Journal of Medicinal Food
https://www.readbyqxmd.com/read/28102837/precise-and-efficient-scarless-genome-editing-in-stem-cells-using-correct
#19
Dylan Kwart, Dominik Paquet, Shaun Teo, Marc Tessier-Lavigne
CRISPR/Cas9 is a promising tool for genome-editing DNA in cells with single-base-pair precision, which allows novel in vitro models of human disease to be generated-e.g., in pluripotent stem cells. However, the accuracy of intended sequence changes can be severely diminished by CRISPR/Cas9's propensity to re-edit previously modified loci, causing unwanted mutations (indels) alongside intended changes. Here we describe a genome-editing framework termed consecutive re-guide or re-Cas steps to erase CRISPR/Cas-blocked targets (CORRECT), which, by exploiting the use of highly efficacious CRISPR/Cas-blocking mutations in two rounds of genome editing, enables accurate, efficient and scarless introduction of specific base changes-for example, in human induced pluripotent (iPS) stem cells...
February 2017: Nature Protocols
https://www.readbyqxmd.com/read/28102546/ataluren-and-similar-compounds-specific-therapies-for-premature-termination-codon-class-i-mutations-for-cystic-fibrosis
#20
REVIEW
Aisha A Aslam, Colin Higgins, Ian P Sinha, Kevin W Southern
BACKGROUND: Cystic fibrosis is a common life-shortening genetic disorder in the Caucasian population (less common in other ethnic groups) caused by the mutation of a single gene that codes for the production of the cystic fibrosis transmembrane conductance regulator protein. This protein coordinates the transport of salt (and bicarbonate) across cell surfaces and the mutation most notably affects the airways. In the lungs of people with cystic fibrosis, defective protein results in a dehydrated surface liquid and compromised mucociliary clearance...
January 19, 2017: Cochrane Database of Systematic Reviews
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