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https://www.readbyqxmd.com/read/27935851/an-analysis-of-the-sequence-of-the-bad-gene-among-patients-with-maturity-onset-diabetes-of-the-young-mody
#1
Karolina Antosik, Piotr Gnyś, Przemysława Jarosz-Chobot, Małgorzata Myśliwiec, Agnieszka Szadkowska, Maciej Małecki, Wojciech Młynarski, Maciej Borowiec
BACKGROUND: Monogenic diabetes is a rare disease caused by single gene mutations. Maturity onset diabetes of the young (MODY) is one of the major forms of monogenic diabetes recognised in the paediatric population. To date, 13 genes have been related to MODY development. The aim of the study was to analyse the sequence of the BCL2-associated agonist of cell death (BAD) gene in patients with clinical suspicion of GCK-MODY, but who were negative for glucokinase (GCK) gene mutations. METHODS: A group of 122 diabetic patients were recruited from the "Polish Registry for Paediatric and Adolescent Diabetes - nationwide genetic screening for monogenic diabetes" project...
December 9, 2016: Journal of Pediatric Endocrinology & Metabolism: JPEM
https://www.readbyqxmd.com/read/27935608/a-peptide-based-synthetic-transcription-factor-selectively-down-regulates-the-proto-oncogene-cfos-in-tumour-cells-and-inhibits-proliferation
#2
Madhumita Chakraborty, Siddhartha Roy
Selectively regulating genes is an important goal in Chemical Biology. We report the development of a peptide-based synthetic transcription factor which binds the targeted DNA sequence with high affinity and single base-pair discrimination capability. When delivered inside a tumor cell, it regulated targeted genes selectively and inhibited cell proliferation.
December 9, 2016: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/27933274/screening-and-identification-of-an-h-2k-b-restricted-ctl-epitope-within-the-glycoprotein-of-hantaan-virus
#3
Rui-Xue Ma, Lin-Feng Cheng, Qi-Kang Ying, Rong-Rong Liu, Tie-Jun Ma, Xiao-Xiao Zhang, Zi-Yu Liu, Liang Zhang, Wei Ye, Fang-Lin Zhang, Zhi-Kai Xu, Fang Wang, Xing-An Wu
The cytotoxic T lymphocyte (CTL) response plays a key role in controlling viral infection, but only a few epitopes within the HTNV glycoprotein (GP) that are recognized by CTLs have been reported. In this study, we identified one murine HTNV GP-derived H2-K(b)-restricted CTL epitope in C57BL/6 mice, which could be used to design preclinical studies of vaccines for HTNV infection. First, 15 8-mer peptides were selected from the HTNV GP amino acid sequence based on a percentile rank of <=1% by IEDB which is the most comprehensive collection of epitope prediction and analysis tool...
2016: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/27932494/loss-of-a-doublecortin-dcx-domain-protein-causes-structural-defects-in-a-tubulin-based-organelle-of-toxoplasma-gondii-and-impairs-host-cell-invasion
#4
Eiji Nagayasu, Yu-Chen Hwang, Jun Liu, John M Murray, Ke Hu
The ∼6000 species in phylum Apicomplexa are single-celled obligate intracellular parasites. Their defining characteristic is the "apical complex", membranous and cytoskeletal elements at the apical end of the cell that participate in host-cell invasion. The apical complex of Toxoplasma gondii and some other apicomplexans includes a cone-shaped assembly, the "conoid", which (in T. gondii) comprises 14 spirally arranged fibers that are non-tubular polymers of tubulin. The tubulin dimers of the conoid fibers make canonical microtubules elsewhere in the same cell, suggesting that non-tubulin protein dictates their special arrangement in the conoid fibers...
December 8, 2016: Molecular Biology of the Cell
https://www.readbyqxmd.com/read/27932387/the-long-non-coding-rna-transcriptome-of-dictyostelium-discoideum-development
#5
Rafael D Rosengarten, Balaji Santhanam, Janez Kokosar, Gad Shaulsky
Dictyostelium discoideum live in the soil as single cells, engulfing bacteria and growing vegetatively. Upon starvation, tens of thousands of amoebae enter a developmental program that includes aggregation, multicellular differentiation, and sporulation. Major shifts across the protein-coding transcriptome accompany these developmental changes. However, no study has presented a global survey of long non-coding RNAs in D. discoideum To characterize the antisense and long intergenic non-coding RNA transcriptome, we analyzed previously published developmental time course samples using an RNA-sequencing library preparation method that selectively depletes ribosomal RNAs...
December 7, 2016: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/27932033/cellular-analysis-of-trophoblast-and-placenta
#6
Frances Wong, Brian J Cox
The placenta is composed of two lineages: the trophoblast and mesoderm. While morphological assessment of the placenta has highlighted major cell types and developmental structures, the human placenta is relatively unexplained on a molecular level. Current molecular analysis of the placenta has largely been confined to assessing whole organs that include both cell lineages and their differentiated progeny. This has confounded our understanding of the processes of placental development and function for two reasons...
November 30, 2016: Placenta
https://www.readbyqxmd.com/read/27931250/tracing-the-origin-of-disseminated-tumor-cells-in-breast-cancer-using-single-cell-sequencing
#7
Jonas Demeulemeester, Parveen Kumar, Elen K Møller, Silje Nord, David C Wedge, April Peterson, Randi R Mathiesen, Renathe Fjelldal, Masoud Zamani Esteki, Koen Theunis, Elia Fernandez Gallardo, A Jason Grundstad, Elin Borgen, Lars O Baumbusch, Anne-Lise Børresen-Dale, Kevin P White, Vessela N Kristensen, Peter Van Loo, Thierry Voet, Bjørn Naume
BACKGROUND: Single-cell micro-metastases of solid tumors often occur in the bone marrow. These disseminated tumor cells (DTCs) may resist therapy and lay dormant or progress to cause overt bone and visceral metastases. The molecular nature of DTCs remains elusive, as well as when and from where in the tumor they originate. Here, we apply single-cell sequencing to identify and trace the origin of DTCs in breast cancer. RESULTS: We sequence the genomes of 63 single cells isolated from six non-metastatic breast cancer patients...
December 9, 2016: Genome Biology
https://www.readbyqxmd.com/read/27931227/epigenetics-of-amphetamine-induced-sensitization-hdac5-expression-and-microrna-in-neural-remodeling
#8
Philip K Liu, Christina H Liu
BACKGROUND: Histone deacetylase (HDAC) activities modify chromatin structure and play a role in learning and memory during developmental processes. Studies of adult mice suggest HDACs are involved in neural network remodeling in brain repair, but its function in drug addiction is less understood. We aimed to examine in vivo HDAC5 expression in a preclinical model of amphetamine-induced sensitization (AIS) of behavior. We generated specific contrast agents to measure HDAC5 levels by in vivo molecular contrast-enhanced (MCE) magnetic resonance imaging (MRI) in amphetamine-naïve mice as well as in mice with AIS...
December 8, 2016: Journal of Biomedical Science
https://www.readbyqxmd.com/read/27929711/dual-effects-of-a-retn-single-nucleotide-polymorphism-snp-at-420-on-plasma-resistin-genotype-and-dna-methylation
#9
Hiroshi Onuma, Yasuharu Tabara, Ryoichi Kawamura, Jun Ohashi, Wataru Nishida, Yasunori Takata, Masaaki Ochi, Tatsuya Nishimiya, Yasumasa Ohyagi, Ryuichi Kawamoto, Katsuhiko Kohara, Tetsuro Miki, Haruhiko Osawa
CONTEXT: We previously reported that SNP (single nucleotide polymorphism) -420 C>G (rs1862513) in the promoter region of RETN was associated with type 2 diabetes. Plasma resistin was tightly correlated with SNP-420 genotypes. SNP-420 is a CpG-SNP affecting the sequence of CpG dinucleotides. OBJECTIVE: To examine whether methylation at SNP-420 affects plasma resistin, we analyzed plasma resistin and methylation at RETN SNP-420. DESIGN AND METHODS: Genomic DNA was extracted from peripheral white blood cells in 2,078 Japanese subjects...
December 8, 2016: Journal of Clinical Endocrinology and Metabolism
https://www.readbyqxmd.com/read/27929523/single-cell-barcoding-and-sequencing-using-droplet-microfluidics
#10
Rapolas Zilionis, Juozas Nainys, Adrian Veres, Virginia Savova, David Zemmour, Allon M Klein, Linas Mazutis
Single-cell RNA sequencing has recently emerged as a powerful tool for mapping cellular heterogeneity in diseased and healthy tissues, yet high-throughput methods are needed for capturing the unbiased diversity of cells. Droplet microfluidics is among the most promising candidates for capturing and processing thousands of individual cells for whole-transcriptome or genomic analysis in a massively parallel manner with minimal reagent use. We recently established a method called inDrops, which has the capability to index >15,000 cells in an hour...
January 2017: Nature Protocols
https://www.readbyqxmd.com/read/27926791/high-prevalence-of-mitf-staining-in-undifferentiated-pleomorphic-sarcoma-caution-in-use-of-melanocytic-markers-in-sarcoma
#11
Bonnie Choy, Elizabeth Hyjek, Anthony G Montag, Peter Pytel, Rex Haydon, Hue H Luu, Chao Jie Zhen, Bradley C Long, Sabah Kadri, Jeremy P Segal, Larissa V Furtado, Nicole A Cipriani
AIMS: Diagnosis of undifferentiated pleomorphic sarcoma (UPS) may be challenging, as other lesions with undifferentiated spindle cell morphology must be excluded, including melanoma. Microphthalmia-associated transcription factor (MiTF) stains nevi and epithelioid melanomas, as well as some mesenchymal neoplasms. We evaluated the prevalence of MiTF and melanocytic markers in UPS and a subset of atypical fibroxanthoma (AFX). METHODS AND RESULTS: MiTF, SOX10, Melan-A, HMB45, and S100 immunostains were performed on resection specimens from 19 UPS and 5 AFX...
December 7, 2016: Histopathology
https://www.readbyqxmd.com/read/27924489/kinetic-analysis-of-target-rna-binding-and-slicing-by-human-argonaute-2-protein
#12
Sarah Willkomm, Tobias Restle
Analyzing the mechanisms of Argonaute-mediated gene silencing is essential to the understanding of RNA interference (RNAi). RNAi is a process to regulate gene expression on a posttranscriptional level. Directed by single-stranded small RNA guides, Argonaute 2 binds complementary target RNAs, and if the guide displays full complementarity to the targeted sequence, Argonaute 2 slices the bound target RNA. This on the one hand is an important mechanism to regulate gene expression in the cell and on the other hand represents a powerful tool to interfere with harmful gene expression levels...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27924045/a-novel-method-for-the-simultaneous-identification-of-methylcytosine-and-hydroxymethylcytosine-at-a-single-base-resolution
#13
Yuki Kawasaki, Yukiko Kuroda, Isao Suetake, Shoji Tajima, Fumitoshi Ishino, Takashi Kohda
Since the discovery of oxidative demethylation of methylcytosine (mC) by Tet enzymes, an analytical method has been urgently needed that would enable the identification of mC and hydroxymethylcytosine (hmC) at the single base resolution level, because their roles in gene regulation are quite different from each other. However, the bisulfite sequencing method, the gold standard for DNA methylation analysis at present, does not distinguish them. Recently reported alternative methods, such as oxBS-seq and TAB-seq, are not even capable of determining mC and hmC simultaneously...
October 24, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27923803/whole-exome-sequencing-validates-a-preclinical-mouse-model-for-the-prevention-and-treatment-of-cutaneous-squamous-cell-carcinoma
#14
Elena V Knatko, Brandon Praslicka, Maureen Higgins, Alan Evans, Karin J Purdie, Catherine A Harwood, Charlotte M Proby, Aikseng Ooi, Albena T Dinkova-Kostova
Cutaneous squamous cell carcinomas (cSCC) are among the most common and highly mutated human malignancies. Solar UV radiation is the major factor in the etiology of cSCC. Whole exome sequencing of 18 microdissected tumor samples (cases) derived from SKH-1 hairless mice that had been chronically exposed to solar-simulated UV (SSUV) radiation showed a median point mutation (single nucleotide polymorphism, SNP) rate of 155 per megabase. The majority (78.6%) of the SNPs are C.G>T.A transitions, a characteristic UVR-induced mutational signature...
December 6, 2016: Cancer Prevention Research
https://www.readbyqxmd.com/read/27923064/sparse-regression-based-structure-learning-of-stochastic-reaction-networks-from-single-cell-snapshot-time-series
#15
Anna Klimovskaia, Stefan Ganscha, Manfred Claassen
Stochastic chemical reaction networks constitute a model class to quantitatively describe dynamics and cell-to-cell variability in biological systems. The topology of these networks typically is only partially characterized due to experimental limitations. Current approaches for refining network topology are based on the explicit enumeration of alternative topologies and are therefore restricted to small problem instances with almost complete knowledge. We propose the reactionet lasso, a computational procedure that derives a stepwise sparse regression approach on the basis of the Chemical Master Equation, enabling large-scale structure learning for reaction networks by implicitly accounting for billions of topology variants...
December 2016: PLoS Computational Biology
https://www.readbyqxmd.com/read/27923045/tumor-evolution-in-two-patients-with-basal-like-breast-cancer-a-retrospective-genomics-study-of-multiple-metastases
#16
Katherine A Hoadley, Marni B Siegel, Krishna L Kanchi, Christopher A Miller, Li Ding, Wei Zhao, Xiaping He, Joel S Parker, Michael C Wendl, Robert S Fulton, Ryan T Demeter, Richard K Wilson, Lisa A Carey, Charles M Perou, Elaine R Mardis
BACKGROUND: Metastasis is the main cause of cancer patient deaths and remains a poorly characterized process. It is still unclear when in tumor progression the ability to metastasize arises and whether this ability is inherent to the primary tumor or is acquired well after primary tumor formation. Next-generation sequencing and analytical methods to define clonal heterogeneity provide a means for identifying genetic events and the temporal relationships between these events in the primary and metastatic tumors within an individual...
December 2016: PLoS Medicine
https://www.readbyqxmd.com/read/27921386/cytotoxicity-of-a-series-of-norcantharidin-inspired-tetrahydroepoxyisoindole-carboxamides
#17
Christopher Peter Gordon, Lawson K Spare, Pasquale Falsetta, Jayne Gilbert, David G Harman, Mark A Baker, Feng Li, Adam McCluskey, Jack K Clegg, Jennette A Sakoff, Janice R Aldrich-Wright
A series of 28 norcantharidin (NorC) inspired analogues were accessed via a robust two-step Ugi intramolecular Diels-Alder (IMDA) sequence. Four analogues displayed equipotent whole cell cytotoxicity to NorC and cisplatin against a number of cancer cell lines and a normal breast cell line (MCF10A). Notably (3S,3aS,6R)-2-benzyl-7-methyl-N-(naphthalen-2-yl)-1-oxo-1,2,3,6-tetrahydro-3a,6-epoxyisoindole-3-carboxamide (trans-27) displayed superior whole cell activity against breast (MCF-7, GI50 = 2.9 µM) and colon (HT29, GI50 = 6...
December 6, 2016: ChemMedChem
https://www.readbyqxmd.com/read/27921343/complete-genome-sequence-of-streptococcus-troglodytae-tku31-isolated-from-an-oral-cavity-of-chimpanzee-pan-troglodytes
#18
Masaaki Okamoto, Mariko Naito, Mayu Miyanohara, Susumu Imai, Yoshiaki Nomura, Wataru Saito, Yasuko Momoi, Kazuko Takada, Takako Miyabe-Nishiwaki, Masaki Tomonaga, Nobuhiro Hanada
Streptococcus troglodytae TKU31 was isolated from an oral cavity of chimpanzee (Pan troglodytes), and it is the most closely related species to Streptococcus mutans among the mutans group streptococci. The complete sequence of TKU31 genome consisted of a single circular chromosome that was 2,097,874 base pairs in length, with a G + C content of 37.18%. It possessed a total of 2,082 coding sequences (CDSs), 65 tRNAs and five rRNA operons (15 rRNAs). Two clustered regularly interspaced short palindromic repeats (CRISPRs), six insertion sequences (IS) and two predicted prophage elements were identified...
December 6, 2016: Microbiology and Immunology
https://www.readbyqxmd.com/read/27920797/genome-wide-association-study-for-identifying-loci-that-affect-fillet-yield-carcass-and-body-weight-traits-in-rainbow-trout-oncorhynchus-mykiss
#19
Dianelys Gonzalez-Pena, Guangtu Gao, Matthew Baranski, Thomas Moen, Beth M Cleveland, P Brett Kenney, Roger L Vallejo, Yniv Palti, Timothy D Leeds
Fillet yield (FY, %) is an economically-important trait in rainbow trout aquaculture that affects production efficiency. Despite that, FY has received little attention in breeding programs because it is difficult to measure on a large number of fish and cannot be directly measured on breeding candidates. The recent development of a high-density SNP array for rainbow trout has provided the needed tool for studying the underlying genetic architecture of this trait. A genome-wide association study (GWAS) was conducted for FY, body weight at 10 (BW10) and 13 (BW13) months post-hatching, head-off carcass weight (CAR), and fillet weight (FW) in a pedigreed rainbow trout population selectively bred for improved growth performance...
2016: Frontiers in Genetics
https://www.readbyqxmd.com/read/27920086/a-role-for-mitotic-bookmarking-of-sox2-in-pluripotency-and-differentiation
#20
Cédric Deluz, Elias T Friman, Daniel Strebinger, Alexander Benke, Mahé Raccaud, Andrea Callegari, Marion Leleu, Suliana Manley, David M Suter
Mitotic bookmarking transcription factors remain bound to chromosomes during mitosis and were proposed to regulate phenotypic maintenance of stem and progenitor cells at the mitosis-to-G1 (M-G1) transition. However, mitotic bookmarking remains largely unexplored in most stem cell types, and its functional relevance for cell fate decisions remains unclear. Here we screened for mitotic chromosome binding within the pluripotency network of embryonic stem (ES) cells and show that SOX2 and OCT4 remain bound to mitotic chromatin through their respective DNA-binding domains...
December 5, 2016: Genes & Development
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