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single-cell sequencing

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https://www.readbyqxmd.com/read/28732199/catch-shiny-droplets-in-suspension-finding-the-needle-in-a-haystack
#1
Nina V Hein-Fuchs, Renate König
In a recent issue of Cell Chemical Biology, Chaipan et al. (2017) described a high-throughput screening methodology to identify epitopes on HIV-1 particles recognized by broadly neutralizing antibodies. The approach utilizes a droplet-based microfluidics platform combining robust phenotypic single-virus sorting with next-generation sequencing of viral quasispecies.
July 20, 2017: Cell Chemical Biology
https://www.readbyqxmd.com/read/28731467/uncultivated-microbes-in-need-of-their-own-taxonomy
#2
Konstantinos T Konstantinidis, Ramon Rosselló-Móra, Rudolf Amann
The great majority of microbial species remains uncultured, severely limiting their taxonomic characterization and thus communication among scientists. Although Candidatus was devised as a provisional category to classify uncultured taxa, it has not been widely accepted owing to technical limitations and lack of priority of Candidatus names in the official nomenclature. High-throughput sequencing provides the potential for data-rich taxonomic descriptions of uncultivated microbes, comparable in quality to those of cultured organisms...
July 21, 2017: ISME Journal
https://www.readbyqxmd.com/read/28731049/composite-hemangioendothelioma-with-neuroendocrine-marker-expression-an-aggressive-variant
#3
Kyle D Perry, Alyaa Al-Lbraheemi, Brian P Rubin, Jin Jen, Hongzheng Ren, Jin Sung Jang, Asha Nair, Jaime Davila, Stefan Pambuccian, Andrew Horvai, William Sukov, Henry D Tazelaar, Andrew L Folpe
Aberrant expression of neuroendocrine markers is extremely rare in endothelial neoplasms, with only a single report describing three cases. Although originally classified as conventional angiosarcoma, further assessment of these tumors revealed a strikingly composite morphology composed of retiform and epithelioid elements reminiscent of composite hemangioendothelioma, a rare subtype of hemangioendothelioma. To further investigate these findings, available materials from 11 morphologically distinctive endothelial tumors showing neuroendocrine marker expression were retrieved from our archives...
July 21, 2017: Modern Pathology: An Official Journal of the United States and Canadian Academy of Pathology, Inc
https://www.readbyqxmd.com/read/28730907/the-rs10229583-polymorphism-near-paired-box-gene-4-is-associated-with-gestational-diabetes-mellitus-in-chinese-women
#4
Tianyi Xu, Yiru Shi, Jiangbo Liu, Yun Liu, Ailin Zhu, Cui Xie, Yan Zhang, Yan Chen, Lirong Ren
Objective The rs10229583 polymorphism near paired box gene 4 ( PAX4) is associated with insulin resistance and type 2 diabetes. Mutations in the PAX4 gene may be associated with impaired differentiation/development of pancreatic islet beta cells during fetal development and, consequently, a compromised insulin response to high blood glucose. To ascertain whether this polymorphism plays a role in gestational diabetes mellitus (GDM), we investigated the genotypic and allele frequency differences between GDM and normal pregnancies...
January 1, 2017: Journal of International Medical Research
https://www.readbyqxmd.com/read/28730820/tryptic-peptides-bearing-c-terminal-dimethyllysine-need-be-considered-during-the-analysis-of-lysine-dimethylation-in-proteomic-study
#5
Ming Chen, Min Zhang, Linhui Zhai, Hao Hu, Ping Liu, Minjia Tan
Lysine methylation plays important roles in structural and functional regulation of chromatin. Although trypsin is the most widely used protease in mass spectrometry-based proteomic analysis for lysine methylation substrates, the proteolytic activity of trypsin on dimethylated lysine residues remains an arguable issue. In this study, we tested the ability of trypsin to cleave dimethylated lysine residues in synthetic peptides, purified albumin and whole cell lysate, and found that the C-terminal of dimethylated lysine residue could be cleaved in a protein sequence-dependent manner...
July 21, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28730439/design-and-preparation-of-aptamer-sirna-chimeras-asics-for-targeted-cancer-therapy
#6
Sven Kruspe, Paloma H Giangrande
Conjugation of cell-internalizing DNA or RNA aptamers to tumor-suppressing siRNAs represents a novel promising approach for cancer therapy. Here we describe how to employ RNA aptamers that bind to cell surface receptors as carriers for cell-targeted siRNA (or miRNA) delivery. This protocol was optimized to improve the efficiency of the aptamer-siRNA/miRNA conjugates and facilitate its implementation in most molecular biology labs. The single working steps include (1) outlining the optimal sequences of the RNA strands bearing the aptamer and siRNA sequence, for which further (2) a dsDNA template is synthesized and then (3) transcribed into an RNA that will be (4) folded and annealed to a chemically synthesized siRNA complementary strand...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28729688/improved-genome-recovery-and-integrated-cell-size-analyses-of-individual-uncultured-microbial-cells-and-viral-particles
#7
Ramunas Stepanauskas, Elizabeth A Fergusson, Joseph Brown, Nicole J Poulton, Ben Tupper, Jessica M Labonté, Eric D Becraft, Julia M Brown, Maria G Pachiadaki, Tadas Povilaitis, Brian P Thompson, Corianna J Mascena, Wendy K Bellows, Arvydas Lubys
Microbial single-cell genomics can be used to provide insights into the metabolic potential, interactions, and evolution of uncultured microorganisms. Here we present WGA-X, a method based on multiple displacement amplification of DNA that utilizes a thermostable mutant of the phi29 polymerase. WGA-X enhances genome recovery from individual microbial cells and viral particles while maintaining ease of use and scalability. The greatest improvements are observed when amplifying high G+C content templates, such as those belonging to the predominant bacteria in agricultural soils...
July 20, 2017: Nature Communications
https://www.readbyqxmd.com/read/28729663/a-comparative-strategy-for-single-nucleus-and-single-cell-transcriptomes-confirms-accuracy-in-predicted-cell-type-expression-from-nuclear-rna
#8
Blue B Lake, Simone Codeluppi, Yun C Yung, Derek Gao, Jerold Chun, Peter V Kharchenko, Sten Linnarsson, Kun Zhang
Significant heterogeneities in gene expression among individual cells are typically interrogated using single whole cell approaches. However, tissues that have highly interconnected processes, such as in the brain, present unique challenges. Single-nucleus RNA sequencing (SNS) has emerged as an alternative method of assessing a cell's transcriptome through the use of isolated nuclei. However, studies directly comparing expression data between nuclei and whole cells are lacking. Here, we have characterized nuclear and whole cell transcriptomes in mouse single neurons and provided a normalization strategy to reduce method-specific differences related to the length of genic regions...
July 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28728983/etv4-and-ap1-transcription-factors-form-multivalent-interactions-with-three-sites-on-the-med25-activator-interacting-domain
#9
Simon L Currie, Jedediah J Doane, Kathryn S Evans, Niraja Bhachech, Bethany J Madison, Desmond K W Lau, Lawrence P McIntosh, Jack J Skalicky, Kathleen A Clark, Barbara J Graves
The recruitment of transcriptional cofactors by sequence-specific transcription factors challenges the basis of high affinity and selective interactions. Extending previous studies that the N-terminal activation domain (AD) of ETV5 interacts with Mediator subunit 25 (MED25), we establish that similar, aromatic-rich motifs located both in the AD and in the DNA-binding domain (DBD) of the related ETS factor ETV4 interact with MED25. These ETV4 regions bind MED25 independently, display distinct kinetics, and combine to contribute to a high-affinity interaction of full-length ETV4 with MED25...
July 17, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/28728979/ploc-mvirus-predict-subcellular-localization-of-multi-location-virus-proteins-via-incorporating-the-optimal-go-information-into-general-pseaac
#10
Xiang Cheng, Xuan Xiao, Kuo-Chen Chou
Knowledge of subcellular locations of proteins is crucially important for in-depth understanding their functions in a cell. With the explosive growth of protein sequences generated in the postgenomic age, it is highly demanded to develop computational tools for timely annotating their subcellular locations based on the sequence information alone. The current study is focused on virus proteins. Although considerable efforts have been made in this regard, the problem is far from being solved yet. Most existing methods can be used to deal with single-location proteins only...
July 17, 2017: Gene
https://www.readbyqxmd.com/read/28728360/isolation-and-characterization-of-a-novel-gossypol-degrading-bacteria-bacillus-subtilis-strain-rbs
#11
Yunhua Zhang, Lijuan Chen, Zhengyou Zhang, Li Dai, Ying Liu, Maoji Cheng
Objective: An experiment was conducted to isolate gossypol-degrading bacteria and assessed its potential for gossypol degradation. Methods: Rumen liquid was collected from the rumen of cows through fistula from the experimental pasture. Approximately 1 ml of the rumen liquid was spread onto basal medium plates containing 2 g/l gossypol as the only source of carbon and was then cultured at 39°C to isolate gossypol-degrading bacteria. The isolated colonies were cultured for 6 h and then observed their size and shape by the microscope and scanning electron microscope...
June 27, 2017: Asian-Australasian Journal of Animal Sciences
https://www.readbyqxmd.com/read/28725235/gateway-compatible-crispr-cas9-vectors-and-a-rapid-detection-by-high-resolution-melting-curve-analysis
#12
Cynthia J Denbow, Samantha Lapins, Nick Dietz, Raelynn Scherer, Zachary L Nimchuk, Sakiko Okumoto
CRISPR-Cas9 system rapidly became an indispensable tool in plant biology to perform targeted mutagenesis. A CRISPR-Cas9-mediated double strand break followed by non-homologous end joining (NHEJ) repair most frequently results in a single base pair deletion or insertions (indels), which is hard to detect using methods based on enzymes that detect heteroduplex DNA. In addition, somatic tissues of the T1 generation inevitably contain a mosaic population, in which the portion of cells carrying the mutation can be too small to be detected by the enzyme-based methods...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28725161/ep300-single-nucleotide-polymorphism-rs20551-correlates-with-prolonged-overall-survival-in-diffuse-large-b-cell-lymphoma-patients-treated-with-r-chop
#13
Jiao Li, Ning Ding, Xiaogan Wang, Lan Mi, Lingyan Ping, Xuan Jin, Yalu Liu, Zhitao Ying, Yan Xie, Weiping Liu, Yuqin Song, Jun Zhu
BACKGROUND: Rituximab combined with cyclophosphamide, doxorubicin, vincristine and prednisone (CHOP) is used as standard frontline regimen for diffuse large B-cell lymphoma (DLBCL). The landscape of somatic mutations in DLBCL revealed that inactivation of EP300 plays an important role in lymphomagenesis. A common EP300 single nucleotide polymorphism (SNP) rs20551 results in the substitution of valine for isoleucine at codon 997 close to the Bromodomain. However, the association between SNP rs20551 and clinical prognosis in DLBCL patients treated with R-CHOP is unknown...
2017: Cancer Cell International
https://www.readbyqxmd.com/read/28724766/a-unique-t-cell-receptor-amino-acid-sequence-selected-by-htlv-i-tax301-309-specific-cytotoxic-t-cells-in-hla-a24-02-asymptomatic-carriers-and-adult-t-cell-leukemia-lymphoma-patients
#14
Yuko Ishihara, Yukie Tanaka, Seiichiro Kobayashi, Koji Kawamura, Hideki Nakasone, Ayumi Gomyo, Jin Hayakawa, Masaharu Tamaki, Yu Akahoshi, Naonori Harada, Machiko Kusuda, Kazuaki Kameda, Tomotaka Ugai, Hidenori Wada, Kana Sakamoto, Miki Sato, Kiriko Terasako-Saito, Misato Kikuchi, Shun-Ichi Kimura, Aki Tanihara, Shinichi Kako, Kaoru Uchimaru, Yoshinobu Kanda
We previously reported that the T-cell receptor (TCR) repertoire of HTLV-I Tax301-309-specific CD8(+) cytotoxic T-cells (Tax-CTLs) was highly restricted and a particular amino acid sequence motif, "PDR", was conserved among HLA-A*24:02(+) ATL patients who have undergone allogeneic hematopoietic cell transplantation (allo-HSCT). Furthermore, we found that donor-derived PDR+CTLs selectively expanded in ATL long-term HSCT survivors with strong CTL activity against HTLV-I. On the other hand, the TCR repertoires in Tax-CTL of asymptomatic HTLV-I carriers (ACs) remain unclear...
July 19, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28724605/heterozygous-loss-of-function-mutation-in-odd-skipped-related-1-osr1-is-associated-with-vesico-ureteric-reflux-duplex-systems-and-hydronephrosis
#15
Marie-Lyne Fillion, Jasmine El Andalousi, Fatima Tokhmafshan, Vasikar Murugapoopathy, Christine L Watt, Inga J Murawski, John-Paul Capolicchio, Mohamed El-Sherbiny, Roman Jednak, Indra Rani Gupta
Osr1 is a transcriptional repressor that plays critical roles in maintaining the mesenchymal stem cell population within the developing kidney. Here, we report that newborn pups with a heterozygous null mutation in Osr1 exhibit a 21% incidence of vesico-ureteric reflux and have hydronephrosis and urinary tract duplications. Newborn pups have a short intravesical ureter resulting in a less competent uretero-vesical junction which arises from a delay in urinary tract development. We describe a new domain of Osr1 expression in the ureteral mesenchyme and within the developing bladder in the mouse...
July 19, 2017: American Journal of Physiology. Renal Physiology
https://www.readbyqxmd.com/read/28724397/partial-uniparental-isodisomy-of-chromosome-16-unmasks-a-deleterious-biallelic-mutation-in-ift140-that-causes-mainzer-saldino-syndrome
#16
Benjamin M Helm, Jason R Willer, Azita Sadeghpour, Christelle Golzio, Eric Crouch, Samantha Schrier Vergano, Nicholas Katsanis, Erica E Davis
BACKGROUND: The ciliopathies represent an umbrella group of >50 clinical entities that share both clinical features and molecular etiology underscored by structural and functional defects of the primary cilium. Despite the advances in gene discovery, this group of entities continues to pose a diagnostic challenge, in part due to significant genetic and phenotypic heterogeneity and variability. We consulted a pediatric case from asymptomatic, non-consanguineous parents who presented as a suspected ciliopathy due to a constellation of retinal, renal, and skeletal findings...
July 19, 2017: Human Genomics
https://www.readbyqxmd.com/read/28723968/new-library-construction-method-for-single-cell-genomes
#17
Larry Xi, Alexander Belyaev, Sandra Spurgeon, Xiaohui Wang, Haibiao Gong, Robert Aboukhalil, Richard Fekete
A central challenge in sequencing single-cell genomes is the accurate determination of point mutations, phasing of these mutations, and identifying copy number variations with few assumptions. Ideally, this is accomplished under as low sequencing coverage as possible. Here we report our attempt to meet these goals with a novel library construction and library amplification methodology. In our approach, single-cell genomic DNA is first fragmented with saturated transposition to make a primary library that uniformly covers the whole genome by short fragments...
2017: PloS One
https://www.readbyqxmd.com/read/28723630/functional-role-of-setd2-bap1-parp-3-and-pbrm1-candidate-genes-on-the-regulation-of-htert-gene-expression
#18
Hannah Linne, Hemad Yasaei, Alison Marriott, Amanda Harvey, Kefah Mokbel, Robert Newbold, Terry Roberts
Narrowing the search for the critical hTERT repressor sequence(s) has identified three regions on chromosome 3p (3p12-p21.1, 3p21.2 and 3p21.3-p22). However, the precise location and identity of the sequence(s) responsible for hTERT transcriptional repression remains elusive. In order to identify critical hTERT repressor sequences located within human chromosome 3p12-p22, we investigated hTERT transcriptional activity within 21NT microcell hybrid clones containing chromosome 3 fragments. Mapping of chromosome 3 structure in a single hTERT-repressed 21NT-#3fragment hybrid clone, revealed a 490kb region of deletion localised to 3p21...
June 27, 2017: Oncotarget
https://www.readbyqxmd.com/read/28723489/immunotherapy-for-renal-cancer-sequencing-and-combinations
#19
REVIEW
Grant D Stewart, Maria De Santis, Bernard Escudier, Thomas Powles, Guru Sonpavde
CONTEXT: Current therapy for renal cell carcinoma (RCC) generally consists of the sequential administration of single agent therapy. Given the advent of T-cell checkpoint inhibitors, the role of combinations including these agents is being intensely interrogated. OBJECTIVE: To evaluate ongoing trials of combinations including immunotherapy and sequencing of agents to treat RCC. EVIDENCE ACQUISITION: Recent data and ongoing trials were analyzed to evaluate the direction of research in this arena...
December 15, 2016: European Urology Focus
https://www.readbyqxmd.com/read/28723342/molecular-analysis-of-circulating-free-dna-from-lung-cancer-patients-in-routine-laboratory-practice-a-cross-platform-comparison-of-three-different-molecular-methods-for-mutation-detection
#20
Stephan Bartels, Sascha Persing, Britta Hasemeier, Elisa Schipper, Hans Kreipe, Ulrich Lehmann
Cell-free DNA (cfDNA), which is isolated from blood plasma, represents a noninvasive source for the detection of mutations conferring resistance against epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors in non-small-cell lung cancer patients. In advanced disease stages, performing regular biopsies is often not possible because of the general health condition of the patients. Furthermore, a biopsy of a single tumor lesion or metastasis may not reflect the heterogeneous genotype of the tumor and its metastases...
July 16, 2017: Journal of Molecular Diagnostics: JMD
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