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https://www.readbyqxmd.com/read/29350029/a-microwell-array-method-for-rapid-generation-of-uniform-agarose-droplets-and-beads-for-single-molecule-analysis
#1
Xingrui Li, Dongfeng Zhang, Huimin Zhang, Zhichao Guan, Yanling Song, Ruochen Liu, Zhi Zhu, Chaoyong James Yang
Compartmentalization of aqueous samples in uniform emulsion droplets has proven to be a useful tool for many chemical, biological, and biomedical applications. Herein, we introduce an array-based emulsification method for rapid and easy generation of monodisperse agarose-in-oil droplets in a PDMS microwell array. The microwells are filled with agarose solution, and subsequent addition of hot oil results in immediate formation of agarose droplets due to the surface-tension of the liquid solution. Because droplet size is determined solely by the array unit dimensions, uniform droplets with pre-selectable diameters ranging from 20 µm to 100 µm can be produced with relative standard deviations less than 3...
January 19, 2018: Analytical Chemistry
https://www.readbyqxmd.com/read/29348659/blm-helicase-suppresses-recombination-at-g-quadruplex-motifs-in-transcribed-genes
#2
Niek van Wietmarschen, Sarra Merzouk, Nancy Halsema, Diana C J Spierings, Victor Guryev, Peter M Lansdorp
Bloom syndrome is a cancer predisposition disorder caused by mutations in the BLM helicase gene. Cells from persons with Bloom syndrome exhibit striking genomic instability characterized by excessive sister chromatid exchange events (SCEs). We applied single-cell DNA template strand sequencing (Strand-seq) to map the genomic locations of SCEs. Our results show that in the absence of BLM, SCEs in human and murine cells do not occur randomly throughout the genome but are strikingly enriched at coding regions, specifically at sites of guanine quadruplex (G4) motifs in transcribed genes...
January 18, 2018: Nature Communications
https://www.readbyqxmd.com/read/29348443/a-general-and-flexible-method-for-signal-extraction-from-single-cell-rna-seq-data
#3
Davide Risso, Fanny Perraudeau, Svetlana Gribkova, Sandrine Dudoit, Jean-Philippe Vert
Single-cell RNA-sequencing (scRNA-seq) is a powerful high-throughput technique that enables researchers to measure genome-wide transcription levels at the resolution of single cells. Because of the low amount of RNA present in a single cell, some genes may fail to be detected even though they are expressed; these genes are usually referred to as dropouts. Here, we present a general and flexible zero-inflated negative binomial model (ZINB-WaVE), which leads to low-dimensional representations of the data that account for zero inflation (dropouts), over-dispersion, and the count nature of the data...
January 18, 2018: Nature Communications
https://www.readbyqxmd.com/read/29348307/non-mammalian-models-of-multiple-endocrine-neoplasia-type-2
#4
REVIEW
Tirtha K Das, Ross L Cagan
Twenty-five years ago, RET was identified as the primary driver of multiple endocrine neoplasia type 2 (MEN2) syndrome. MEN2 is characterized by several transformation events including pheochromocytoma, parathyroid adenoma and, especially penetrant, medullary thyroid carcinoma (MTC). Overall, MTC is a rare but aggressive type of thyroid cancer for which no effective treatment currently exists. Surgery, radiation, radioisotope treatment and chemotherapeutics have all shown limited success, and none of these approaches have proven durable in advanced disease...
February 2018: Endocrine-related Cancer
https://www.readbyqxmd.com/read/29346760/single-cell-transcriptional-profiling-reveals-cellular-diversity-and-intercommunication-in-the-mouse-heart
#5
Daniel A Skelly, Galen T Squiers, Micheal A McLellan, Mohan T Bolisetty, Paul Robson, Nadia A Rosenthal, Alexander R Pinto
Characterization of the cardiac cellulome, the network of cells that form the heart, is essential for understanding cardiac development and normal organ function and for formulating precise therapeutic strategies to combat heart disease. Recent studies have reshaped our understanding of cardiac cellular composition and highlighted important functional roles for non-myocyte cell types. In this study, we characterized single-cell transcriptional profiles of the murine non-myocyte cardiac cellular landscape using single-cell RNA sequencing (scRNA-seq)...
January 16, 2018: Cell Reports
https://www.readbyqxmd.com/read/29346103/wavedec-a-wavelet-approach-to-identify-both-shared-and-individual-patterns-of-copy-number-variations
#6
Hongmin Cai, Peihua Chen, Jiazhou Chen, Jiulun Cai, Yan Song, Guoqiang Han
Copy-number variations (CNVs) are associated with complex diseases and particular tumor types. Array-based comparative genomic hybridization (aCGH) is a common approach for the detection of CNVs. Traditional CNV detection methods for multiple aCGH samples mainly use batch samples to find common variations, not accounting for the individual characteristics of each sample. Accurately differentiating both the commonly shared and the individual CNV patterns is pivotal to identify cell populations, or to distinguish cell growth (as in cancer) from invasion of new cells...
February 2018: IEEE Transactions on Bio-medical Engineering
https://www.readbyqxmd.com/read/29344856/next-generation-sequencing-analysis-of-laser-microdissected-formalin-fixed-and-paraffin-embedded-ffpe-tissue-specimens
#7
Lavinia Mägel, Stephan Bartels, Ulrich Lehmann
In recent years, next-generation sequencing (NGS) became widely used in molecular pathology. Comprehensive mutational profiling improved diagnosis and prognosis, as well as the identification of therapeutically relevant genetic alterations. However, the vast majority of studies analyzing tissue samples use DNA extracted from bulk tissue or only manually microdissected specimens. Laser-assisted microdissection offers the possibility of isolating morphologically defined small tissue compartments (like individual glands) or even of single cells for further molecular analysis...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29343825/a-survey-of-validation-strategies-for-crispr-cas9-editing
#8
Monica F Sentmanat, Samuel T Peters, Colin P Florian, Jon P Connelly, Shondra M Pruett-Miller
The T7 endonuclease 1 (T7E1) mismatch detection assay is a widely used method for evaluating the activity of site-specific nucleases, such as the clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 system. To determine the accuracy and sensitivity of this assay, we compared the editing estimates derived by the T7E1 assay with that of targeted next-generation sequencing (NGS) in pools of edited mammalian cells. Here, we report that estimates of nuclease activity determined by T7E1 most often do not accurately reflect the activity observed in edited cells...
January 17, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29343640/single-cell-transcriptomics-of-the-developing-lateral-geniculate-nucleus-reveals-insights-into-circuit-assembly-and-refinement
#9
Brian T Kalish, Lucas Cheadle, Sinisa Hrvatin, M Aurel Nagy, Samuel Rivera, Megan Crow, Jesse Gillis, Rory Kirchner, Michael E Greenberg
Coordinated changes in gene expression underlie the early patterning and cell-type specification of the central nervous system. However, much less is known about how such changes contribute to later stages of circuit assembly and refinement. In this study, we employ single-cell RNA sequencing to develop a detailed, whole-transcriptome resource of gene expression across four time points in the developing dorsal lateral geniculate nucleus (LGN), a visual structure in the brain that undergoes a well-characterized program of postnatal circuit development...
January 17, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29343303/comparison-of-modified-wet-suction-technique-and-dry-suction-technique-in-endoscopic-ultrasound-guided-fine-needle-aspiration-eus-fna-for-solid-lesions-study-protocol-for-a-randomized-controlled-trial
#10
Yun Wang, Qian Chen, Jinlin Wang, Xiaoli Wu, Yaqi Duan, Ping Yin, Qiaozhen Guo, Wei Hou, Bin Cheng
BACKGROUND: Several suction techniques have been developed recently to enhance tissue acquisition when sampling solid lesions using endoscopic ultrasound-guided fine-needle aspiration (EUS-FNA). The aim of this study is to determine whether a new modified wet suction technique (MWST) compared with the conventional dry suction technique (DRST) shall present better outcomes with respect to diagnostic yield and specimen quality of solid lesions in the intra-abdomen and mediastinum. METHODS/DESIGN: This is a single-blind, randomized, controlled, superiority trial conducted at four large tertiary care centers in China...
January 17, 2018: Trials
https://www.readbyqxmd.com/read/29342275/hot-spot-kif5a-mutations-cause-familial-als
#11
David Brenner, Rüstem Yilmaz, Kathrin Müller, Torsten Grehl, Susanne Petri, Thomas Meyer, Julian Grosskreutz, Patrick Weydt, Wolfgang Ruf, Christoph Neuwirth, Markus Weber, Susana Pinto, Kristl G Claeys, Berthold Schrank, Berit Jordan, Antje Knehr, Kornelia Günther, Annemarie Hübers, Daniel Zeller, Christian Kubisch, Sibylle Jablonka, Michael Sendtner, Thomas Klopstock, Mamede de Carvalho, Anne Sperfeld, Guntram Borck, Alexander E Volk, Johannes Dorst, Joachim Weis, Markus Otto, Joachim Schuster, Kelly Del Tredici, Heiko Braak, Karin M Danzer, Axel Freischmidt, Thomas Meitinger, Tim M Strom, Albert C Ludolph, Peter M Andersen, Jochen H Weishaupt
Heterozygous missense mutations in the N-terminal motor or coiled-coil domains of the kinesin family member 5A (KIF5A) gene cause monogenic spastic paraplegia (HSP10) and Charcot-Marie-Tooth disease type 2 (CMT2). Moreover, heterozygous de novo frame-shift mutations in the C-terminal domain of KIF5A are associated with neonatal intractable myoclonus, a neurodevelopmental syndrome. These findings, together with the observation that many of the disease genes associated with amyotrophic lateral sclerosis disrupt cytoskeletal function and intracellular transport, led us to hypothesize that mutations in KIF5A are also a cause of amyotrophic lateral sclerosis...
January 12, 2018: Brain: a Journal of Neurology
https://www.readbyqxmd.com/read/29342233/quantumclone-clonal-assessment-of-functional-mutations-in-cancer-based-on-a-genotype-aware-method-for-clonal-reconstruction
#12
Paul Deveau, Leo Colmet Daage, Derek Oldridge, Virginie Bernard, Angela Bellini, Mathieu Chicard, Nathalie Clement, Eve Lapouble, Valerie Combaret, Anne Boland, Vincent Meyer, Jean-Francois Deleuze, Isabelle Janoueix-Lerosey, Emmanuel Barillot, Olivier Delattre, John Maris, Gudrun Schleiermacher, Valentina Boeva
Motivation: In cancer, clonal evolution is assessed based on information coming from single nucleotide variants and copy number alterations. Nonetheless, existing methods often fail to accurately combine information from both sources to truthfully reconstruct clonal populations in a given tumor sample or in a set of tumor samples coming from the same patient. Moreover, previously published methods detect clones from a single set of variants. As a result, compromises have to be done between stringent variant filtering (reducing dispersion in variant allele frequency estimates, VAFs) and using all biologically relevant variants...
January 12, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29341473/somatic-mosaic-deletions-involving-scn1a-cause-dravet-syndrome
#13
Tojo Nakayama, Atsushi Ishii, Takeshi Yoshida, Hirosato Nasu, Keiko Shimojima, Toshiyuki Yamamoto, Shigeo Kure, Shinichi Hirose
Somatic mosaicism in single nucleotide variants of SCN1A is known to occur in a subset of parents of children with Dravet syndrome (DS). Here, we report recurrent somatic mosaic microdeletions involving SCN1A in children diagnosed with DS. Through the evaluation of 237 affected individuals with DS who did not show SCN1A or PCHD19 mutations in prior sequencing analyzes, we identified two children with mosaic microdeletions covering the entire SCN1A region. The allele frequency of the mosaic deletions estimated by multiplex ligation-dependent probe amplification and array comparative genomic hybridization was 25-40%, which was comparable to the mosaic ratio in lymphocytes and buccal mucosa cells observed by fluorescence in situ hybridization analysis...
January 17, 2018: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/29340109/development-of-a-targeted-sequencing-approach-to-identify-prognostic-predictive-and-diagnostic-markers-in-paediatric-solid-tumours
#14
Elisa Izquierdo, Lina Yuan, Sally George, Michael Hubank, Chris Jones, Paula Proszek, Janet Shipley, Susanne A Gatz, Caedyn Stinson, Andrew S Moore, Steven C Clifford, Debbie Hicks, Janet C Lindsey, Rebecca M Hill, Thomas S Jacques, Jane Chalker, Khin Thway, Simon O'Connor, Lynley Marshall, Lucas Moreno, Andrew Pearson, Louis Chesler, Brian A Walker, David Gonzalez De Castro
The implementation of personalised medicine in childhood cancers has been limited by a lack of clinically validated multi-target sequencing approaches specific for paediatric solid tumours. In order to support innovative clinical trials in high-risk patients with unmet need, we have developed a clinically relevant targeted sequencing panel spanning 311 kb and comprising 78 genes involved in childhood cancers. A total of 132 samples were used for the validation of the panel, including Horizon Discovery cell blends (n=4), cell lines (n=15), formalin-fixed paraffin embedded (FFPE, n=83) and fresh frozen tissue (FF, n=30) patient samples...
December 19, 2017: Oncotarget
https://www.readbyqxmd.com/read/29340026/evaluating-the-bias-of-circrna-predictions-from-total-rna-seq-data
#15
Jinzeng Wang, Kang Liu, Ya Liu, Qi Lv, Fan Zhang, Haiyun Wang
CircRNAs are a group of endogenous noncoding RNAs. The quickly developing high throughput RNA sequencing technologies along with novel bioinformatics approaches have enabled researchers to systematically identify circRNAs and their biological functions in cells. Deep sequencing of rRNA-depleted RNAs treated with RNase R, which digests linear RNAs and leaves circRNAs enriched, is an efficient way to identify circRNAs. However, very few of RNase R treated data are at hand but a large amount of total RNA-Seq data with no sequencing costs is available, for circRNA predictions...
December 19, 2017: Oncotarget
https://www.readbyqxmd.com/read/29339469/the-bardet-biedl-syndrome-protein-complex-is-an-adapter-expanding-the-cargo-range-of-intraflagellar-transport-trains-for-ciliary-export
#16
Peiwei Liu, Karl F Lechtreck
Bardet-Biedl syndrome (BBS) is a ciliopathy resulting from defects in the BBSome, a conserved protein complex. BBSome mutations affect ciliary membrane composition, impairing cilia-based signaling. The mechanism by which the BBSome regulates ciliary membrane content remains unknown. Chlamydomonas bbs mutants lack phototaxis and accumulate phospholipase D (PLD) in the ciliary membrane. Single particle imaging revealed that PLD comigrates with BBS4 by intraflagellar transport (IFT) while IFT of PLD is abolished in bbs mutants...
January 16, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29339440/repurposing-tin-mesoporphyrin-as-an-immune-checkpoint-inhibitor-shows-therapeutic-efficacy-in-preclinical-models-of-cancer
#17
Tamara Muliaditan, James W Opzoomer, Jonathan Caron, Mary Okesola, Paris Kosti, Sharanpreet Lall, Mieke Van Hemelrijck, Francesco Dazzi, Andrew Tutt, Anita Grigoriadis, Cheryl Gillett, Stephen F Madden, Joy M Burchell, Shahram Kordasti, Sandra S Diebold, James Spicer, James N Arnold
PURPOSE: Unprecedented clinical outcomes have been achieved in a variety of cancers by targeting immune checkpoint molecules. This preclinical study investigates heme oxygenase-1 (HO-1), an immune suppressive enzyme that is expressed in a wide variety of cancers, as a potential immune checkpoint target in the context of a chemotherapy-elicited anti-tumor immune response. We evaluate repurposing tin mesoporphyrin (SnMP), which has demonstrated safety and efficacy targeting hepatic HO in the clinic for the treatment of hyperbilirubinaemia, as an immune checkpoint blockade therapy for the treatment of cancer...
January 16, 2018: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/29339412/the-sequence-specific-peptide-binding-activity-of-the-protein-sulfide-isomerase-agr2-directs-its-stable-binding-to-the-oncogenic-receptor-epcam
#18
M Aiman Mohtar, Lenka Hernychova, Robert O'Neill, Melanie Lawrence, Euan Murray, Borek Vojtesek, Ted R Hupp
AGR2 is an oncogenic endoplasmic reticulum (ER)-resident protein disulfide isomerase. AGR2 protein has a relatively unique property for a chaperone in that it can bind sequence-specifically to a specific peptide motif (TTIYY). A synthetic TTIYY-containing peptide column was used to affinity-purify AGR2 from crude lysates highlighting peptide selectivity in complex mixtures. Hydrogen-deuterium exchange mass spectrometry localized the dominant region in AGR2 that interacts with the TTIYY peptide to within a structural loop from amino acids 131-135 (VDPSL)...
January 16, 2018: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/29339403/a-phase-1-study-of-azacitidine-combined-with-chemotherapy-in-childhood-leukemia-a-report-from-tacl-consortium
#19
Weili Sun, Timothy Triche, Jemily Malvar, Paul Gaynon, Richard Sposto, Xiaojing Yang, Henrique Bittencourt, Andrew E Place, Yoav Messinger, Chris Fraser, Luciano Dalla-Pozza, Bodour Salhia, Peter Jones, Alan S Wayne, Lia Gore, Todd M Cooper, Gangning Liang
Growing evidence indicates that aberrant DNA hypermethylation is associated with leukemogenesis, chemotherapy resistance, and relapse. DNA methyltransferase inhibitors such as azacitidine and decitabine have been shown to reverse drug resistance and prime leukemia cells to cytotoxic agents in vitro. Here we report the first pediatric phase 1 study using azacitidine in sequence with chemotherapy in patients with relapsed/refractory leukemia. Fourteen patients were enrolled, twelve with acute myeloid leukemia (AML) and two with acute lymphoblastic leukemia (ALL)...
January 16, 2018: Blood
https://www.readbyqxmd.com/read/29337374/pooled-lentiviral-delivery-genetic-screens
#20
Federica Piccioni, Scott T Younger, David E Root
Pooled cell-based screens of mammalian genetic perturbations enable systematic large-scale, even genome-scale, evaluation of gene function. Pooled screens introduce genetic perturbations into a cell population through viral transduction such that each cell integrates into its DNA a single or small number of library perturbations with barcodes identifying the perturbations. One then selects and physically isolates the subset of cells that exhibit the phenotype of interest. Sequencing the barcodes in the hit cells reveals which genes favored or inhibited the hit phenotype...
January 16, 2018: Current Protocols in Molecular Biology
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