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https://www.readbyqxmd.com/read/27932033/cellular-analysis-of-trophoblast-and-placenta
#1
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/27930944/high-throughput-sequencing-in-acute-lymphoblastic-leukemia-follow-up-of-minimal-residual-disease-and-emergence-of-new-clones
#2
Mikaël Salson, Mathieu Giraud, Aurélie Caillault, Nathalie Grardel, Nicolas Duployez, Yann Ferret, Marc Duez, Ryan Herbert, Tatiana Rocher, Shéhérazade Sebda, Sabine Quief, Céline Villenet, Martin Figeac, Claude Preudhomme
Minimal residual disease (MRD) is known to be an independent prognostic factor in patients with acute lymphoblastic leukemia (ALL). High-throughput sequencing (HTS) is currently used in routine practice for the diagnosis and follow-up of patients with hematological neoplasms. In this retrospective study, we examined the role of immunoglobulin/T-cell receptor-based MRD in patients with ALL by HTS analysis of immunoglobulin H and/or T-cell receptor gamma chain loci in bone marrow samples from 11 patients with ALL, at diagnosis and during follow-up...
November 21, 2016: Leukemia Research
https://www.readbyqxmd.com/read/27929523/single-cell-barcoding-and-sequencing-using-droplet-microfluidics
#3
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/27929461/isolation-of-high-density-lipoproteins-for-non-coding-small-rna-quantification
#4
Danielle L Michell, Ryan M Allen, Stuart R Landstreet, Shilin Zhao, Cynthia L Toth, Quanhu Sheng, Kasey C Vickers
The diversity of small non-coding RNAs (sRNA) is rapidly expanding and their roles in biological processes, including gene regulation, are emerging. Most interestingly, sRNAs are also found outside of cells and are stably present in all biological fluids. As such, extracellular sRNAs represent a novel class of disease biomarkers and are likely involved in cell signaling and intercellular communication networks. To assess their potential as biomarkers, sRNAs can be quantified in plasma, urine, and other fluids...
November 28, 2016: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/27919782/understanding-zebrafish-cognition
#5
REVIEW
Darya A Meshalkina, Marina N Kizlyk, Elana V Kysil, Adam D Collier, David J Echevarria, Murilo S Abreu, Leonardo J G Barcellos, Cai Song, Allan V Kalueff
Zebrafish (Danio rerio) are rapidly becoming a popular model organism in translational and cognitive neuroscience research. Both larval and adult zebrafish continue to increase our understanding of cognitive mechanisms and their genetic and pharmacological modulation. Here, we discuss the developing utility of zebrafish in understanding cognitive phenotypes and their deficits, relevant to a wide range human brain disorders. We also discuss the potential of zebrafish models for high-throughput genetic mutant and small molecule screening (e...
December 2, 2016: Behavioural Processes
https://www.readbyqxmd.com/read/27918638/small-molecule-microarray-based-discovery-of-parp14-inhibitors
#6
Bo Peng, Ann-Gerd Thorsell, Tobias Karlberg, Herwig Schüler, Shao Q Yao
Poly(ADP-ribose) polymerases (PARPs) are key enzymes in a variety of cellular processes. Most small-molecule PARP inhibitors developed to date have been against PARP1, and suffer from poor selectivity. PARP14 has recently emerged as a potential therapeutic target, but its inhibitor development has trailed behind. Herein, we describe a small molecule microarray-based strategy for high-throughput synthesis, screening of >1000 potential bidentate inhibitors of PARPs, and the successful discovery of a potent PARP14 inhibitor H10 with >20-fold selectivity over PARP1...
December 5, 2016: Angewandte Chemie
https://www.readbyqxmd.com/read/27918438/minimum-interference-channel-assignment-algorithm-for-multicast-in-a-wireless-mesh-network
#7
Sangil Choi, Jong Hyuk Park
Wireless mesh networks (WMNs) have been considered as one of the key technologies for the configuration of wireless machines since they emerged. In a WMN, wireless routers provide multi-hop wireless connectivity between hosts in the network and also allow them to access the Internet via gateway devices. Wireless routers are typically equipped with multiple radios operating on different channels to increase network throughput. Multicast is a form of communication that delivers data from a source to a set of destinations simultaneously...
December 2, 2016: Sensors
https://www.readbyqxmd.com/read/27913513/minimal-residual-disease-in-mantle-cell-lymphoma-insights-into-biology-and-impact-on-treatment
#8
Eva Hoster, Christiane Pott
Despite the recent substantial improvement of clinical outcome in mantle cell lymphoma (MCL), resistance to immunochemotherapy and common relapses are challenges for long-term tumor control. The assessment of minimal residual disease (MRD) by real-time quantitative polymerase chain reaction has emerged as a widely feasible and standardized tool for direct assessment of therapy-induced reduction of tumor burden and regrowth after cytotoxic treatment in MCL, with much improved sensitivity compared with conventional staging procedures...
December 2, 2016: Hematology—the Education Program of the American Society of Hematology
https://www.readbyqxmd.com/read/27911841/high-performance-multiplexed-fluorescence-in-situ-hybridization-in-culture-and-tissue-with-matrix-imprinting-and-clearing
#9
Jeffrey R Moffitt, Junjie Hao, Dhananjay Bambah-Mukku, Tian Lu, Catherine Dulac, Xiaowei Zhuang
Highly multiplexed single-molecule FISH has emerged as a promising approach to spatially resolved single-cell transcriptomics because of its ability to directly image and profile numerous RNA species in their native cellular context. However, background-from off-target binding of FISH probes and cellular autofluorescence-can become limiting in a number of important applications, such as increasing the degree of multiplexing, imaging shorter RNAs, and imaging tissue samples. Here, we developed a sample clearing approach for FISH measurements...
November 22, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27910067/next-generation-sequencing
#10
Matthieu Le Gallo, Fred Lozy, Daphne W Bell
Endometrial cancers are the most frequently diagnosed gynecological malignancy and were expected to be the seventh leading cause of cancer death among American women in 2015. The majority of endometrial cancers are of serous or endometrioid histology. Most human tumors, including endometrial tumors, are driven by the acquisition of pathogenic mutations in cancer genes. Thus, the identification of somatic mutations within tumor genomes is an entry point toward cancer gene discovery. However, efforts to pinpoint somatic mutations in human cancers have, until recently, relied on high-throughput sequencing of single genes or gene families using Sanger sequencing...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/27909234/a-high-throughput-screening-strategy-for-development-of-rnf8-ubc13-protein-protein-interaction-inhibitors
#11
Elisabeth Weber, Ina Rothenaigner, Stefanie Brandner, Kamyar Hadian, Kenji Schorpp
The ubiquitin-proteasome system plays an essential role in a broad range of cellular signaling pathways. Ubiquitination is a posttranslational protein modification that involves the action of an enzymatic cascade (E1, E2, and E3 enzymes) for the covalent attachment of ubiquitin to target proteins. The emerging knowledge of the molecular mechanisms and correlation of deregulation of the ubiquitin system in human diseases is uncovering new opportunities for therapeutics development. The E3 ligase RNF8 acts in cooperation with the heterodimeric E2 enzyme Ubc13/Uev1a to generate ubiquitin conjugates at the sides of DNA double-strand breaks, and recent findings suggest RNF8 as a potential therapeutic target for the treatment of breast cancer...
December 1, 2016: Journal of Biomolecular Screening
https://www.readbyqxmd.com/read/27907891/analysis-of-translation-using-polysome-profiling
#12
Héloïse Chassé, Sandrine Boulben, Vlad Costache, Patrick Cormier, Julia Morales
During the past decade, there has been growing interest in the role of translational regulation of gene expression in many organisms. Polysome profiling has been developed to infer the translational status of a specific mRNA species or to analyze the translatome, i.e. the subset of mRNAs actively translated in a cell. Polysome profiling is especially suitable for emergent model organisms for which genomic data are limited. In this paper, we describe an optimized protocol for the purification of sea urchin polysomes and highlight the critical steps involved in polysome purification...
October 7, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27906308/linear-and-nonlinear-optical-characterization-of-self-assembled-large-area-gold-nanosphere-metasurfaces-with-sub-nanometer-gaps
#13
Jake Fontana, Melissa Maldonado, Nicholas Charipar, Scott A Trammell, Rafaela Nita, Jawad Naciri, Alberto Pique, Banahalli Ratna, Anderson S L Gomes
We created centimeter-scale area metasurfaces consisting of a quasi-hexagonally close packed monolayer of gold nanospheres capped with alkanethiol ligands on glass substrates using a directed self-assembly approach. We experimentally characterized the morphology and the linear and nonlinear optical properties of metasurfaces. We show these metasurfaces, with interparticle gaps of 0.6 nm, are modeled well using a classical (without charge transfer) description. We find a large dispersion of linear refractive index, ranging from values less than vacuum, 0...
November 28, 2016: Optics Express
https://www.readbyqxmd.com/read/27904140/restrictions-in-the-t-cell-repertoire-of-chronic-lymphocytic-leukemia-high-throughput-immunoprofiling-supports-selection-by-shared-antigenic-elements
#14
A Vardi, E Vlachonikola, M Karypidou, E Stalika, V Bikos, K Gemenetzi, C Maramis, A Siorenta, A Anagnostopoulos, S Pospisilova, N Maglaveras, I Chouvarda, K Stamatopoulos, A Hadzidimitriou
Immunoglobulin (IG) gene repertoire restrictions strongly support antigen selection in the pathogenesis of chronic lymphocytic leukemia (CLL). Given the emerging multifarious interactions between CLL and bystander T cells, we sought to determine whether antigen(s) are also selecting T cells in CLL. We performed a large-scale, next-generation sequencing (NGS) study of the T-cell repertoire, focusing on major stereotyped subsets representing CLL subgroups with undisputed antigenic drive, but also included patients carrying non-subset IG rearrangements to seek for T-cell immunogenetic signatures ubiquitous in CLL...
December 1, 2016: Leukemia: Official Journal of the Leukemia Society of America, Leukemia Research Fund, U.K
https://www.readbyqxmd.com/read/27902747/joint-profiling-of-mirnas-and-mrnas-reveals-mirna-mediated-gene-regulation-in-the-g%C3%A3-ttingen-minipig-obesity-model
#15
Caroline M Junker Mentzel, Ferhat Alkan, Helle Keinicke, Mette J Jacobsen, Jan Gorodkin, Merete Fredholm, Susanna Cirera
Obesity and its comorbidities are an increasing challenge for both affected individuals and health care systems, worldwide. In obese individuals, perturbation of expression of both protein-coding genes and microRNAs (miRNA) are seen in obesity-relevant tissues (i.e. adipose tissue, liver and skeletal muscle). miRNAs are small non-coding RNA molecules which have important regulatory roles in a wide range of biological processes, including obesity. Rodents are widely used animal models for human diseases including obesity...
2016: PloS One
https://www.readbyqxmd.com/read/27897988/reciprocally-benefited-secure-transmission-for-spectrum-sensing-based-cognitive-radio-sensor-networks
#16
Dawei Wang, Pinyi Ren, Qinghe Du, Li Sun, Yichen Wang
The rapid proliferation of independently-designed and -deployed wireless sensor networks extremely crowds the wireless spectrum and promotes the emergence of cognitive radio sensor networks (CRSN). In CRSN, the sensor node (SN) can make full use of the unutilized licensed spectrum, and the spectrum efficiency is greatly improved. However, inevitable spectrum sensing errors will adversely interfere with the primary transmission, which may result in primary transmission outage. To compensate the adverse effect of spectrum sensing errors, we propose a reciprocally-benefited secure transmission strategy, in which SN's interference to the eavesdropper is employed to protect the primary confidential messages while the CRSN is also rewarded with a loose spectrum sensing error probability constraint...
November 25, 2016: Sensors
https://www.readbyqxmd.com/read/27896771/selective-reaction-monitoring-for-quantitation-of-cellular-proteins
#17
Vitor M Faça
Proteins and proteomes are dynamic and complex. The accurate identification and measurement of their properties such as abundance, location, and turnover are challenging tasks. Even though high-throughput proteomics has significantly evolved, the technique still lacks fully quantitative and reproducible qualities. A mass spectrometry-based targeted proteomic strategy called selective reaction monitoring (SRM) has emerged in recent years as an important multiplex platform to precisely quantify sets of proteins in multiple samples...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27896376/reducing-the-bottleneck-in-discovery-of-novel-antibiotics
#18
Marcus B Jones, William C Nierman, Yue Shan, Bryan C Frank, Amy Spoering, Losee Ling, Aaron Peoples, Ashley Zullo, Kim Lewis, Karen E Nelson
Most antibiotics were discovered by screening soil actinomycetes, but the efficiency of the discovery platform collapsed in the 1960s. By now, more than 3000 antibiotics have been described and most of the current discovery effort is focused on the rediscovery of known compounds, making the approach impractical. The last marketed broad-spectrum antibiotics discovered were daptomycin, linezolid, and fidaxomicin. The current state of the art in the development of new anti-infectives is a non-existent pipeline in the absence of a discovery platform...
November 28, 2016: Microbial Ecology
https://www.readbyqxmd.com/read/27884742/antifungals
#19
REVIEW
Sonia Campoy, José L Adrio
The need for new antifungal agents is undeniable. Current therapeutics choices for the treatment of invasive fungal infections are limited to three classes of drugs. Most used antifungals agents are not completely effective due to the development of resistance, host toxicity and undesirable side effects that limit their use in medical practice. Invasive fungal infections have significantly increased over the last decades and the mortality rates remain unacceptably high. More threatening, new resistance patterns have been observed including simultaneous resistance to different antifungal classes...
November 21, 2016: Biochemical Pharmacology
https://www.readbyqxmd.com/read/27884207/potential-contribution-of-the-uterine-microbiome-in-the-development-of-endometrial-cancer
#20
Marina R S Walther-António, Jun Chen, Francesco Multinu, Alexis Hokenstad, Tammy J Distad, E Heidi Cheek, Gary L Keeney, Douglas J Creedon, Heidi Nelson, Andrea Mariani, Nicholas Chia
BACKGROUND: Endometrial cancer studies have led to a number of well-defined but mechanistically unconnected genetic and environmental risk factors. One of the emerging modulators between environmental triggers and genetic expression is the microbiome. We set out to inquire about the composition of the uterine microbiome and its putative role in endometrial cancer. METHODS: We undertook a study of the microbiome in samples taken from different locations along the female reproductive tract in patients with endometrial cancer (n = 17), patients with endometrial hyperplasia (endometrial cancer precursor, n = 4), and patients afflicted with benign uterine conditions (n = 10)...
November 25, 2016: Genome Medicine
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