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https://www.readbyqxmd.com/read/28749987/dude-seq-fast-flexible-and-robust-denoising-for-targeted-amplicon-sequencing
#1
Byunghan Lee, Taesup Moon, Sungroh Yoon, Tsachy Weissman
We consider the correction of errors from nucleotide sequences produced by next-generation targeted amplicon sequencing. The next-generation sequencing (NGS) platforms can provide a great deal of sequencing data thanks to their high throughput, but the associated error rates often tend to be high. Denoising in high-throughput sequencing has thus become a crucial process for boosting the reliability of downstream analyses. Our methodology, named DUDE-Seq, is derived from a general setting of reconstructing finite-valued source data corrupted by a discrete memoryless channel and effectively corrects substitution and homopolymer indel errors, the two major types of sequencing errors in most high-throughput targeted amplicon sequencing platforms...
2017: PloS One
https://www.readbyqxmd.com/read/28749472/retinoic-acid-induced-upregulation-of-mir-219-promotes-the-differentiation-of-embryonic-stem-cells-into-neural-cells
#2
Haibo Wu, Jiamin Zhao, Beibei Fu, Songna Yin, Chao Song, Jingcheng Zhang, Shanting Zhao, Yong Zhang
MicroRNAs (miRNAs) regulate critical cell processes, such as apoptosis, proliferation, and development. However, the role of miRNAs in embryonic stem cell (ESC) neural differentiation induced by retinoic acid (RA) and factors that govern neural directional differentiation remain poorly understood. In this study, we demonstrated that miR-219 is sufficient in promoting mouse ESCs to undergo neural differentiation. We discovered that Foxj3 and Zbtb18, two target genes of miR-219, are not able to determine the process of RA-induced differentiation, however they prevent ESCs from differentiating into neural cells...
July 27, 2017: Cell Death & Disease
https://www.readbyqxmd.com/read/28748760/visible-light-therapy-molecular-mechanisms-and-therapeutic-opportunities
#3
Zandra C Félix Garza, Matthias Born, Peter A J Hilbers, Natal A W van Riel, Joerg Liebmann
Visible light is absorbed by photoacceptors in pigmented and non-pigmented mammalian cells, activating signaling cascades and downstream mechanisms that lead to the modulation of cellular processes. Most studies have investigated the molecular mechanisms and therapeutic applications of UV and the red to near infrared regions of the visible spectrum. However, considerably less effort has been dedicated to the UV-free blue part of the spectrum. In this review we discuss the current advances in the understanding of the molecular photoacceptors, downstream signaling mechanisms and the corresponding therapeutic opportunities in the context of inflammatory skin conditions of blue light photoreception in mammalian cells...
July 27, 2017: Current Medicinal Chemistry
https://www.readbyqxmd.com/read/28745977/zap70-and-downstream-ranbp2-are-required-for-the-exact-timing-of-the-meiotic-cell-cycle-in-oocytes
#4
Hyun-Jung Kim, Su-Yeon Lee, Hyun-Seo Lee, Eun-Young Kim, Jung-Jae Ko, Kyung-Ah Lee
In previous studies, we observed that Zeta-chain-associated protein kinase 70 (Zap70) regulates spindle assembly and chromosome alignment in mouse oocyte and that Ran binding protein 2 (RanBP2) is highly associated gene with Zap70 based on a microarray analysis. Because RanBP2 is related to nuclear envelope breakdown (NEBD) during mitosis, the aim of the present study was to elucidate the molecular mechanism of Zap70 with respect to RanBP2 in the germinal vesicle breakdown (GVBD) of oocytes. Results indicated that RanBP2 expression was regulated by Zap70 and that depletion of RanBP2 using RanBP2 RNAi manifested comparable phenotypes to those observed in Zap70 RNAi-treated oocytes, which presented faster processing of GVBD...
July 26, 2017: Cell Cycle
https://www.readbyqxmd.com/read/28745623/a-standardized-approach-for-multispecies-purification-of-mammalian-male-germ-cells-by-mechanical-tissue-dissociation-and-flow-cytometry
#5
Ana C Lima, Min Jung, Jannette Rusch, Abul Usmani, Alexandra M Lopes, Donald F Conrad
Fluorescence-activated cell sorting (FACS) has been one of the methods of choice to isolate enriched populations of mammalian testicular germ cells. Currently, it allows the discrimination of up to 9 murine germ cell populations with high yield and purity. This high-resolution in discrimination and purification is possible due to unique changes in chromatin structure and quantity throughout spermatogenesis. These patterns can be captured by flow cytometry of male germ cells stained with fluorescent DNA-binding dyes such as Hoechst-33342 (Hoechst)...
July 12, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28743039/exogenous-application-of-poly-%C3%AE-glutamic-acid-enhances-stress-defense-in-brassica-napus-l-seedlings-by-inducing-cross-talks-between-ca-2-h2o2-brassinolide-and-jasmonic-acid-in-leaves
#6
Zongqi Xu, Peng Lei, Xiao Pang, Huashan Li, Xiaohai Feng, Hong Xu
Poly-γ-glutamic acid (γ-PGA) is a microbe-secreted isopeptide shown to promote growth and enhance crop stress tolerance. However, its downstream signaling pathways are unknown. Here, we studied γ-PGA-induced tolerance to salt and cold stresses. Pretreatment with γ-PGA contributed to enhance stress tolerance of canola seedlings by promoting proline accumulation and total antioxidant capacity (T-AOC) improvement. Further, Ca(2+), H2O2, brassinolide, and jasmonic acid were found to be involved in the γ-PGA-induced process...
July 17, 2017: Plant Physiology and Biochemistry: PPB
https://www.readbyqxmd.com/read/28742189/novel-endogenous-negative-modulators-of-platelet-function-as-potential-anti-thrombotic-targets
#7
Y-J Li, H-X Zhu, D Zhang, H-C Li, P Ma, L-Y Huang
Platelets are megakaryocyte-derived nuclear-free fragments that participate in cardiovascular diseases including acute myocardial infarction, ischemic stroke, hypertension, and atherosclerosis. At the endothelium damage site, platelets interact with sub-endothelial matrix proteins such as glycoprotein VI/Fc receptor γ-chain (GPVI/FcRγ), G protein-coupled receptor/phospholipase Cγ(β) (GPCR/PLCγ(β)), Rho/RhoK and integrin. The activation of these signaling pathways triggers intracellular calcium increase and causes platelet adhesion, aggregation, granule release and finally thrombus formation...
July 2017: European Review for Medical and Pharmacological Sciences
https://www.readbyqxmd.com/read/28742002/cdc42-activation-state-affects-its-localization-and-protein-levels-in-fission-yeast
#8
Miguel Estravís, Sergio Antonio Rincón, Elvira Portales, Pilar Pérez, Beatriz Santos
Rho GTPases control polarized cell growth and are well-known regulators of exocytic and endocytic processes. Cdc42 is an essential GTPase, conserved from yeast to humans, that is critical for cell polarization. Cdc42 is negatively regulated by the GTPase-activating proteins (GAPs) and the GDP dissociation inhibitors (GDIs), and positively regulated by guanine nucleotide exchange factors (GEFs). Cdc42 GTPase can be found in a GTP- or GDP-bound state, which determines the ability to bind downstream effector proteins and activate signalling pathways...
July 26, 2017: Microbiology
https://www.readbyqxmd.com/read/28741645/inflammasome-and-autophagy-regulation-a-two-way-street
#9
Qian Sun, Jie Fan, Timothy R Billiar, Melanie J Scott
Inflammation plays a significant role in protecting hosts against pathogens. Inflammation induced by non-infectious, endogenous agents can be detrimental, and if excessive can result in organ and tissue damage. The inflammasome is a major innate immune pathway that can be activated via both exogenous pathogen-associated molecular patterns (PAMPs) and endogenous damage-associated molecular patterns (DAMPs). Inflammasome activation involves formation and oligomerization of a protein complex including a NOD-like receptor (NLR), an adaptor protein (ASC) and procaspase-1...
July 24, 2017: Molecular Medicine
https://www.readbyqxmd.com/read/28738544/a-xylanase-aided-enzymatic-pretreatment-facilitates-cellulose-nanofibrillation
#10
Lingfeng Long, Dong Tian, Jinguang Hu, Fei Wang, Jack Saddler
Although biological pretreatment of cellulosic fiber based on endoglucanases has shown some promise to facilitate cellulose nanofibrillation, its efficacy is still limited. In this study, a xylanase-aided endoglucanase pretreatment was assessed on the bleached hardwood and softwood Kraft pulps to facilitate the downstream cellulose nanofibrillation. Four commercial xylanase preparations were compared and the changes of major fiber physicochemical characteristics such as cellulose/hemicellulose content, gross fiber properties, fiber morphologies, cellulose accessibility/degree of polymerization (DP)/crystallinity were systematically evaluated before and after enzymatic pretreatment...
July 9, 2017: Bioresource Technology
https://www.readbyqxmd.com/read/28738385/pharmacological-and-nonpharmacological-interventions-to-arrest-neuroprogression-in-psychiatric-disorders
#11
Fotini Boufidou, Angelos Halaris
The concept of neuroprogression describes the progressive course of the disorder and stresses the progressive, recurrent, and chronic course of the disease entity under consideration. It subsumes clinical manifestations of the disease process and may also entail morphological, biochemical, neurochemical, immunological, physiological, and genetic aspects that contribute to the progressive course of the disease in question. In an attempt to identify the appropriate agent or method that could arrest neuroprogression in psychiatric patients, we conducted an evaluation of the use of anti-inflammatory drugs under the perspective of current pharmacological and neurophysiological data...
2017: Modern Trends in Pharmacopsychiatry
https://www.readbyqxmd.com/read/28738304/bacteria-contribute-to-pesticide-degradation-in-cryoconite-holes-in-an-alpine-glacier
#12
Claudia Ferrario, Francesca Pittino, Ilario Tagliaferri, Isabella Gandolfi, Giuseppina Bestetti, Roberto Sergio Azzoni, Guglielmina Diolaiuti, Andrea Franzetti, Roberto Ambrosini, Sara Villa
Organic contaminants deposited on glacier snow and ice are subject to partitioning and degradation processes that determine their environmental fate and, consequently, their accumulation in ice bodies. Among these processes, organic compound degradation by supraglacial bacteria has been investigated to a lesser extent than photo- and chemical degradation. We investigated biodegradation of the organophosphorus insecticide chlorpyrifos (CPF), a xenobiotic tracer that accumulates on glaciers after atmospheric medium- and long-range transport, by installing in situ microcosms on an Alpine glacier to simulate cryoconite hole systems...
July 21, 2017: Environmental Pollution
https://www.readbyqxmd.com/read/28738086/an-essential-ebv-latent-antigen-3c-binds-bcl6-for-targeted-degradation-and-cell-proliferation
#13
Yonggang Pei, Shuvomoy Banerjee, Hem Chandra Jha, Zhiguo Sun, Erle S Robertson
The latent EBV nuclear antigen 3C (EBNA3C) is required for transformation of primary human B lymphocytes. Most mature B-cell malignancies originate from malignant transformation of germinal center (GC) B-cells. The GC reaction appears to have a role in malignant transformation, in which a major player of the GC reaction is Bcl6, a key regulator of this process. We now demonstrate that EBNA3C contributes to B-cell transformation by targeted degradation of Bcl6. We show that EBNA3C can physically associate with Bcl6...
July 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28738082/short-term-sleep-deprivation-leads-to-decreased-systemic-redox-metabolites-and-altered-epigenetic-status
#14
Malav S Trivedi, Dana Holger, Anh Tuyet Bui, Travis J A Craddock, Jaime L Tartar
Sleep is critical for repair as well as the rejuvenation processes in the body and many of these functions are regulated via underlying cellular metabolic homeostasis. Changes in sleep pattern are reported to alter such metabolic function resulting in altered disease susceptibility or behavior. Here, we measured the extent to which overnight total sleep deprivation (SD) in young adult humans can influence systemic (plasma-derived) redox-metabolism including the major antioxidant, glutathione as well as DNA methylation levels...
2017: PloS One
https://www.readbyqxmd.com/read/28737002/nanofiltration-enabled-in-situ-solvent-and-reagent-recycle-for-sustainable-continuous-flow-synthesis
#15
Tamas Fodi, Christos Didaskalou, Jozsef Kupai, Gyorgy T Balogh, Peter Huszthy, Gyorgy Szekely
The solvent usage in the pharmaceutical sector accounts for as much as 90% of the overall mass during manufacturing processes. Consequently, solvent consumption poses significant costs and environmental burden. Continuous processing, in particular continuous-flow reactors have a great potential in the sustainable production of pharmaceuticals but subsequent downstream processing remains challenging. Separation processes for the concentration and purification of chemicals can account for as much as 80% of the total manufacturing costs...
July 23, 2017: ChemSusChem
https://www.readbyqxmd.com/read/28736556/ras-signaling-inhibitors-attenuate-disease-in-adjuvant-induced-arthritis-via-targeting-pathogenic-antigen-specific-th17-type-cells
#16
Morad Zayoud, Victoria Marcu-Malina, Einav Vax, Jasmine Jacob-Hirsch, Galit Elad-Sfadia, Iris Barshack, Yoel Kloog, Itamar Goldstein
The Ras family of GTPases plays an important role in signaling nodes downstream to T cell receptor and CD28 activation, potentially lowering the threshold for T-cell receptor activation by autoantigens. Somatic mutation in NRAS or KRAS may cause a rare autoimmune disorder coupled with abnormal expansion of lymphocytes. T cells from rheumatoid arthritis (RA) patients show excessive activation of Ras/MEK/ERK pathway. The small molecule farnesylthiosalicylic acid (FTS) interferes with the interaction between Ras GTPases and their prenyl-binding chaperones to inhibit proper plasma membrane localization...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/28735898/genome-wide-single-molecule-footprinting-reveals-high-rna-polymerase-ii-turnover-at-paused-promoters
#17
Arnaud R Krebs, Dilek Imanci, Leslie Hoerner, Dimos Gaidatzis, Lukas Burger, Dirk Schübeler
Transcription initiation entails chromatin opening followed by pre-initiation complex formation and RNA polymerase II recruitment. Subsequent polymerase elongation requires additional signals, resulting in increased residence time downstream of the start site, a phenomenon referred to as pausing. Here, we harnessed single-molecule footprinting to quantify distinct steps of initiation in vivo throughout the Drosophila genome. This identifies the impact of promoter structure on initiation dynamics in relation to nucleosomal occupancy...
July 19, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28735097/protecting-the-heart-through-mk2-modulation-toward-a-role-in-diabetic-cardiomyopathy-and-lipid-metabolism
#18
REVIEW
Matthieu Ruiz, Lise Coderre, Bruce Gordon Allen, Christine Des Rosiers
Various signaling pathways have been identified in the heart as important players during development, physiological adaptation or pathological processes. This includes the MAPK families, particularly p38MAPK, which is involved in several key cellular processes, including differentiation, proliferation, apoptosis, inflammation, metabolism and survival. Disrupted p38MAPK signaling has been associated with several diseases, including cardiovascular diseases (CVD) as well as diabetes and its related complications...
July 19, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28734608/sequence-specific-dna-solid-phase-extraction-in-an-on-chip-monolith-towards-detection-of-antibiotic-resistance-genes
#19
Radim Knob, Daniel B Nelson, Richard A Robison, Adam T Woolley
Antibiotic resistance of bacteria is a growing problem and presents a challenge for prompt treatment in patients with sepsis. Currently used methods rely on culturing or amplification; however, these steps are either time consuming or suffer from interference issues. A microfluidic device was made from black polypropylene, with a monolithic column modified with a capture oligonucleotide for sequence selective solid-phase extraction of a complementary target from a lysate sample. Porous properties of the monolith allow flow and hybridization of a target complementary to the probe immobilized on the column surface...
July 10, 2017: Journal of Chromatography. A
https://www.readbyqxmd.com/read/28733662/probing-the-gas-phase-dynamics-of-graphene-chemical-vapour-deposition-using-in-situ-uv-absorption-spectroscopy
#20
Abhay Shivayogimath, David Mackenzie, Birong Luo, Ole Hansen, Peter Bøggild, Timothy J Booth
The processes governing multilayer nucleation in the chemical vapour deposition (CVD) of graphene are important for obtaining high-quality monolayer sheets, but remain poorly understood. Here we show that higher-order carbon species in the gas-phase play a major role in multilayer nucleation, through the use of in-situ ultraviolet (UV) absorption spectroscopy. These species are the volatilized products of reactions between hydrogen and carbon contaminants that have backstreamed into the reaction chamber from downstream system components...
July 21, 2017: Scientific Reports
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