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https://www.readbyqxmd.com/read/27879314/genetic-variation-in-the-slc8a1-calcium-signaling-pathway-is-associated-with-susceptibility-to-kawasaki-disease-and-coronary-artery-abnormalities
#1
Chisato Shimizu, Hariklia Eleftherohorinou, Victoria J Wright, Jihoon Kim, Martin P Alphonse, James C Perry, Rolando Cimaz, David Burgner, Nagib Dahdah, Long T Hoang, Chiea-Chuen Khor, Andrea Salgado, Adriana H Tremoulet, Sonia Davila, Taco W Kuijpers, Martin L Hibberd, Todd A Johnson, Atsushi Takahashi, Tatsuhiko Tsunoda, Michiaki Kubo, Toshihiro Tanaka, Yoshihiro Onouchi, Rae S M Yeung, Lachlan J M Coin, Michael Levin, Jane C Burns
BACKGROUND: -Kawasaki disease (KD) is an acute pediatric vasculitis in which host genetics influence both susceptibility to KD and the formation of coronary artery aneurysms. Variants discovered by genome-wide association studies (GWAS) and linkage studies only partially explain the influence of genetics on KD susceptibility. METHODS AND RESULTS: -To search for additional functional genetic variation, we performed pathway and gene stability analysis on a GWAS dataset...
November 21, 2016: Circulation. Cardiovascular Genetics
https://www.readbyqxmd.com/read/27874299/cooling-effectiveness-of-a-modified-cold-water-immersion-method-after-exercise-induced-hyperthermia
#2
Katherine E Luhring, Cory L Butts, Cody R Smith, Jeffrey A Bonacci, Ramon C Ylanan, Matthew S Ganio, Brendon P McDermott
CONTEXT:  Recommended treatment for exertional heat stroke includes whole-body cold-water immersion (CWI). However, remote locations or monetary or spatial restrictions can challenge the feasibility of CWI. Thus, the development of a modified, portable CWI method would allow for optimal treatment of exertional heat stroke in the presence of these challenges. OBJECTIVE:  To determine the cooling rate of modified CWI (tarp-assisted cooling with oscillation [TACO]) after exertional hyperthermia...
November 22, 2016: Journal of Athletic Training
https://www.readbyqxmd.com/read/27869815/taco-produces-robust-multisample-transcriptome-assemblies-from-rna-seq
#3
Yashar S Niknafs, Balaji Pandian, Hariharan K Iyer, Arul M Chinnaiyan, Matthew K Iyer
Accurate transcript structure and abundance inference from RNA sequencing (RNA-seq) data is foundational for molecular discovery. Here we present TACO, a computational method to reconstruct a consensus transcriptome from multiple RNA-seq data sets. TACO employs novel change-point detection to demarcate transcript start and end sites, leading to improved reconstruction accuracy compared with other tools in its class. The tool is available at http://tacorna.github.io and can be readily incorporated into RNA-seq analysis workflows...
November 21, 2016: Nature Methods
https://www.readbyqxmd.com/read/27863252/the-allelic-landscape-of-human-blood-cell-trait-variation-and-links-to-common-complex-disease
#4
William J Astle, Heather Elding, Tao Jiang, Dave Allen, Dace Ruklisa, Alice L Mann, Daniel Mead, Heleen Bouman, Fernando Riveros-Mckay, Myrto A Kostadima, John J Lambourne, Suthesh Sivapalaratnam, Kate Downes, Kousik Kundu, Lorenzo Bomba, Kim Berentsen, John R Bradley, Louise C Daugherty, Olivier Delaneau, Kathleen Freson, Stephen F Garner, Luigi Grassi, Jose Guerrero, Matthias Haimel, Eva M Janssen-Megens, Anita Kaan, Mihir Kamat, Bowon Kim, Amit Mandoli, Jonathan Marchini, Joost H A Martens, Stuart Meacham, Karyn Megy, Jared O'Connell, Romina Petersen, Nilofar Sharifi, Simon M Sheard, James R Staley, Salih Tuna, Martijn van der Ent, Klaudia Walter, Shuang-Yin Wang, Eleanor Wheeler, Steven P Wilder, Valentina Iotchkova, Carmel Moore, Jennifer Sambrook, Hendrik G Stunnenberg, Emanuele Di Angelantonio, Stephen Kaptoge, Taco W Kuijpers, Enrique Carrillo-de-Santa-Pau, David Juan, Daniel Rico, Alfonso Valencia, Lu Chen, Bing Ge, Louella Vasquez, Tony Kwan, Diego Garrido-Martín, Stephen Watt, Ying Yang, Roderic Guigo, Stephan Beck, Dirk S Paul, Tomi Pastinen, David Bujold, Guillaume Bourque, Mattia Frontini, John Danesh, David J Roberts, Willem H Ouwehand, Adam S Butterworth, Nicole Soranzo
Many common variants have been associated with hematological traits, but identification of causal genes and pathways has proven challenging. We performed a genome-wide association analysis in the UK Biobank and INTERVAL studies, testing 29.5 million genetic variants for association with 36 red cell, white cell, and platelet properties in 173,480 European-ancestry participants. This effort yielded hundreds of low frequency (<5%) and rare (<1%) variants with a strong impact on blood cell phenotypes. Our data highlight general properties of the allelic architecture of complex traits, including the proportion of the heritable component of each blood trait explained by the polygenic signal across different genome regulatory domains...
November 17, 2016: Cell
https://www.readbyqxmd.com/read/27863251/genetic-drivers-of-epigenetic-and-transcriptional-variation-in-human-immune-cells
#5
Lu Chen, Bing Ge, Francesco Paolo Casale, Louella Vasquez, Tony Kwan, Diego Garrido-Martín, Stephen Watt, Ying Yan, Kousik Kundu, Simone Ecker, Avik Datta, David Richardson, Frances Burden, Daniel Mead, Alice L Mann, Jose Maria Fernandez, Sophia Rowlston, Steven P Wilder, Samantha Farrow, Xiaojian Shao, John J Lambourne, Adriana Redensek, Cornelis A Albers, Vyacheslav Amstislavskiy, Sofie Ashford, Kim Berentsen, Lorenzo Bomba, Guillaume Bourque, David Bujold, Stephan Busche, Maxime Caron, Shu-Huang Chen, Warren Cheung, Oliver Delaneau, Emmanouil T Dermitzakis, Heather Elding, Irina Colgiu, Frederik O Bagger, Paul Flicek, Ehsan Habibi, Valentina Iotchkova, Eva Janssen-Megens, Bowon Kim, Hans Lehrach, Ernesto Lowy, Amit Mandoli, Filomena Matarese, Matthew T Maurano, John A Morris, Vera Pancaldi, Farzin Pourfarzad, Karola Rehnstrom, Augusto Rendon, Thomas Risch, Nilofar Sharifi, Marie-Michelle Simon, Marc Sultan, Alfonso Valencia, Klaudia Walter, Shuang-Yin Wang, Mattia Frontini, Stylianos E Antonarakis, Laura Clarke, Marie-Laure Yaspo, Stephan Beck, Roderic Guigo, Daniel Rico, Joost H A Martens, Willem H Ouwehand, Taco W Kuijpers, Dirk S Paul, Hendrik G Stunnenberg, Oliver Stegle, Kate Downes, Tomi Pastinen, Nicole Soranzo
Characterizing the multifaceted contribution of genetic and epigenetic factors to disease phenotypes is a major challenge in human genetics and medicine. We carried out high-resolution genetic, epigenetic, and transcriptomic profiling in three major human immune cell types (CD14(+) monocytes, CD16(+) neutrophils, and naive CD4(+) T cells) from up to 197 individuals. We assess, quantitatively, the relative contribution of cis-genetic and epigenetic factors to transcription and evaluate their impact as potential sources of confounding in epigenome-wide association studies...
November 17, 2016: Cell
https://www.readbyqxmd.com/read/27851971/distinct-trends-of-dna-methylation-patterning-in-the-innate-and-adaptive-immune-systems
#6
Ronald P Schuyler, Angelika Merkel, Emanuele Raineri, Lucia Altucci, Edo Vellenga, Joost H A Martens, Farzin Pourfarzad, Taco W Kuijpers, Frances Burden, Samantha Farrow, Kate Downes, Willem H Ouwehand, Laura Clarke, Avik Datta, Ernesto Lowy, Paul Flicek, Mattia Frontini, Hendrik G Stunnenberg, José I Martín-Subero, Ivo Gut, Simon Heath
DNA methylation and the localization and post-translational modification of nucleosomes are interdependent factors that contribute to the generation of distinct phenotypes from genetically identical cells. With 112 whole-genome bisulfite sequencing datasets from the BLUEPRINT Epigenome Project, we analyzed the global development of DNA methylation patterns during lineage commitment and maturation of a range of immune system effector cells and the cancers that arise from them. We show clear trends in methylation patterns that are distinct in the innate and adaptive arms of the human immune system, both globally and in relation to consistently positioned nucleosomes...
November 15, 2016: Cell Reports
https://www.readbyqxmd.com/read/27833934/data-on-the-characterization-of-native-soy-globulin-by-sds-page-light-scattering-and-titration
#7
Nannan Chen, Mouming Zhao, Christophe Chassenieux, Taco Nicolai
The data presented in this article are related to the research article entitled Structure of Self-assembled Native Soy Globulin in Aqueous Solution as a Function of the Concentration and the pH by N. Chen, M. Zhao C. Chassenieux, T. Nicolai (2016) [1]. Please refer to this article for interpretation of the data. The protein composition of soy protein isolate (SPI) was characterized by SDS-Page. The molar mass of native soy globulin aggregates formed at different protein concentrations was determined by light scattering as a function of the waiting time...
December 2016: Data in Brief
https://www.readbyqxmd.com/read/27815426/gata1-deficient-dendritic-cells-display-impaired-ccl21-dependent-migration-toward-lymph-nodes-due-to-reduced-levels-of-polysialic-acid
#8
Maaike R Scheenstra, Iris M De Cuyper, Filipe Branco-Madeira, Pieter de Bleser, Mirjam Kool, Marjolein Meinders, Mark Hoogenboezem, Erik Mul, Monika C Wolkers, Fiamma Salerno, Benjamin Nota, Yvan Saeys, Sjoerd Klarenbeek, Wilfred F J van IJcken, Hamida Hammad, Sjaak Philipsen, Timo K van den Berg, Taco W Kuijpers, Bart N Lambrecht, Laura Gutiérrez
Dendritic cells (DCs) play a pivotal role in the regulation of the immune response. DC development and activation is finely orchestrated through transcriptional programs. GATA1 transcription factor is required for murine DC development, and data suggest that it might be involved in the fine-tuning of the life span and function of activated DCs. We generated DC-specific Gata1 knockout mice (Gata1-KO(DC)), which presented a 20% reduction of splenic DCs, partially explained by enhanced apoptosis. RNA sequencing analysis revealed a number of deregulated genes involved in cell survival, migration, and function...
November 4, 2016: Journal of Immunology: Official Journal of the American Association of Immunologists
https://www.readbyqxmd.com/read/27801680/broad-spectrum-antibodies-against-self-antigens-and-cytokines-in-rag-deficiency
#9
Jolan E Walter, Lindsey B Rosen, Krisztian Csomos, Jacob M Rosenberg, Divij Mathew, Marton Keszei, Boglarka Ujhazi, Karin Chen, Yu Nee Lee, Irit Tirosh, Kerry Dobbs, Waleed Al-Herz, Morton J Cowan, Jennifer Puck, Jack J Bleesing, Michael S Grimley, Harry Malech, Suk See De Ravin, Andrew R Gennery, Roshini S Abraham, Avni Y Joshi, Thomas G Boyce, Manish J Butte, Kari C Nadeau, Imelda Balboni, Kathleen E Sullivan, Javeed Akhter, Mehdi Adeli, Reem A El-Feky, Dalia H El-Ghoneimy, Ghassan Dbaibo, Rima Wakim, Chiara Azzari, Paolo Palma, Caterina Cancrini, Kelly Capuder, Antonio Condino-Neto, Beatriz T Costa-Carvalho, Joao Bosco Oliveira, Chaim Roifman, David Buchbinder, Attila Kumanovics, Jose Luis Franco, Tim Niehues, Catharina Schuetz, Taco Kuijpers, Christina Yee, Janet Chou, Michel J Masaad, Raif Geha, Gulbu Uzel, Rebecca Gelman, Steven M Holland, Mike Recher, Paul J Utz, Sarah K Browne, Luigi D Notarangelo
No abstract text is available yet for this article.
November 1, 2016: Journal of Clinical Investigation
https://www.readbyqxmd.com/read/27799929/the-high-prevalence-of-functional-complement-defects-induced-by-chemotherapy
#10
Mischa P Keizer, Angela M Kamp, Cathelijn Aarts, Judy Geisler, Huib N Caron, Marianne D van de Wetering, Diana Wouters, Taco W Kuijpers
INTRODUCTION: To date, oncology patients are more dependent on non-cellular host defense against pathogens due to intensive (chemo)therapy-related bone marrow suppression. Since data on complement functionality in oncology patients are limited, we aimed to investigate the innate complement function in relation to the type of malignancy and therapy in a longitudinal cohort of patients. METHODS: A large single-center, prospective non-intervention study was conducted, in which blood samples were taken from patients before, during, and after treatment with chemotherapy and/or subsequent admittance for (febrile) neutropenia...
2016: Frontiers in Immunology
https://www.readbyqxmd.com/read/27792871/found-in-translation-international-initiatives-pursuing-interleukin-1-blockade-for-treatment-of-acute-kawasaki-disease
#11
REVIEW
Jane C Burns, Isabelle Koné-Paut, Taco Kuijpers, Chisato Shimizu, Adriana Tremoulet, Moshe Arditi
The decision to move forward with three clinical trials of IL-1 blockade for treatment of acute Kawasaki disease is a case study in translational science. These trials were born on the one hand from transcriptome studies of host response during the acute disease coupled with animal model investigations of key immune signaling pathways and, on the other hand, out of clinical desperation to intervene in patients with severe inflammation in the setting of acute Kawasaki disease. The convergence of laboratory science and clinical observations led to the clinical trials described here and serves as a model for how such observations can be translated into new therapies...
October 28, 2016: Arthritis & Rheumatology
https://www.readbyqxmd.com/read/27779207/hbv-core-promoter-mutations-and-akt-upregulate-s-phase-kinase-associated-protein-2-to-promote-postoperative-hepatocellular-carcinoma-progression
#12
Lubiao Chen, Lin Gu, Yurong Gu, Hongbo Wang, Meihai Deng, Zania Stamataki, Ye Htun Oo, Yuehua Huang
Mutations in the hepatitis B virus (HBV) core promoter (CP) have been shown to be associated with hepatocellular carcinoma (HCC). The CP region overlaps HBV X gene, which activates AKT to regulate hepatocyte survival. However, the cooperation between these two cascades in HCC progression remains poorly understood. Here, we assayed virological factors and AKT expression in liver tissues from 56 HCC patients with better prognoses (BHCC, ≥5-year survival) and 58 with poor prognoses (PHCC, <5-year survival) after partial liver resection...
October 25, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27777981/extrapulmonary-aspergillus-infection-in-patients-with-card9-deficiency
#13
Nikolaus Rieber, Roel P Gazendam, Alexandra F Freeman, Amy P Hsu, Amanda L Collar, Janyce A Sugui, Rebecca A Drummond, Chokechai Rongkavilit, Kevin Hoffman, Carolyn Henderson, Lily Clark, Markus Mezger, Muthulekha Swamydas, Maik Engeholm, Rebecca Schüle, Bettina Neumayer, Frank Ebel, Constantinos M Mikelis, Stefania Pittaluga, Vinod K Prasad, Anurag Singh, Joshua D Milner, Kelli W Williams, Jean K Lim, Kyung J Kwon-Chung, Steven M Holland, Dominik Hartl, Taco W Kuijpers, Michail S Lionakis
Invasive pulmonary aspergillosis is a life-threatening mycosis that only affects patients with immunosuppression, chemotherapy-induced neutropenia, transplantation, or congenital immunodeficiency. We studied the clinical, genetic, histological, and immunological features of 2 unrelated patients without known immunodeficiency who developed extrapulmonary invasive aspergillosis at the ages of 8 and 18. One patient died at age 12 with progressive intra-abdominal aspergillosis. The other patient had presented with intra-abdominal candidiasis at age 9, and developed central nervous system aspergillosis at age 18 and intra-abdominal aspergillosis at age 25...
October 20, 2016: JCI Insight
https://www.readbyqxmd.com/read/27712058/inhibition-and-promotion-of-heat-induced-gelation-of-whey-proteins-in-the-presence-of-calcium-by-addition-of-sodium-caseinate
#14
Bach Trong Nguyen, Gireesh Balakrishan, Boris Jacquette, Taco Nicolai, Christophe Chassenieux, Christophe Schmitt, Lionel Bovetto
Heat-induced aggregation and gelation of aqueous solutions of whey protein isolate (WPI) in the presence of sodium caseinate (SC) and CaCl2 was studied at pH 6.6. The effect of adding SC (0-100 g/L) on the structure of the aggregates and the gels was investigated by light scattering and confocal laser scanning microscopy at different CaCl2 concentration ([CaCl2]=0-30 mM). The gelation process was studied by oscillatory shear rheology. At the whey protein concentrations studied here (34 g/L, 60 g/L), no gels were formed in the absence of CaCl2 and SC...
October 6, 2016: Biomacromolecules
https://www.readbyqxmd.com/read/27701145/decreased-somatic-hypermutation-induces-an-impaired-peripheral-b-cell-tolerance-checkpoint
#15
Tineke Cantaert, Jean-Nicolas Schickel, Jason M Bannock, Yen-Shing Ng, Christopher Massad, Fabien R Delmotte, Natsuko Yamakawa, Salome Glauzy, Nicolas Chamberlain, Tuure Kinnunen, Laurence Menard, Aubert Lavoie, Jolan E Walter, Luigi D Notarangelo, Julie Bruneau, Waleed Al-Herz, Sara Sebnem Kilic, Hans D Ochs, Charlotte Cunningham-Rundles, Mirjam van der Burg, Taco W Kuijpers, Sven Kracker, Hideo Kaneko, Yujin Sekinaka, Shigeaki Nonoyama, Anne Durandy, Eric Meffre
Patients with mutations in AICDA, which encodes activation-induced cytidine deaminase (AID), display an impaired peripheral B cell tolerance. AID mediates class-switch recombination (CSR) and somatic hypermutation (SHM) in B cells, but the mechanism by which AID prevents the accumulation of autoreactive B cells in blood is unclear. Here, we analyzed B cell tolerance in AID-deficient patients, patients with autosomal dominant AID mutations (AD-AID), asymptomatic AICDA heterozygotes (AID+/-), and patients with uracil N-glycosylase (UNG) deficiency, which impairs CSR but not SHM...
November 1, 2016: Journal of Clinical Investigation
https://www.readbyqxmd.com/read/27694492/inositol-triphosphate-3-kinase-c-mediates-inflammasome-activation-and-treatment-response-in-kawasaki-disease
#16
Martin Prince Alphonse, Trang T Duong, Chisato Shumitzu, Truong Long Hoang, Brian W McCrindle, Alessandra Franco, Stéphane Schurmans, Dana J Philpott, Martin L Hibberd, Jane Burns, Taco W Kuijpers, Rae S M Yeung
Kawasaki disease (KD) is a multisystem vasculitis that predominantly targets the coronary arteries in children. Phenotypic similarities between KD and recurrent fever syndromes point to the potential role of inflammasome activation in KD. Mutations in NLRP3 are associated with recurrent fever/autoinflammatory syndromes. We show that the KD-associated genetic polymorphism in inositol-triphosphate 3-kinase C (ITPKC) (rs28493229) has important functional consequences, governing ITPKC protein levels and thereby intracellular calcium, which in turn regulates NLRP3 expression and production of IL-1β and IL-18...
September 30, 2016: Journal of Immunology: Official Journal of the American Association of Immunologists
https://www.readbyqxmd.com/read/27666011/mesenchymal-inflammation-drives-genotoxic-stress-in-hematopoietic-stem-cells-and-predicts-disease-evolution-in-human-pre-leukemia
#17
Noemi A Zambetti, Zhen Ping, Si Chen, Keane J G Kenswil, Maria A Mylona, Mathijs A Sanders, Remco M Hoogenboezem, Eric M J Bindels, Maria N Adisty, Paulina M H Van Strien, Cindy S van der Leije, Theresia M Westers, Eline M P Cremers, Chiara Milanese, Pier G Mastroberardino, Johannes P T M van Leeuwen, Bram C J van der Eerden, Ivo P Touw, Taco W Kuijpers, Roland Kanaar, Arjan A van de Loosdrecht, Thomas Vogl, Marc H G P Raaijmakers
Mesenchymal niche cells may drive tissue failure and malignant transformation in the hematopoietic system, but the underlying molecular mechanisms and relevance to human disease remain poorly defined. Here, we show that perturbation of mesenchymal cells in a mouse model of the pre-leukemic disorder Shwachman-Diamond syndrome (SDS) induces mitochondrial dysfunction, oxidative stress, and activation of DNA damage responses in hematopoietic stem and progenitor cells. Massive parallel RNA sequencing of highly purified mesenchymal cells in the SDS mouse model and a range of human pre-leukemic syndromes identified p53-S100A8/9-TLR inflammatory signaling as a common driving mechanism of genotoxic stress...
September 10, 2016: Cell Stem Cell
https://www.readbyqxmd.com/read/27593624/response-contingency-directs-long-term-cocaine-induced-neuroplasticity-in-prefrontal-and-striatal-dopamine-terminals
#18
Joost Wiskerke, Anton N M Schoffelmeer, Taco J De Vries
Exposure to addictive substances such as cocaine is well-known to alter brain organisation. Cocaine-induced neuroadaptations depend on several factors, including drug administration paradigm. To date, studies addressing the consequences of cocaine exposure on dopamine transmission have either not been designed to investigate the role of response contingency or focused only on short-term neuroplasticity. We demonstrate a key role of response contingency in directing long-term cocaine-induced neuroplasticity throughout projection areas of the mesocorticolimbic dopamine system...
October 2016: European Neuropsychopharmacology: the Journal of the European College of Neuropsychopharmacology
https://www.readbyqxmd.com/read/27589902/field-deployable-reverse-transcription-insulated-isothermal-pcr-rt-iipcr-assay-for-rapid-and-sensitive-detection-of-foot-and-mouth-disease-virus
#19
A Ambagala, M Fisher, M Goolia, C Nfon, T Furukawa-Stoffer, R Ortega Polo, O Lung
Foot-and-mouth disease (FMD) is a highly contagious viral disease of cloven-hoofed animals, which can decimate the livestock industry and economy of countries previously free of this disease. Rapid detection of foot-and-mouth disease virus (FMDV) is critical to containing an FMD outbreak. Availability of a rapid, highly sensitive and specific, yet simple and field-deployable assay would support local decision-making during an FMDV outbreak. Here we report validation of a novel reverse transcription-insulated isothermal PCR (RT-iiPCR) assay that can be performed on a commercially available, compact and portable POCKIT(™) analyser that automatically analyses data and displays '+' or '-' results...
September 3, 2016: Transboundary and Emerging Diseases
https://www.readbyqxmd.com/read/27584941/gelation-kinetics-and-network-structure-of-cellulose-nanocrystals-in-aqueous-solution
#20
Karthik R Peddireddy, Isabelle Capron, Taco Nicolai, Lazhar Benyahia
Cellulose nanocrystals (CNC) are rod-like biosourced nanoparticles that are widely used in a range of applications. Charged CNC was obtained by acid extraction from cotton and dispersed in aqueous solution using ultrasound and characterized by light scattering. Aggregation and gelation of CNC induced by addition of NaCl was investigated by light scattering as a function of the NaCl concentration (30-70 mM), the CNC concentration (0.5-5 g/L), and the temperature (10-60 °C). Formation of fractal aggregates was observed that grow with time until they percolate and form a weak system spanning network...
October 10, 2016: Biomacromolecules
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