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Repertoire Sequencing

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https://www.readbyqxmd.com/read/29684201/dysregulation-of-epstein-barr-virus-infection-in-hypomorphic-zap70-mutation
#1
Akihiro Hoshino, Takehiro Takashima, Kenichi Yoshida, Akira Morimoto, Yuta Kawahara, Tzu-Wen Yeh, Tsubasa Okano, Motoi Yamashita, Noriko Mitsuiki, Kohsuke Imai, Takashi Sakatani, Atsuko Nakazawa, Yusuke Okuno, Yuichi Shiraishi, Kenichi Chiba, Hiroko Tanaka, Satoru Miyano, Seishi Ogawa, Seiji Kojima, Tomohiro Morio, Hirokazu Kanegane
Background: Some patients with genetic defects develop Epstein-Barr virus (EBV)-associated lymphoproliferative disorder (LPD)/lymphoma as the main feature. Hypomophic mutations can cause different clinical and laboratory manifestations from null mutations in the same genes. Methods: We sought to describe the clinical and immunologic phenotype of a 21-month-old boy having EBV-associated LPD who was in good health till then. A genetic and immunologic analysis was performed...
April 19, 2018: Journal of Infectious Diseases
https://www.readbyqxmd.com/read/29681477/a-forward-genetic-screen-in-zebrafish-identifies-the-g-protein-coupled-receptor-casr-as-a-modulator-of-sensorimotor-decision-making
#2
Roshan A Jain, Marc A Wolman, Kurt C Marsden, Jessica C Nelson, Hannah Shoenhard, Fabio A Echeverry, Christina Szi, Hannah Bell, Julianne Skinner, Emilia N Cobbs, Keisuke Sawada, Amy D Zamora, Alberto E Pereda, Michael Granato
Animals continuously integrate sensory information and select contextually appropriate responses. Here, we show that zebrafish larvae select a behavioral response to acoustic stimuli from a pre-existing choice repertoire in a context-dependent manner. We demonstrate that this sensorimotor choice is modulated by stimulus quality and history, as well as by neuromodulatory systems-all hallmarks of more complex decision making. Moreover, from a genetic screen coupled with whole-genome sequencing, we identified eight mutants with deficits in this sensorimotor choice, including mutants of the vertebrate-specific G-protein-coupled extracellular calcium-sensing receptor (CaSR), whose function in the nervous system is not well understood...
April 6, 2018: Current Biology: CB
https://www.readbyqxmd.com/read/29679709/unique-glandular-ex-vivo-th1-and-th17-receptor-motifs-in-sj%C3%A3-gren-s-syndrome-patients-using-single-cell-analysis
#3
Alexandria Voigt, Katherine Bohn, Sukesh Sukumaran, Carol M Stewart, Indraneel Bhattacharya, Cuong Q Nguyen
Primary Sjögren's syndrome (pSS) is an autoimmune disease in which the underlying cause has yet to be elucidated. The main objective of this study was to determine the T cell receptor (TCR) repertoires of individual infiltrating T helper (Th)-1 and 17 cells of pSS patients using single-cell analysis. Single-cell analysis of ex-vivo infiltrating T cells demonstrated that pSS patients had higher frequencies of activated Th17 cells. Single-cell TCR sequencing revealed that TCRβ variable (TRBV)3-1/joint (J)1-2 (CLFLSMSACVW) and TRBV20-1/J1-1 (SVGSTAIPP*T) were expressed by activated Th1 and Th17 cells in both cohorts...
April 18, 2018: Clinical Immunology: the Official Journal of the Clinical Immunology Society
https://www.readbyqxmd.com/read/29678917/genomic-inference-of-recombination-mediated-evolution-in-xanthomonas-euvesicatoria-and-x-perforans
#4
Mustafa O Jibrin, Neha Potnis, Sujan Timilsina, Gerald V Minsavage, Gary E Vallad, Pamela D Roberts, Jeffrey B Jones, Erica M Goss
Recombination is a major driver of evolution in bacterial populations because it can spread and combine independently evolved beneficial mutations. Recombinant lineages of plant bacterial pathogens are typically associated with colonization of novel hosts and emergence of new diseases. Here, we show that recombination between evolutionarily and phenotypically distinct plant pathogenic lineages generated recombinant lineages with unique combinations of pathogenicity and virulence factors. X. euvesicatoria ( Xe ) and X...
April 20, 2018: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29678843/analytical-and-workflow-evaluation-of-the-aries-sample-to-result-molecular-assay-for-clostridium-difficile
#5
Steven K Lawson, David Chung, Shubhagata Das, Jeremy Friesen, Susan Sefers, Sherry Dunbar, Jonathan E Schmitz
We evaluated the analytical and workflow characteristics of the ARIES Clostridium difficile assay, a recently developed qPCR-based test for toxigenic C. difficile ARIES was compared to the illumigene C. difficile assay, a commonly employed, loop-mediated amplification technique with similar sample-to-result capabilities. Following illumigene analysis, 122 positive and 164 negative stool specimens were banked for subsequent ARIES testing. The analytical agreement between the platforms was high: 93.4% positive agreement (89...
March 2018: Annals of Clinical and Laboratory Science
https://www.readbyqxmd.com/read/29677397/two-ancestral-genes-shaped-the-xanthomonas-campestris-tal-effector-gene-repertoire
#6
Nicolas Denancé, Boris Szurek, Erin L Doyle, Emmanuelle Lauber, Lisa Fontaine-Bodin, Sébastien Carrère, Endrick Guy, Ahmed Hajri, Aude Cerutti, Tristan Boureau, Stéphane Poussier, Matthieu Arlat, Adam J Bogdanove, Laurent D Noël
Xanthomonas transcription activator-like effectors (TALEs) are injected inside plant cells to promote host susceptibility by enhancing transcription of host susceptibility genes. TALE-encoding (tal) genes were thought to be absent from Brassicaceae-infecting Xanthomonas campestris (Xc) genomes based on four reference genomic sequences. We discovered tal genes in 26 of 49 Xc strains isolated worldwide and used a combination of single molecule real time (SMRT) and tal amplicon sequencing to yield a near-complete description of the TALEs found in Xc (Xc TALome)...
April 20, 2018: New Phytologist
https://www.readbyqxmd.com/read/29673315/inter-genome-comparison-of-the-quorn-fungus-fusarium-venenatum-and-the-closely-related-plant-infecting-pathogen-fusarium-graminearum
#7
Robert King, Neil Andrew Brown, Martin Urban, Kim E Hammond-Kosack
BACKGROUND: The soil dwelling saprotrophic non-pathogenic fungus Fusarium venenatum, routinely used in the commercial fermentation industry, is phylogenetically closely related to the globally important cereal and non-cereal infecting pathogen F. graminearum. This study aimed to sequence, assemble and annotate the F. venenatum (strain A3/5) genome, and compare this genome with F. graminearum. RESULTS: Using shotgun sequencing, a 38,660,329 bp F. venenatum genome was assembled into four chromosomes, and a 78,618 bp mitochondrial genome...
April 19, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29669837/amino-acid-substitutions-within-hla-b-27-restricted-t-cell-epitopes-prevent-recognition-by-hepatitis-delta-virus-specific-cd8-t-cells
#8
Hadi Karimzadeh, Muthamia M Kiraithe, Anna D Kosinska, Manuel Glaser, Melanie Fiedler, Valerie Oberhardt, Elahe Salimi Alizei, Maike Hofmann, Juk Yee Mok, Melanie Nguyen, Wim J E van Esch, Bettina Budeus, Jan Grabowski, Maria Homs, Antonella Olivero, Hossein Keyvani, Francisco Rodríguez-Frías, David Tabernero, Maria Buti, Andreas Heinold, Seyed Moayed Alavian, Tanja Bauer, Julian Schulze Zur Wiesch, Bijan Raziorrouh, Daniel Hoffmann, Antonina Smedile, Mario Rizzetto, Heiner Wedemeyer, Jörg Timm, Iris Antes, Christoph Neumann-Haefelin, Ulrike Protzer, Michael Roggendorf
Virus-specific CD8 T-cell response seems to play a significant role in the outcome of hepatitis delta virus (HDV) infection. However, the HDV-specific T-cell epitope repertoire and mechanisms of CD8 T-cell failure in HDV infection have merely been characterized. We therefore aimed to characterize HDV-specific CD8 T cell epitopes and the impact of viral mutations on immune escape. In this study, we predicted peptide epitopes binding the most frequent HLA types and assessed their HLA binding capacity. These epitopes were characterized in HDV-infected patients by intracellular IFN-γ staining...
April 18, 2018: Journal of Virology
https://www.readbyqxmd.com/read/29669518/irprofiler-a-software-toolbox-for-high-throughput-immune-receptor-profiling
#9
Christos Maramis, Athanasios Gkoufas, Anna Vardi, Evangelia Stalika, Kostas Stamatopoulos, Anastasia Hatzidimitriou, Nicos Maglaveras, Ioanna Chouvarda
BACKGROUND: The study of the huge diversity of immune receptors, often referred to as immune repertoire profiling, is a prerequisite for diagnosis, prognostication and monitoring of hematological disorders. In the era of high-throughput sequencing (HTS), the abundance of immunogenetic data has revealed unprecedented opportunities for the thorough profiling of T-cell receptors (TR) and B-cell receptors (BcR). However, the volume of the data to be analyzed mandates for efficient and ease-to-use immune repertoire profiling software applications...
April 18, 2018: BMC Bioinformatics
https://www.readbyqxmd.com/read/29668996/brepertoire-a-user-friendly-web-server-for-analysing-antibody-repertoire-data
#10
Christian Margreitter, Hui-Chun Lu, Catherine Townsend, Alexander Stewart, Deborah K Dunn-Walters, Franca Fraternali
Antibody repertoire analysis by high throughput sequencing is now widely used, but a persisting challenge is enabling immunologists to explore their data to discover discriminating repertoire features for their own particular investigations. Computational methods are necessary for large-scale evaluation of antibody properties. We have developed BRepertoire, a suite of user-friendly web-based software tools for large-scale statistical analyses of repertoire data. The software is able to use data preprocessed by IMGT, and performs statistical and comparative analyses with versatile plotting options...
April 14, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29666626/next-generation-immune-repertoire-sequencing-as-a-clue-to-elucidate-the-landscape-of-immune-modulation-by-host-gut-microbiome-interactions
#11
Tatsuo Ichinohe, Takahiko Miyama, Takakazu Kawase, Yasuko Honjo, Kazutaka Kitaura, Hiroyuki Sato, Tadasu Shin-I, Ryuji Suzuki
The human immune system is a fine network consisted of the innumerable numbers of functional cells that balance the immunity and tolerance against various endogenous and environmental challenges. Although advances in modern immunology have revealed a role of many unique immune cell subsets, technologies that enable us to capture the whole landscape of immune responses against specific antigens have been not available to date. Acquired immunity against various microorganisms including host microbiome is principally founded on T cell and B cell populations, each of which expresses antigen-specific receptors that define a unique clonotype...
2018: Frontiers in Immunology
https://www.readbyqxmd.com/read/29666193/lmo1656-is-a-secreted-virulence-factor-of-listeria-monocytogenes-that-interacts-with-the-sortin-nexin-6-bar-complex
#12
Daryl Jason David, Alessandro Pagliuso, Lilliana Radoshevich, Marie-Anne Nahori, Pascale Cossart
Listeria monocytogenes (Lm) is a facultative intracellular bacterial pathogen, the causative agent of listeriosis, a rare but fatal disease.  During infection, Lm can traverse several physiological barriers; it can cross the intestine and placenta, and in immunocompromised individuals, the blood-brain barrier. With the recent plethora of sequenced genomes available for Lm, it is clear that the complete repertoire of genes used by Lm to interact with its host remains to be fully explored.  Recently, we focused on secreted Lm proteins, since they are likely to interact with host cell components...
April 17, 2018: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29661185/madagascar-ground-gecko-genome-analysis-characterizes-asymmetric-fates-of-duplicated-genes
#13
Yuichiro Hara, Miki Takeuchi, Yuka Kageyama, Kaori Tatsumi, Masahiko Hibi, Hiroshi Kiyonari, Shigehiro Kuraku
BACKGROUND: Conventionally, comparison among amniotes - birds, mammals, and reptiles - has often been approached through analyses of mammals and, for comparison, birds. However, birds are morphologically and physiologically derived and, moreover, some parts of their genomes are recognized as difficult to sequence and/or assemble and are thus missing in genome assemblies. Therefore, sequencing the genomes of reptiles would aid comparative studies on amniotes by providing more comprehensive coverage to help understand the molecular mechanisms underpinning evolutionary changes...
April 16, 2018: BMC Biology
https://www.readbyqxmd.com/read/29659703/b-cell-receptor-reconstruction-from-single-cell-rna-seq-with-vdjpuzzle
#14
Simone Rizzetto, David N P Koppstein, Jerome Samir, Mandeep Singh, Joanne H Reed, Curtis H Cai, Andrew R Lloyd, Auda A Eltahla, Christopher C Goodnow, Fabio Luciani
Motivation: The B-cell receptor (BCR) performs essential functions for the adaptive immune system including recognition of pathogen-derived antigens. The vast repertoire and adaptive variation of BCR sequences due to V(D)J recombination and somatic hypermutation (SHM) necessitates single-cell characterization of BCR sequences. Single-cell RNA sequencing (scRNA-seq) presents the opportunity for simultaneous capture of paired BCR heavy and light chains and the transcriptomic signature. Results: We developed VDJPuzzle, a novel bioinformatic tool that reconstructs productive, full-length B-cell receptor sequences of both heavy and light chains and extract somatic mutations on the VDJ region...
April 5, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29658117/mapping-the-tumour-hla-ligandome-by-mass-spectrometry
#15
REVIEW
Lena Katharina Freudenmann, Ana Marcu, Stefan Stevanović
The entirety of HLA-presented peptides is referred to as the HLA ligandome of a cell or tissue, in tumours often termed immunopeptidome. Mapping the tumour immunopeptidome by mass spectrometry (MS) comprehensively views the pathophysiologically relevant antigenic signature of human malignancies. MS is an unbiased approach stringently filtering the candidates to be tested as opposed to epitope prediction algorithms. In the setting of peptide-specific immunotherapies, MS-based strategies significantly diminish the risk of lacking clinical benefit, as they yield highly enriched amounts of truly presented peptides...
April 15, 2018: Immunology
https://www.readbyqxmd.com/read/29657315/author-correction-next-generation-sequencing-reveals-changes-of-the-%C3%AE-%C3%AE-t-cell-receptor-repertoires-in-patients-with-pulmonary-tuberculosis
#16
Chaofei Cheng, Bei Wang, Lei Gao, Jianmin Liu, Xinchun Chen, He Huang, Zhendong Zhao
A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has not been fixed in the paper.
April 16, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29657145/hla-drb1-shared-epitope-alleles-and-disease-activity-are-correlated-with-reduced-t-cell-receptor-repertoire-diversity-in-cd4-t-cells-in-rheumatoid-arthritis
#17
Keiichi Sakurai, Kazuyoshi Ishigaki, Hirofumi Shoda, Yasuo Nagafuchi, Yumi Tsuchida, Shuji Sumitomo, Hiroko Kanda, Akari Suzuki, Yuta Kochi, Kazuhiko Yamamoto, Keishi Fujio
OBJECTIVE: Shared epitope (SE) alleles are the most significant genetic susceptibility locus in rheumatoid arthritis (RA); however, their target populations in CD4+ T cells are not well elucidated. We analyzed the association between SE alleles and the T cell receptor (TCR) repertoire diversity of naive and memory CD4+ T cells using next-generation sequencing (NGS). METHODS: The TCR beta chains in naive and memory CD4+ T cells from the peripheral blood of 22 patients with RA and 18 age- and sex-matched healthy donors (HD) were analyzed by NGS...
April 15, 2018: Journal of Rheumatology
https://www.readbyqxmd.com/read/29651461/limiting-parental-interaction-during-vocal-development-affects-acoustic-call-structure-in-marmoset-monkeys
#18
Yasemin B Gultekin, Steffen R Hage
Human vocal development is dependent on learning by imitation through social feedback between infants and caregivers. Recent studies have revealed that vocal development is also influenced by parental feedback in marmoset monkeys, suggesting vocal learning mechanisms in nonhuman primates. Marmoset infants that experience more contingent vocal feedback than their littermates develop vocalizations more rapidly, and infant marmosets with limited parental interaction exhibit immature vocal behavior beyond infancy...
April 2018: Science Advances
https://www.readbyqxmd.com/read/29651249/ontogenetic-and-experience-dependent-changes-in-defensive-behavior-in-captive-bred-hawaiian-bobtail-squid-euprymna-scolopes
#19
Kia Seehafer, Samantha Brophy, Sara R Tom, Robyn J Crook
Cephalopod molluscs are known for their extensive behavioral repertoire and their impressive learning abilities. Their primary defensive behaviors, such as camouflage, have received detailed study, but knowledge is limited to intensive study of relatively few species. A considerable challenge facing cephalopod research is the need to establish new models that can be captive bred, are tractable for range of different experimental procedures, and that will address broad questions in biological research. The Hawaiian Bobtail Squid ( Euprymna scolopes ) is a small, tropical cephalopod that has a long history of research in the field of microbial symbiosis, but offers great promise as a novel behavioral and neurobiological model...
2018: Frontiers in Physiology
https://www.readbyqxmd.com/read/29651132/compositional-characteristics-of-human-peripheral-trbv-pseudogene-rearrangements
#20
Bin Shi, Long Ma, Xiaoyan He, Peipei Wu, Peng Wang, Xiaomei Wang, Rui Ma, Xinsheng Yao
The diversity of the T cell receptor (TCR) complementarity determining region 3 (CDR3) repertoire is the result of random combinations, insertions and deletions during recombination of the germline V, D and J gene fragments. During evolution, some human TCR beta chain variable (TRBV) pseudogenes have been retained. Many previous studies have focused on functional TRBV genes, while little attention has been given to TRBV pseudogenes. To describe the compositional characteristics of TRBV pseudogene rearrangements, we compared and analysed TRBV pseudogenes, TRBV open reading frames (ORFs) and functional TRBV genes via high-throughput sequencing of DNA obtained from the peripheral blood of 4 healthy volunteers and 4 patients...
April 12, 2018: Scientific Reports
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