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Repertoire Sequencing

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https://www.readbyqxmd.com/read/28092796/global-open-data-management-in-metabolomics
#1
REVIEW
Kenneth Haug, Reza M Salek, Christoph Steinbeck
Chemical Biology employs chemical synthesis, analytical chemistry and other tools to study biological systems. Recent advances in both molecular biology such as next generation sequencing (NGS) have led to unprecedented insights towards the evolution of organisms' biochemical repertoires. Because of the specific data sharing culture in Genomics, genomes from all kingdoms of life become readily available for further analysis by other researchers. While the genome expresses the potential of an organism to adapt to external influences, the Metabolome presents a molecular phenotype that allows us to asses the external influences under which an organism exists and develops in a dynamic way...
January 13, 2017: Current Opinion in Chemical Biology
https://www.readbyqxmd.com/read/28091735/comprehensive-assessment-of-peripheral-blood-tcr%C3%AE-repertoire-in-infectious-mononucleosis-and-chronic-active-ebv-infection-patients
#2
Shenglin Liu, Qian Zhang, Dongli Huang, Wenli Zhang, Fengluan Zhong, Jia Feng, Xueru Chen, Qingxiang Meng, Xiaofan Chen, Wei Zhang, Hongyu Zhang
Epstein-Barr virus (EBV) primary infection is usually asymptomatic, but it sometimes progresses to infectious mononucleosis (IM). Occasionally, some people develop chronic active EBV infection (CAEBV) with underlying immunodeficiency, which belongs to a continuous spectrum of EBV-associated lymphoproliferative disorders (EBV(+) LPD) with heterogeneous clinical presentations and high mortality. It has been well established that T cell-mediated immune response plays a critical role in the disease evolution of EBV infection...
January 14, 2017: Annals of Hematology
https://www.readbyqxmd.com/read/28088364/antibodies-from-novel-repertoires-to-defining-and-refining-the-structure-of-biologically-important-targets
#3
REVIEW
Paul J Conroy, Ruby H P Law, Tom Caradoc-Davies, James C Whisstock
Antibodies represent a highly successful class of molecules that bind a wide-range of targets in therapeutic-, diagnostic- and research-based applications. The antibody repertoire is composed of the building blocks required to develop an effective adaptive immune response against foreign insults. A number of species have developed novel genetic and structural mechanisms from which they derive these antibody repertoires, however, traditionally antibodies are derived from human, and rodent sources. Due to their high-value therapeutic, diagnostic, biotechnological and research applications, much innovation has resulted in techniques and approaches to isolate novel antibodies...
January 11, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28087666/dysregulation-of-b-cell-repertoire-formation-in-myasthenia-gravis-patients-revealed-through-deep-sequencing
#4
Jason A Vander Heiden, Panos Stathopoulos, Julian Q Zhou, Luan Chen, Tamara J Gilbert, Christopher R Bolen, Richard J Barohn, Mazen M Dimachkie, Emma Ciafaloni, Teresa J Broering, Francois Vigneault, Richard J Nowak, Steven H Kleinstein, Kevin C O'Connor
Myasthenia gravis (MG) is a prototypical B cell-mediated autoimmune disease affecting 20-50 people per 100,000. The majority of patients fall into two clinically distinguishable types based on whether they produce autoantibodies targeting the acetylcholine receptor (AChR-MG) or muscle specific kinase (MuSK-MG). The autoantibodies are pathogenic, but whether their generation is associated with broader defects in the B cell repertoire is unknown. To address this question, we performed deep sequencing of the BCR repertoire of AChR-MG, MuSK-MG, and healthy subjects to generate ∼518,000 unique VH and VL sequences from sorted naive and memory B cell populations...
January 13, 2017: Journal of Immunology: Official Journal of the American Association of Immunologists
https://www.readbyqxmd.com/read/28086979/b-cell-repertoires-in-hla-sensitized-kidney-transplant-candidates-undergoing-desensitization-therapy
#5
John F Beausang, H Christina Fan, Rene Sit, Maria U Hutchins, Kshama Jirage, Rachael Curtis, Edward Hutchins, Stephen R Quake, Julie M Yabu
BACKGROUND: Kidney transplantation is the most effective treatment for end-stage renal disease. Sensitization refers to pre-existing antibodies against human leukocyte antigen (HLA) protein and remains a major barrier to successful transplantation. Despite implementation of desensitization strategies, many candidates fail to respond. Our objective was to determine whether measuring B cell repertoires could differentiate candidates that respond to desensitization therapy. METHODS: We developed an assay based on high-throughput DNA sequencing of the variable domain of the heavy chain of immunoglobulin genes to measure changes in B cell repertoires in 19 highly HLA-sensitized kidney transplant candidates undergoing desensitization and 7 controls with low to moderate HLA sensitization levels...
January 13, 2017: Journal of Translational Medicine
https://www.readbyqxmd.com/read/28077776/odour-based-discrimination-of-similarity-at-the-major-histocompatibility-complex-in-birds
#6
Sarah Leclaire, Maria Strandh, Jérôme Mardon, Helena Westerdahl, Francesco Bonadonna
Many animals are known to preferentially mate with partners that are dissimilar at the major histocompatibility complex (MHC) in order to maximize the antigen binding repertoire (or disease resistance) in their offspring. Although several mammals, fish or lizards use odour cues to assess MHC similarity with potential partners, the ability of birds to assess MHC similarity using olfactory cues has not yet been explored. Here we used a behavioural binary choice test and high-throughput-sequencing of MHC class IIB to determine whether blue petrels can discriminate MHC similarity based on odour cues alone...
January 11, 2017: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/28077600/ibrutinib-therapy-increases-t-cell-repertoire-diversity-in-patients-with-chronic-lymphocytic-leukemia
#7
Qingsong Yin, Mariela Sivina, Harlan Robins, Erik Yusko, Marissa Vignali, Susan O'Brien, Michael J Keating, Alessandra Ferrajoli, Zeev Estrov, Nitin Jain, William G Wierda, Jan A Burger
The Bruton's tyrosine kinase inhibitor ibrutinib is a highly effective, new targeted therapy for chronic lymphocytic leukemia (CLL) that thwarts leukemia cell survival, growth, and tissue homing. The effects of ibrutinib treatment on the T cell compartment, which is clonally expanded and thought to support the growth of malignant B cells in CLL, are not fully characterized. Using next-generation sequencing technology, we characterized the diversity of TCRβ-chains in peripheral blood T cells from 15 CLL patients before and after 1 y of ibrutinib therapy...
January 11, 2017: Journal of Immunology: Official Journal of the American Association of Immunologists
https://www.readbyqxmd.com/read/28077404/high-throughput-sequencing-of-the-t-cell-receptor-repertoire-pitfalls-and-opportunities
#8
James M Heather, Mazlina Ismail, Theres Oakes, Benny Chain
T-cell specificity is determined by the T-cell receptor, a heterodimeric protein coded for by an extremely diverse set of genes produced by imprecise somatic gene recombination. Massively parallel high-throughput sequencing allows millions of different T-cell receptor genes to be characterized from a single sample of blood or tissue. However, the extraordinary heterogeneity of the immune repertoire poses significant challenges for subsequent analysis of the data. We outline the major steps in processing of repertoire data, considering low-level processing of raw sequence files and high-level algorithms, which seek to extract biological or pathological information...
January 10, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28074285/t-cell-receptor-repertoire-usage-in-cancer-as-a-surrogate-marker-for-immune-responses
#9
REVIEW
David Schrama, Cathrin Ritter, Jürgen C Becker
Characterizing the interaction of cancer cells with the host adaptive immune system is critical for understanding tumor immunology and the modus operandi of immunotherapeutic interventions to treat cancer. As the key cellular effectors of adaptive immunity, T cells are endowed with specialized receptors (the T cell receptor; TCR), to recognize and to eliminate cancer cells. The diversity of the TCR repertoire results from specialized genetic diversification mechanisms that generate an incredible variability allowing recognizing extensive collections of antigens...
January 10, 2017: Seminars in Immunopathology
https://www.readbyqxmd.com/read/28073756/feature-selection-using-a-one-dimensional-na%C3%A3-ve-bayes-classifier-increases-the-accuracy-of-support-vector-machine-classification-of-cdr3-repertoires
#10
Mattia Cinelli, Yuxin Sun, Katharine Best, James M Heather, Shlomit Reich-Zeliger, Eric Shifrut, Nir Friedman, John Shawe-Taylor, Benny Chain
MOTIVATION: Somatic DNA recombination, the hallmark of vertebrate adaptive immunity, has the potential to generate a vast diversity of antigen receptor sequences. How this diversity captures antigen specificity remains incompletely understood. In this study we use high throughput sequencing to compare the global changes in T cell receptor β chain complementarity determining region 3 (CDR3β) sequences following immunization with ovalbumin administered with complete Freund's adjuvant (CFA) or CFA alone...
January 10, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28073357/long-noncoding-rna-repertoire-in-chicken-liver-and-adipose-tissue
#11
Kévin Muret, Christophe Klopp, Valentin Wucher, Diane Esquerré, Fabrice Legeai, Frédéric Lecerf, Colette Désert, Morgane Boutin, Frédéric Jehl, Hervé Acloque, Elisabetta Giuffra, Sarah Djebali, Sylvain Foissac, Thomas Derrien, Sandrine Lagarrigue
BACKGROUND: Improving functional annotation of the chicken genome is a key challenge in bridging the gap between genotype and phenotype. Among all transcribed regions, long noncoding RNAs (lncRNAs) are a major component of the transcriptome and its regulation, and whole-transcriptome sequencing (RNA-Seq) has greatly improved their identification and characterization. We performed an extensive profiling of the lncRNA transcriptome in the chicken liver and adipose tissue by RNA-Seq. We focused on these two tissues because of their importance in various economical traits for which energy storage and mobilization play key roles and also because of their high cell homogeneity...
January 10, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28070679/diversity-of-microbial-carbohydrate-active-enzymes-cazymes-associated-with-freshwater-and-soil-samples-from-caatinga-biome
#12
Ana Camila Andrade, Adriana Fróes, Fabyano Álvares Cardoso Lopes, Fabiano L Thompson, Ricardo Henrique Krüger, Elizabeth Dinsdale, Thiago Bruce
Semi-arid and arid areas occupy about 33% of terrestrial ecosystems. However, little information is available about microbial diversity in the semi-arid Caatinga, which represents a unique biome that extends to about 11% of the Brazilian territory and is home to extraordinary diversity and high endemism level of species. In this study, we characterized the diversity of microbial genes associated with biomass conversion (carbohydrate-active enzymes, or so-called CAZYmes) in soil and freshwater of the Caatinga...
January 9, 2017: Microbial Ecology
https://www.readbyqxmd.com/read/28067677/the-microbiome-in-mechanically-ventilated-patients
#13
Yudong Yin, Peter Hountras, Richard G Wunderink
PURPOSE OF REVIEW: Discovery of a normal lung microbiome requires reassessment of our concepts of HAP/VAP pathogenesis and has important implications for clinical diagnosis and management. RECENT FINDINGS: Changes in the microbiome of dental plaque are associated with increased risk of HAP/VAP. A transition to a lung microbiome enriched with gut flora is found in ARDS with an increased inflammatory response in patients with this change in microbial flora. A characteristic microbiome pattern of higher amounts of bacterial DNA, lower community diversity, and greater relative abundance of a single species characterize pneumonia and occasionally identify bacteria not found in culture...
January 6, 2017: Current Opinion in Infectious Diseases
https://www.readbyqxmd.com/read/28067254/unusual-respiratory-capacity-and-nitrogen-metabolism-in-a-parcubacterium-od1-of-the-candidate-phyla-radiation
#14
Cindy J Castelle, Christopher T Brown, Brian C Thomas, Kenneth H Williams, Jillian F Banfield
The Candidate Phyla Radiation (CPR) is a large group of bacteria, the scale of which approaches that of all other bacteria. CPR organisms are inferred to depend on other community members for many basic cellular building blocks and all appear to be obligate anaerobes. To date, there has been no evidence for any significant respiratory capacity in an organism from this radiation. Here we report a curated draft genome for 'Candidatus Parcunitrobacter nitroensis' a member of the Parcubacteria (OD1) superphylum of the CPR...
January 9, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28063478/developmental-expression-of-b-cell-molecules-in-equine-lymphoid-tissues
#15
J M B Prieto, R L Tallmadge, M J B Felippe
Identification and classification of B cell subpopulations has been shown to be challenging and inconsistent among different species. Our study tested aspects of ontogeny, phenotype, tissue distribution, and function of equine CD5(hi) B cells, which represented a greater proportion of B cells early in development and in the peritoneal cavity. CD5(hi) and CD5(lo) B cells differentially expressed B cell markers (CD2, CD21, IgM) measured using flow cytometry, but similar mRNA expression of signature genes (DGKA, FGL2, PAX5, IGHM, IL10) measured using quantitative RT-PCR...
January 2017: Veterinary Immunology and Immunopathology
https://www.readbyqxmd.com/read/28061744/comprehensive-evaluation-of-extracellular-small-rna-isolation-methods-from-serum-in-high-throughput-sequencing
#16
Yan Guo, Kasey Vickers, Yanhua Xiong, Shilin Zhao, Quanhu Sheng, Pan Zhang, Wanding Zhou, Charles R Flynn
BACKGROUND: DNA and RNA fractions from whole blood, serum and plasma are increasingly popular analytes that are currently under investigation for their utility in the diagnosis and staging of disease. Small non-coding ribonucleic acids (sRNAs), specifically microRNAs (miRNAs) and their variant isoforms (isomiRs), and transfer RNA (tRNA)-derived small RNAs (tDRs) comprise a repertoire of molecules particularly promising in this regard. RESULTS: In this designed study, we compared the performance of various methods and kits for isolating circulating extracellular sRNAs (ex-sRNAs)...
January 7, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28060363/genomic-repertoire-of-the-woeseiaceae-jtb255-cosmopolitan-and-abundant-core-members-of-microbial-communities-in-marine-sediments
#17
Marc Mußmann, Petra Pjevac, Karen Krüger, Stefan Dyksma
To date, very little is known about the bacterial core community of marine sediments. Here we study the environmental distribution, abundance and ecogenomics of the gammaproteobacterial Woeseiaceae/JTB255 marine benthic group. A meta-analysis of published work shows that the Woeseiaceae/JTB255 are ubiquitous and consistently rank among the most abundant 16S rRNA gene sequences in diverse marine sediments. They account for up to 22% of bacterial amplicons and 6% of total cell counts in European and Australian coastal sediments...
January 6, 2017: ISME Journal
https://www.readbyqxmd.com/read/28060302/a-platform-of-anti-biofilm-assays-suited-to-the-exploration-of-natural-compound-libraries
#18
Malena E Skogman, Pia M Vuorela, Adyary Fallarero
Biofilms are regarded as one of the most challenging topics of modern biomedicine, and they are potentially responsible for over 80% of antibiotic-tolerant infections. Biofilms have displayed an exceptionally high tolerance for chemotherapy, which is thought to be multifactorial. For instance, the matrix provides a physical barrier that decreases the penetration of antibiotics into the biofilm. Also, cells within the biofilms are phenotypically diverse. Likely, biofilm resilience arises from a combination of these and other, yet unknown, mechanisms...
December 27, 2016: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28057863/mutational-landscape-of-antibody-variable-domains-reveals-a-switch-modulating-the-interdomain-conformational-dynamics-and-antigen-binding
#19
Patrick Koenig, Chingwei V Lee, Benjamin T Walters, Vasantharajan Janakiraman, Jeremy Stinson, Thomas W Patapoff, Germaine Fuh
Somatic mutations within the antibody variable domains are critical to the immense capacity of the immune repertoire. Here, via a deep mutational scan, we dissect how mutations at all positions of the variable domains of a high-affinity anti-VEGF antibody G6.31 impact its antigen-binding function. The resulting mutational landscape demonstrates that large portions of antibody variable domain positions are open to mutation, and that beneficial mutations can be found throughout the variable domains. We determine the role of one antigen-distal light chain position 83, demonstrating that mutation at this site optimizes both antigen affinity and thermostability by modulating the interdomain conformational dynamics of the antigen-binding fragment...
January 5, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28055305/generation-of-a-highly-diverse-panel-of-antagonistic-chicken-monoclonal-antibodies-against-the-gip-receptor
#20
Jennifer D Könitzer, Shreya Pramanick, Qi Pan, Robert Augustin, Sebastian Bandholtz, William Harriman, Shelley Izquierdo
Raising functional antibodies against G protein-coupled receptors (GPCRs) is challenging due to their low density expression, instability in the absence of the cell membrane's lipid bilayer and frequently short extracellular domains that can serve as antigens. In addition, a particular therapeutic concept may require an antibody to not just bind the receptor, but also act as a functional receptor agonist or antagonist. Antagonizing the glucose-dependent insulinotropic polypeptide (GIP) receptor may open up new therapeutic modalities in the treatment of diabetes and obesity...
January 5, 2017: MAbs
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