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Repertoire Sequencing

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https://www.readbyqxmd.com/read/28212502/a-new-mechanism-shapes-the-na%C3%A3-ve-cd8-t-cell-repertoire-the-selection-for-full-diversity
#1
Pedro Gonçalves, Marco Ferrarini, Carmen Molina-Paris, Grant Lythe, Florence Vasseur, Annik Lim, Benedita Rocha, Orly Azogui
During thymic T cell differentiation, TCR repertoires are shaped by negative, positive and agonist selection. In the thymus and in the periphery, repertoires are also shaped by strong inter-clonal and intra-clonal competition to survive death by neglect. Understanding the impact of these events on the T cell repertoire requires direct evaluation of TCR expression in peripheral naïve T cells. Several studies have evaluated TCR diversity, with contradictory results. Some of these studies had intrinsic technical limitations since they used material obtained from T cell pools, preventing the direct evaluation of clone sizes...
February 14, 2017: Molecular Immunology
https://www.readbyqxmd.com/read/28212410/a-high-throughput-genetic-screen-identifies-previously-uncharacterized-borrelia-burgdorferi-genes-important-for-resistance-against-reactive-oxygen-and-nitrogen-species
#2
Meghan E Ramsey, Jenny A Hyde, Diana N Medina-Perez, Tao Lin, Lihui Gao, Maureen E Lundt, Xin Li, Steven J Norris, Jon T Skare, Linden T Hu
Borrelia burgdorferi, the causative agent of Lyme disease in humans, is exposed to reactive oxygen and nitrogen species (ROS and RNS) in both the tick vector and vertebrate reservoir hosts. B. burgdorferi contains a limited repertoire of canonical oxidative stress response genes, suggesting that novel gene functions may be important for protection of B. burgdorferi against ROS or RNS exposure. Here, we use transposon insertion sequencing (Tn-seq) to conduct an unbiased search for genes involved in resistance to nitric oxide, hydrogen peroxide, and tertiary-butyl hydroperoxide in vitro...
February 17, 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28212378/sequencing-the-extrachromosomal-circular-mobilome-reveals-retrotransposon-activity-in-plants
#3
Sophie Lanciano, Marie-Christine Carpentier, Christel Llauro, Edouard Jobet, Dagmara Robakowska-Hyzorek, Eric Lasserre, Alain Ghesquière, Olivier Panaud, Marie Mirouze
Retrotransposons are mobile genetic elements abundant in plant and animal genomes. While efficiently silenced by the epigenetic machinery, they can be reactivated upon stress or during development. Their level of transcription not reflecting their transposition ability, it is thus difficult to evaluate their contribution to the active mobilome. Here we applied a simple methodology based on the high throughput sequencing of extrachromosomal circular DNA (eccDNA) forms of active retrotransposons to characterize the repertoire of mobile retrotransposons in plants...
February 17, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28209129/orthograph-a-versatile-tool-for-mapping-coding-nucleotide-sequences-to-clusters-of-orthologous-genes
#4
Malte Petersen, Karen Meusemann, Alexander Donath, Daniel Dowling, Shanlin Liu, Ralph S Peters, Lars Podsiadlowski, Alexandros Vasilikopoulos, Xin Zhou, Bernhard Misof, Oliver Niehuis
BACKGROUND: Orthology characterizes genes of different organisms that arose from a single ancestral gene via speciation, in contrast to paralogy, which is assigned to genes that arose via gene duplication. An accurate orthology assignment is a crucial step for comparative genomic studies. Orthologous genes in two organisms can be identified by applying a so-called reciprocal search strategy, given that complete information of the organisms' gene repertoire is available. In many investigations, however, only a fraction of the gene content of the organisms under study is examined (e...
February 16, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28201988/molecular-characterization-of-mhc-class-iib-genes-of-sympatric-neotropical-cichlids
#5
Melinda J Hofmann, Seraina E Bracamonte, Christophe Eizaguirre, Marta Barluenga
BACKGROUND: The Major Histocompatibility Complex (MHC) is a key component of the adaptive immune system of all vertebrates and consists of the most polymorphic genes known to date. Due to this complexity, however, MHC remains to be characterized in many species including any Neotropical cichlid fish. Neotropical crater lake cichlids are ideal models to study evolutionary processes as they display one of the most convincing examples of sympatric and repeated parallel radiation events within and among isolated crater lakes...
February 15, 2017: BMC Genetics
https://www.readbyqxmd.com/read/28196891/insights-into-immune-system-development-and-function-from-mouse-t-cell-repertoires
#6
Zachary Sethna, Yuval Elhanati, Chrissy S Dudgeon, Curtis G Callan, Arnold J Levine, Thierry Mora, Aleksandra M Walczak
The ability of the adaptive immune system to respond to arbitrary pathogens stems from the broad diversity of immune cell surface receptors. This diversity originates in a stochastic DNA editing process (VDJ recombination) that acts on the surface receptor gene each time a new immune cell is created from a stem cell. By analyzing T-cell receptor (TCR) sequence repertoires taken from the blood and thymus of mice of different ages, we quantify the changes in the VDJ recombination process that occur from embryo to young adult...
February 14, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28193177/anopheline-salivary-protein-genes-and-gene-families-an-evolutionary-overview-after-the-whole-genome-sequence-of-sixteen-anopheles-species
#7
Bruno Arcà, Fabrizio Lombardo, Claudio J Struchiner, José M C Ribeiro
BACKGROUND: Mosquito saliva is a complex cocktail whose pharmacological properties play an essential role in blood feeding by counteracting host physiological response to tissue injury. Moreover, vector borne pathogens are transmitted to vertebrates and exposed to their immune system in the context of mosquito saliva which, in virtue of its immunomodulatory properties, can modify the local environment at the feeding site and eventually affect pathogen transmission. In addition, the host antibody response to salivary proteins may be used to assess human exposure to mosquito vectors...
February 13, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28190732/the-macronuclear-genome-of-stentor-coeruleus-reveals-tiny-introns-in-a-giant-cell
#8
Mark M Slabodnick, J Graham Ruby, Sarah B Reiff, Estienne C Swart, Sager Gosai, Sudhakaran Prabakaran, Ewa Witkowska, Graham E Larue, Susan Fisher, Robert M Freeman, Jeremy Gunawardena, William Chu, Naomi A Stover, Brian D Gregory, Mariusz Nowacki, Joseph Derisi, Scott W Roy, Wallace F Marshall, Pranidhi Sood
The giant, single-celled organism Stentor coeruleus has a long history as a model system for studying pattern formation and regeneration in single cells. Stentor [1, 2] is a heterotrichous ciliate distantly related to familiar ciliate models, such as Tetrahymena or Paramecium. The primary distinguishing feature of Stentor is its incredible size: a single cell is 1 mm long. Early developmental biologists, including T.H. Morgan [3], were attracted to the system because of its regenerative abilities-if large portions of a cell are surgically removed, the remnant reorganizes into a normal-looking but smaller cell with correct proportionality [2, 3]...
February 8, 2017: Current Biology: CB
https://www.readbyqxmd.com/read/28188172/t-cell-repertoires-in-refractory-coeliac-disease
#9
Julia Ritter, Karin Zimmermann, Korinna Jöhrens, Stefanie Mende, Anke Seegebarth, Britta Siegmund, Steffen Hennig, Kremena Todorova, Andreas Rosenwald, Severin Daum, Michael Hummel, Michael Schumann
OBJECTIVE: Refractory coeliac disease (RCD) is a potentially hazardous complication of coeliac disease (CD). In contrast to RCD type I, RCD type II is a precursor entity of enteropathy-associated T-cell lymphoma (EATL), which is associated with clonally expanding T-cells that are also found in the sequentially developing EATL. Using high-throughput sequencing (HTS), we aimed to establish the small-intestinal T-cell repertoire (TCR) in CD and RCD to unravel the role of distinct T-cell clonotypes in RCD pathogenesis...
February 10, 2017: Gut
https://www.readbyqxmd.com/read/28187283/applications-of-immunogenomics-to-cancer
#10
REVIEW
X Shirley Liu, Elaine R Mardis
Cancer immunogenomics originally was framed by research supporting the hypothesis that cancer mutations generated novel peptides seen as "non-self" by the immune system. The search for these "neoantigens" has been facilitated by the combination of new sequencing technologies, specialized computational analyses, and HLA binding predictions that evaluate somatic alterations in a cancer genome and interpret their ability to produce an immune-stimulatory peptide. The resulting information can characterize a tumor's neoantigen load, its cadre of infiltrating immune cell types, the T or B cell receptor repertoire, and direct the design of a personalized therapeutic...
February 9, 2017: Cell
https://www.readbyqxmd.com/read/28182967/the-suppression-of-tomato-defence-response-genes-upon-potato-cyst-nematode-infection-indicates-a-key-regulatory-role-of-mirnas
#11
Magdalena Święcicka, Waldemar Skowron, Piotr Cieszyński, Joanna Dąbrowska-Bronk, Mateusz Matuszkiewicz, Marcin Filipecki, Marek Daniel Koter
Potato cyst nematode Globodera rostochiensis is an obligate parasite of solanaceous plants, triggering metabolic and morphological changes in roots which may result in substantial crop yield losses. Previously, we used the cDNA-AFLP to study the transcriptional dynamics in nematode infected tomato roots. Now, we present the rescreening of already published, upregulated transcript-derived fragment dataset using the most current tomato transcriptome sequences. Our reanalysis allowed to add 54 novel genes to 135, already found as upregulated in tomato roots upon G...
January 30, 2017: Plant Physiology and Biochemistry: PPB
https://www.readbyqxmd.com/read/28182777/correction-vidjil-a-web-platform-for-analysis-of-high-throughput-repertoire-sequencing
#12
Marc Duez, Mathieu Giraud, Ryan Herbert, Tatiana Rocher, Mikaël Salson, Florian Thonier
[This corrects the article DOI: 10.1371/journal.pone.0166126.].
2017: PloS One
https://www.readbyqxmd.com/read/28179494/hierarchical-clustering-can-identify-b-cell-clones-with-high-confidence-in-ig-repertoire-sequencing-data
#13
Namita T Gupta, Kristofor D Adams, Adrian W Briggs, Sonia C Timberlake, Francois Vigneault, Steven H Kleinstein
Adaptive immunity is driven by the expansion, somatic hypermutation, and selection of B cell clones. Each clone is the progeny of a single B cell responding to Ag, with diversified Ig receptors. These receptors can now be profiled on a large scale by next-generation sequencing. Such data provide a window into the microevolutionary dynamics that drive successful immune responses and the dysregulation that occurs with aging or disease. Clonal relationships are not directly measured, but they must be computationally inferred from these sequencing data...
February 8, 2017: Journal of Immunology: Official Journal of the American Association of Immunologists
https://www.readbyqxmd.com/read/28178945/comparative-genomics-of-canine-hemoglobin-genes-reveals-primacy-of-beta-subunit-delta-in-adult-carnivores
#14
Sara Zaldívar-López, Jennie L Rowell, Elise M Fiala, Isain Zapata, C Guillermo Couto, Carlos E Alvarez
BACKGROUND: The main function of hemoglobin (Hb) is to transport oxygen in the circulation. It is among the most highly studied proteins due to its roles in physiology and disease, and most of our understanding derives from comparative research. There is great diversity in Hb gene evolution in placental mammals, mostly in the repertoire and regulation of the β-globin subunits. Dogs are an ideal model in which to study Hb genes because: 1) they are members of Laurasiatheria, our closest relatives outside of Euarchontoglires (including primates, rodents and rabbits), 2) dog breeds are isolated populations with their own Hb-associated genetics and diseases, and 3) their high level of health care allows for development of biomedical investigation and translation...
February 8, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28177902/identification-of-patient-specific-and-tumor-shared-t-cell-receptor-sequences-in-renal-cell-carcinoma-patients
#15
Chiara Massa, Harlan Robins, Cindy Desmarais, Dagmar Riemann, Corinna Fahldieck, Paolo Fornara, Barbara Seliger
A major requirement for cancer immunotherapy is the development of biomarkers for prognosis and for monitoring therapy response. In an attempt to evaluate the immune response of renal cell carcinoma (RCC) patients, tumor lesions and / or blood samples from 12 RCC patients underwent deep T cell receptor (TCR) sequencing. Despite the low number of samples, different TCR distribution patterns could be detected. Most of the RCC patients presented "patient-specific" TCR sequences, and those clonotypes were present at higher frequency in tumor lesions suggesting a specific extravasation from the blood...
February 3, 2017: Oncotarget
https://www.readbyqxmd.com/read/28172667/dop054-high-throughput-sequencing-of-t-cell-receptors-from-pediatric-ulcerative-colitis-patients-reveals-distinct-tissue-specific-repertoires
#16
L Werner, M Nunberg, Y Haberman, A Lahad, D Turner, B Weiss, D Shouval
No abstract text is available yet for this article.
February 1, 2017: Journal of Crohn's & Colitis
https://www.readbyqxmd.com/read/28167670/salmonella-typhi-lipopolysaccharide-o-antigen-modifications-impact-on-serum-resistance-and-antibody-recognition
#17
Erica Kintz, Christian Heiss, Ian Black, Nicholas Donohue, Naj Brown, Mark R Davies, Parastoo Azadi, Stephen Baker, Paul M Kaye, Marjan van der Woude
Salmonella Typhi is a human restricted Gram-negative bacterial pathogen, responsible for causing an estimated 27 million cases of typhoid fever annually leading to 217,000 deaths, and current vaccines do not offer full protection. The O-antigen side chain of the lipopolysaccharide is an immunodominant antigen, can define host-pathogen interactions, and is under consideration as a vaccine target for some Gram-negative species. The composition of the O-antigen can be modified by activity of glycosyltransferase (gtr) operons acquired by horizontal gene transfer...
February 6, 2017: Infection and Immunity
https://www.readbyqxmd.com/read/28167275/single-amino-acid-fingerprinting-of-the-human-antibody-repertoire-with-high-density-peptide-arrays
#18
Laura K Weber, Andrea Palermo, Jonas Kügler, Olivier Armant, Awale Isse, Simone Rentschler, Thomas Jaenisch, Jürgen Hubbuch, Stefan Dübel, Alexander Nesterov-Mueller, Frank Breitling, Felix F Loeffler
The antibody species that patrol in a patient's blood are an invaluable part of the immune system. While most of them shield us from life-threatening infections, some of them do harm in autoimmune diseases. If we knew exactly all the antigens that elicited all the antibody species within a group of patients, we could learn which ones correlate with immune protection, are irrelevant, or do harm. Here, we demonstrate an approach to this question: First, we use a plethora of phage-displayed peptides to identify many different serum antibody binding peptides...
February 3, 2017: Journal of Immunological Methods
https://www.readbyqxmd.com/read/28164855/from-culture-to-high-throughput-sequencing-and-beyond-a-layperson-s-guide-to-the-omics-and-diagnostic-potential-of-the-microbiome
#19
REVIEW
Paul W O'Toole, Burkhardt Flemer
Detailed knowledge of the community of organisms in the gut has become possible in recent years because of the development of culture-independent methods. Largely based on latest DNA sequencing platforms, it is now possible to establish the composition of the microbiota and the repertoire of biochemical functions it encodes. Variations in either or both of these parameters have been linked to intestinal and extraintestinal disease. This article summarizes how these methods are applied, with special reference to gastroenterology, and describes the achievements and future potential of microbiota analysis as a diagnostic tool...
March 2017: Gastroenterology Clinics of North America
https://www.readbyqxmd.com/read/28164597/visual-system-homeobox-1-vsx1-gene-analysis-in-keratoconus-design-of-specific-primers-and-dna-amplification-protocols-for-accurate-molecular-characterization
#20
Jun B Ng, Rozaida Y Y Poh, Kenneth R Lee, Visvaraja Subrayan, Jenny P Deva, Amy Y L Lau, Jin A M A Tan
BACKGROUND: Keratoconus is an ocular degeneration characterized by the thinning of corneal stroma that may lead to varying degrees of myopia and visual impairment. Genetic factors have been reported in the pathology of keratoconus where Asians have a higher incidence, earlier onset, and undergo earlier corneal grafts compared to Caucasians. The visual system homeobox 1 (VSX1) gene forms part of a paired-like homeodomain transcription factor which is responsible for ocular development...
September 1, 2016: Clinical Laboratory
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