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Repertoire Sequencing

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https://www.readbyqxmd.com/read/29453107/body-fluid-identification-using-a-targeted-mrna-massively-parallel-sequencing-approach-results-of-a-euroforgen-ednap-collaborative-exercise
#1
S Ingold, G Dørum, E Hanson, A Berti, W Branicki, P Brito, P Elsmore, K B Gettings, F Giangasparo, T E Gross, S Hansen, E N Hanssen, M-L Kampmann, M Kayser, F-X Laurent, N Morling, A Mosquera-Miguel, W Parson, C Phillips, M J Porto, E Pośpiech, A D Roeder, P M Schneider, K Schulze Johann, C R Steffen, D Syndercombe-Court, M Trautmann, M van den Berge, K J van der Gaag, J Vannier, V Verdoliva, A Vidaki, C Xavier, J Ballantyne, C Haas
In a previous study we presented an assay for targeted mRNA sequencing for the identification of human body fluids, optimised for the Illumina MiSeq/FGx MPS platform. This assay, together with an additional in-house designed assay for the Ion Torrent PGM/S5 platform, was the basis for a collaborative exercise within 17 EUROFORGEN and EDNAP laboratories, in order to test the efficacy of targeted mRNA sequencing to identify body fluids. The task was to analyse the supplied dried body fluid stains and, optionally, participants' own bona fide or mock casework samples of human origin, according to specified protocols...
January 31, 2018: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/29451876/comparative-genomic-analysis-of-the-multispecies-probiotic-marketed-product-vsl-3
#2
François P Douillard, Diego Mora, Robyn T Eijlander, Michiel Wels, Willem M de Vos
Several probiotic-marketed formulations available for the consumers contain live lactic acid bacteria and/or bifidobacteria. The multispecies product commercialized as VSL#3 has been used for treating various gastro-intestinal disorders. However, like many other products, the bacterial strains present in VSL#3 have only been characterized to a limited extent and their efficacy as well as their predicted mode of action remain unclear, preventing further applications or comparative studies. In this work, the genomes of all eight bacterial strains present in VSL#3 were sequenced and characterized, to advance insights into the possible mode of action of this product and also to serve as a basis for future work and trials...
2018: PloS One
https://www.readbyqxmd.com/read/29449843/insights-into-the-structural-basis-of-antibody-affinity-maturation-from-next-generation-sequencing
#3
REVIEW
Arjun K Mishra, Roy A Mariuzza
Affinity maturation is the process whereby the immune system generates antibodies of higher affinities during a response to antigen. It is unique in being the only evolutionary mechanism known to operate on a molecule in an organism's own body. Deciphering the structural mechanisms through which somatic mutations in antibody genes increase affinity is critical to understanding the evolution of immune repertoires. Next-generation sequencing (NGS) has allowed the reconstruction of antibody clonal lineages in response to viral pathogens, such as HIV-1, which was not possible in earlier studies of affinity maturation...
2018: Frontiers in Immunology
https://www.readbyqxmd.com/read/29447068/microbial-culturomics-broadens-human-vaginal-flora-diversity-genome-sequence-and-description-of-prevotella-lascolaii-sp-nov-isolated-from-a-patient-with-bacterial-vaginosis
#4
Khoudia Diop, Awa Diop, Anthony Levasseur, Oleg Mediannikov, Catherine Robert, Nicholas Armstrong, Carine Couderc, Florence Bretelle, Didier Raoult, Pierre-Edouard Fournier, Florence Fenollar
Microbial culturomics is a new subfield of postgenomic medicine and omics biotechnology application that has broadened our awareness on bacterial diversity of the human microbiome, including the human vaginal flora bacterial diversity. Using culturomics, a new obligate anaerobic Gram-stain-negative rod-shaped bacterium designated strain khD1 T was isolated in the vagina of a patient with bacterial vaginosis and characterized using taxonogenomics. The most abundant cellular fatty acids were C 15:0 anteiso (36%), C 16:0 (19%), and C 15:0 iso (10%)...
February 15, 2018: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/29444930/immunophenotyping-of-newly-diagnosed-and-recurrent-glioblastoma-defines-distinct-immune-exhaustion-profiles-in-peripheral-and-tumor-infiltrating-lymphocytes
#5
Malte Mohme, Simon Schliffke, Cecile L Maire, Alessandra Rünger, Laura Glau, Klaus C Mende, Jakob Matschke, Christina Gehbauer, Nuray Akyüz, Svenja Zapf, Mareike Holz, Miriam Schaper, Tobias Martens, Nils O Schmidt, Sven Peine, Manfred Westphal, Mascha Binder, Eva Tolosa, Katrin Lamszus
PURPOSE: Immunotherapeutic treatment strategies for glioblastoma (GBM) are under investigation in clinical trials. However, our understanding of the immune phenotype of GBM-infiltrating T-cells (TILs) and changes during disease progression is limited. Deeper insight is urgently needed to therapeutically overcome tumor-induced immune exhaustion. EXPERIMENTAL DESIGN: We used flow-cytometry and cytokine assays to profile TILs and blood lymphocytes (PBL) from GBM patients, comparing newly diagnosed or recurrent GBM to long-term survivors (LTS) and healthy donors...
February 14, 2018: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/29444302/rab-gtpases-in-the-basal-land-plant-marchantia-polymorpha
#6
Naoki Minamino, Takehiko Kanazawa, Atsuko Era, Kazuo Ebine, Akihiko Nakano, Takashi Ueda
The RAB GTPase is an evolutionarily conserved machinery component of membrane trafficking, which is the fundamental system for cell viability and higher-order biological functions. The composition of RAB GTPases in each organism is closely related to the complexity and organization of the membrane-trafficking pathway, which has been developed uniquely to realize the organism-specific membrane trafficking system. Comparative genomics has suggested that terrestrialization and/or multicellularization were associated with the expansion of membrane trafficking pathways in green plants, which has yet to be validated in basal land plant lineages...
February 10, 2018: Plant & Cell Physiology
https://www.readbyqxmd.com/read/29444117/an-ancestral-tmem16-homolog-from-dictyostelium-discoideum-forms-a-scramblase
#7
Thomas Pelz, Daniela R Drose, David Fleck, Bastian Henkel, Tobias Ackels, Marc Spehr, Eva M Neuhaus
TMEM16 proteins are a recently identified protein family comprising Ca2+-activated Cl- channels that generate outwardly rectifying ionic currents in response to intracellular Ca2+ elevations. Some TMEM16 family members, such as TMEM16F/ANO6 are also essential for Ca2+-dependent phospholipid scrambling. TMEM16-like genes are present in the genomes of most eukaryotic species, the function(s) of TMEM16 family members from evolutionary ancient eukaryotes is not completely clear. Here, we provide insight into the evolution of these TMEM16 proteins by similarity searches for ancestral sequences...
2018: PloS One
https://www.readbyqxmd.com/read/29443062/generation-of-discriminative-human-monoclonal-antibodies-from-rare-antigen-specific-b-cells-circulating-in-blood
#8
Marie-Claire Devilder, Mélinda Moyon, Xavier Saulquin, Laetitia Gautreau-Rolland
Monoclonal antibodies (mAbs) are powerful tools useful for both fundamental research and in biomedicine. Their high specificity is indispensable when the antibody needs to distinguish between highly related structures (e.g., a normal protein and a mutated version thereof). The current way of generating such discriminative mAbs involves extensive screening of multiple Ab-producing B cells, which is both costly and time consuming. We propose here a rapid and cost-effective method for the generation of discriminative, fully human mAbs starting from human blood circulating B lymphocytes...
February 6, 2018: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/29440283/evolution-of-neuropeptide-signalling-systems
#9
REVIEW
Maurice R Elphick, Olivier Mirabeau, Dan Larhammar
Neuropeptides are a diverse class of neuronal signalling molecules that regulate physiological processes and behaviour in animals. However, determining the relationships and evolutionary origins of the heterogeneous assemblage of neuropeptides identified in a range of phyla has presented a huge challenge for comparative physiologists. Here, we review revolutionary insights into the evolution of neuropeptide signalling that have been obtained recently through comparative analysis of genome/transcriptome sequence data and by 'deorphanisation' of neuropeptide receptors...
February 9, 2018: Journal of Experimental Biology
https://www.readbyqxmd.com/read/29435243/genotyping-strategy-matters-when-analyzing-hypervariable-major-histocompatibility-complex-experience-from-a-passerine-bird
#10
Silje L Rekdal, Jarl Andreas Anmarkrud, Arild Johnsen, Jan T Lifjeld
Genotyping of classical major histocompatibility complex (MHC) genes is challenging when they are hypervariable and occur in multiple copies. In this study, we used several different approaches to genotype the moderately variable MHC class I exon 3 (MHCIe3) and the highly polymorphic MHC class II exon 2 (MHCIIβe2) in the bluethroat (Luscinia svecica). Two family groups (eight individuals) were sequenced in replicates at both markers using Ion Torrent technology with both a single- and a dual-indexed primer structure...
February 2018: Ecology and Evolution
https://www.readbyqxmd.com/read/29435138/personalized-adoptive-immunotherapy-for-patients-with-ebv-associated-tumors-and-complications-evaluation-of-novel-naturally-processed-and-presented-ebv-derived-t-cell-epitopes
#11
Maren Bieling, Sabine Tischer, Ulrich Kalinke, Rainer Blasczyk, Søren Buus, Britta Maecker-Kolhoff, Britta Eiz-Vesper
Morbidity and mortality of immunocompromised patients are increased by primary infection with or reactivation of Epstein-Barr virus (EBV), possibly triggering EBV+ post-transplant lymphoproliferative disease (PTLD). Adoptive transfer of EBV-specific cytotoxic T cells (EBV-CTLs) promises a non-toxic immunotherapy to effectively prevent or treat these complications. To improve immunotherapy and immunomonitoring this study aimed at identifying and evaluating naturally processed and presented HLA-A*03:01-restricted EBV-CTL epitopes as immunodominant targets...
January 12, 2018: Oncotarget
https://www.readbyqxmd.com/read/29434576/candidatus-nitrosocaldus-cavascurensis-an-ammonia-oxidizing-extremely-thermophilic-archaeon-with-a-highly-mobile-genome
#12
Sophie S Abby, Michael Melcher, Melina Kerou, Mart Krupovic, Michaela Stieglmeier, Claudia Rossel, Kevin Pfeifer, Christa Schleper
Ammonia oxidizing archaea (AOA) of the phylum Thaumarchaeota are widespread in moderate environments but their occurrence and activity has also been demonstrated in hot springs. Here we present the first enrichment of a thermophilic representative with a sequenced genome, which facilitates the search for adaptive strategies and for traits that shape the evolution of Thaumarchaeota. Candidatus Nitrosocaldus cavascurensis has been enriched from a hot spring in Ischia, Italy. It grows optimally at 68°C under chemolithoautotrophic conditions on ammonia or urea converting ammonia stoichiometrically into nitrite with a generation time of approximately 23 h...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29432186/adaptive-antibody-diversification-through-n-linked-glycosylation-of-the-immunoglobulin-variable-region
#13
Fleur S van de Bovenkamp, Ninotska I L Derksen, Pleuni Ooijevaar-de Heer, Karin A van Schie, Simone Kruithof, Magdalena A Berkowska, C Ellen van der Schoot, Hanna IJspeert, Mirjam van der Burg, Ann Gils, Lise Hafkenscheid, René E M Toes, Yoann Rombouts, Rosina Plomp, Manfred Wuhrer, S Marieke van Ham, Gestur Vidarsson, Theo Rispens
A hallmark of B-cell immunity is the generation of a diverse repertoire of antibodies from a limited set of germline V(D)J genes. This repertoire is usually defined in terms of amino acid composition. However, variable domains may also acquire N -linked glycans, a process conditional on the introduction of consensus amino acid motifs ( N -glycosylation sites) during somatic hypermutation. High levels of variable domain glycans have been associated with autoantibodies in rheumatoid arthritis, as well as certain follicular lymphomas...
February 5, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29429614/inversely-active-striatal-projection-neurons-and-interneurons-selectively-delimit-useful-behavioral-sequences
#14
Nuné Martiros, Alexandra A Burgess, Ann M Graybiel
Understanding neural representations of behavioral routines is critical for understanding complex behavior in health and disease. We demonstrate here that accentuated activity of striatal projection neurons (SPNs) at the beginning and end of such behavioral repertoires is a supraordinate representation specifically marking previously rewarded behavioral sequences independent of the individual movements making up the behavior. We recorded spike activity in the striatum and primary motor cortex as individual rats learned specific rewarded lever-press sequences, each one unique to a given rat...
February 1, 2018: Current Biology: CB
https://www.readbyqxmd.com/read/29429564/genomic-comparison-between-members-of-the-salinibacteraceae-family-and-description-of-a-new-species-of-salinibacter-salinibacter-altiplanensis-sp-nov-isolated-from-high-altitude-hypersaline-environments-of-the-argentinian-altiplano
#15
Tomeu Viver, Luis Orellana, Pedro González-Torres, Sara Díaz, Mercedes Urdiain, María Eugenia Farías, Vladimir Benes, Peter Kaempfer, Azadeh Shahinpei, Mohammad Ali Amoozegar, Rudolf Amann, Josefa Antón, Konstantinos T Konstantinidis, Ramon Rosselló-Móra
The application of tandem MALDI-TOF MS screening with 16S rRNA gene sequencing of selected isolates has been demonstrated to be an excellent approach for retrieving novelty from large-scale culturing. The application of such methodologies in different hypersaline samples allowed the isolation of the culture-recalcitrant Salinibacter ruber second phylotype (EHB-2) for the first time, as well as a new species recently isolated from the Argentinian Altiplano hypersaline lakes. In this study, the genome sequences of the different species of the phylum Rhodothermaeota were compared and the genetic repertoire along the evolutionary gradient was analyzed together with each intraspecific variability...
January 31, 2018: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/29425228/kshv-oral-shedding-and-plasma-viremia-result-in-significant-changes-in-the-extracellular-tumorigenic-mirna-expression-profile-in-individuals-infected-with-the-malaria-parasite
#16
Minako Ikoma, Soren Gantt, Corey Casper, Yuko Ogata, Qing Zhang, Ryan Basom, Michael R Dyen, Timothy M Rose, Serge Barcy
Kaposi's sarcoma herpesvirus (KSHV) is the etiological agent of Kaposi's sarcoma (KS). Both KSHV and HIV infections are endemic in Uganda, where KS is among the most common cancers in HIV-infected individuals. Recent studies examined the use of small RNAs as biomarkers of disease, including microRNAs (miRNAs), with viral and tumor-derived miRNAs being detected in exosomes from individuals with KSHV-associated malignancies. In the current study, the host and viral extracellular mature miRNA expression profiles were analyzed in blood of KS-negative individuals in Uganda, comparing those with or without KSHV detectable from the oropharynx...
2018: PloS One
https://www.readbyqxmd.com/read/29423137/mouse-obox-and-crxos-modulate-preimplantation-transcriptional-profiles-revealing-similarity-between-paralogous-mouse-and-human-homeobox-genes
#17
Amy H Royall, Ignacio Maeso, Thomas L Dunwell, Peter W H Holland
Background: ETCHbox genes are eutherian-specific homeobox genes expressed during preimplantation development at a time when the first cell lineage decisions are being made. The mouse has an unusual repertoire of ETCHbox genes with several gene families lost in evolution and the remaining two, Crxos and Obox, greatly divergent in sequence and number. Each has undergone duplication to give a double homeodomain Crxos locus and a large cluster of over 60 Obox loci. The gene content differences between species raise important questions about how evolution can tolerate loss of genes implicated in key developmental events...
2018: EvoDevo
https://www.readbyqxmd.com/read/29422654/high-throughput-immune-repertoire-analysis-with-igor
#18
Quentin Marcou, Thierry Mora, Aleksandra M Walczak
High-throughput immune repertoire sequencing is promising to lead to new statistical diagnostic tools for medicine and biology. Successful implementations of these methods require a correct characterization, analysis, and interpretation of these data sets. We present IGoR (Inference and Generation Of Repertoires)-a comprehensive tool that takes B or T cell receptor sequence reads and quantitatively characterizes the statistics of receptor generation from both cDNA and gDNA. It probabilistically annotates sequences and its modular structure can be used to investigate models of increasing biological complexity for different organisms...
February 8, 2018: Nature Communications
https://www.readbyqxmd.com/read/29419434/deep-sequencing-and-flow-cytometric-characterization-of-expanded-effector-memory-cd8-cd57-t-cells-frequently-reveals-t-cell-receptor-v%C3%AE-oligoclonality-and-cdr3-homology-in-acquired-aplastic-anemia
#19
Valentina Giudice, Xingmin Feng, Zenghua Lin, Wei Hu, Fanmao Zhang, Wangmin Qiao, Maria Del Pilar Fernandez Ibanez, Olga Rios, Neal S Young
Oligoclonal expansion of CD8+CD28- lymphocytes has been considered indirect evidence for a pathogenic immune response in acquired aplastic anemia. A subset of CD8+CD28- cells with CD57 expression termed effector memory cells is expanded in several immune mediated diseases and may have a role in immune surveillance. We hypothesized that effector memory CD8+CD28-CD57+ cells may drive aberrant oligoclonal expansion in aplastic anemia. We found CD8+CD57+ cells frequently expanded in the blood of aplastic anemia patients, with oligoclonal characteristics by flow cytometric Vβ usage analysis: skewing in 1 to 5 Vβ families and frequencies of immunodominant clones ranging from 1...
February 1, 2018: Haematologica
https://www.readbyqxmd.com/read/29419284/dna-s-encounter-with-ultraviolet-light-an-instinct-for-self-preservation
#20
Adam Barlev, Dipankar Sen
Photochemical modification is the major class of environmental damage suffered by DNA, the genetic material of all free-living organisms. Photolyases are enzymes that carry out direct photochemical repair (photoreactivation) of covalent pyrimidine dimers formed in DNA from exposure to ultraviolet light. The discovery of catalytic RNAs in the 1980s led to the "RNA world hypothesis", which posits that early in evolution RNA or a similar polymer served both genetic and catalytic functions. Intrigued by the RNA world hypothesis, we set out to test whether a catalytic RNA (or a surrogate, a catalytic DNA) with photolyase activity could be contemplated...
February 8, 2018: Accounts of Chemical Research
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