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Repertoire Sequencing

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https://www.readbyqxmd.com/read/28323873/a-three-monoclonal-antibody-combination-potently-neutralizes-multiple-botulinum-neurotoxin-serotype-f-subtypes
#1
Yongfeng Fan, Consuelo Garcia-Rodriguez, Jianlong Lou, Weihua Wen, Fraser Conrad, Wenwu Zhai, Theresa J Smith, Leonard A Smith, James D Marks
Human botulism is primarily caused by botulinum neurotoxin (BoNT) serotypes A, B and E, with around 1% caused by serotype F (BoNT/F). BoNT/F comprises at least seven different subtypes with the amino acid sequence difference between subtypes as high as 36%. The sequence differences present a significant challenge for generating monoclonal antibodies (mAbs) that can bind, detect and neutralize all BoNT/F subtypes. We used repertoire cloning of immune mouse antibody variable (V) regions and yeast display to generate a panel of 33 lead single chain Fv (scFv) mAbs that bound one or more BoNT/F subtypes with a median equilibrium dissociation constant (KD) of 4...
2017: PloS One
https://www.readbyqxmd.com/read/28318808/t-cell-receptor-assessment-in-autoimmune-disease-requires-access-to-the-most-adjacent-immunologically-active-organ
#2
Bergithe E Oftedal, Brita Ardesjö Lundgren, David Hamm, Poh-Yi Gan, Stephen R Holdsworth, Christopher N Hahn, Andreas W Schreiber, Hamish S Scott
Next generation sequencing of T and B cell receptors is emerging as a valuable and effective method to diagnose and monitor hematopoietic malignancies. So far, this approach has not been fully explored in regard to autoimmune diseases. T cells develop in the thymus where they undergo positive and negative selection, and the autoimmune regulator (Aire) is central in the establishment of immunological tolerance. Loss of Aire leads to severe multiorgan autoimmune disease with infiltration of autoreactive T cells in affected organs...
March 15, 2017: Journal of Autoimmunity
https://www.readbyqxmd.com/read/28306506/crystal-structure-of-the-minimal-cas9-from-campylobacter-jejuni-reveals-the-molecular-diversity-in-the-crispr-cas9-systems
#3
Mari Yamada, Yuto Watanabe, Jonathan S Gootenberg, Hisato Hirano, F Ann Ran, Takanori Nakane, Ryuichiro Ishitani, Feng Zhang, Hiroshi Nishimasu, Osamu Nureki
The RNA-guided endonuclease Cas9 generates a double-strand break at DNA target sites complementary to the guide RNA and has been harnessed for the development of a variety of new technologies, such as genome editing. Here, we report the crystal structures of Campylobacter jejuni Cas9 (CjCas9), one of the smallest Cas9 orthologs, in complex with an sgRNA and its target DNA. The structures provided insights into a minimal Cas9 scaffold and revealed the remarkable mechanistic diversity of the CRISPR-Cas9 systems...
March 16, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28301469/global-analysis-of-translation-termination-in-e-coli
#4
Natalie E Baggett, Yan Zhang, Carol A Gross
Terminating protein translation accurately and efficiently is critical for both protein fidelity and ribosome recycling for continued translation. The three bacterial release factors (RFs) play key roles: RF1 and 2 recognize stop codons and terminate translation; and RF3 promotes disassociation of bound release factors. Probing release factors mutations with reporter constructs containing programmed frameshifting sequences or premature stop codons had revealed a propensity for readthrough or frameshifting at these specific sites, but their effects on translation genome-wide have not been examined...
March 16, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28300170/cd8-t-cells-specific-for-the-islet-autoantigen-igrp-are-restricted-in-their-t-cell-receptor-chain-usage
#5
Yannick F Fuchs, Anne Eugster, Sevina Dietz, Christian Sebelefsky, Denise Kühn, Carmen Wilhelm, Annett Lindner, Anita Gavrisan, Jan Knoop, Andreas Dahl, Anette-G Ziegler, Ezio Bonifacio
CD8(+) T cells directed against beta cell autoantigens are considered relevant for the pathogenesis of type 1 diabetes. Using single cell T cell receptor sequencing of CD8(+) T cells specific for the IGRP265-273 epitope, we examined whether there was expansion of clonotypes and sharing of T cell receptor chains in autoreactive CD8(+) T cell repertoires. HLA-A*0201 positive type 1 diabetes patients (n = 19) and controls (n = 18) were analysed. TCR α- and β-chain sequences of 418 patient-derived IGRP265-273-multimer(+) CD8(+) T cells representing 48 clonotypes were obtained...
March 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28289082/use-of-a-phosphorylation-site-mutant-to-identify-distinct-modes-of-gene-repression-by-the-control-of-virulence-regulator-covr-in-streptococcus-pyogenes
#6
Nicola Horstmann, Pranoti Sahasrabhojane, Hui Yao, Xiaoping Su, Samuel A Shelburne
The control of virulence regulator/sensor kinase (CovRS) two-component system (TCS) serves as a model for investigating the impact of signaling pathways on the pathogenesis of Gram-positive bacteria. However the molecular mechanisms by which CovR, an OmpR/PhoB family response regulator, controls virulence gene expression are poorly defined partly due to the labile nature of its aspartate phosphorylation site. To better understand the regulatory effect of phosphorylated CovR, we generated the phosphorylation site mutant strain 10870-CovR-D53E, which we predicted to have a constitutive CovR phosphorylation phenotype...
March 13, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/28289056/expression-and-trafficking-of-placental-micrornas-at-the-feto-maternal-interface
#7
Guojing Chang, Jean-François Mouillet, Takuya Mishima, Tianjiao Chu, Elena Sadovsky, Carolyn B Coyne, W Tony Parks, Urvashi Surti, Yoel Sadovsky
During pregnancy, placental trophoblasts at the feto-maternal interface produce a broad repertoire of microRNA (miRNA) species. These species include miRNA from the primate-specific chromosome 19 miRNA cluster (C19MC), which is expressed nearly exclusively in the placenta. Trafficking of these miRNAs among the maternal, placental, and fetal compartments is unknown. To determine miRNA expression and trafficking patterns during pregnancy, we sequenced miRNAs in triads of human placenta and of maternal and fetal blood and found large subject-to-subject variability, with C19MC exhibiting compartment-specific expression...
March 13, 2017: FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology
https://www.readbyqxmd.com/read/28284194/clonocalc-and-clonoplot-immune-repertoire-analysis-from-raw-files-to-publication-figures-with-graphical-user-interface
#8
Anke Fähnrich, Moritz Krebbel, Normann Decker, Martin Leucker, Felix D Lange, Kathrin Kalies, Steffen Möller
BACKGROUND: Next generation sequencing (NGS) technologies enable studies and analyses of the diversity of both T and B cell receptors (TCR and BCR) in human and animal systems to elucidate immune functions in health and disease. Over the last few years, several algorithms and tools have been developed to support respective analyses of raw sequencing data of the immune repertoire. These tools focus on distinct aspects of the data processing and require a strong bioinformatics background...
March 11, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28283778/plk1-associated-micrornas-are-correlated-with-pediatric-medulloblastoma-prognosis
#9
Julia Alejandra Pezuk, María Sol Brassesco, Ricardo Santos de Oliveira, Hélio Rubens Machado, Luciano Neder, Carlos Alberto Scrideli, Luiz Gonzaga Tone
PURPOSE: Medulloblastoma (MB) is the most common malignant tumor of the central nervous system (CNS) in children. Despite its relative good survival rates, treatment can cause long time sequels and may impair patients' lifespan and quality, making the search for new treatment options still necessary. Polo like kinases (PLKs) constitute a five-member serine/threonine kinases family (PLK 1-5) that regulates different stages during cell cycle. Abnormal PLKs expression has been observed in several cancer types, including MB...
March 10, 2017: Child's Nervous System: ChNS: Official Journal of the International Society for Pediatric Neurosurgery
https://www.readbyqxmd.com/read/28281773/b-cell-epitopes-of-african-horse-sickness-virus-serotype-4-recognised-by-immune-horse-sera
#10
Evans M Mathebula, Frederika E Faber, Wouter Van Wyngaardt, Antoinette Van Schalkwyk, Alri Pretorius, Jeanni Fehrsen
Identifying antigenic proteins and mapping their epitopes is important for the development of diagnostic reagents and recombinant vaccines. B-cell epitopes of African horse sickness virus (AHSV) have previously been mapped on VP2, VP5, VP7 and NS1, using mouse, rabbit and chicken monoclonal antibodies. A comprehensive study of the humoral immune response of five vaccinated horses to AHSV-4 antigenic peptides was undertaken. A fragmented-genome phage display library expressing a repertoire of AHSV-4 peptides spanning the entire genome was constructed...
February 24, 2017: Onderstepoort Journal of Veterinary Research
https://www.readbyqxmd.com/read/28280485/characterization-of-the-prophage-repertoire-of-african-salmonella-typhimurium-st313-reveals-high-levels-of-spontaneous-induction-of-novel-phage-btp1
#11
Siân V Owen, Nicolas Wenner, Rocío Canals, Angela Makumi, Disa L Hammarlöf, Melita A Gordon, Abram Aertsen, Nicholas A Feasey, Jay C D Hinton
In the past 30 years, Salmonella bloodstream infections have become a significant health problem in sub-Saharan Africa and are responsible for the deaths of an estimated 390,000 people each year. The disease is predominantly caused by a recently described sequence type of Salmonella Typhimurium: ST313, which has a distinctive set of prophage sequences. We have thoroughly characterized the ST313-associated prophages both genetically and experimentally. ST313 representative strain D23580 contains five full-length prophages: BTP1, Gifsy-2(D23580), ST64B(D23580), Gifsy-1(D23580), and BTP5...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28271616/evolutionary-ecology-of-opsin-gene-sequence-expression-and-repertoire
#12
Gregory L Owens, Diana J Rennison
Linking molecular evolution to biological function is a long-standing challenge in evolutionary biology. Some of the best examples of this involve opsins, the genes that encode the molecular basis of light reception. In this issue of Molecular Ecology, three studies examine opsin gene sequence, expression and repertoire to determine how natural selection has shaped the visual system. First, Escobar-Camacho et al. () use opsin repertoire and expression in three Amazonian cichlid species to show that a shift in sensitivity towards longer wavelengths is coincident with the long-wavelength-dominated Amazon basin...
March 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28266108/role-of-microbial-communities-in-the-pathogenesis-of-periodontal-diseases-and-caries
#13
Alex Mira, A Simon-Soro, M A Curtis
The microbiological characteristics of both caries and periodontal disease show significant change from those in health. In both instances, there is evidence of co-association of different organisms into consortia. AIM: We review and summarize a number of issues pertinent to the community organization and functional activity of the bacterial populations resident on supra- and subgingival tooth surface and the influence of these populations on disease. METHODS: A literature review was undertaken with a particular emphasis on recent publications involving high-throughput, deep sequencing approaches to the analysis of microbial populations and their functional activity...
March 2017: Journal of Clinical Periodontology
https://www.readbyqxmd.com/read/28264664/experience-dependent-modulation-of-alpha-and-beta-during-action-observation-and-motor-imagery
#14
Paula M Di Nota, Julie M Chartrand, Gabriella R Levkov, Rodrigo Montefusco-Siegmund, Joseph F X DeSouza
BACKGROUND: EEG studies investigating the neural networks that facilitate action observation (AO) and kinaesthetic motor imagery (KMI) have shown reduced, or desynchronized, power in the alpha (8-12 Hz) and beta (13-30 Hz) frequency bands relative to rest, reflecting efficient activation of task-relevant areas. Functional modulation of these networks through expertise in dance has been established using fMRI, with greater activation among experts during AO. While there is evidence for experience-dependent plasticity of alpha power during AO of dance, the influence of familiarity on beta power during AO, and alpha and beta activity during KMI, remain unclear...
March 6, 2017: BMC Neuroscience
https://www.readbyqxmd.com/read/28264647/the-repertoire-dissimilarity-index-as-a-method-to-compare-lymphocyte-receptor-repertoires
#15
Christopher R Bolen, Florian Rubelt, Jason A Vander Heiden, Mark M Davis
BACKGROUND: The B and T cells of the human adaptive immune system leverage a highly diverse repertoire of antigen-specific receptors to protect the human body from pathogens. The sequencing and analysis of immune repertoires is emerging as an important tool to understand immune responses, whether beneficial or harmful (in the case of autoimmunity). However, methods for studying these repertoires, and for directly comparing different immune repertoires, are lacking. RESULTS: In this paper, we present a non-parametric method for directly comparing sequencing repertoires, with the goal of rigorously quantifying differences in V, D, and J gene segment utilization...
March 7, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28262836/dynamics-of-mirna-transcriptome-during-gonadal-development-of-zebrafish
#16
Christopher Presslauer, Teshome Tilahun Bizuayehu, Martina Kopp, Jorge M O Fernandes, Igor Babiak
Studies in non-teleost vertebrates have found microRNAs (miRNAs) to be essential for proper gonadal development. However, comparatively little is known about their role during gonadal development in teleost fishes. So far in zebrafish, a model teleost, transcript profiling throughout gonadal development has not been established because of a tiny size of an organ in juvenile stages and its poor distinguishability from surrounding tissues. We performed small RNA sequencing on isolated gonads of See-Thru-Gonad line, from the undifferentiated state at 3 weeks post fertilization (wpf) to fully mature adults at 24 wpf...
March 6, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28261241/analysis-of-plant-pan-genomes-and-transcriptomes-with-get_homologues-est-a-clustering-solution-for-sequences-of-the-same-species
#17
Bruno Contreras-Moreira, Carlos P Cantalapiedra, María J García-Pereira, Sean P Gordon, John P Vogel, Ernesto Igartua, Ana M Casas, Pablo Vinuesa
The pan-genome of a species is defined as the union of all the genes and non-coding sequences found in all its individuals. However, constructing a pan-genome for plants with large genomes is daunting both in sequencing cost and the scale of the required computational analysis. A more affordable alternative is to focus on the genic repertoire by using transcriptomic data. Here, the software GET_HOMOLOGUES-EST was benchmarked with genomic and RNA-seq data of 19 Arabidopsis thaliana ecotypes and then applied to the analysis of transcripts from 16 Hordeum vulgare genotypes...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28261218/the-t-cell-response-to-the-contact-sensitizer-paraphenylenediamine-is-characterized-by-a-polyclonal-diverse-repertoire-of-antigen-specific-receptors
#18
Theres Oakes, Amy Lee Popple, Jason Williams, Katharine Best, James M Heather, Mazlina Ismail, Gavin Maxwell, Nichola Gellatly, Rebecca J Dearman, Ian Kimber, Benny Chain
Paraphenylenediamine (PPD) is a common component of hair dyes and black henna tattoos and can cause skin sensitization and allergic contact dermatitis (ACD). The cutaneous inflammatory reaction associated with ACD is driven by both CD4+ and CD8+ T cells. However, the characteristics of such responses with respect to clonal breadth and magnitude are poorly defined. In this study, we have characterized the in vitro recall response of peripheral blood T cells prepared from PPD-allergic individuals to a PPD-human serum albumin (HSA) conjugate (PPD-HSA)...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/28259700/describing-the-diversity-of-ag-specific-receptors-in-vertebrates-contribution-of-repertoire-deep-sequencing
#19
Rosario Castro, Sofie Navelsaker, Aleksei Krasnov, Louis Du Pasquier, Pierre Boudinot
During the last decades, gene and cDNA cloning identified TCR and Ig genes across vertebrates; genome sequencing of TCR and Ig loci in many species revealed the different organizations selected during evolution under the pressure of generating diverse repertoires of Ag receptors. By detecting clonotypes over a wide range of frequency, deep sequencing of Ig and TCR transcripts provides a new way to compare the structure of expressed repertoires in species of various sizes, at different stages of development, with different physiologies, and displaying multiple adaptations to the environment...
March 1, 2017: Developmental and Comparative Immunology
https://www.readbyqxmd.com/read/28259047/the-tripartite-leader-sequence-is-required-for-ectopic-expression-of-hadv-b-and-hadv-e-e3-cr1-genes
#20
Camden R Bair, Poornima Kotha Lakshmi Narayan, Adriana E Kajon
The unique repertoire of genes that characterizes the early region 3 (E3) of the different species of human adenovirus (HAdV) likely contributes to their distinct pathogenic traits. The function of many E3 CR1 proteins remains unknown possibly due to unidentified intrinsic properties that make them difficult to express ectopically. This study shows that the species HAdV-B- and HAdV-E-specific E3 CR1 genes can be expressed from vectors carrying the HAdV tripartite leader (TPL) sequence but not from traditional mammalian expression vectors...
March 1, 2017: Virology
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