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1.
Microbiol Resour Announc ; 11(9): e0063622, 2022 Sep 15.
Artigo em Inglês | MEDLINE | ID: mdl-35969062

RESUMO

Subcluster L3 bacteriophage Finnry was isolated from soil collected in Charleston, South Carolina, using Mycobacterium smegmatis mc2155 as a host. The genome of this temperate siphovirus is 75,632 bp long (130 predicted protein-coding genes, 9 tRNAs, and no transfer-messenger RNAs), and BLASTn alignment revealed 99.86% identity with the genome of L3 mycobacteriophage Samty.

2.
Microbiol Resour Announc ; 10(26): e0049321, 2021 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-34197200

RESUMO

Lolalove, a B4 subcluster soil bacteriophage of Mycobacterium smegmatis, was isolated in Charleston, SC. It possesses a 71,111-bp linear double-stranded DNA (dsDNA) genome with 99 protein-coding genes and a GC content of 68.9%. genome BLASTn alignments indicate high sequence identity to the related B4 subcluster M. smegmatis phages BrownCNA, Mithril, and Hangman.

3.
Genome Announc ; 5(43)2017 Oct 26.
Artigo em Inglês | MEDLINE | ID: mdl-29074662

RESUMO

Seven mycobacteriophages from distinct geographical locations were isolated, using Mycobacterium smegmatis mc2155 as the host, and then purified and sequenced. All of the genomes are related to cluster A mycobacteriophages, BobSwaget and Lokk in subcluster A2; Fred313, KADY, Stagni, and StepMih in subcluster A3; and MyraDee in subcluster A18, the first phage to be assigned to that subcluster.

4.
Immunogenetics ; 65(5): 387-96, 2013 May.
Artigo em Inglês | MEDLINE | ID: mdl-23417322

RESUMO

The gene segments encoding antibodies have been studied in many capacities and represent some of the best-characterized gene families in traditional animal disease models (mice and humans). To date, multiple immunoglobulin light chain (IgL) isotypes have been found in vertebrates and it is unclear as to which isotypes might be more primordial in nature. Sequence data emerging from an array of fish genome projects is a valuable resource for discerning complex multigene assemblages in this critical branch point of vertebrate phylogeny. Herein, we have analyzed the genomic organization of medaka (Oryzias latipes) IgL gene segments based on recently released genome data. The medaka IgL locus located on chromosome 11 contains at least three clusters of IgL gene segments comprised of multiple gene assemblages of the kappa light chain isotype. These data suggest that medaka IgL gene segments may undergo both intra- and inter-cluster rearrangements as a means to generate additional diversity. Alignments of expressed sequence tags to concordant gene segments which revealed each of the three IgL clusters are expressed. Collectively, these data provide a genomic framework for IgL genes in medaka and indicate that Ig diversity in this species is achieved from at least three distinct chromosomal regions.


Assuntos
Genes de Cadeia Leve de Imunoglobulina/genética , Variação Genética , Oryzias/genética , Sequência de Aminoácidos , Animais , Genes de Cadeia Leve de Imunoglobulina/imunologia , Genoma , Dados de Sequência Molecular , Oryzias/imunologia , Filogenia , Homologia de Sequência de Aminoácidos
5.
Mol Immunol ; 48(15-16): 2220-3, 2011 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-21820179

RESUMO

The zebrafish is an emerging model for comparative immunology and biomedical research. In contrast to the five heavy chain isotype system of mice and human (IgD, IgM, IgA, IgG, IgE), zebrafish harbor gene segments for IgD, IgM, and novel heavy chain isotype called IgZ/T which appears restricted to bony fishes. The purpose of this study was to design and validate a suite of quantitative real time RT-PCR protocols to measure IgH expression in a vertebrate model which has considerable promise for modeling both pathogenic infection and chronic conditions leading to immune dysfunction. Specific primers were designed and following verification of their specificty, relative expression levels of IgD, IgM, and IgZ/T were measured in triplicate for zebrafish raised under standard laboratory conditions. During embryonic stages, low levels of each heavy chain isotype (IgH) were detected with each increasing steadily between 2 and 17 weeks post fertilization. Overall IgM>IgZ>IgD throughout zebrafish development with the copy number of IgM being several fold higher than that of IgD or IgZ/T. IgD exon usage was also characterized, as its extremely long size and presence of a stop codon in the second IgD exon in zebrafish, raised questions as to how this antibody might be expressed. Zebrafish IgD was found to be a chimeric immunoglobulin, with the third IgD exon spliced to the first IgM constant exon thereby circumventing the first and second IgD exons. Collectively, the qRT-PCR results represent the first comparative profile of IgD, IgM, IgZ/T expression over the lifespan of any fish species and the primers and assay parameters reported should prove useful in enabling researchers to rapidly quantify changes in IgH expression in zebrafish models of disease where altered IgH expression is manifested.


Assuntos
Perfilação da Expressão Gênica , Imunoglobulina D/genética , Cadeias Pesadas de Imunoglobulinas/genética , Reação em Cadeia da Polimerase Via Transcriptase Reversa/métodos , Peixe-Zebra/genética , Peixe-Zebra/imunologia , Animais , Éxons , Expressão Gênica , Rearranjo Gênico do Linfócito B/genética , Cadeias Pesadas de Imunoglobulinas/análise , Isotipos de Imunoglobulinas/genética , Isotipos de Imunoglobulinas/imunologia , Imunoglobulina M/genética , Imunoglobulina M/imunologia , Splicing de RNA , Peixe-Zebra/crescimento & desenvolvimento
6.
Fish Shellfish Immunol ; 31(5): 697-703, 2011 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-20933599

RESUMO

Genomic organization, composition, and microsynteny of immunoglobulin light chain (IgL) gene segments in the zebrafish were analyzed through the identification and annotation of overlapping BAC clone insert sequences and an Illumina de novo assembly. The resultant gap-free IgL annotation confirmed a number of previous conclusions about teleost IgL including: suites of (V(L)-J(L)-C(L)) clusters on multiple chromosomes; V(L) in the same or opposite transcriptional orientation as J(L) and C(L); and the apparent absence of lambda IgL in the zebrafish model. In addition, palindromic heptamers (CACAGTG or CACTGTG) within the 3' region of zebrafish C(L) were identified. In mammals, heptamers within J(κ)-C(κ) introns can recombine with downstream kappa deleting elements (Kde) to ablate C(κ) regions prior to rearrangements of V(λ)-J(λ) gene segments. The presence of palindromic heptamers within zebrafish C(L) is intriguing as their recombination with intact RSS might result in the deletion of a large portion of the C(L) thereby permanently silencing C(L) exons within the IgL locus. Given that bony fish have appreciably more C(L) spread over more chromosomes than mice and humans, it is plausible the presence of recombining sequences within C(L) may be tied to a need for heightened mechanisms to facilitate allelic exclusion or receptor editing. Collectively, with this report, gap-free annotations of the heavy and light chain Ig loci have now been completed for Danio rerio, the only teleost for which this has been accomplished, thereby strengthening the overall utility of zebrafish as a model organism for both comparative immunology and biomedical research.


Assuntos
Genes de Cadeia Leve de Imunoglobulina/genética , Regiões Constantes de Imunoglobulina/genética , Anotação de Sequência Molecular , Peixe-Zebra/genética , Sequência de Aminoácidos , Animais , Sequência de Bases , Cromossomos Artificiais Bacterianos/genética , Células Clonais , Ordem dos Genes , Regiões Constantes de Imunoglobulina/química , Dados de Sequência Molecular , Alinhamento de Sequência
7.
Immunology ; 132(2): 240-55, 2011 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-21070232

RESUMO

In mammals, somatic hypermutation (SHM) of immunoglobulin (Ig) genes is critical for the generation of high-affinity antibodies and effective immune responses. Knowledge of sequence-specific biases in the targeting of somatic mutations can be useful for studies aimed at understanding antibody repertoires produced in response to infections, B-cell neoplasms, or autoimmune disease. To evaluate potential nucleotide targets of somatic mutation in zebrafish (Danio rerio), an enriched IgL cDNA library was constructed and > 250 randomly selected clones were sequenced and analysed. In total, 55 unique VJ-C sequences were identified encoding a total of 125 mutations. Mutations were most prevalent in V(L) with a bias towards single base transitions and increased mutation in the complementarity-determining regions (CDRs). Overall, mutations were overrepresented at WRCH/DGYW motifs suggestive of activation-induced cytidine deaminase (AID) targeting which is common in mice and humans. In contrast to mammalian models, N and P addition was not observed and mutations at AID hotspots were largely restricted to palindromic WRCH/DGYW motifs. Mutability indexes for di- and trinucleotide combinations confirmed C/G targets within WRCH/DGYW motifs to be statistically significant mutational hotspots and showed trinucleotides ATC and ATG to be mutation coldspots. Additive mutations in VJ-C sequences revealed patterns of clonal expansion consistent with affinity maturation responses seen in higher vertebrates. Taken together, the data reveal specific nucleotide targets of SHM in zebrafish and suggest that AID and affinity maturation contribute to antibody diversification in this emerging immunological model.


Assuntos
Genes de Cadeia Leve de Imunoglobulina/genética , Cadeias Leves de Imunoglobulina/genética , Hipermutação Somática de Imunoglobulina/genética , Peixe-Zebra/genética , Peixe-Zebra/imunologia , Motivos de Aminoácidos , Animais , Citidina/metabolismo , Citidina Desaminase/metabolismo , Biblioteca Gênica , Modelos Imunológicos , Dados de Sequência Molecular , Mutação , Análise de Sequência de DNA , Peixe-Zebra/metabolismo
8.
Dev Comp Immunol ; 32(4): 421-34, 2008.
Artigo em Inglês | MEDLINE | ID: mdl-18022691

RESUMO

In mammals, Immunoglobulin light chain (IgL) are localized to two chromosomal regions (designated kappa and lambda). Here we report a genome-wide survey of IgL genes in the zebrafish revealing (V(L)-J(L)-C(L)) clusters spanning 5 separate chromosomes. To elucidate IgL loci present in the zebrafish genome assembly (Zv6), conventional sequence similarity searches and a novel scanning approach based on recombination signal sequence (RSS) motifs were applied. RT-PCR with zebrafish cDNA was used to confirm annotations, evaluate VJ-rearrangement possibilities and show that each chromosomal locus is expressed. In contrast to other vertebrates in which IgL exon usage has been studied, inversional rearrangement between (V(L)-J(L)-C(L)) clusters were found. Inter-cluster rearrangements may convey a selective advantage for editing self-reactive receptors and poise zebrafish by virtue of their extensive numbers of V(L), J(L) and C(L) to have greater potential for immunoglobulin gene shuffling than traditionally studied mice and human models.


Assuntos
Rearranjo Gênico de Cadeia Leve de Linfócito B , Genes de Cadeia Leve de Imunoglobulina , Cadeias Leves de Imunoglobulina/genética , Peixe-Zebra/genética , Peixe-Zebra/imunologia , Sequência de Aminoácidos , Animais , Cromossomos/genética , Regiões Constantes de Imunoglobulina/genética , Região de Junção de Imunoglobulinas/genética , Cadeias Leves de Imunoglobulina/química , Cadeias Leves de Imunoglobulina/imunologia , Região Variável de Imunoglobulina/genética , Dados de Sequência Molecular , Família Multigênica , Filogenia , Alinhamento de Sequência , Análise de Sequência de DNA
9.
Immunogenetics ; 55(12): 825-35, 2004 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-14968267

RESUMO

We report the identification of a single major chromosomal region controlling natural killer (NK) cell-like activity in rainbow trout (Oncorhynchus mykiss). A genetic map based on 484 AFLP and 39 microsatellite genotypes from 106 doubled haploid fish was constructed. These fish were produced by androgenesis from a hybrid of two clonal lines divergent in NK-like activity. NK-like activities for 75 of the doubled haploids were quantified by an in vitro chromium release assay utilizing (51)Cr-labeled YAC-1 target cells. Composite interval mapping revealed a single major quantitative trait locus (QTL) associated with NK-like activity in this rainbow trout model. Genetic mapping revealed this QTL to also be unlinked to: fragmented MHC class I and MHC class II regions, the leukocyte receptor cluster, the natural killer cell enhancement factor ( NKEF) gene, the RAG-1 gene, and two QTL associated with resistance to infectious pancreatic necrosis virus in rainbow trout. Collectively, these results extend the utility of rainbow trout as an immunological model and are consistent with the idea that a single chromosomal region homologous to the natural killer cell complex (NKC) located on syntenic portions of mouse chromosome (Chr) 6, human Chr 12, and rat Chr 4 may exist in a lower vertebrate model.


Assuntos
Mapeamento Cromossômico , Cromossomos/genética , Células Matadoras Naturais/imunologia , Oncorhynchus mykiss/genética , Característica Quantitativa Herdável , Animais , Cromo/metabolismo , Feminino , Genótipo , Haploidia , Antígenos de Histocompatibilidade Classe I/genética , Antígenos de Histocompatibilidade Classe I/imunologia , Escore Lod , Masculino , Repetições de Microssatélites , Polimorfismo de Fragmento de Restrição
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