Antibody heavy chain recombination that results in the incorporation of multiple diversity (D) genes, although uncommon, contributes substantially to the diversity of the human antibody repertoire. Such recombination allows the generation of HCDR3 regions of extreme length and enables junctional regions that, due to the nucleotide bias of N-addition regions, ...

ABSTRACT: BACKGROUND: Exome sequencing using next-generation sequencing technologies is a cost efficient approachto selectively sequencing coding regions of human genome for detection of disease variants.A significant amount of DNA fragments from the capture process fall outside target regions,and sequence data for positions outside target regions have been mostly ignored afteralignment.ResultWe ...

Lactococcus garvieae is recognized as an emerging pathogen in fish. Several PCR-based methods have been developed for the detection and identification of L. garvieae; however, the sensitivity of these methods is still in question regarding the discrimination of this organism from other closely related species. Two primers, ITSLg30F and ITSLg319R, were ...

Fifteen gene-containing BACs with accumulated length of 1.82-Mb from the Rht-D1b locus region were sequenced and compared in detail with the orthologous regions of rice, sorghum, and maize. Our results show that Rht-D1b represents a conserved genomic region as implied by high gene sequence identity, good maintenance of gene colinearity, ...

Mycoplasma genitalium is expected to metabolize RNA using unique pathways because its minimal genome encodes very few ribonucleases. In this work, we report that the only exoribonuclease identified in M. genitalium, RNase R, is able to remove tRNA 3' trailers and generate mature 3' ends. Several sequence and structural features ...

Our study demonstrates that the genetic investigation of forkhead box O3A gene (FOXO3A), a validated human longevity gene, is greatly hampered by the fact that its exonic regions have 99% sequence homology with the FOXO3B pseudogene. If unaccounted for, this high degree of homology can cause serious genotyping or sequencing ...

High-throughput sequencing (HTS) of lymphoid receptor genes is an emerging technology that can comprehensively assess the diversity of the immune system. Here, we applied HTS to the diagnosis of T-lineage acute lymphoblastic leukemia/lymphoma. Using 43 paired patient samples, we then assessed minimal residual disease (MRD) at day 29 after treatment. ...

The study of 5-hydroxylmethylcytosines (5hmC) has been hampered by the lack of a method to map it at single-base resolution on a genome-wide scale. Affinity purification-based methods cannot precisely locate 5hmC nor accurately determine its relative abundance at each modified site. We here present a genome-wide approach, Tet-assisted bisulfite sequencing ...

PGC-1α has been implicated in the pathogenesis of neurodegenerative disorders. Several SNPs, located in two separate haplotype blocks of PPARGC1A, have shown associations with Huntington and Parkinson diseases, but causative SNPs have not been identified. One SNP (rs7665116) was located in a highly conserved 233 bp region of intron 2. ...

Genetic testing of PKD1 and PKD2 is useful for the diagnosis and prognosis of autosomal dominant polycystic kidney disease; however, analysis is complicated by the large transcript size, the complexity of the gene region, and the high level of gene variations. We developed a novel mutation screening assay for PKD1 ...

This month's Genome Watch reviews a recent paper that used a metagenomics approach to characterize the plasmid content of bovine rumen samples.

ABSTRACT: BACKGROUND: Pentatricopeptide repeat (PPR) proteins are required for numerous RNA processing events in plant organelles including C-to-U editing, splicing, stabilization, and cleavage. Fifteen PPR proteins are known to be required for RNA editing at 21 sites in Arabidopsis chloroplasts, and belong to the PLS class of PPR proteins. In ...

We generated a high-quality reference genome sequence for foxtail millet (Setaria italica). The ∼400-Mb assembly covers ∼80% of the genome and >95% of the gene space. The assembly was anchored to a 992-locus genetic map and was annotated by comparison with >1.3 million expressed sequence tag reads. We produced more ...

The use of a priori knowledge in the alignment of targeted sequencing data is investigated using computational experiments. Adapting a Needleman-Wunsch algorithm to incorporate the genomic position information from the targeted capture, we demonstrate that alignment can be done to just the target region of interest. When in addition use ...

Antibody switching involves class switch recombination (CSR) events between switch (S) regions located upstream of heavy chain constant (C) genes. Mechanisms targeting CSR to S-regions are not clear. Deletion of Sμ tandem repeat (SμTR) sequences causes CSR to shift into downstream regions that do not undergo CSR in WT B-cells, ...

ABSTRACT: BACKGROUND: Detecting duplication segments within completely sequenced genomes provides valuable information to address genome evolution and in particular the important question of the emergence of novel functions. The usual approach to gene duplication detection, based on all-pairs protein gene comparisons, provides only a restricted view of duplication. RESULTS: In ...

The mosaic structure of the cagA gene has been suggested to affect Helicobacter pylori CagA-associated pathogenesis. An improved polymerase chain reaction assay allowed for a rapid and detailed molecular analysis of the cagA gene 3'-region in a single amplification step, followed by amplicon sequencing using universal M13 and T7 sequencing ...

Biophysical and mechanistic investigation of RNA function requires site-specific incorporation of spectroscopic and chemical probes, which is difficult to achieve using current technologies. We have in vitro reconstituted a functional box C/D small ribonucleoprotein RNA 2'-O-methyltransferase (C/D RNP) from the thermophilic archaeon Pyrococcus abyssi and demonstrated its ability to transfer ...

Abundant nsSNPs have been found in genes coding for human solute carrier (SLC) transporters, but there is little known about the relationship between the genotype and phenotype of nsSNPs in these membrane proteins. It is unknown which prediction method is better suited for the prediction of nonneutral nsSNPs of SLC ...

ABSTRACT: BACKGROUND: Various aspects of genome organization have been explored based on data from distincttechnologies, including histone modification ChIP-Seq, 3C, and its derivatives. Recentlydeveloped Hi-C techniques enable the genome wide mapping of DNA interactomes, therebyproviding the opportunity to study genome organization in detail, but these methods also posechallenges in methodology ...

Abstract Clonality analysis of viral vector-transduced cell populations represents a convincing approach to dissect the physiology of tissue and organ regeneration, to monitor the fate of individual gene-corrected cells in vivo, and to assess vector biosafety. With the decoding of mammalian genomes and the introduction of next-generation sequencing technologies, the ...

To develop a multi-antigen-specific immunoglobulin new antigen receptor (IgNAR) variable (V) region phage display library, CDR3 in the V region of IgNAR from banded houndshark (Triakis scyllium) was artificially randomized, and clones specific for hen egg white lysozyme (HEL) were obtained by the biopanning method. The nucleotide sequence of CDR3 ...

ABSTRACT: BACKGROUND: Expressed Sequence Tag (EST) sequences are widely used in applications such as genome annotation, gene discovery and gene expression studies. However, some of GenBank dbEST sequences have proven to be "unclean". Identification of cDNA termini/ends and their structures in raw ESTs not only facilitates data quality control and ...

Recombination rates vary across the genome and in many species show significant relationships with several genomic features including distance to the centromere, gene density and GC content. Studies of fine-scale recombination rates have also revealed that in several species there are recombination hotspots, i.e. short regions with recombination rates 10-100 ...

The role of natural selection in speciation has received increasing attention and support in recent years. Different types of approaches have been developed that can detect genomic regions influenced by selection. Here, we address the question whether two highly different methods-F(ST) outlier analysis and admixture analysis-detect largely the same set ...

ABSTRACT: The dramatic fall in the cost of genomic sequencing, and the increasing convenience of distributed cloud computing resources, positions the MapReduce coding pattern as a cornerstone of scalable bioinformatics algorithm development. In some cases an algorithm will find a natural distribution via use of map functions to process vectorized ...

OBJECTIVES: Nalidixic acid-resistant Salmonella enterica serovars Kentucky (n = 5) and Virchow (n = 6) cultured from individuals were investigated for the presence of plasmid-mediated quinolone resistance (PMQR) determinants. METHODS: PMQR markers and mutations within the quinolone resistance-determining regions of the target genes were investigated by PCR followed by DNA sequencing. Conjugation, plasmid profiling ...

Rhodococcus fascians is currently the only phytopathogen of which the virulence genes occur on a linear plasmid. To get insight into the origin of this replicon and into the virulence strategy of this broad-spectrum phytopathogen, the sequence of the linear plasmid of strain D188, pFiD188, was determined. Analysis of the ...

ABSTRACT: BACKGROUND: The leishmaniases are a group of clinically diverse diseases caused by parasites of the genus Leishmania. To distinguish between species is crucial for correct diagnosis and prognosis as well as for treatment decisions. Recently, sequencing of the HSP70 coding region has been applied in phylogenetic studies and for ...

Many populations of the narrow-clawed crayfish Astacus leptodactylus in Turkey, including those inhabiting Lake Eğirdir, declined drastically in the mid-1980s due to introduction of crayfish plague Aphanomyces astaci. However, unlike many other localities, there has been some recovery in the A. leptodactylus population inhabiting this lake even though crayfish plague ...

The risk of developing tauopathic neurodegenerative disease depends in part on the levels and composition of six naturally occurring tau isoforms in human brain. These proteins, which form filamentous aggregates in disease, vary only by the presence or absence of three inserts encoded by alternatively spliced exons 2, 3, and ...

A new recombinant human species D adenovirus (HAdV-D) was isolated from the stool of a pharyngitis patient in Japan, and genetic characterization was performed via sequencing variable regions between HAdV types. The nucleotide sequences of the penton base gene and loops 1 and 2 in the hexon gene showed 100% ...

The VapBC toxin-antitoxin (TA) family is the largest of nine identified TA families. The toxin, VapC, is a metal-dependent ribonuclease that is inhibited by its cognate antitoxin, VapB. Although the VapBCs are the largest TA family, little is known about their biological roles. Here we describe a new general method ...

In a recent Technical Advance article, Vachon and Freeland (2011, Molecular Ecology Resources, 11, 279-285.) evaluate the utility of repetitive and non-repetitive variation in the chloroplast genome for phylogeographic inference, using variation in Phragmites australis as an example. While we agree that repetitive and nonrepetitive regions evolve at different rates ...

Abstract Chromatin immunoprecipitation followed by massively parallel sequencing (ChIP-Seq) has become a routine for detecting genome-wide protein-DNA interaction. The success of ChIP-Seq data analysis highly depends on the quality of peak calling (i.e., to detect peaks of tag counts at a genomic location and evaluate if the peak corresponds to ...

A 1D motif usually comprises conserved essential residues involved in catalysis, ligand binding, or maintaining a specific structure. However, it cannot be easily detected in proteins with low sequence identity because it is difficult to (1) identify protein sequences suspected to contain the motif, and (2) align sequences with little ...

This study reports the complete chloroplast (cp) DNA sequence of Eleutherococcus senticosus (GenBank: JN 637765), an endangered endemic species. The genome is 156,768 bp in length, and contains a pair of inverted repeat (IR) regions of 25,930 bp each, a large single copy (LSC) region of 86,755 bp and a ...

ABSTRACT: BACKGROUND: Adenosine-to-inosine (A-to-I) editing is a site-selective post-transcriptional alteration of double-stranded RNA by ADAR deaminases that is crucial for homeostasis and development. Recently the Mouse Genomes Project generated genome sequences for 17 laboratory mouse strains and rich catalogues of variants. We also generated RNA-seq data from whole brain RNA ...

In the present study, we made further investigation into the diversity of Trichoderma in China than previous ones utilizing comprehensive approaches of morphological microscopic observation and phylogenetic analysis by detecting molecular markers. One thousand nine hundred ten Trichoderma strains were isolated from soil or other materials in China: East (Anhui, ...

A rapid and efficient organocatalytic cascade sequence for the direct construction of spirocyclopentane bioxindoles has been carried out by using a chiral squaramide catalyst in the presence of a base. This process constitutes a powerful approach to the preparation of biologically important bispirooxindoles in high enantioselectivities.

Oaks, chestnuts, and beeches are economically important species of the Fagaceae. To understand the relationship between these members of this family, a deep knowledge of their genome composition and organization is needed. In this work, we have isolated and characterized several AFLP fragments obtained from Quercus rotundifolia Lam. through homology ...

Thirty-one members of the genus Marichromatium were analysed based on multilocus sequence analysis (MLSA) of four concatenated protein-coding genes (fusA, pufM, dnaK, recA) along with the internal transcribed spacer (ITS; 16S-23S rRNA) region and 16S rRNA gene. The restriction patterns obtained from the in silico analysis of the concatenated sequences ...

DNA methylation mediates imprinted gene expression by passing an epigenomic state across generations and differentially marking specific regulatory regions on maternal and paternal alleles. Imprinting has been tied to the evolution of the placenta in mammals and defects of imprinting have been associated with human diseases. Although recent advances in ...

We report on the effectiveness of a custom-designed oligonucleotide-based comparative genomic hybridization microarray (array-CGH) to interrogate copy number across the entire 2.2-Mb genomic region of the DMD gene and its applicability in diagnosis. The high-resolution array-CGH, we developed, successfully detected a series of 42 previously characterized large rearrangements of various ...

Bioinformatic evidence of the presence of a large conjugative transposon in ruminal bacterium Prevotella bryantii B(1)4(T) is presented. The described transposon appears to be related to another large conjugative transposon CTnBST, described in Bacteroides uniformis WH207 and to the conjugative transposon CTn3-Bf, which was observed in the genome of Bacteroides ...

ABSTRACT: BACKGROUND: Halomonas boliviensis is a halophilic bacterium that is included in the gamma-Proteobacteria sub-group, and is able to assimilate different types of carbohydrates. H. boliviensis is also able to produce poly(3-hydroxybutyrate) (PHB) in high yields using glucose as the carbon precursor. Accumulation of PHB by microorganisms is induced by ...

The finished human genome-assemblies comprise several hundred un-sequenced euchromatic gaps, which may be rich in long polypurine/polypyrimidine stretches. Human chromosome 20 (chr 20) currently has three unfinished gaps remaining on its q-arm. All three gaps are within gene-dense regions and/or overlap disease-associated loci, including the DLGAP4 locus. In this study, ...

Genome-Wide association studies (GWAS) routinely apply principal component analysis (PCA) to infer population structure within a sample to correct for confounding due to ancestry. GWAS implementation of PCA uses tens of thousands of single-nucleotide polymorphisms (SNPs) to infer structure, despite the fact that only a small fraction of such SNPs ...

Cysteine proteases (CPs) from the C1 family, which are similar to papain, can be found in animals and plants, as well as some viruses and prokaryotes. These enzymes have diverse physiological functions and are thus very attractive for science and industry. Jacaratia mexicana, a member of the Caricaceae plant family, ...

Excision from the chromosome is the first step during transfer of conjugative transposons (CTn) to a recipient. We previously showed that excision of CTnDOT is more complex than excision of lambdoid phages and CTns such as Tn916. Excision in vivo of CTnDOT utilizes four CTnDOT-encoded proteins: IntDOT, Xis2c, Xis2d, Exc ...