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At least 109 records · Page 6Linked to original sources
PubMed1997

A large-insert (130 kbp) bacterial artificial chromosome library of the rice blast fungus Magnaporthe grisea: genome analysis, contig assembly, and gene cloning.

Magnaporthe grisea (Hebert) Barr causes rice blast, one of the most devastating diseases of rice (Oryza sativa) worldwide. This fungus is an ideal organism for studying a number of aspects of plant-pathogen interactions, including infection-related morphogenesis, avirulence, and pathogen evolution. To facilitate M. grisea genome analysis, physical mapping, and positional cloning, we have constructed a bacterial artificial chromosome (BAC) library from the rice infecting strain 70-15. A new method was developed for separation of partially digested large-molecular-weight DNA fragments that facilitated library construction with large inserts. The library contains 9216 clones, with an average insert size of 130 kbp (> 25 genome equivalents) stored in 384-well microtiter plates that can be double spotted robotically on to a single nylon membrane. Several unlinked single-copy DNA probes were used to screen 4608 clones in the library and an average of 13 (minimum of 6) overlapping BAC clones was found in each case. Hybridization of total genomic DNA to the library and analysis of individual clones indicated that approximately 26% of the clones contain single-copy DNA. Approximately 35% of BAC clones contained the retrotransposon MAGGY. The library was used to identify BAC clones containing a adenylate cyclase gene (mac1). In addition, a 550-kbp contig composed of 6 BAC clones was constructed that encompassed two adjacent RFLP markers on chromosome 2. These data show that the BAC library is suitable for genome analysis of M. grisea. Copies of colony hybridization membranes are available upon request.

Ascomycota↗
PubMed2003

[Genomic analysis in Candida albicans].

With the recent advances in DNA sequencing technology, a succession of entire genome sequences have been published. A number of genome projects are underway in pathogenic fungi. From these, we present the history and current status of the genomic analysis of Candida albicans. The sequencing project for this organism has been undertaken at Stanford University, and is now nearing the end.

Candida albicans↗
PubMed2005

Automatic detection of subsystem/pathway variants in genome analysis.

MOTIVATION: Proteins work together in pathways and networks, collectively comprising the cellular machinery. A subsystem (a generalization of pathway concept) is a group of related functional roles (such as enzymes) jointly involved in a specific aspect of the cellular machinery. Subsystems provide a natural framework for comparative genome analysis and functional annotation. A subsystem may be implemented in a number of different functional variants in individual species. In order to reliably project functional assignments across multiple genomes, we have to be able to identify the variants implemented in each genome. The analysis of such variants across diverse species is an interesting problem by itself and may provide new evolutionary insights. However, no computational techniques are presently available for an automated detection and analysis of subsystem variants. RESULTS: Here we formulate the subsystem variant detection problem as finding the minimum number of subgraphs of a subsystem, which is represented as a graph, and solve the optimization problem by integer programming approach. The performance of our method was tested on subsystems encoded in the SEED, a genomic integration platform developed by the Fellowship for Interpretation of Genomes as a component of a large-scale effort on comparative analysis and annotation of multiple diverse genomes. Here we illustrate the results obtained for two expert-encoded subsystems of the biosynthesis of Coenzyme A and FMN/FAD cofactors. Applications of variant detection, to support genomic annotations and to assess divergence of species, are briefly discussed in the context of these universally conserved and essential metabolic subsystems. SUPPLEMENTARY INFORMATION: The details of the variant detection results are available at http://ffas.burnham.org/svar/supp.html.

Animals↗
PubMed2006

Genomic analysis of a 1 Mb region near the telomere of Hessian fly chromosome X2 and avirulence gene vH13.

BACKGROUND: To have an insight into the Mayetiola destructor (Hessian fly) genome, we performed an in silico comparative genomic analysis utilizing genetic mapping, genomic sequence and EST sequence data along with data available from public databases. RESULTS: Chromosome walking and FISH were utilized to identify a contig of 50 BAC clones near the telomere of the short arm of Hessian fly chromosome X2 and near the avirulence gene vH13. These clones enabled us to correlate physical and genetic distance in this region of the Hessian fly genome. Sequence data from these BAC ends encompassing a 760 kb region, and a fully sequenced and assembled 42.6 kb BAC clone, was utilized to perform a comparative genomic study. In silico gene prediction combined with BLAST analyses was used to determine putative orthology to the sequenced dipteran genomes of the fruit fly, Drosophila melanogaster, and the malaria mosquito, Anopheles gambiae, and to infer evolutionary relationships. CONCLUSION: This initial effort enables us to advance our understanding of the structure, composition and evolution of the genome of this important agricultural pest and is an invaluable tool for a whole genome sequencing effort.

Animals↗
PubMed2003

Whole genome analysis of genetic alterations in small DNA samples using hyperbranched strand displacement amplification and array-CGH.

Structural genetic alterations in cancer often involve gene loss or gene amplification. With the advent of microarray approaches for the analysis of the genome, as exemplified by array-CGH (Comparative Genomic Hybridization), scanning for gene-dosage alterations is limited only by issues of DNA microarray density. However, samples of interest to the pathologist often comprise small clusters of just a few hundred cells, which do not provide sufficient DNA for array-CGH analysis. We sought to develop a simple method that would permit amplification of the whole genome without the use of thermocycling or ligation of DNA adaptors, because such a method would lend itself to the automated processing of a large number of tissue samples. We describe a method that permits the isothermal amplification of genomic DNA with high fidelity and limited sequence representation bias. The method is based on strand displacement reactions that propagate by a hyperbranching mechanism, and generate hundreds, or even thousands, of copies of the genome in a few hours. Using whole genome isothermal amplification, in combination with comparative genomic hybridization on cDNA microarrays, we demonstrate the ability to detect gene losses in yeast and gene dosage imbalances in human breast tumor cell lines. Although sequence representation bias in the amplified DNA presents potential problems for CGH analysis, these problems have been overcome by using amplified DNA in both control and tester samples. Gene-dosage alterations of threefold or more can be observed with high reproducibility with as few as 1000 cells of starting material.

Breast Neoplasms↗
PubMed1997

Isolation and genomic analysis of the rat polymeric immunoglobulin receptor gene terminal domain and transcriptional control region.

The polymeric immunoglobulin receptor (pIgR) transports IgA and IgM across secretory epithelial cells and is essential in external immunity maintenance. We report here the structural characterization of the single-copy rat gene distributed over 30 kb of chromosomal DNA and analysis of its transcriptional control region. RNA sequencing and genomic analysis show a 5' terminal region originates at a major (+1) and a minor site producing an unusual 124-bp nontranslated exon I separated from a small 96-bp initiator ATG coding exon II by a 7.5-kb intron. The pIgR 5' region comprises a structured promoter with abundant helix-loop-helix (bHLH) cis elements positioned within an equivalent internal -70, -290, -528, and three centered at -745. The three latter bHLH elements each occur within 30-bp repeats at -690 to -780. Transient expression assays show a 1.3-kb 5' region is sufficient to drive expression in rat primary hepatocyte monolayer cultures, transformed human hepatic (HepG2) cells, and a mammary epithelial tumor cell line MCF-7, but is inactive in the rodent fibroblast 3T3 cell line. A minimal transcriptional promoter domain was deduced from sequentially deleted vectors revealing a +40 to -922 sequence to be sufficient for full activity. Further deletions within this region yield incremental losses in cis activity, indicating that multiple subregions comprise an extended transcriptional control region.

Animals↗
PubMed1993

[Application of the chromosome sorting technique to the human genome analysis].

The flow-sorted human chromosome is an ideal DNA source for genome analysis research, particularly gene mapping and construction of cosmid library. For gene mapping, 50,000 chromosomes each were sorted on a membrane filter and hybridized with a radio-labeled gene probe. Using this Spot Blot Hybridization method in combination with FISH, we have mapped more than 30 new genes including 6 neuron-specific ones. For construction of a chromosome-specific cosmid library, nearly 10 million chromosomes were flow-sorted. The chromosome 21-specific cosmid library consisting of 33,000 clones and the 22pter-q11 region-specific library consisting of 9,200 clones were established. Grouping of cosmid clones from the library using high density replica filters and YAC DNAs to make cosmid contigs within specific regions is under way.

Base Sequence↗
PubMed1992

A human genome analysis system (HUGA-I) developed in Japan.

A part of the Japanese human genome project has resulted in the development of a world original human genome analysis system. Circumstances of the project, objective, design concept, and constitution of the system are described in the paper.

Base Sequence↗
PubMed2000

Whole-genome analysis of human astrocytic tumors by comparative genomic hybridization.

Frozen sections of 35 astrocytic tumors of various histologic malignancies were analyzed by comparative genomic hybridization in an attempt to characterize the profile of genetic aberrations. Over 94% of the samples revealed DNA copy number aberrations, which increased with higher histological malignancy grades, and also involvement of more than one chromosome was seen in 85% of instances. The aberrations observed were mainly deletions and most frequently incorporated chromosomes 1p, 10, 19q, and 22q. On the other hand, gains or amplifications were detected only in glioblastomas. Additionally, such gains or amplifications were present in all tumor samples where the initial histopathological diagnosis was glioblastoma and immunohistochemical study disclosed p53 tumor suppressor protein negative and epidermal growth factor receptor positive immunoreactivity; such glioblastomas possessing p53 tumor suppressor protein positive and epidermal growth factor receptor negative immunoreactivity seldom displayed any gain. Thus, glioblastomas exhibiting two different profiles of genetic aberrations were recognized--one with and the other without any gains/ amplifications. We speculate that the former variety is de novo glioblastoma.

Adult↗
PubMed2002

Applications of InterPro in protein annotation and genome analysis.

The applications of InterPro span a range of biologically important areas that includes automatic annotation of protein sequences and genome analysis. In automatic annotation of protein sequences InterPro has been utilised to provide reliable characterisation of sequences, identifying them as candidates for functional annotation. Rules based on the InterPro characterisation are stored and operated through a database called RuleBase. RuleBase is used as the main tool in the sequence database group at the EBI to apply automatic annotation to unknown sequences. The annotated sequences are stored and distributed in the TrEMBL protein sequence database. InterPro also provides a means to carry out statistical and comparative analyses of whole genomes. In the Proteome Analysis Database, InterPro analyses have been combined with other analyses based on CluSTr, the Gene Ontology (GO) and structural information on the proteins.

Amino Acid Sequence↗
PubMed2026

Quantile Tensor Regression for Integrative Genomic Analysis of Oesophageal Carcinoma.

Recent integrative genomic studies have increasingly exploited the tensor structure of multi-omics data to develop statistical methods that jointly model the relationship between clinical outcomes and multiple genomes. However, genomic measurements and clinical outcomes are frequently contaminated by outliers or heavy-tailed noise, necessitating robust tensor-based inference approaches. In this paper, we investigate the quantile tensor regression with an emphasis on the region selection problem. We introduce a novel estimator that integrates quantile regression for robustness with a nonconvex penalty to encourage sparsity in the tensor coefficient, thereby enabling the identification of localized genomic regions that significantly influence the clinical response. To solve the resulting optimization problem, we devise an effective algorithm tailored to the nonconvex objective and tensor architecture. We establish the asymptotic properties of the proposed nonconvex penalized estimator. Extensive simulations demonstrate the excellent finite-sample performance of the proposed estimator. We further illustrate the practical utility of the proposed estimator through an application to esophageal carcinoma data, providing empirical validation.

Humans↗
PubMed2020

Genomic Analysis of Circulating Tumor Cells at the Single-Cell Level.

Circulating tumor cells (CTCs) have a great potential for noninvasive diagnosis and real-time monitoring of cancer. A comprehensive evaluation of four whole genome amplification (WGA)/next-generation sequencing workflows for genomic analysis of single CTCs, including PCR-based (GenomePlex and Ampli1), multiple displacement amplification (Repli-g), and hybrid PCR- and multiple displacement amplification-based [multiple annealing and loop-based amplification cycling (MALBAC)] is reported herein. To demonstrate clinical utilities, copy number variations (CNVs) in single CTCs isolated from four patients with squamous non-small-cell lung cancer were profiled. Results indicate that MALBAC and Repli-g WGA have significantly broader genomic coverage compared with GenomePlex and Ampli1. Furthermore, MALBAC coupled with low-pass whole genome sequencing has better coverage breadth, uniformity, and reproducibility and is superior to Repli-g for genome-wide CNV profiling and detecting focal oncogenic amplifications. For mutation analysis, none of the WGA methods were found to achieve sufficient sensitivity and specificity by whole exome sequencing. Finally, profiling of single CTCs from patients with non-small-cell lung cancer revealed potentially clinically relevant CNVs. In conclusion, MALBAC WGA coupled with low-pass whole genome sequencing is a robust workflow for genome-wide CNV profiling at single-cell level and has great potential to be applied in clinical investigations. Nevertheless, data suggest that none of the evaluated single-cell sequencing workflows can reach sufficient sensitivity or specificity for mutation detection required for clinical applications.

Carcinoma, Non-Small-Cell Lung↗
PubMed2026

Genomic analysis of community-associated multidrug-resistant Klebsiella quasipneumoniae subsp. similipneumoniae and the identification of the ST2059-KL1 clone in the U.S.

UNLABELLED: Klebsiella quasipneumoniae subsp. similipneumoniae is an important member of the K. pneumoniae species complex (KpSC) and is increasingly reported as multidrug-resistant (MDR) in healthcare- and community-associated infections. Since clinical laboratories do not routinely distinguish K. quasipneumoniae subsp. similipneumoniae from K. pneumoniae, national prevalence estimates, particularly for MDR, are lacking. In this study, a total of 2,006 community-associated MDR KpSC isolates were collected from 42 U.S. states, with 30 K. quasipneumoniae subsp. similipneumoniae isolates originating from 12 states identified using whole genome sequencing. All isolates were resistant to ceftriaxone and exhibited high rates of resistance to other antimicrobial agents, including ampicillin-sulbactam (56.7%, 17/30), levofloxacin (75.9%, 22/29), and trimethoprim-sulfamethoxazole (53.3%, 16/30). Notably, five isolates were also carbapenem-resistant. Genomic analysis resolved 10 sequence types (STs), with ST2059 (n = 13) and ST414 (n = 9) predominating. Ceftriaxone resistance in most isolates (90%, 27/30) was conferred by an extended-spectrum β-lactamase gene, predominantly blaCTX-M-15 (73.3%, 22/30); the remaining isolates carried either a carbapenemase (blaKPC-3) or an AmpC β-lactamase (blaCMY-2). Nanopore sequencing identified blaCTX-M-15 harbored on two types of IncFIB(Kpn3) antimicrobial resistance (AMR) plasmids, either with or without the conjugative tra gene cluster. Interestingly, the KL1 locus, associated with canonical hypervirulent K. pneumoniae strains, was detected in all ST2059 isolates. Further analysis of public genomic data showed that the KL1 locus is widely distributed across KpSC. KL1 phylogenetic analyses indicated frequent intrasubspecies recombination but limited intersubspecies exchange of KL1. The identification of the dominant MDR K. quasipneumoniae subsp. similipneumoniae KL1-ST2059 clone in the U.S. underscores the importance of ongoing genomic surveillance. IMPORTANCE: Klebsiella quasipneumoniae subsp. similipneumoniae is an underrecognized member of the Klebsiella pneumoniae species complex that is frequently misidentified in clinical laboratories, leading to an incomplete understanding of its role in antimicrobial resistance. In this study, we used large-scale genomic surveillance of community-associated multidrug-resistant isolates across the U.S. to identify this subspecies as a reservoir of clinically relevant resistance plasmids. Notably, we detected a widely distributed ST2059 lineage carrying the K1 capsular locus, a feature traditionally associated with hypervirulent K. pneumoniae. These findings highlight the convergence of resistance and virulence-associated traits in an overlooked species and underscore the need for genomic surveillance to monitor emerging high-risk lineages in community settings.

Drug Resistance, Multiple, Bacterial↗
PubMed2006

Sequence and comparative genomic analysis of lactococcal bacteriophages jj50, 712 and P008: evolutionary insights into the 936 phage species.

The complete genome sequences of three lactococcal 936-type bacteriophages, 712, jj50 and P008, were determined. Comparative genomic analysis of these phages with the previously sequenced 936-type phages, sk1 and bIL170, reveals a strict conservation of the overall genetic organization of this geographically diverse phage group. Genetic divergence was mainly observed in the early expressed region of the phage genomes, where a number of deletions, exchanges and insertions appear to have occurred. These genetic differences may be responsible for the observed differential sensitivity to the lactococcal DNA injection blocking protein, Sie(2009), and the abortive infection system, AbiA.

Bacterial Proteins↗
PubMed1998

A competence regulon in Streptococcus pneumoniae revealed by genomic analysis.

Transformation in bacteria is the uptake and incorporation of exogenous DNA into a cell's genome. Several species transform naturally during a regulated state defined as competence. Genetic elements in Streptococcus pneumoniae induced during transformation were identified by combining a genetic screen with genomic analysis. Six loci were discovered that composed a competence-induced regulon. These loci shared a consensus promoter sequence and encoded proteins, some of which were similar to proteins involved in DNA processing during transformation in other bacteria. Each locus was induced during competence and essential for genetic transformation.

Consensus Sequence↗
PubMed1999

Status of protozoan genome analysis: trypanosomatids.

The three trypanosomatid genome projects have employed common strategies which include: analysis of pulsed-field gel electrophoretic chromosomal karyotypes; physical mapping using big DNA (cosmid, pacmid P1, bacterial artificial chromosome, yeast artificial chromosome) libraries; partial cDNA sequence analysis to develop sets of expressed sequence tags (ESTs) for gene discovery and use as markers in physical mapping; genomic sequencing; dissemination of information through development of web-sites and ACeDB-based fully integrated databases; and establishment of functional genomics programmes to maximize useful application of genome data. Highlights of the projects to date have been the demonstration that, despite extensive chromosomal size polymorphisms for diploid homologues within Africa trypanosomes, T. cruzi or Leishmania, the physical linkage groups for markers on each chromosome are retained across all isolates/species studied within each group. For African trypanosomes, detailed analysis of chromosome 1 has demonstrated that repetitive sequences and the two retroposon-like elements RIME and INGI are localized to a defined region at one end of the chromosome, with the bulk of the central region of the chromosome containing genes coding for expressed proteins. Comparative mapping shows that, although subtelomeric changes account for a large proportion of the polymorphism in chromosome size in African trypanosomes, there are significant expansions and contractions in regions across the entire chromosome. The highlight of the genomic sequencing projects has been the demonstration of just 2 putative transcriptional units of chromosome 1 of Leishmania major, extending on opposite strands from a point in the central region of the chromosome. A similar observation made on 93.4 kb of contiguous sequence for T. cruzi chromosome 3 suggests the presence of promoter and regulatory elements at the junctions of large polycistronic transcriptional units. All data obtained from the genome projects are made available through the public domain, which has prompted changing philosophies in how we approach analysis of the biology of these organisms, and strategies that we can employ now in the search for new therapies and vaccines.

Animals↗
PubMed2006

Genomic analysis of influenza A viruses, including avian flu (H5N1) strains.

This study was designed to conduct genomic analysis in two steps, such as the overall relative synonymous codon usage (RSCU) analysis of the five virus species in the orthomyxoviridae family, and more intensive pattern analysis of the four subtypes of influenza A virus (H1N1, H2N2, H3N2, and H5N1) which were isolated from human population. All the subtypes were categorized by their isolated regions, including Asia, Europe, and Africa, and most of the synonymous codon usage patterns were analyzed by correspondence analysis (CA). As a result, influenza A virus showed the lowest synonymous codon usage bias among the virus species of the orthomyxoviridae family, and influenza B and influenza C virus were followed, while suggesting that influenza A virus might have an advantage in transmitting across the species barrier due to their low codon usage bias. The ENC values of the host-specific HA and NA genes represented their different HA and NA types very well, and this reveals that each influenza A virus subtype uses different codon usage patterns as well as the amino acid compositions. In NP, PA and PB2 genes, most of the virus subtypes showed similar RSCU patterns except for H5N1 and H3N2 (A/HK/1774/1999) subtypes which were suspected to be transmitted across the species barrier, from avian and porcine species to human beings, respectively. This distinguishable synonymous codon usage patterns in non-human origin viruses might be useful in determining the origin of influenza A viruses in genomic levels as well as the serological tests. In this study, all the process, including extracting sequences from GenBank flat file and calculating codon usage values, was conducted by Java codes, and these bioinformatics-related methods may be useful in predicting the evolutionary patterns of pandemic viruses.

Africa↗
PubMed1998

Comparative genome analysis of Bacillus sphaericus by ribotyping, M13 hybridization, and M13 polymerase chain reaction fingerprinting.

A comparative genome analysis of 15 strains representing the five homology groups of the highly heterogeneous species Bacillus sphaericus was performed by M13 hybridization fingerprinting, M13 polymerase chain reaction fingerprinting, and ribotyping with the whole rrn operon. The computer cluster analyses of the polymorphic patterns, presented in dendrograms, showed that these methods allow the differentiation of the individual strains and some homology groups. Our results confirm the close genetic relatedness of the mosquito pathogenic strains of group IIA and support the idea for differentiation of a separate species. At the same time, we present additional proof of the significant genetic heterogeneity of B. sphaericus and the necessity of reconsideration of its present classification.

Bacillus↗