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At least 55 records · Page 3Linked to original sources
PubMed2006

Comparative genomic analysis links karyotypic evolution with genomic evolution in the Indian muntjac (Muntiacus muntjak vaginalis).

The karyotype of Indian muntjacs (Muntiacus muntjak vaginalis) has been greatly shaped by chromosomal fusion, which leads to its lowest diploid number among the extant known mammals. We present, here, comparative results based on draft sequences of 37 bacterial artificial clones (BAC) clones selected by chromosome painting for this special muntjac species. Sequence comparison on these BAC clones uncovered sequence syntenic relationships between the muntjac genome and those of other mammals. We found that the muntjac genome has peculiar features with respect to intron size and evolutionary rates of genes. Inspection of more than 80 pairs of orthologous introns from 15 genes reveals a significant reduction in intron size in the Indian muntjac compared to that of human, mouse, and dog. Evolutionary analysis using 19 genes indicates that the muntjac genes have evolved rapidly compared to other mammals. In addition, we identified and characterized sequence composition of the first BAC clone containing a chromosomal fusion site. Our results shed new light on the genome architecture of the Indian muntjac and suggest that chromosomal rearrangements have been accompanied by other salient genomic changes.

Animals↗
PubMed1995

Sse8387I, a useful eight base cutter for mammalian genome analysis (influence of methylation on the activity of Sse8387I).

To develop restriction enzymes that are useful for genome analysis, we previously performed screening and isolated Sse8387I from Streptomyces sp. strain 8387. Sse8387I is a restriction enzyme that recognizes 5'-CCTGCA/GG-3' and cleaves DNA at the site shown by the diagonal (Nucleic Acid Res., 18, 5637-5640). The present study evaluated the effects of methylation that is important when Sse8387I is used for genome analysis. Sse8387I lost cleavage activity after methylation of adenine or methylation of cytosine at any site in the recognition sequence. However, the recognition sequence of Sse8387I contains no CG sequence, which is the mammalian methylation sequence. In addition, we evaluated the effects of methylation of CG at sites other than the recognition sequence. The cleavage activity of Sse8387I was maintained even when CG sequences were present immediately before or after, or near the recognition sequence, and cytosine was methylated. These results suggest that CG methylation does not affect the cleavage activity of Sse8387I. Therefore, Sse8387I seems to be very useful for mammalian genome analysis.

5-Methylcytosine↗
PubMed1997

Genomic analysis of single cells from human basal cell cancer using laser-assisted capture microscopy.

In this study, we show that direct mutational analysis of genomic DNA can be performed on single somatic cells extracted from a frozen, immunohistochemically stained tissue section using laser-assisted capture microscopy. Eighty-nine single tumor cells were separately dissected from one case of human basal cell cancer (BCC) and p53 mutations were analyzed by direct semi-automated sequencing of PCR fragments. Amplification was obtained for at least one of the two analyzed exons from approximately 50% of the single tumor cells. Identical p53 mutations were found in widely spread areas of the tumor, suggesting a clonal proliferation originating from one cell. Interestingly, comparison between results of immunohistochemistry and genetic analysis of the single cells revealed the same p53 mutations irrespective of the p53 immunoreactivity. We propose that this approach has a great potential to allow investigation of genotypic differences in single cells and more specifically to resolve important and fundamental questions determining cancer heterogeneity.

Aged↗
PubMed1991

Applications of the polymerase chain reaction to genome analysis.

The objectives of the Human Genome Project are to create high-resolution genetic and physical maps, and ultimately to determine the complete nucleotide sequence of the human genome. The result of this initiative will be to localize the estimated 50,000-100,000 human genes, and acquire information that will enable development of a better understanding of the relationship between genome structure and function. To achieve these goals, new methodologies that provide more rapid, efficient, and cost effective means of genomic analysis will be required. From both conceptual and practical perspectives, the polymerase chain reaction (PCR) represents a fundamental technology for genome mapping and sequencing. The availability of PCR has allowed definition of a technically credible form that the final composite map of the human genome will take, as described in the sequence-tagged site proposal. Moreover, applications of PCR have provided efficient approaches for identifying, isolating, mapping, and sequencing DNA, many of which are amenable to automation. The versatility and power provided by PCR have encouraged its involvement in almost every aspect of human genome research, with new applications of PCR being developed on a continual basis.

Base Sequence↗
PubMed2003

Integration of data and methods for genome analysis.

The development of genomic and post-genomic technologies has created an explosion in the quantity, diversity and availability of both biological data and methods of analysis. Biologists are currently facing the problem of using all these resources to convert raw data into new valuable knowledge. This review presents software platforms designed to handle data and/or methods in the context of genome analysis.

Animals↗
PubMed1997

Comparative genomic analysis of isolates belonging to the six species of the genus Thermus using pulsed-field gel electrophoresis and ribotyping.

Fifty isolates belonging to the six validly described species of the genus Thermus (T. aquaticus, T. filiformis, T. thermophilus, T. scotoductus, T. brockianus, and T. oshimai) isolated from hot springs of different geographical areas were compared using macrorestriction analysis of genomic DNA and ribotyping. With the exception of presumed clones, the macrorestriction patterns of isolates obtained with EcoRI or NdeI were distinct. However, isolates belonging to the same species exhibited similar profiles particularly when they were isolated from the same hot spring. The estimated genomic size of strains of the Thermus spp. varied between approximately 1.8 and 2.5 Mbp. Ribotyping with BamHI and HindIII produced 30 and 35 distinct ribotypes, respectively. In spite of the variability of the hybridization patterns produced, the ribotypes obtained for isolates belonging to the same species also shared, in general, several fragments of identical size, and these fragments were similar when isolates originated from the same spring.

Bacterial Typing Techniques↗
PubMed2005

Comparative genome analysis of Bacillus cereus group genomes with Bacillus subtilis.

Genome features of the Bacillus cereus group genomes (representative strains of Bacillus cereus, Bacillus anthracis and Bacillus thuringiensis sub spp. israelensis) were analyzed and compared with the Bacillus subtilis genome. A core set of 1381 protein families among the four Bacillus genomes, with an additional set of 933 families common to the B. cereus group, was identified. Differences in signal transduction pathways, membrane transporters, cell surface structures, cell wall, and S-layer proteins suggesting differences in their phenotype were identified. The B. cereus group has signal transduction systems including a tyrosine kinase related to two-component system histidine kinases from B. subtilis. A model for regulation of the stress responsive sigma factor sigmaB in the B. cereus group different from the well studied regulation in B. subtilis has been proposed. Despite a high degree of chromosomal synteny among these genomes, significant differences in cell wall and spore coat proteins that contribute to the survival and adaptation in specific hosts has been identified.

Bacillus anthracis↗
PubMed1991

Genome analysis of adenovirus type 31 strains from immunocompromised and immunocompetent patients.

Adenovirus type 31 (Ad31) was isolated from 15 immunocompromised patients in 12 of whom seroconversion was also recorded. Ad31 infection has a substantial clinical relevance since 8 of 10 with lower respiratory tract infection and 4 of 4 with hepatitis died. Therefore, Ad31 isolates from immunocompetent and immunodeficient hosts were compared by restriction endonuclease analysis. Nine genome types were identified among the 79 Ad31 isolates. Pairwise comparison of comigrating restriction fragments indicated that the genome types could be divided into three genomic clusters. Several Ad31 genome types were isolated from immunocompromised patients, but no highly virulent genome type could be found. A genome type was identified in a child with severe combined immunodeficiency who originally was infected with another genome type. This observation is suggested to have evolutionary implications.

Adenovirus Infections, Human↗
PubMed1992

[Ethical and social issues on the human genome analysis].

The modern technologies for human genome analysis raise a variety of ethical and social questions. The pre-symptomatic diagnostic of diseases of late expression is becoming possible for a rapidly increasing number of situations. The use of that knowledge by employers, insurance companies, schools, and society in general, could lead to discriminations and stigmatizations, in addition to adverse psychological reactions. DNA fingerprinting raises questions of privacy and personal autonomy in its applications to paternity proof, criminal proceedings, and establishment of data banks. The project of the immediate and complete sequencing of the human genome will lead to questions of economical ethics, as well as of access, commercialization and property rights of scientific information and materials obtained. It also favours a reducionistic mentality and international unbalances. The molecular biology of humans, which will follow the complete sequencing of the genome, may foster a rethinking of the concepts of freedom of self-determination (basic for moral responsibility) and of equality. The gene therapy and its possible extension to the betterment of the human species, pose questions of ethical limits to this technology. All these problems will have to be answered in terms of the application of the principle of ethical freedom for self-fulfillment, as a right of the human person, as well as of science and society. Scientific, economic and social interests have to be subordinated to the dignity of the human person.

DNA Fingerprinting↗
PubMed2003

The ERGO genome analysis and discovery system.

The ERGO (http://ergo.integratedgenomics.com/ERGO/) genome analysis and discovery suite is an integration of biological data from genomics, biochemistry, high-throughput expression profiling, genetics and peer-reviewed journals to achieve a comprehensive analysis of genes and genomes. Far beyond any conventional systems that facilitate functional assignments, ERGO combines pattern-based analysis with comparative genomics by visualizing genes within the context of regulation, expression profiling, phylogenetic clusters, fusion events, networked cellular pathways and chromosomal neighborhoods of other functionally related genes. The result of this multifaceted approach is to provide an extensively curated database of the largest available integration of genomes, with a vast collection of reconstructed cellular pathways spanning all domains of life. Although access to ERGO is provided only under subscription, it is already widely used by the academic community. The current version of the system integrates 500 genomes from all domains of life in various levels of completion, 403 of which are available for subscription.

Animals↗
PubMed2006

Comparative genomic analysis of 18 Pseudomonas aeruginosa bacteriophages.

A genomic analysis of 18 P. aeruginosa phages, including nine newly sequenced DNA genomes, indicates a tremendous reservoir of proteome diversity, with 55% of open reading frames (ORFs) being novel. Comparative sequence analysis and ORF map organization revealed that most of the phages analyzed displayed little relationship to each other.

DNA, Viral↗
PubMed2004

Cross-validation for linear model with unequal variances in genomic analysis.

In recent years, genomic studies are usually conducted to identify genes that may have an impact on clinical outcomes. The identified genes are then used to establish a predictive model for identifying subjects who are most likely to respond to the test treatment in clinical trials. This information is useful in early and later phases of clinical development. The United States Food and Drug Administration (FDA) requires that such a predictive model be validated before it can be used in clinical development. Shao [Shao, J. (1993). Linear model selection by cross-validation. J. Amer. Statist. Assoc. 88(422):486-494] proposed a cross-validation method for linear model with equal variances, which is found useful in genomic studies. In practice, however, genomic data may be obtained from different sources with unequal variances. As a result, Shao's method may not be applied directly. In this paper, we extend Shao's method for cross-validation of a linear model with unequal variances. Along this line, two re-sampling methods were proposed to account for the heterogeneity in variance. Several simulations were performed to evaluate the finite samples performances of the proposed methods. An example concerning a breast cancer research is present to illustrate the use of the proposed methods.

Algorithms↗
PubMed2002

SIGNAL-Sequence Information and GeNomic AnaLysis.

An integrated software package has been developed to provide convenient graphical and textual analysis of a variety of genomic sequence features, free of charge to the biomedical research community. This package, called sequence information and genomic analysis, is available as either a stand-alone or a web-based version to enable greater versatility in access and utilization. The package can be accessed or downloaded at the following URL: http://innovation.swmed.edu/signal.htm.

Algorithms↗
PubMed2026

Whole-Genome Analysis Reveals Antimicrobial Resistance and Population Structure of Environmental and Veterinary Acinetobacter baumannii.

Acinetobacter (A.) baumannii is an important multidrug-resistant pathogen increasingly recognized across animal and environmental settings, and carbapenem-resistant A. baumannii (CRAB) is classified as a critical-priority pathogen by the World Health Organization. This study investigated the antimicrobial resistance (AMR) and genomic characteristics of 122 A. baumannii isolates comprising 72 veterinary and 50 environmental isolates collected in Andhra Pradesh, India. Antimicrobial susceptibility testing, whole-genome sequencing (WGS), resistance and virulence gene profiling, multilocus sequence typing (MLST), core-genome analysis, single nucleotide polymorphism (SNP) phylogeny, and pan-genome analysis were performed. Overall, 58.2% of isolates were multidrug-resistant (MDR), and 41.8% were extensively drug-resistant (XDR). Sequence type (ST) 52 predominated among veterinary isolates, whereas ST2 was more frequent among environmental isolates. The presence of carbapenem-resistant isolates along with the ST2 lineage enhances the similarity to clinical A. baumannii. Several intrinsic resistance genes, including blaOXA-23, armA, aph(3″)-Ib, aph(6)-Id, tet(B), mph(E), and msr(E), were more prevalent in the ST2-associated population. Virulence-associated determinants were widely conserved. Core-genome MLST (cgMLST) and core-genome SNP (cgSNP) analyses identified highly related isolates within both lineages, while pairwise SNP differences were 0-7. Pan-genome analysis identified 4204 gene clusters and distinct accessory gene patterns between ST2 and ST52. These findings indicate that resistance gene distribution was closely associated with lineage structure and support integrated genomic surveillance of A. baumannii across animal and environmental reservoirs.

Acinetobacter baumannii↗
PubMed1999

An archaeal aminoacyl-tRNA synthetase missing from genomic analysis.

The complete genomic sequencing of Methanococcus jannaschii cannot identify the gene for the cysteine-specific member of aminoacyl-tRNA synthetases. However, we show here that enzyme activity is present in the cell lysate of M. jannaschii. The demonstration of this activity suggests a direct pathway for the synthesis of cysteinyl-tRNA(Cys) during protein synthesis.

Amino Acyl-tRNA Synthetases↗
PubMed1994

[Genomic analysis of Japanese patients with adult-type metachromatic leukodystrophy].

We performed the genomic analysis of arylsulfatase A (ASA) gene in five Japanese patients with adult-type metachromatic leukodystrophy (MLD) including two sibling cases. Sequencing of amino acid coding region of ASA gene of proband case of family A disclosed 426Pro (CCG)-->Leu (CTG) mutation, which was reported to be frequently found in Caucasian patients with late-onset MLD. We developed mismatch primer PCR/RFLP method for detection of this mutation. If 426Pro-->Leu mutation exists in genomic DNA, Pst I site is newly created by PCR with a 3'-primer mismatched at one nucleotide. Genomic analysis of family A members using this method revealed that younger patient was homozygote of 426Pro-->Leu mutation and patient's parents and her younger brother were heterozygotes, which were confirmed by sequencing of exon 8 of ASA gene. Screening of this mutation using mismatch primer PCR/RFLP method was performed in one sibling case and one autopsy case. This point mutation was found in the sibling case. These results showed the possibility of world-wide spread of 426Pro-->Leu mutation in late-onset MLD patients and usefulness of our mismatch primer PCR/RFLP method for screening of this mutation.

Adult↗
PubMed2026

Comprehensive genomic and computational insights into Brucella suis: pan-genome analysis, evolutionary perspectives, and in-silico vaccine design.

BACKGROUND: Brucella suis is a zoonotic intracellular pathogen responsible for brucellosis, mainly in swine and humans. Although numerous genome sequences are publicly available, an integrative genomic analysis combining pan-genome architecture, structural organization, evolutionary relationships, and vaccine-associated targets remains limited. RESULTS: In this study, we analyzed 91 publicly available B.suis genomes to characterize their pan-genome composition and genomic structure. The pan-genome exhibited an open configuration, indicating continued genomic diversification. A total of 2,146 core genes were identified, representing conserved functions essential for species maintenance, while the accessory genome reflected strain-level variability. Phylogenetic reconstruction based on single-copy orthologs revealed distinct evolutionary clades among the strains. A complementary phylogenetic analysis of pan-genome gene presence-absence patterns further supported clade differentiation and highlighted variation in accessory gene repertoires. Comparative synteny and genome structural analyses demonstrated largely conserved chromosomal organization with localized rearrangements across strains. Screening of the core proteome identified 64 putative antigenic proteins with predicted surface localization and immunogenic properties. Additionally, resistance-associated determinants related to tetracycline and doxycycline were detected in one genome within the dataset. CONCLUSIONS: This comprehensive genomic analysis defines the pan-genome structure, evolutionary relationships, and genome organization of B.suis. The integration of core and pan-genome-based phylogenies provides complementary insights into strain diversification, while the identified conserved antigenic candidates offer a foundation for future experimental validation and rational vaccine development strategies.

Genome, Bacterial↗
PubMed1999

[Impact of human genome analysis on the future medicine].

The human genome project is considered to be the most important project in biology and medicine. The discovery of an entire human genes through this project should revolutionize biological medicine including molecular diagnosis of various diseases and development of novel treatment. The entire genome DNA sequence is expected to be completed by 2003, and 90% of the genes will be identified by 2001. The information will accelerate discovery of genes susceptible to or causing various diseases and contribute to screening of novel drugs that target these disease-gene products. In addition, the field of "phamacogenetics" will become more important. Phamacogenetic studies focusing on inherited variations in drug metabolism and polymorphisms in drug metabolisms of the genes encoding drug-metabolizing enzymes are also very important to determine an appropriate dose of certain drugs to obtain the maximum effect and avoid serious toxicity. In this regard, the recent world-wide effort of the SNP (single nucleotide polymorphism) project in which scientists attempt to discover 100,000 genetic variations in our genome will generate very variable resources. In this review, I will be describing the recent progress and future direction of human genome analysis and its impact on medicine and pharmacology.

Gene Expression↗