Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Genome analysis”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 163 records · Page 9Linked to original sources
PubMed2004

Possibilities and results in the wide-scale genomic analysis of inflammation. Looking for the child among many midwives.

Only recently, available microarray methods have been extended to the investigation of such complex pathophysiological conditions as inflammatory disease. Genome analysis gives the possibility of looking for susceptibility gene loci and their allelic combinations. By the analysis of mRNAs (transcriptome), novel players, functional groups of participants and regulatory pathways involved in the inflammation can be revealed. The possibility of comparing several samples is ideal to increase our knowledge about the kinetics of inflammation. The effects and post-receptor signalling events of individual pro- or anti-inflammatory mediators can also be tested. The use of human post mortem samples could yield otherwise inaccessible information on molecular mechanisms of chronic inflammatory diseases. However, the analysis and interpretation of a huge amount of data, the selection of appropriate experimental systems and time points may hide some pitfalls, which emphasize the need to confirm results with independent methods such as e.g. semi-quantitative Northern, real time PCR, RNA-ase protection assay as well as functional studies.

Acute-Phase Reaction↗
PubMed1995

Application of fluorescence in situ hybridization in genome analysis of the mouse.

Fluorescence in situ hybridization (FISH) is an effective technique for localizing cloned DNA probes directly onto metaphase chromosomes. Human genome mapping using FISH has been significantly enhanced by the development of new techniques, especially high-resolution gene mapping with direct R-banding FISH and physical gene ordering with multi-color FISH. By contrast, FISH techniques have not been put to practical use for the analysis of the mouse genome compared with the human. We have developed and modified FISH techniques for use in mouse genome analysis. In this article we summarize and review our recent results with FISH analyses in the following studies: (i) high-resolution gene mapping with the direct R-banding FISH, (ii) analysis of chromosomal rearrangement with multi-color FISH, (iii) establishment of centromere mapping with the major satellite DNA probe, (iv) analysis of chromatin structure in meiotic cells, and (v) application of FISH in cytogenetic studies of genetic variation in the mouse, showing that these applications of FISH are very useful for mouse genome analysis.

Animals↗
PubMed2003

[A new dimension of DNA analysis: genomic profiling by matrix CGH].

Analysis of genetic alterations in tumor cells represent a first step to understand the molecular mechanism of cancer etiology and development. Due to the progress in genome research, it is feasible to assess the complexity of genomic changes on a large scale. Protocols for gene expression profiling using cDNA arrays have been developed allowing to test the activity of almost all human genes in tumor cells. Another important approach is matrix-CGH which was recently developed to assess gains and losses on the genomic level with high resolution. This method not only allows to narrow down the position of novel oncogenes or tumor suppressor-genes but also contributes to a refinement of tumor classifications. Since matrix-CGH can be performed under highly standardized conditions in a fully automatized way, it is suited for diagnostics in clinical laboratories.

Chromosome Aberrations↗
PubMed1992

Genomic analysis of Pediococcus starter cultures used to control Listeria monocytogenes in turkey summer sausage.

The pulsed-field technique of clamped homogeneous electric field electrophoresis was employed to characterize and size genomic DNA of three pediocin-producing (Ped+) and two non-pediocin-producing (Ped-) strains of Pediococcus acidilactici. Comparison of genomic fingerprints obtained by digestion with the low-frequency-cleavage endonuclease AscI revealed identical restriction profiles for four of the five strains analyzed. Summation of results for 10 individually sized AscI fragments estimated the genome length to be 1,861 kb for the four strains (H, PAC1.0, PO2, and JBL1350) with identical fingerprints. Genomic analysis of the pediocin-sensitive, plasmid-free strain P. acidilactici LB42 with the unique fingerprint revealed nine AscI fragments and a genome length of about 2,133 kb. Ped- (JBL1350) and Ped+ (JBL1095) starter cultures (one each) were used to separately prepare turkey summer sausage coinoculated with a four-strain Listeria monocytogenes mixture (ca. 10(5) CFU/g). The starter cultures produced equivalent amounts of acid during fermentation, but counts of L. monocytogenes were reduced to a greater extent in the presence of the Ped+ starter culture (3.4 log10 unit decrease) than in the presence of the Ped- starter culture (0.9 log10 unit decrease). Although no listeriae were recovered from sausages following the cook/shower, appreciable pediocin activity was recovered from sausages prepared with the Ped+ strain for at least 60 days during storage at 4 degrees C. The results of this study revealed genomic similarities among pediococcal starter cultures and established that pediocins produced during fermentation provide an additional measure of safety against listerial proliferation in turkey summer sausage.

Acids↗
PubMed2003

Genome analysis technologies: towards species identification by genotype.

Traditional identification of species has been based on phenotypic traits, although it is clear that, theoretically, genotype-based classification is more accurate. This is especially the case for microorganisms which possess less identifiable traits and are more easily influenced by environment. Therefore, technology that allows identification of species based on genotype is highly desirable. Whole genome sequencing can provide a sufficient amount of information and can be determinative for this purpose but is very impractical for routine use. Thus, a competent technology is needed that allows a reproducible reduction in the amount of information required about a whole genome, while still providing sufficiently accurate identification. It is almost imperative for such a technology to be of a high cost-performance and of easy handling. Universality and portability are also strongly desired. Based on these criteria, the current state of genome analysis technologies are reviewed. Among various methodologies discussed here, amplified fragment length polymorphism (AFLP), genome profiling (GP) and microarrays are the subject of particular attention. As species identification is a base for most fields of biology including microbiology, ecology, epidemiology and for various biotechnologies, it is of paramount importance to establish a more efficient, easily handled and more objective methodology, in parallel with conventional phenotype-based methodologies. GP is currently considered to have the most optimal nature for identification of species since it can reproducibly reduce a huge amount of genome information to a manageable size by way of random polymerase chain reaction and can extract a sufficient amount of information for species identification from the DNA fragments thus profiled by temperature gradient gel electrophoresis. The potential ability of DNA microarrays for this purpose is also discussed and promises much for the future.

Genome↗
PubMed2025

Pan-Genome Analysis Reveals Local Adaptation to Climate Driven by Introgression in Oak Species.

The genetic base of local adaptation has been extensively studied in natural populations. However, a comprehensive genome-wide perspective on the contribution of structural variants (SVs) and adaptive introgression to local adaptation remains limited. In this study, we performed de novo assembly and annotation of 22 representative accessions of Quercus variabilis, identifying a total of 543,372 SVs. These SVs play crucial roles in shaping genomic structure and influencing gene expression. By analyzing range-wide genomic data, we identified both SNPs and SVs associated with local adaptation in Q. variabilis and Quercus acutissima. Notably, SV-outliers exhibit selection signals that did not overlap with SNP-outliers, indicating that SNP-based analyses may not detect the same candidate genes associated with SV-outliers. Remarkably, 29%-37% of candidate SNPs were located in a 250 kb region on chromosome 9, referred to as Chr9-ERF. This region contains 8 duplicated ethylene-responsive factor (ERF) genes, which may have contributed to local adaptation of Q. variabilis and Q. acutissima. We also found that a considerable number of candidate SNPs were shared between Q. variabilis and Q. acutissima in the Chr9-ERF region, suggesting a pattern of repeated selection. We further demonstrated that advantageous variants in this region were introgressed from western populations of Q. acutissima into Q. variabilis, providing compelling evidence that introgression facilitates local adaptation. This study offers a valuable genomic resource for future studies on oak species and highlights the importance of pan-genome analysis in understating mechanism driving adaptation and evolution.

Quercus↗
PubMed2006

Genome analysis and phylogenetic relationships between east, central and west African isolates of Yellow fever virus.

Yellow fever virus (YFV), a reemerging disease agent in Africa and South America, is the prototype member of the genus Flavivirus. Based on examination of the prM/M, E and 3' non-coding regions of the YFV genome, previous studies have identified seven genotypes of YFV, including the Angolan, east/central African and east African genotypes, which are highly divergent from the prototype strain Asibi. In this study, full genome analysis was used to expand upon these genetic relationships as well as on the very limited full genome database for YFV. This study was the first to investigate genomic sequences of YFV strains from east and central Africa (Angola71, Uganda48a and Ethiopia61b). All three viruses had genomes of 10 823 nt in length. Compared with the prototype strain Asibi (from west Africa) they were approximately 25 % divergent in nucleotide sequence and 7 % divergent in amino acid sequence. Comparison of multiple flaviviruses in the N-terminal region of NS4B showed that amino acid sequences were variable and that west African strains of YFV had an amino acid deletion at residue 21. Additionally, N-linked glycosylation sites were conserved between viral genotypes, while codon usage varied between strains.

Africa, Central↗
PubMed1995

Parallel genome analysis by one- and two-dimensional DNA fingerprinting in human gliomas.

The detection of DNA variation in cancers is an important step in elucidating the mechanism of tumorigenesis. Using the strategy of multipoint genome analysis we detected many differences between glioma-derived and constitutional DNA by customary DNA fingerprinting with simple repetitive oligonucleotide probes. Amplification of the epidermal growth factor receptor (EGFR) gene has been found to be easily detectable as new or highly intensified bands in one-dimensional (1-D) DNA fingerprints of glioblastoma DNA generated with probes (GTG)5 or (GT)8. However, in most low-grade astrocytomas, 1-D DNA fingerprinting has failed to reveal any genomic abnormalities. In these cases a two-dimensional (2-D) technique was successfully employed that is based on size separation in neutral gels followed by sequence-dependent separation in denaturing gradient gels and hybridization with several mini- and microsatellite core probes. The hundreds of spots visualized with this technique were used to detect subtle changes probably occurring as the initial steps of tumorigenesis in human gliomas. On average, five of the approximately 580 spots generated by probes CAC and 33.6 were found to be altered in tumor DNA; 80% of the alterations were spot losses, the rest being spot gains or amplifications. Computer-based image analysis using an external lambda marker provided a stringent way to compare spot patterns generated by 2-D DNA fingerprinting. In comparisons performed between typing patterns generated on the same gel, 99% of truly identical spots were confirmed by the software. In intergel comparisons 84% of identical spots were matched on the basis of the marker information alone.

Base Sequence↗
PubMed2025

Joint, multifaceted genomic analysis enables diagnosis of diverse, ultra-rare monogenic presentations.

Genomics for rare disease diagnosis has advanced at a rapid pace due to our ability to perform in-depth analyses on individual patients with ultra-rare diseases. The increasing sizes of ultra-rare disease cohorts internationally newly enables cohort-wide analyses for new discoveries, but well-calibrated statistical genetics approaches for jointly analyzing these patients are still under development. The Undiagnosed Diseases Network (UDN) brings multiple clinical, research and experimental centers under the same umbrella across the United States to facilitate and scale case-based diagnostic analyses. Here, we present the first joint analysis of whole genome sequencing data of UDN patients across the network. We introduce new, well-calibrated statistical methods for prioritizing disease genes with de novo recurrence and compound heterozygosity. We also detect pathways enriched with candidate and known diagnostic genes. Our computational analysis, coupled with a systematic clinical review, recapitulated known diagnoses and revealed new disease associations. We further release a software package, RaMeDiES, enabling automated cross-analysis of deidentified sequenced cohorts for new diagnostic and research discoveries. Gene-level findings and variant-level information across the cohort are available in a public-facing browser ( https://dbmi-bgm.github.io/udn-browser/ ). These results show that case-level diagnostic efforts should be supplemented by a joint genomic analysis across cohorts.

Humans↗
PubMed2002

Genomic analysis of uncultured marine viral communities.

Viruses are the most common biological entities in the oceans by an order of magnitude. However, very little is known about their diversity. Here we report a genomic analysis of two uncultured marine viral communities. Over 65% of the sequences were not significantly similar to previously reported sequences, suggesting that much of the diversity is previously uncharacterized. The most common significant hits among the known sequences were to viruses. The viral hits included sequences from all of the major families of dsDNA tailed phages, as well as some algal viruses. Several independent mathematical models based on the observed number of contigs predicted that the most abundant viral genome comprised 2-3% of the total population in both communities, which was estimated to contain between 374 and 7,114 viral types. Overall, diversity of the viral communities was extremely high. The results also showed that it would be possible to sequence the entire genome of an uncultured marine viral community.

Bacteriophages↗
PubMed2026

Spatiotemporal genomic analysis and risk assessment of the plasmids carrying blaOXA-48-like genes based on a large-scale international dataset.

BACKGROUND: The spread of OXA-48-like carbapenemases represents a major public health challenge. Although previous studies have investigated OXA-48-like carbapenemases risk factors, nosocomial dissemination, and plasmid dynamics, an integrated plasmid-centered framework combining complete plasmid mining, transmission-unit analysis, phylogenetic reconstruction, and machine learning-based risk assessment remains limited. METHODS: We systematically collected 747 complete plasmid sequences carrying blaOXA-48-like genes from the NCBI database, establishing the largest collections of complete plasmid sequences to date. Using an integrative framework of population genomics, phylogenetic dating, and machine learning, this study aimed to characterize the dissemination patterns, plasmid replicon diversity, transmission units, mobile genetic elements, co-resistance profiles, and risk classification of these plasmid. RESULTS: Plasmids carrying blaOXA-48-like genes were detected across 50 countries on six continents, with blaOXA-48 predominating in Europe, blaOXA-181 in South Asia, and blaOXA-232 largely in Asia. IncL and ColKP3/IncX3 replicons, together with Tn1999.2 and other MGEs, were central drivers of plasmid maintenance and spread. Sixteen transmission units were defined, with AA068_Cluster3 estimated to have originated in the Netherlands around 2005 before expanding to Europe, the Middle East, Asia, and North America. Co-resistance analyses revealed frequent modules involving aminoglycoside and quinolone resistance, with qnrS1 and aph(3'')-Ib most prevalent. Notably, high-risk transposon structures were often identified in non-clinical environments, underscoring their cross-ecological transmission potential. Machine learning-based classification models showed good internal performance for predefined composite-risk categories, with plasmid mobility, clinical/non-clinical source composition, and host background contributing to the classification results. CONCLUSIONS: This study provides a large-scale plasmid-centered genomic analysis of publicly available complete plasmid sequences carrying blaOXA-48-like genes, integrating transmission-unit inference, phylogeographic reconstruction, mobile genetic element and co-resistance profiling, and composite genomic risk stratification. This gene-centered framework may support future One Health-oriented antimicrobial resistance surveillance and prioritization of plasmids with higher dissemination and resistance potential.

Plasmids↗
PubMed2003

Genome analysis of F. nucleatum sub spp vincentii and its comparison with the genome of F. nucleatum ATCC 25586.

We present the draft genome sequence and its analysis for Fusobacterium nucleatum sub spp. vincentii (FNV), and compare that genome with F. nucleatum ATCC 25586 (FN). A total of 441 FNV open reading frames (ORFs) with no orthologs in FN have been identified. Of these, 118 ORFs have no known function and are unique to FNV, whereas 323 ORFs have functional orthologs in other organisms. In addition to the excretion of butyrate, H2S and ammonia-like FN, FNV has the additional capability to excrete lactate and aminobutyrate. Unlike FN, FNV is likely to incorporate galactopyranose, galacturonate, and sialic acid into its O-antigen. It appears to transport ferrous iron by an anaerobic ferrous transporter. Genes for eukaryotic type serine/threonine kinase and phosphatase, transpeptidase E-transglycosylase Pbp1A are found in FNV but not in FN. Unique ABC transporters, cryptic phages, and three types of restriction-modification systems have been identified in FNV. ORFs for ethanolamine utilization, thermostable carboxypeptidase, gamma glutamyl-transpeptidase, and deblocking aminopeptidases are absent from FNV. FNV, like FN, lacks the classical catalase-peroxidase system, but thioredoxin/glutaredoxin enzymes might alleviate oxidative stress. Genes for resistance to antibiotics such as acriflavin, bacitracin, bleomycin, daunorubicin, florfenicol, and other general multidrug resistance are present. These capabilities allow Fusobacteria to survive in a mixed culture in the mouth.

ATP-Binding Cassette Transporters↗
PubMed1998

Purification of Cowdria ruminantium organisms for use in genome analysis by pulsed-field gel electrophoresis.

Cowdria ruminantium is an obligate intracellular rickettsial pathogen which is responsible for a tick-borne disease of domestic and wild ruminants called heartwater or cowdriosis. Although several genes have been cloned and partially sequenced, the genome size, gross structure, and organization of the C. ruminantium genome is unknown. Genome analysis of the organism has been hindered because it is difficult to obtain C. ruminantium DNA free from contaminating host cell DNA, and this probably accounts for the lack of genome size data for this organism. In this study we investigated several methods for purifying C. ruminantium from bovine cellular contaminants and organisms of a relatively high purity were obtained. These were used to prepare Cowdria DNA which was analyzed by pulsed-field gel electrophoresis (PFGE) and which revealed a genome approximately 1900 kbp in length plus an additional extra-chromosomal fragment migrating with an apparent size of 815 kbp. This is the first time that the genome size of C. ruminantium has been determined and the first demonstration of an extrachromosomal element.

Animals↗
PubMed2006

Population genomic analysis of outcrossing and recombination in yeast.

The budding yeast Saccharomyces cerevisiae has been used by humans for millennia to make wine, beer and bread. More recently, it became a key model organism for studies of eukaryotic biology and for genomic analysis. However, relatively little is known about the natural lifestyle and population genetics of yeast. One major question is whether genetically diverse yeast strains mate and recombine in the wild. We developed a method to infer the evolutionary history of a species from genome sequences of multiple individuals and applied it to whole-genome sequence data from three strains of Saccharomyces cerevisiae and the sister species Saccharomyces paradoxus. We observed a pattern of sequence variation among yeast strains in which ancestral recombination events lead to a mosaic of segments with shared genealogy. Based on sequence divergence and the inferred median size of shared segments (approximately 2,000 bp), we estimated that although any two strains have undergone approximately 16 million cell divisions since their last common ancestor, only 314 outcrossing events have occurred during this time (roughly one every 50,000 divisions). Local correlations in polymorphism rates indicate that linkage disequilibrium in yeast should extend over kilobases. Our results provide the initial foundation for population studies of association between genotype and phenotype in S. cerevisiae.

Crosses, Genetic↗
PubMed1997

Proteome analysis: genomics via the output rather than the input code.

A knowledge of the 'proteome,' total protein output encoded by a genome, provides information on (1) if and when predicted gene products are translated, (2) the relative concentrations of gene products, and (3) the extent of posttranslational modification, none of which can be accurately predicted from the nucleic acid sequence alone. The current status of proteome analysis is reviewed with respect to some of the techniques employed, automation, relevance to genomic studies, mass spectrometry and bioinformatics, limitations, and recent improvements in resolution and sensitivity for the detection of protein expression in whole cells, tissues, or organisms. The concept of 'proteomic contigs' is introduced for the first time. Traditional approaches to genomic analysis call upon a number of strategies to produce contiguous DNA sequence information, while 'proteomic contigs' are derived from multiple molecular mass and isoelectric point windows in order to construct a picture of the total protein expression within living cells. In higher eukaryotes, the latter may require several dozen image subsets of protein spots to be stitched together using advanced image analysis. The utility of both experimental and theoretical peptide-mass fingerprinting (PMF) and associated bioinformatics is outlined. A previously unknown motif within the peptide sequence of Elongation Factor Tu from Thermus aquaticus was discovered using PMF. This motif was shown to possess potential significance in maintaining structural integrity of the entire molecule.

DNA↗
PubMed2006

Whole genome analysis of non-optimal codon usage in secretory signal sequences of Streptomyces coelicolor.

Non-optimal (rare) codons have been suggested to reduce translation rate and facilitate secretion in Escherichia coli. In this study, the complete genome analysis of non-optimal codon usage in secretory signal sequences and non-secretory sequences of Streptomyces coelicolor was performed. The result showed that there was a higher proportion of non-optimal codons in secretory signal sequences than in non-secretory sequences. The increased tendency was more obvious when tested with the experimental data of secretory proteins from proteomics analysis. Some non-optimal codons for Arg (AGA, CGU and CGA), Ile (AUA) and Lys (AAA) were significantly over presented in the secretary signal sequences. It may reveal that a balanced non-optimal codon usage was necessary for protein secretion and expression in Streptomyces.

Base Sequence↗
PubMed2005

Recent advances in the genomic analysis of Candida albicans.

The release of the diploid genomic sequence of Candida albicans and its recent community-based annotation have permitted a number of studies which have significantly advanced our understanding of the biology of this important human pathogen. These advances range from analysis of genomic changes to differential gene expression under a variety of conditions. A few general conclusions can be drawn from the data presently in hand; one can expect more and more new insights as the number and kind of experiments grows.

Candida albicans↗
PubMed2006

Comparative genomic analysis of two strains of human adenovirus type 3 isolated from children with acute respiratory infection in southern China.

Human adenovirus type 3 (HAdV-3) is a causative agent of acute respiratory disease, which is prevalent throughout the world, especially in Asia. Here, the complete genome sequences of two field strains of HAdV-3 (strains GZ1 and GZ2) isolated from children with acute respiratory infection in southern China are reported (GenBank accession nos DQ099432 and DQ105654, respectively). The genomes were 35,273 bp (GZ1) and 35,269 bp (GZ2) and both had a G+C content of 51 mol%. They shared 99% nucleotide identity and the four early and five late regions that are characteristic of human adenoviruses. Thirty-nine protein- and two RNA-coding sequences were identified in the genome sequences of both strains. Protein pX had a predicted molecular mass of 8.3 kDa in strain GZ1; this was lower (7.6 kDa) in strain GZ2. Both strains contained 10 short inverted repeats, in addition to their inverted terminal repeats (111 bp). Comparative whole-genome analysis revealed 93 mismatches and four insertions/deletions between the two strains. Strain GZ1 infection produced a typical cytopathic effect, whereas strain GZ2 did not; non-synonymous substitutions in proteins of GZ2 may be responsible for this difference.

Acute Disease↗