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At least 649 records · Page 36Linked to original sources
PubMed2003

The phylogenetic diversity of eukaryotic transcription.

Eukaryotic transcription is a highly regulated process involving interactions between large numbers of proteins. To analyse the phylogenetic distribution of the components of this process, six crown eukaryote group genomes were queried with a reference set of transcription-associated (TA) proteins. On average, one in 10 proteins encoded by these genomes were found to be homologous to sequences in the reference set. Analysis of families identified using an accurate sequence clustering algorithm and containing both TA proteins and eukaryotic sequences showed that in two-thirds of the families the homologues originate from a single kingdom. Furthermore, in only 15% of the fungal-specific clusters are the homologues present in both budding and fission yeast, as compared with the metazoan-specific clusters where 53% of the homologues originate from two or more species. Families whose members comprise general transcription factor or RNA polymerase subunits exhibit a low degree of taxon specificity, suggesting that the transcription initiation complex is highly conserved. This contrasts with transcriptional regulator families, that are primarily taxon-specific, indicating proteins controlling gene activation exhibit considerable sequence diversity across the eukaryotic domain.

Animals↗
PubMed2004

Gene expression analysis in the hippocampal formation of tree shrews chronically treated with cortisol.

Adrenal corticosteroids influence the function of the hippocampus, the brain structure in which the highest expression of glucocorticoid receptors is found. Chronic high levels of cortisol elicited by stress or through exogenous administration can cause irreversible damage and cognitive deficits. In this study, we searched for genes expressed in the hippocampal formation after chronic cortisol treatment in male tree shrews. Animals were treated orally with cortisol for 28 days. At the end of the experiments, we generated two subtractive hippocampal hybridization libraries from which we sequenced 2,246 expressed sequenced tags (ESTs) potentially regulated by cortisol. To validate this approach further, we selected some of the candidate clones to measure mRNA expression levels in hippocampus using real-time PCR. We found that 66% of the sequences tested (10 of 15) were differentially represented between cortisol-treated and control animals. The complete set of clones was subjected to a bioinformatic analysis, which allowed classification of the ESTs into four different main categories: 1) known proteins or genes (approximately 28%), 2) ESTs previously published in the database (approximately 16%), 3) novel ESTs matching only the reference human or mouse genome (approximately 5%), and 4) sequences that do not match any public database (50%). Interestingly, the last category was the most abundant. Hybridization assays revealed that several of these clones are indeed expressed in hippocampal tissue from tree shrew, human, and/or rat. Therefore, we discovered an extensive inventory of new molecular targets in the hippocampus that serves as a reference for hippocampal transcriptional responses under various conditions. Finally, a detailed analysis of the genomic localization in human and mouse genomes revealed a survey of putative novel splicing variants for several genes of the nervous system.

Animals↗
PubMed2000

Yeast two-hybrid systems and protein interaction mapping projects for yeast and worm.

The availability of complete genome sequences necessitates the development of standardized functional assays to analyse the tens of thousands of predicted gene products in high-throughput experimental settings. Such approaches are collectively referred to as 'functional genomics'. One approach to investigate the properties of a proteome of interest is by systematic analysis of protein-protein interactions. So far, the yeast two-hybrid system is the most commonly used method for large-scale, high-throughput identification of potential protein-protein interactions. Here, we discuss several technical features of variants of the two-hybrid systems in light of data recently obtained from different protein interaction mapping projects for the budding yeast Saccharomyces cerevisiae and the nematode Caenorhabditis elegans.

Animals↗
PubMed2006

Development and evaluation of canine reference genes for accurate quantification of gene expression.

In determining relative gene expression by quantitative measurements of mRNA levels using real-time quantitative PCR, internal standards such as reference genes are essential. Large-scale studies evaluating (candidate) reference genes for veterinary research have not been conducted as thoroughly as for human research, although they are equally important. Our goal was to design and evaluate a genome-wide panel of reference genes from different functional classes. First, primers were optimized using mRNA from canine cell lines and from 30 tissues of one dog as template and SYBR green as fluorescent probe. Second, the expression variation and stability of a gene within one specific tissue were determined. Prostate, kidney, mammary gland, left ventricle, and liver tissues from five to nine dogs of different breeds, sexes, ages, body weights, and disease status were used. Averaging relative stabilities over these tissues revealed the usefulness of individual genes as reference genes. Furthermore, according to expression variation of a reference gene within a specific tissue, usually two to four reference genes are sufficient. Taken together, ribosomal protein S19 (RPS19), ribosomal protein S5 (RPS5), beta-2-microglobulin (B2M), and hypoxanthine phosphoribosyltransferase (HPRT) are advocated. However, the optimal set of reference genes depends on the tissue and should be selected and evaluated for each series of experiments.

Animals↗
PubMed2005

Analysis of CpG methylation in the killifish CYP1A promoter.

Fundulus heteroclitus (Atlantic killifish or mummichog) inhabiting a creosote-contaminated Superfund site on the Elizabeth River (VA, USA), exhibit a lack of induction of cytochrome P4501A (CYP1A) mRNA, immunodetectable protein, and catalytic activity after exposure to typical inducers. This "refractory CYP1A phenotype" is not explained by alterations in mRNA expression of known CYP1A transcription factors. Furthermore, the refractory phenotype is lost progressively during development in laboratory-reared F1 generation fish. Thus, while heritable, the refractory CYP1A phenotype does not appear to be genetically based. To test the hypothesis that cytosine methylation at CpG sites in the promoter region of CYP1A underlies the refractory CYP1A phenotype, we employed bisulfite sequencing to compare the methylation status of CpG sites in the CYP1A promoter region of DNA from killifish from the Elizabeth River and a reference site. We examined genomic DNA both from livers of wild-caught adult killifish and from pools of F1 generation embryos raised in the laboratory. In fish from both the contaminated and the reference site, cytosine methylation was not detectable at any of the 34 CpG sites examined, including 3 that are part of putative xenobiotic response elements.

Animals↗
PubMed2002

Identification of strain-specific genes located outside the plasticity zone in nine clinical isolates of Helicobacter pylori.

Helicobacter pylori is a Gram-negative bacterium that is associated with the development of peptic ulcers and gastric carcinoma in humans. This species appears to be one of the most genetically variable bacteria described to date. The overall level of heterogeneity within strains of this organism was determined by comparing the genome sequences of two reference strains, J99 and 26695. The aim of this study was to measure the genetic diversity within strains of H. pylori by looking for strain-specific genes in nine H. pylori strains isolated from patients suffering from chronic gastritis (n=3), duodenal ulcers (n=3) or gastric cancer (n=3). Seven loci that contained strain-specific genes in strains J99 and 26695 were studied. These regions were subsequently amplified from most of the clinical isolates studied and their sequences were determined. ORFs were predicted from the sequence data and were compared to sequences within the databases. The results showed that the genes flanking the ORFs specific to either strain J99 or strain 26695 were also present in a similar configuration in the genomes of the nine clinical isolates. Moreover, in most regions, ORFs homologous to those found in the corresponding loci in the two reference strains were detected. However, in 10 regions, genes similar to those located at another locus in the genome of J99 or 26695 were found. Finally, six strain-specific genes were identified in three regions of three of the H. pylori strains isolated from patients with duodenal ulcers (n=2) and gastric cancer (n=1). Of these six genes, five were putative genes and one was an orthologue of a gene encoding a transposase in Thermotoga maritima. However, no association with disease was found for these genes.

Gene Amplification↗
PubMed1995

Structural gene analysis of a Quebec reference strain or porcine reproductive and respiratory syndrome virus (PRRSV).

The 3' end genomic region of a Québec PRRSV reference strain (IAF-exp91), propagated in porcine alveolar macrophages (PAM), was sequenced and compared to the prototype European strain, the Lelystad virus (LV). The sequence, which represents the 3'-terminal 2834 nucleotides, encompassed 5 ORFs corresponding to ORFs 3 to 7 of LV. Extensive genomic variations resulting from an important rate of nucleotide additions, substitutions, and deletions were demonstrated between the two viruses. Indeed, the two corresponding sequences displayed a total of 66% and 63% identity at the nucleotide and amino acid levels, respectively. The predicted products of ORFs 5, 3, and 7, showed the highest rate of amino acid variations with percentages of identity of 52, 54, and 59, respectively. Sequence analysis of an additional Québec strain that could be propagated in a continuous cell line (MARC-145), suggested that Québec PRRSV strains belong to a genotype distinct from that of LV, thus confirming previous serological results which allowed to divide PRRSV isolates into two distinct antigenic subgroups (U.S. and European). Six viral major polypeptides with apparent M(rs) of 14.5K, 15K, 19K, 24.5K, 29K, and 42K could be identified from lysates of viral infected cells, of which the 15, 19 and 24.5K species seemed to be structural. In vitro translation products of ORFs 7 and 6 comigrated with the 15 and 19 K viral proteins, whereas that of ORF 5 may be associated to the 24.5K when translated in presence of microsomes. Consequently, it is likely that ORFs 7 to 5, encode the three major structural proteins.

Animals↗
PubMed2004

Use of genome level-informed PCR as a new investigational approach for analysis of outbreak-associated Mycobacterium tuberculosis isolates.

Mycobacterium tuberculosis strain CH, the index isolate linked to a major tuberculosis outbreak associated with high levels of transmissibility and virulence, was characterized by microarray analysis by use of a PCR product array representative of the genome of M. tuberculosis strain H37Rv. Seven potential genomic deletions were identified in CH, five of which were confirmed by PCR analysis across the predicted deletion points. The panel of five PCRs required to individually interrogate these loci was collectively referred to as the genome level-informed PCR (GLIP) assay. GLIP analysis was performed with CH, 12 other epidemiologically linked isolates, and 43 recent, non-outbreak-associated isolates derived from patients within the local area. All 13 outbreak-linked isolates showed a profile corresponding to the presence of all five deletions. These 13 isolates were also found to share common variable-number tandem repeat and mycobacterial interspersed repetitive unit profiles. None of the 43 non-outbreak-associated isolates exhibited the five-deletion profile. Although three individual deletions were present in upwards of 44% of the non-outbreak-associated isolates, no single-deletion isolates were detected. Interestingly, none of these deletions had been previously recognized, and sequence analysis of the immediate flanking regions in CH failed to identify a likely mechanism of deletion for four of the five loci. The GLIP assay also proved valuable in ongoing surveillance of the outbreak, rapidly identifying a further two outbreak-associated cases months after the initial cluster and, importantly, dismissing a further 12 epidemiologically suspect cases, which allowed the optimum deployment of public health resources.

Base Sequence↗
PubMed1985

[Restriction polymorphism of 3 human genomic probes on the short arm of the X chromosome in a reference population, and applications in prenatal and carrier female diagnosis of Duchenne's muscular dystrophy].

Restriction polymorphisms of three human genomic probes (RC8, L1-28 and p754), located on the short arm of the X chromosome, are studied in a French population panel after digestion with taq I and Pst I endonucleases. Informativeness of these three probes in that population are, respectively, 0.18, 0.41 and 0.50. Two kinds of strategies for utilizing these polymorphisms to prenatal and carrier diagnosis of the Duchenne muscular dystrophy (DMD) are given. The last probe available, p754, is of great interest, cumulating advantages that being nearly the DMD gene (3 centiMorgans) and presenting the maximal informativeness theoretically possible.

DNA↗
PubMed2026

ALPAR: automated learning pipeline for antimicrobial resistance.

SUMMARY: The field of machine learning in antimicrobial resistance (AMR) research has experienced rapid growth, fueled by advancements in high-throughput genome sequencing and the growing capacity of computational resources. However, the complexity and lack of standardized data preparation and bioinformatic analyses present significant challenges, especially for newcomers to the domain. In response to these challenges, we introduce ALPAR (Automated Learning Pipeline for Antimicrobial Resistance), a comprehensive AMR data analysis tool covering the entire process from processing of raw genomic data to training machine learning models to interpretation of results. Our method relies on a reproducible pipeline that integrates widely used bioinformatics tools, presenting a simplified, automatic workflow specifically tailored for single-reference AMR analysis. Accepting genomic data in the form of FASTA files as input, ALPAR facilitates the generation of machine learning-ready data tables and both the training of machine learning and the execution of genome-wide association studies (GWAS) experiments. Additionally, our tool offers supplementary functionalities such as phylogeny-based analysis of the distribution of mutations, enhancing its utility for researchers. The tool has also proven its performance in competitive benchmarks, winning the 2024 CAMDA Anti-Microbial Resistance Prediction Challenge and placing third in the 2025 edition. AVAILABILITY AND IMPLEMENTATION: ALPAR is open-source and freely accessible via GitHub (https://github.com/kalininalab/ALPAR). The pipeline is fully reproducible and can be easily installed as a Conda package (https://anaconda.org/kalininalab/ALPAR).

Machine Learning↗
PubMed2004

Pi30 DNA probe may be useful for the identification of Prevotella intermedia at the species or strain level.

Recently, we introduced a new method for the rapid screening of bacterial species-or subspecies-specific DNA probes, named the "inverted dot blot hybridization screening method." This method has subsequently been then applied to develop species-or strain-specific DNA probes for Prevotella intermedia and Prevotella nigrescens. In a previous study, the inverted dot blot hybridization data showed that a probe, Pi30, was specific for P. intermedia. In this study, the DNA probe Pi30 was evaluated by Southern blot analysis to determine if it could distinguish P. intermedia from P. nigrescens. The data showed that the probe Pi30 reacted with the genomic DNAs from the reference strains and clinical isolates of both P. intermedia and P. nigrescens, but the size of the signal bands was different. In addition, the probe Pi30 reacted with a 1.4 kbp fragment from the genomic DNAs digested with Pst I of the P. intermedia strains but not with any fragments of P. nigrescens strains. The result indicates that the probe Pi30 could be useful for the identification of P. intermedia by restriction fragment length polymorphism (RFLP) at the species or strain level.

Bacteroidaceae Infections↗
PubMed1993

Sequence-tagged microsatellite sites as markers in chicken reference and resource populations.

Two chicken genomic libraries were screened for the presence of poly(TG/AC) microsatellite tracts. The number of positive clones was low, confirming the low frequency of such microsatellites in the chicken genome relative to mammalian genomes. Polymorphism of 29 microsatellite tracts, comprising 11 from the library screening and 18 obtained from GenBank, was examined in the East Lansing and Compton reference families, in a resource population formed by a cross between a single White Rock broiler and inbred Leghorn females, and in a panel of birds from five layer stocks. Twenty microsatellites, primarily of the poly(TG/AC) type, were polymorphic in at least one of the populations. Thirteen of the microsatellites were polymorphic in the East Lansing reference family and 13 were also polymorphic in the resource population, confirming that the genetic distance between White Rock and White Leghorn is about as great as between Jungle fowl and White Leghorn. Only six microsatellites were polymorphic in the Compton reference family, formed by a cross between two White Leghorn strains. Twelve of the microsatellites were mapped in the East Lansing and/or Compton reference families. These were well dispersed among the various linkage groups and did not show any indications of terminal clustering.

Animals↗
PubMed2003

Creating a saturated reference map for the apple (Malus x domestica Borkh.) genome.

The availability of a high quality linkage map is essential for the detection and the analysis of quantitative traits. Such a map should cover a significant part of the genome, should be densely populated with markers, and in order to gain the maximum advantage should be transferable to populations or cultivars other than the ones on which it has been constructed. An apple genetic linkage map has been constructed on the basis of a segregating population of the cross between the cultivars Fiesta and Discovery. A total of 840 molecular markers, 475 AFLPs, 235 RAPDs, 129 SSRs and 1 SCAR, were used for the two parental maps constructed with JoinMap and spanning 1,140 cM and 1,450 cM, respectively. Large numbers of codominant markers, like SSRs, enable a rapid transfer of the map to other populations or cultivars, allowing the investigation of any chosen trait in another genetic background. This map is currently the most advanced linkage map in apple with regard to genome coverage and marker density. It represents an ideal starting point for future mapping projects in Malus since the stable and transferable SSR frame of the map can be saturated quickly with dominant AFLP markers.

Automation↗
PubMed1997

Discrimination of Acinetobacter genomic species by AFLP fingerprinting.

AFLP is a novel genomic fingerprinting method based on the selective PCR amplification of restriction fragments. The usability of this method for the differentiation of genomic species in the genus Acinetobacter was investigated. A total of 151 classified strains (representing 18 genomic species, including type, reference, and field strains) and 8 unclassified strains were analyzed. By using a single set of restriction enzymes (HindIII and TaqI) and one particular set of selective PCR primers, all strains could be allocated to the correct genomic species and all groups were properly separated, with minimal intraspecific similarity levels ranging from 29 to 74%. Strains belonging to genomic species 8 (Acinetobacter lwoffii sensu stricto) and 9 grouped together in one cluster. The closely related DNA groups 1 (Acinetobacter calcoaceticus), 2 (Acinetobacter baumannii), 3 and 13TU (sensu Tjernberg & Ursing 1989) were clearly distinguishable, with intraspecific linkage levels above 50%. Strains of the independently described genomic species 13BJ (sensu Bouvet & Jeanjean 1989) and 14TU linked together at a relatively low level (33%). Although a previous DNA-DNA hybridization study seemed to justify the unification of these genomic species, AFLP analysis actually divides the 13BJ-14TU group into three well-separated subgroups. Finally, four unclassified strains obtained from diverse sources and origins grouped convincingly together, with a similarity linkage level of approximately 50%. These strains showed no similarities in their AFLP patterns with any of the other 155 strains studied and may represent a thus-far-undescribed Acinetobacter species. Based on these results, AFLP should be regarded as an important auxiliary method for the delineation of genomic species. Furthermore, because AFLP provides a detailed insight into the infraspecific structure of Acinetobacter taxa, the method also represents a highly effective means for the confirmation of strain identity in the epidemiology of acinetobacters.

Acinetobacter↗
PubMed2005

[Meiotic recombination hotspots in eukaryotes].

Meiotic recombination may occur more frequently in some regions of the eukaryotic genome. These regions are referred to as meiotic recombination hotspot loci. Genetic studies in the yeast have revealed that these hotspots contain special sites for recombination initiation and result in heterogeneous distribution of recombination (along the chromosome length or across the genome). However, the data for recombination hotspot is so far limited to organisms such as fungi, maize and human. In the present paper, we listed several typical approaches to characterizing recombination hotspots in different organisms, summarizing current progress in mapping of the meiotic recombination hotspots and discussing the factors and mechanisms for activation of eukaryotic meiotic recombination. Some unresolved questions and future prospects were also discussed.

Animals↗
PubMed2026

Genomes of the ex-type strains of Elsinoë mangiferae and E. perseae, the causal agents of scab on mango and avocado.

Elsinoë species are slow-growing, hemibiotrophic to necrotrophic fungi that cause scab diseases on economically important fruit crops. Genome resources for many host-specific species remain limited. We report high-quality draft genome assemblies for the ex-type strains of Elsinoë mangiferae (CBS 226.50) and E. perseae (CBS 406.34), causal agents of mango and avocado scab, respectively. Among 5 approaches tested, a Nanopore-only NextDenovo assembly produced the most contiguous genomes, yielding 24.5 Mb (E. mangiferae) and 25.1 Mb (E. perseae) assemblies with 13 and 18 contigs, respectively, BUSCO completeness scores of ∼94%, and multiple putative telomere-to-telomere chromosomes. Gene prediction identified 9,134 and 9,243 genes, respectively. Functional annotation revealed enrichment of metabolic and regulatory pathways, including those involved in posttranslational modification, protein transport, and secondary metabolism. Carbohydrate-active enzyme repertoires were small but conserved, consistent with stealth pathogenicity strategies and low plant cell wall degradation. Both genomes encoded large secretomes (>850 proteins), diverse protease repertoires (>300 proteins), Ecp2-like effector proteins, and multiple biosynthetic gene clusters, including clusters with similarity to those associated with elsinochrome and ACT-toxin II biosynthesis, some of which may contribute to host-pathogen interactions and disease development. A large fraction of genes lacked functional characterization, suggesting incomplete databases and/or the presence of lineage-specific genes potentially involved in virulence or host adaptation. These genome resources fill critical gaps for underrepresented Elsinoë species and provide taxonomically anchored references essential for diagnostics, comparative genomics, and research into the molecular basis of host specificity and pathogenicity in scab-causing fungi.

Persea↗
PubMed1996

Mapping the Trypanosoma cruzi genome: analyses of representative cosmid libraries.

In order to generate contiguous cosmid coverage of the genome of the protozoan parasite Trypanosoma cruzi for large-scale sequence analysis, a cosmid library of 36864 individual, primary clones was generated. Total genomic DNA of the reference strain CL Brener was fragmented both by partial digestion with MboI and by physical shearing. For cloning, a modified cosmid vector was used that simplifies analyses such as restriction mapping. The library's representation is about 25 genome equivalents, assuming a size of 55 Mb per haploid genome. No chimerism of inserts in the clones could be detected. The colinearity between cosmid inserts and genomic DNA was verified. Also, hybridizations to the gel-separated karyotype of the organism were carried out as a quality check. Gridded onto two nylon filters, the library was analyzed with a variety of probes. Apart from being used for combined physical and transcriptional mapping of the genome, library filters and clones are also available to interested parties.

Animals↗