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At least 649 records · Page 36Linked to original sources
PubMed2006

Identification of cDNAs encoding pterocarpan reductase involved in isoflavan phytoalexin biosynthesis in Lotus japonicus by EST mining.

Isoflavans and pterocarpans are the major biosynthetically connected phytoalexins in legumes. A search of the expressed sequence tag library of a model legume Lotus japonicus, which produces an (-)-isoflavan, for homologs of phenylcoumaran benzylic ether reductase catalyzing the reductive cleavage of dihydrofurans, yielded seven full-length cDNAs, and the encoded proteins were analyzed in vitro. Four of them cleaved the dihydrofuran of a pterocarpan medicarpin to yield an isoflavan (-)-vestitol and were designated pterocarpan reductase (PTR). Two PTRs displayed enantiospecificity to (-)-medicarpin, representing genuine L. japonicus PTRs, while the other two lacked enantiospecificity and were presumed to be evolutionarily primitive types.

DNA, Complementary↗
PubMed2004

Characterization of SCAR markers of Eimeria spp. of domestic fowl and construction of a public relational database (The Eimeria SCARdb).

This study reports the development and characterization of 151 sequence characterized amplified region (SCAR) markers for the seven Eimeria species that infect the domestic fowl. From this set, 84 markers are species-specific and 67 present partial specificity. The complete nucleotide sequence was derived for all markers, revealing the presence of micro- and minisatellite repetitive units in 22 SCARs, with up to five distinct repeat units being observed per marker. Only 15 markers showed significant hits in similarity searches against public sequence databases, thus confirming their anonymous and non-coding character. Finally, a relational database of the markers (the Eimeria SCARdb) was developed and made available on the Internet, providing a valuable resource of SCAR markers that can be useful for molecular diagnosis, and also for epizootiological, genetic variability and genome mapping studies.

Animals↗
PubMed2005

Identification of strain specific markers in Bacillus anthracis by random amplification of polymorphic DNA.

Classification and differentiation of Bacillus anthracis isolates by genetic markers play an important role in anthrax research. We used a PCR based method--Random Amplification of Polymorphic DNA (RAPD)--to identify genetic markers in B. anthracis strains. Twenty-five differential genetic markers were identified which divided the strains into five different groups. Three selected RAPD-markers were cloned and sequenced. The five RAPD-derived genotypes could be defined by integration of these three markers. This system offers a simple non-expensive method to classify B. anthracis strains in laboratories involved in the research of this bacterium.

Bacillus↗
PubMed2005

Comparative and functional genomics of lactococci.

Whole-genome nucleotide sequencing has revolutionized the genetic, biochemical and molecular biology research on bacteria and indeed, many higher organisms. The genome sequences of the strains of two subspecies of Lactococcus lactis, L. lactis subsp. lactis and L. lactis subsp. cremoris, have been determined. These genomic sequences have permitted two important new approaches to be applied in the research of L. lactis. The analysis of the regulation of expression of all genes under specific circumstances at a given point in time is now possible by DNA microarray technology. The elucidation of the full protein complement of the organism as a function of intrinsic or external factors has been made possible by high-throughput protein identification and analysis techniques combined with the gene-derived know-how of the total protein encoding capacity of the genome. These techniques from the genomics arena, transcriptomics and proteomics, have been recently implemented in the study of various aspects of growth and functioning of L. lactis. In this paper we discuss a number of similarities and differences between the two lactococcal genome sequences and review the current status of genomics research in L. lactis. We also propose future directions with respect to both answering fundamental questions more quickly and more completely, as well as opening new avenues for biotechnological applications.

DNA Transposable Elements↗
PubMed2006

Reevaluation of azoospermic factor c microdeletions using sequence-tagged site markers with confirmed physical positions from the GenBank database.

OBJECTIVE: To investigate microdeletions and palindrome complexes in the azoospermic factor (AZF) c regions of the Y chromosome, by polymerase chain reaction (PCR) with sequence-tagged site (STS) markers with known physical positions, after verification of the exact physical locations of candidate STSs and exclusion of those that would give ambiguous results on PCR. DESIGN: Retrospective STS deletion study in infertile Japanese men. SETTING: University hospital and reproductive clinic. PATIENT(S): A total of 410 men with nonobstructive azoospermia and severe oligospermia (sperm concentrations of <5 x 10(6)/mL). INTERVENTION(S): Polymerase chain reaction was performed for all STS markers confirmed to be physically located in the partial AZFb and AZFc regions of the Y chromosome. All STSs were retrieved from the University of California at Santa Cruz database, and their location and specificity were verified. MAIN OUTCOME MEASURE(S): Presence or absence of appropriately sized PCR products. RESULT(S): Sixty-nine markers were retrieved, 32 of which were not specific to the long arm of the Y chromosome (Yq). The markers retained for test use were contiguous deletions classified as P1+P2 (AZFc) or P3 proximal/P1 (AZFb+c). The prevalence of accurately mapped microdeletions was 5.1% (21 of 410) in this patient population. CONCLUSION(S): Although noncontiguous deletions were observed, considerable confusion remained until the genome sequence was finally determined because many of the STSs were either repetitive sequences or polymorphic between individuals or races.

Animals↗
PubMed2003

The development of simple sequence repeat markers for Magnaporthe grisea and their integration into an established genetic linkage map.

Although microsatellite or simple sequence repeat (SSR) markers have several advantages, few have been developed in fungi. The goal of this study was to identify and characterize SSR-containing loci in the filamentous ascomycete Magnaporthe grisea, the causal agent of rice blast disease, and to add these markers to an integrated genetic map of this species [Theor. Appl. Genet. 95 (1997) 20]. We have constructed and screened a microsatellite-enriched small-insert genomic library as well as exploited both publicly available and one proprietary databases for identification of M. grisea SSR containing sequences. Twenty-four out of 49 primer pairs designed to amplify SSR, produced unambiguous polymorphic products in our test population of six isolates. The number of alleles at each locus ranged from two to six when assayed on 3% agarose gels. Twenty-three of the primer pairs amplified polymorphic products between Guy11 and 2539, the parents of a cross from which a genetic map for M. grisea has been established. Genetic analysis showed that all the markers segregated in the expected 1:1 ratio and map positions were determined for all 23 loci.

Base Sequence↗
PubMed2004

A comparison of the nature and abundance of microsatellites in 14 fungal genomes.

An overview of the character of microsatellites in 14 fungal genomes was obtained by analyzing databases containing complete or nearly complete genome sequences. Low GC content, rather than genome size, was the best predictor of high microsatellite density, although very long iterations of tandem repeats were less common in small genomes. Motif type correlated with %GC in that low-GC genomes were more likely to be dominated by A/T-rich motifs, and vice versa, although some exceptions were noted. The experimentally useful dinucleotide and trinucleotide arrays were analyzed in greater detail. Although these varied in sequence and length among fungal species, some that are likely to be universally useful were identified. This information will be useful for researchers wanting to identify the most useful microsatellites to analyze for the fungi included in this survey and provides a platform for choosing microsatellites to target in fungi that are not yet sequenced.

Base Sequence↗
PubMed2005

An oligonucleotide barcode for species identification in Trichoderma and Hypocrea.

One of the biggest obstructions to studies on Trichoderma has been the incorrect and confused application of species names to isolates used in industry, biocontrol of plant pathogens and ecological surveys, thereby making the comparison of results questionable. Here we provide a convenient, on-line method for the quick molecular identification of Hypocrea/Trichoderma at the genus and species levels based on an oligonucleotide barcode: a diagnostic combination of several oligonucleotides (hallmarks) specifically allocated within the internal transcribed spacer 1 and 2 (ITS1 and 2) sequences of the rDNA repeat. The barcode was developed on the basis of 979 sequences of 88 vouchered species which displayed in total 135 ITS1 and 2 haplotypes. Oligonucleotide sequences which are constant in all known ITS1 and 2 of Hypocrea/Trichoderma but different in closely related fungal genera, were used to define genus-specific hallmarks. The library of species-, clade- and genus-specific hallmarks is stored in the MySQL database and integrated in the TrichOKey v. 1.0 - barcode sequence identification program with the web interface located on . TrichOKey v. 1.0 identifies 75 single species, 5 species pairs and 1 species triplet. Verification of the DNA-barcode was done by a blind test on 53 unknown isolates of Trichoderma, collected in Central and South America. The obtained results were in a total agreement with phylogenetic identification based on tef1 (large intron), NCBI BLAST of vouchered records and postum morphological analysis. We conclude that oligonucleotide barcode is a powerful tool for the routine identification of Hypocrea/Trichoderma species and should be useful as a complement to traditional methods.

Base Sequence↗
PubMed2006

Computational analysis of the Phanerochaete chrysosporium v2.0 genome database and mass spectrometry identification of peptides in ligninolytic cultures reveal complex mixtures of secreted proteins.

The white-rot basidiomycete Phanerochaete chrysosporium employs extracellular enzymes to completely degrade the major polymers of wood: cellulose, hemicellulose, and lignin. Analysis of a total of 10,048 v2.1 gene models predicts 769 secreted proteins, a substantial increase over the 268 models identified in the earlier database (v1.0). Within the v2.1 'computational secretome,' 43% showed no significant similarity to known proteins, but were structurally related to other hypothetical protein sequences. In contrast, 53% showed significant similarity to known protein sequences including 87 models assigned to 33 glycoside hydrolase families and 52 sequences distributed among 13 peptidase families. When grown under standard ligninolytic conditions, peptides corresponding to 11 peptidase genes were identified in culture filtrates by mass spectrometry (LS-MS/MS). Five peptidases were members of a large family of aspartyl proteases, many of which were localized to gene clusters. Consistent with a role in dephosphorylation of lignin peroxidase, a mannose-6-phosphatase (M6Pase) was also identified in carbon-starved cultures. Beyond proteases and M6Pase, 28 specific gene products were identified including several representatives of gene families. These included 4 lignin peroxidases, 3 lipases, 2 carboxylesterases, and 8 glycosyl hydrolases. The results underscore the rich genetic diversity and complexity of P. chrysosporium's extracellular enzyme systems.

Carboxylic Ester Hydrolases↗
PubMed2006

Identification and genetic mapping of highly polymorphic microsatellite loci from an EST database of the septoria tritici blotch pathogen Mycosphaerella graminicola.

A database of 30,137 EST sequences from Mycosphaerella graminicola, the septoria tritici blotch fungus of wheat, was scanned with a custom software pipeline for di- and trinucleotide units repeated tandemly six or more times. The bioinformatics analysis identified 109 putative SSR loci, and for 99 of them, flanking primers were developed successfully and tested for amplification and polymorphism by PCR on five field isolates of diverse origin, including the parents of the standard M. graminicola mapping population. Seventy-seven of the 99 primer pairs generated an easily scored banding pattern and 51 were polymorphic, with up to four alleles per locus, among the isolates tested. Among these 51 loci, 23 were polymorphic between the parents of the mapping population. Twenty-one of these as well as two previously published microsatellite loci were positioned on the existing genetic linkage map of M. graminicola on 13 of the 24 linkage groups. Most (66%) of the primer pairs also amplified bands in the closely related barley pathogen Septoria passerinii, but only six were polymorphic among four isolates tested. A subset of the primer pairs also revealed polymorphisms when tested with DNA from the related banana black leaf streak (Black Sigatoka) pathogen, M. fijiensis. The EST database provided an excellent source of new, highly polymorphic microsatellite markers that can be multiplexed for high-throughput genetic analyses of M. graminicola and related species.

Alleles↗
PubMed2004

The EDNAP mitochondrial DNA population database (EMPOP) collaborative exercises: organisation, results and perspectives.

This paper presents an overview of the organisation and the results of the collaborative exercises (CE) of the European DNA Profiling (EDNAP) Group's mitochondrial DNA population database project (EMPOP). The aim of the collaborative exercises was to determine whether uniformity of mtDNA sequencing results could be achieved among different laboratories. These were asked to sequence either the complete mtDNA control region or the two hypervariable regions HVI (16024-16365) and HVII (73-340) from DNA extracts, buccal swabs or bloodstains, proceeding in accordance with the protocol and strategies used in each individual laboratory. The results of the collaborative exercises were employed to identify possible sources of errors that could arise during the analysis and interpretation of mtDNA profiles. These findings were taken as a basis to tentatively make suitable arrangements for the construction of a high quality mtDNA database. One hundred fifty mtDNA profiles were submitted to the evaluating laboratory, and disaccording profiles were classified into four groups corresponding to the source of error: clerical errors, sample mix-ups, contaminations and discrepancies with respect to the mtDNA nomenclature. Overall, 14 disaccording haplotypes (16 individual errors) were observed. The errors included 10 clerical errors, 3 interpretation problems, 2 cases of sample mix-up and 1 case of point heteroplasmic mixture, where the 2 sequencing reactions brought inconsistent base calls. This corresponds to an error rate of 10.7% in a virtual mtDNA database consisting of the collaborative exercise results. However, this estimate is still conservative compared to conclusions drawn by authors of meanwhile numerous publications critically reviewing published mtDNA population databases. Our results and earlier published concerns strongly emphasize the need for appropriate safety regulations when mtDNA profiles are compiled for database purposes in order to accomplish the high standard required for mtDNA databases that are used in the forensic context.

Clinical Laboratory Techniques↗
PubMed2004

Forensic DNA databases.

Genetic databases have been created in several countries: the United Kingdom was the first European country to have, in 1995, a DNA database. Subsequently, the Netherlands and Austria (1997), Germany (1998), Finland and Norway (1999) and many others have introduced or are preparing databases. Different national legal systems have conditioned the DNA databases and so there is a great heterogeneity between countries. The criteria for an entry of a DNA profile, the criteria for a removal, the criteria for a search, etc., can lead to very distinct databases.

DNA Fingerprinting↗
PubMed2004

Toward increased utility of mtDNA in forensic identifications.

The utility of mtDNA in forensic identifications is limited by its low power of discrimination and the absence of high quality mtDNA databases. Single nucleotide polymorphisms (SNPs) in the control region outside of hypervariable regions I and II (HVI/HVII), and in the coding region of the mtDNA genome, can provide additional discrimination in mtDNA testing. We have identified particularly useful SNP sites via high throughput sequencing of the entire mtDNA genome. We report here two cases in which an 11-plex SNP assay (panel "A") targeting the most common HVI/HVII type successfully resolved two cases in which identifications could not be made on the basis of HVI/HVII sequencing. Additionally, we established a database of 286 samples for SNP panel "A" generated with robotic protocols. We have addressed the need for high quality mtDNA control region (CR) databases by developing robotic protocols for lab processing, and a carefully devised electronic data review process. A large-scale databasing effort targeting several populations underrepresented in current mtDNA databases is underway.

Complementarity Determining Regions↗
PubMed2004

Differences in non-LTR retrotransposons within C. elegans and C. briggsae genomes.

An exhaustive study of the Sam/Frodo family of non-LTR retrotransposons in the Caenorhabditis elegans and Caenorhabditis briggsae genomes demonstrated that C. briggsae contains 60 Sam/Frodo elements including a new subfamily designated Merry, while at least 1000 elements are present in C. elegans. In contrast to C. elegans, C. briggsae does not contain any other non-LTR retrotransposons. The Sam/Frodo/Merry sequences in C. briggsae are shorter and less complete than the Sam/Frodo sequences in C. elegans probably because they all lack a functional first open reading frame (ORF1) and because the genome only encodes one functional reverse transcriptase gene of a non-LTR retrotransposon. Evidence of purifying selection for a functional reverse transcriptase sequence in master/leader elements was found in both nematodes in spite of low copy numbers in C. briggsae. Sam elements in C. elegans are the most abundant Sam/Frodo/Merry family members. They contain the only functional ORF1 copies and, unlike Frodo and Merry members, have a higher GC content than the genomic regions in which they reside. This may indicate a higher transcription rate within this subfamily.

Animals↗
PubMed2004

Evolution of the mdg1 lineage of the Ty3/gypsy group of LTR retrotransposons in Anopheles gambiae.

So far, only a few retrovirus-like transposable elements (TEs) have been reported in Anopheles mosquitoes, although a large fraction of their genomes is made up of these middle repetitive sequences. By screening the A. gambiae genome databases, we have found 10 element families belonging to the mdg1 lineage of the Ty3/gypsy group of long terminal repeat (LTR) retrotransposons. These Anopheles families constitute a sister clade of the Drosophila representatives of this same lineage. According to the phylogenetic reconstruction of their open reading frame (ORF)2 enzymatic domains, the analysis of patterns of nucleotide substitution therein, and the estimation of the age of particular insertions, all these elements must have been active until quite recently, and some of them must be very young. On the other hand, the fact that all these element families are primarily composed of fragmentary copies (mostly solos) or full-length copies with inactivating mutations indicates that their turnover rate has been probably very low. Finally, incongruent phylogenies obtained from different regions of the elements strongly suggest that recombination has played a significant role in their evolutionary history.

Animals↗