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At least 829 records · Page 46Linked to original sources
PubMed1992

Autosomal dominant polycystic kidney disease: from molecular genetics to the patients.

One of the gene loci (PKD1) responsible for autosomal dominant polycystic kidney disease was located in 1985 to the short arm of chromosome 16. The clinical consequences of this finding are analyzed. Genetic heterogeneity has been demonstrated since 5%-15% of the families inherit a non-PKD1 mutation. Progress in molecular genetics allows better classification of patients with some atypical manifestations, e.g., those with early renal failure or those with congenital hepatic fibrosis. Identification of the gene(s) and of their defects will provide further progress.

Chromosome Mapping↗
PubMed2004

Genetic diversity within Pisum sativum using protein- and PCR-based markers.

A collection of 148 Pisum accessions, mostly from Western Europe, and including both primitive germplasm and cultivated types, was structured using 121 protein- and PCR-based markers. This molecular marker-based classification allowed us to trace back major lineages of pea breeding in Western Europe over the last decades, and to follow the main breeding objectives: increase of seed weight, introduction of the afila foliage type and white flowers, and improvement of frost tolerance for winter-sown peas. The classification was largely consistent with the available pedigree data, and clearly resolved the different main varietal types according to their end-uses (fodder, food and feed peas) from exotic types and wild forms. Fodder types were further separated into two sub-groups. Feed peas, corresponding to either spring-sown or winter-sown types, were also separated, with two apparently different gene pools for winter-sown peas. The garden pea group was the most difficult to structure, probably due to a continuum in breeding of feed peas from garden types. The classification also stressed the paradox between the narrowness of the genetic basis of recent cultivars and the very large diversity available within P. sativum. A sub-collection of 43 accessions representing 96% of the whole allelic variability is proposed as a starting point for the construction of a core collection.

Agriculture↗
PubMed1997

Comparison of partial 16S rRNA gene sequences obtained from activated sludge bacteria.

The cultivated and uncultivated bacterial communities of an activated sludge plant were studied. Two samples were taken and a total of 516 bacterial isolates were classified into groups using their whole-cell protein patterns. The distribution of bacteria into protein-pattern groups differed significantly between the two samples, suggesting variation in culturable bacterial flora. Partial 16S rRNA gene sequences were determined for representatives of the commonest protein-pattern groups. Most of the sequences obtained were previously unknown, but relatively closely related to known sequences of organisms belonging to the alpha, beta or gamma subclasses of the proteobacteria, the first two subclasses being predominant. This classification of bacteria isolated on a diluted nutrient-rich medium differed from recent culture-dependent studies using nutrient-rich media. The uncultivated bacterial community was studied by analyzing ten partial 16S rRNA gene sequences cloned directly from activated sludge. None of the cloned sequences was identical to those determined for culturable organisms; or to those in the GenBank database. They were, however, related to the alpha or beta subclasses of the proteobacteria, or to the gram-positive bacteria with a high G + C DNA content.

Bacteria↗
PubMed2003

[Pathology and genetic hereditary kidney cysts].

The classification of cystic kidney diseases according to the pathologic-anatomic potter classification may be difficult. New molecular genetic findings are important to understand the underlying pathogenesis, but less useful to classify the hereditary diseases. An exact classification of polycystic kidney disease in fetus and children is very important for the human genetic consultation. Therefore, the investigation of pathological anatomy of kidney and liver, as well as the evaluation of additional malformations and family history is necessary. For clinical use the mode of inheritance (autosomal dominant and autosomal recessive) is used to differentiate hereditary polycystic kidney diseases.

Humans↗
PubMed2001

Crypt1, an active Ac-like transposon from the chestnut blight fungus, Cryphonectria parasitica.

A moderately repetitive element was identified previously in the nuclear genome of the chestnut blight fungus, Cryphonectria parasitica, and has been used as a probe for population studies of the fungus. We report here that the repetitive element is a class II transposon of the hAT family of Activator (Ac)-like transposable elements. The element, named Crypt1, has a size of 3563 bp, including 21-bp terminal inverted repeats. A unique 8-bp direct repeat sequence flanking Crypt1 was identified in each of three clones examined. A single large ORF with the potential to encode a putative transposase of 946 amino acid residues was deduced from the sequence of Crypt1. Based on amino acid sequence alignments, Crypt1 is most closely related to other Ac-like transposons of filamentous ascomycetes. A single transcript of approximately 3.0 kb was identified by Northern hybridization experiments from Crypt1-containing isolates, suggesting that Crypt1 is an active element. An isolate containing a single, possibly defective, copy of Crypt1 was identified in C. parasitica isolates from China; no Crypt1 transcript was identified in this isolate. Transposition of Crypt1 was inferred from Southern and inverse PCR analyses of C. parasitica isolates maintained in the laboratory, but transposition appears to be a rare event.

Amino Acid Sequence↗
PubMedDate not supplied

Classification of a large anticancer data set by adaptive fuzzy partition.

An Adaptive Fuzzy Partition (AFP) algorithm, derived from Fuzzy Logic concepts, was used to classify an anticancer data set, including about 1300 compounds subdivided into eight mechanisms of action. AFP classification builds relationships between molecular descriptors and bio-activities by dynamically dividing the descriptor hyperspace into a set of fuzzy subspaces. These subspaces are described by simple linguistic rules, from which scores ranging between 0 and 1 can be derived. The latter values define, for each compound, the degrees of membership of the different mechanisms analyzed. A particular attention was devoted to develop structure-activity relations that have a real utility. Then, well-defined and widely accepted protocols were used to validate the models by defining their robustness and prediction ability. More particularly, after selecting the most relevant descriptors with help of a genetic algorithm, a training set of 640 compounds was isolated by a rational procedure based on Self-Organizing Maps. The related AFP model was then validated with help of a validation set and, above all, of cross-validation and Y-randomization procedures. Good validation scores of about 80% were obtained, underlining the robustness of the model. Moreover, the prediction ability was evaluated with 374 test compounds that had not been used to establish the model and 77% of them were predicted correctly.

Algorithms↗
PubMed2005

Animal phylogeny: fatal attraction.

MPhylogenetic analyses of hundreds of genes from model animals have placed flies closer to vertebrates than to nematodes; recent work suggests this may be due to an artefact known as long branch attraction.

Animals↗
PubMed2005

The complete mitochondrial genome of Anisakis simplex (Ascaridida: Nematoda) and phylogenetic implications.

We determined the nucleotide sequence of the complete mitochondrial genome of the nematode species Anisakis simplex. The genome is circular, 13,916 bp in size and conforms to the general characteristics of nematode mitochondrial DNAs. The gene arrangement of A. simplex is the same as that of Ascaris suum and almost identical to those of rhabditid species with a minor exception concerning the relative position of the AT-rich and non-coding regions and radically different from those of spirurid species. Along with comparisons of gene arrangement, phylogenetic analyses (maximum parsimony, neighbour joining and maximum likelihood methods) based on concatenated amino acid sequences of 12 protein-coding genes from 13 nematode species provided strong support for the sister-group relationship between Ascaridida and Rhabditida. The Shimodaira-Hasegawa and Templeton's tests both rejected the alternative hypothesis of a closer relationship between Ascaridida and Spirurida. These results contradicted the traditional view of nematode classification and a recent molecular phylogenetic study of 18S rDNA data that assigned Ascaridida and Spirurida as being a sister-group. Mapping of gene arrangement across the phylogenetic tree lead to the assumption that the conserved gene arrangement found in Ascaridida-Rhabditida members might have been acquired after the most recent common ancestor of ascaridid/rhabditid members branched off from the basal stock of the rhabditid lineage.

Amino Acid Sequence↗
PubMed2025

Methylation Signatures Identify Two Distinct Clusters of Uterine Leiomyosarcoma With Unique Histologic and Clinical Behaviors.

Uterine leiomyosarcoma (uLMS) is a rare and deadly gynecologic malignancy. uLMS is histologically heterogeneous and presents with a wide spectrum of tumor differentiation, with a broad range of genomic DNA instability, which can make the diagnosis and prognosis of uLMS challenging. Methylation has emerged as a useful molecular tool in tumor classification and diagnosis in certain neoplasms. We initiated this study to investigate the role of global methylation in the differential diagnosis of uLMS from its mimics in correlation with pathologic characteristics and clinical outcomes. In this study, we performed array-based global methylation profiling analysis in a total of 71 uLMS and compared the methylation signatures of uLMS with several other uterine mesenchymal tumors and soft tissue leiomyosarcoma. We found that uLMS demonstrated distinct methylation patterns differing from all other tumor types. Notably, methylation profiling defines 2 distinct subgroups of uLMS with differing copy number alterations, resulting in unique histologic and clinical behaviors, further emphasized by differences in methylation pathway analysis. This study is the first to report methylation profiling as a useful diagnostic tool in differentiating uLMS from mimics and defines 2 subtypes of uLMS based on methylation signatures.

Humans↗
PubMed2005

Are plant DNA barcodes a search for the Holy Grail?

In a recent study, Kress et al. compared two plant genomes to seek out plant DNA barcodes. Two promising markers balanced the variability that is needed to distinguish species with conserved primer regions that enable universal amplification. Although this study is the most rigorous effort to date, problems from earlier barcoding efforts, such as the use of non-evolutionary species concepts and differential sorting of genes and species, could reemerge. Single-gene barcoding might not be universally effective owing to inherent inaccuracies. Kress et al. suggest the use of multiple genes, reflecting an integrated approach that is likely to be the best answer to identifying species quickly and accurately.

Biodiversity↗
PubMed2004

Revised definition of Actinobacillus sensu stricto isolated from animals. A review with special emphasis on diagnosis.

The taxonomy of the members of the genus Actinobacillus associated with animals has been reviewed with focus on classification and identification including molecular based characterization, typing and identification. Out of the 22 species or species like taxa reported as Actinobacillus, 19 are associated with animals. When classified on the basis of 16S rRNA sequence based phylogenetic analysis, DNA-DNA hybridizations and phenotypic analysis, Actinobacillus sensu stricto is restricted to include A. lignieresii, A. pleuropneumoniae, A. equuli subsp. equuli, A. equuli subsp. haemolyticus (taxon 11 of Bisgaard), A. hominis, A. suis, A. ureae, A. arthritidis (taxon 9 of Bisgaard), Actinobacillus genomospecies 1 and 2 and the taxa 8 and 26 of Bisgaard. The remaining 11 species of Actinobacillus are unrelated to A. sensu stricto and should consequently be grouped with other genera or be renamed as new genera depending on new data. Identification of members of Actinobacillus at species level is possible through phenotypic characterization combined with information on host of isolation. PCR tests are available for specific detection of A. pleuropneumoniae. Only A. pleuropneumoniae is presently considered as a primary pathogen. Based on different types of RTX genes it is possible to PCR type A. pleuropneumoniae to serotype level. PCR might also be used for the specific detection of A. equuli subsp. haemolyticus. Epidemiological investigations and surveillance have so far included serotyping, multilocus enzyme electrophoresis (MLEE), ribotyping and restriction fragment length profiling.

Actinobacillus↗
PubMed2004

Taxon-specific evolution of glandular kallikrein genes and identification of a progenitor of prostate-specific antigen.

In a previous study we demonstrated that repeated duplications of the tissue kallikrein gene (Klk1) had resulted in 24 paralogs in mouse. Here we demonstrate a different evolution of rat glandular kallikrein genes. Repeated duplications of an approximately 30-kb region, encompassing Klk1, Klk15, and Klk2-ps, resulted in 10 copies of each gene, but only the Klk1 paralogs are functional. The number of genes varies also between nonrodent mammals, e.g., there are probably no paralogs to KLK1 in cow and pig, whereas horse could have up to 5. In the dog, the gene encoding the prostatic arginine esterase was identified as an ortholog to the progenitor of the PSA and hK2 genes, and it carries the same conserved androgen-responsive elements directing prostate transcription as these genes. This is highly interesting with respect to animal models of benign prostate hyperplasia and prostate adenocarcinoma--diseases that have been described only in humans and dogs.

Adenocarcinoma↗
PubMed2004

The phylogeny of acorn weevils (genus Curculio) from mitochondrial and nuclear DNA sequences: the problem of incomplete data.

We considered the contribution of two mitochondrial and two nuclear data sets for the phylogenetic reconstruction of 22 species of seed beetles in the genus Curculio (Coleoptera: Cuculionidae). A phylogenetic tree from representatives found on various hosts was inferred from a combined data set of mitochondrial DNA cytochrome oxidase subunit I, mitochondrial cytochrome b, nuclear elongation factor 1alpha, and nuclear phosphoglycerate mutase, used for the first time as a molecular marker. Separate parsimony analyses of each data set showed that individual gene trees were mainly congruent and often complementary in the support of clades but the analysis was complicated by failure of PCR amplification of nuclear genes for many taxa and hence missing data entries. When the four gene partitions were combined in a simultaneous analysis despite the missing data, this increased the resolution and taxonomic coverage compared to the individual source trees. Alternative approaches of combining the information via supertree methodology produced a comparatively less resolved tree, and hence seem inferior to combining data matrices even in cases where numerous taxa are missing. The molecular data suggest a classification of the European species into two species groups that are in accordance with morphological characteristics but the data do no support any of the previously recognised American species groups.

Animals↗
PubMed2004

Relative character-state space, amount of potential phylogenetic information, and heterogeneity of nucleotide and amino acid characters.

We examined a broad selection of protein-coding loci from a diverse array of clades and genomes to quantify three factors that determine whether nucleotide or amino acid characters should be preferred for phylogenetic inference. First, we quantified the difference in observed character-state space between nucleotides and amino acids. Second, we quantified the loss of potential phylogenetic signal from silent substitutions when amino acids are used. Third, we used the disparity index to quantify the relative compositional heterogeneity of nucleotides and amino acids and then determined how commonly convergent (rather than unique) shifts in nucleotide and amino acid composition occur in a phylogenetic context. The greater potential phylogenetic signal for nucleotide characters was found to be enormous (on average 440% that of amino acids), whereas the greater observed character-state space for amino acids was less impressive (on average 150.4% that of nucleotides). While matrices of amino acid sequences had less compositional heterogeneity than their corresponding nucleotide sequences, heterogeneity in amino acid composition may be more homoplasious than heterogeneity in nucleotide composition. Given the ability of increased taxon sampling to better utilize the greater potential phylogenetic signal of nucleotide characters and decrease the potential for artifacts caused by heterogeneous nucleotide composition among taxa, we suggest that increased taxon sampling be performed whenever possible instead of restricting analyses to amino acid characters.

Amino Acids↗
PubMed2005

Genus Tetrastemma Ehrenberg, 1831 (Phylum Nemertea)--a natural group? Phylogenetic relationships inferred from partial 18S rRNA sequences.

We investigated the monophyletic status of the hoplonemertean taxon Tetrastemma by reconstructing the phylogeny for 22 specimens assigned to this genus, together with another 25 specimens from closely related hoplonemertean genera. The phylogeny was based on partial 18S rRNA sequences using Bayesian and maximum likelihood analyses. The included Tetrastemma-species formed a well-supported clade, although the within-taxon relationships were unsettled. We conclude that the name Tetrastemma refers to a monophyletic taxon, but that it cannot be defined by morphological synapomorphies, and our results do not imply that all the over 100 species assigned to this genus belong to it. The results furthermore indicate that the genera Amphiporus and Emplectonema are non-monophyletic.

Animals↗
PubMed1997

Organization of the equine immunoglobulin constant heavy chain genes. I. c epsilon and c alpha genes.

We provide a restriction map of the equine c epsilon and c alpha genes as a molecular basis for isotype classification. Human and murine DNA probes were used for identification of homologous equine DNA sequences and for isolation of the equine c epsilon and c alpha genes from a genomic DNA library. A detailed map of the equine 5'-s epsilon/c epsilon-s alpha/c alpha-3' gene region was obtained. Equine c epsilon and c alpha DNA probes were prepared and used for restriction analysis of immunoglobulin heavy chain gene loci from different horses. This analysis indicated the presence of only one equine c epsilon and one c alpha gene in the haploid equine genome. In addition, for the equine c alpha gene, four haplotypes were identified according to BamHI restriction fragment length polymorphism (RFLP) of genomic DNA. The relative location of the c epsilon and c alpha genes 3' of the equine c mu and c gamma genes was determined by restriction analysis of equi-murine heterohybridomas.

Animals↗
PubMed2002

Signaling and transcriptional control of pituitary development.

Many common morphogenic, signaling and transcriptional hierarchy themes exist with respect to a number of different model systems representing mammalian organogenesis. The developing pituitary gland defines a fundamentally ideal system for the study and classification of biochemical and molecular events associated with biological transitions such as organ and cellular positional determination as well as lineage-specific terminal differentiation. Recent advances in defining the extrinsic and intrinsic biological cascades behind pituitary development have shed light on the crosstalk between signaling molecules and transcription factors as well as the combinatorial regulatory codes guiding gland maturation. A thorough assessment of these codes is critical to a comprehensive understanding of pituitary organogenesis and the mechanisms which may go awry during tumorigenesis.

Animals↗