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Results for “Molecular Classification”

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At least 883 records · Page 49Linked to original sources
PubMed2005

Understanding iron homeostasis through genetic analysis of hemochromatosis and related disorders.

Genetic analysis of hemochromatosis has led to the discovery of a number of genes whose mutations disrupt iron homeostasis and lead to iron overload. The introduction of molecular tests into clinical practice has provided a tool for early diagnosis of these conditions. It has become clear that hemochromatosis includes a spectrum of disorders that range from simple biochemical abnormalities to chronic asymptomatic tissue damage in midlife to serious life-threatening diseases in young subjects. Molecular studies have identified the systemic loop that controls iron homeostasis and is centered on the hepcidin-ferroportin interaction. The complexity of this regulatory pathway accounts for the genetic heterogeneity of hemochromatosis and related disorders and raises the possibility that genes encoding components of the pathway may be modifiers of the main genotype. Molecular diagnosis has improved the classification of the genetic conditions leading to iron overload and identified novel entities, characterized by both iron loading and variable degrees of anemia. Despite the progress in the diagnosis, classification, and mechanisms of iron overload disorders, the treatment of affected patients continues to rely on regular phlebotomy. Understanding the molecular circuitry of iron control may lead to the identification of potential therapeutic targets for novel treatment strategies to be used in association with or as an alternative to phlebotomy.

Genetic Predisposition to Disease↗
PubMed2005

An edit script for taxonomic classifications.

BACKGROUND: The NCBI taxonomy provides one of the most powerful ways to navigate sequence data bases but currently users are forced to formulate queries according to a single taxonomic classification. Given that there is not universal agreement on the classification of organisms, providing a single classification places constraints on the questions biologists can ask. However, maintaining multiple classifications is burdensome in the face of a constantly growing NCBI classification. RESULTS: In this paper, we present a solution to the problem of generating modifications of the NCBI taxonomy, based on the computation of an edit script that summarises the differences between two classification trees. Our algorithms find the shortest possible edit script based on the identification of all shared subtrees, and only take time quasi linear in the size of the trees because classification trees have unique node labels. CONCLUSION: These algorithms have been recently implemented, and the software is freely available for download from http://darwin.zoology.gla.ac.uk/~rpage/forest/.

Algorithms↗
PubMed2006

Multilocus sequence typing method for identification and genotypic classification of pathogenic Leptospira species.

BACKGROUND: Leptospira are the parasitic bacterial organisms associated with a broad range of mammalian hosts and are responsible for severe cases of human Leptospirosis. The epidemiology of leptospirosis is complex and dynamic. Multiple serovars have been identified, each adapted to one or more animal hosts. Adaptation is a dynamic process that changes the spatial and temporal distribution of serovars and clinical manifestations in different hosts. Serotyping based on repertoire of surface antigens is an ambiguous and artificial system of classification of leptospiral agents. Molecular typing methods for the identification of pathogenic leptospires up to individual genome species level have been highly sought after since the decipherment of whole genome sequences. Only a few resources exist for microbial genotypic data based on individual techniques such as Multiple Locus Sequence Typing (MLST), but unfortunately no such databases are existent for leptospires. RESULTS: We for the first time report development of a robust MLST method for genotyping of Leptospira. Genotyping based on DNA sequence identity of 4 housekeeping genes and 2 candidate genes was analyzed in a set of 120 strains including 41 reference strains representing different geographical areas and from different sources. Of the six selected genes, adk, icdA and secY were significantly more variable whereas the LipL32 and LipL41 coding genes and the rrs2 gene were moderately variable. The phylogenetic tree clustered the isolates according to the genome-based species. CONCLUSION: The main advantages of MLST over other typing methods for leptospires include reproducibility, robustness, consistency and portability. The genetic relatedness of the leptospires can be better studied by the MLST approach and can be used for molecular epidemiological and evolutionary studies and population genetics.

Animals↗
PubMed2000

Where does fission yeast sit on the tree of life?

The budding yeast Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe are as different from each other as either is from animals: their ancestors separated about 420 to 330 million years ago. Now that S. pombe is poised to join the post-genome era, its evolutionary position should become much clearer.

Classification↗
PubMedDate not supplied

Determinants of the gonococcal serovar pattern in Edinburgh, Scotland: a multivariate analysis.

The geographical and temporal variety of gonococcal serovar patterns are well described but it remains uncertain what characteristics possessed by the organism, or sexual behaviour pattern in the patients, determine the particular serovar pattern in a given area at a given time. This study was designed to assess the relative contribution of various demographic and clinical features of infection to the observed pattern of serovars in Edinburgh between 1990 and 1993. Five hundred and eight isolates were included in a multivariate analysis model to control for potential interactions between variables. Associations were noted between certain serovars and an asymptomatic clinical presentation, method of acquisition and site of infection. Certain physical characteristics of Neisseria gonorrhoeae in conjunction with the sexual behaviour patterns of patients are partially responsible for observed serovar patterns but more detailed analysis requires further sub-classification of serovars using molecular techniques.

Adult↗
PubMed1998

The acetylcholinesterase gene Ace: a diagnostic marker for the Pipiens and Quinquefasciatus forms of the Culex pipiens complex.

The taxonomy of the Culex pipiens complex remains a controversial issue in mosquito systematics. Based on morphologic characters, 2 allopatric taxa are recognized, namely Cx. pipiens (including the form "molestus") in temperate areas and Cx. quinquefasciatus in tropical areas. Here we report on variability at the nucleotide level of an acetylcholinesterase gene in several strains and natural populations of this species complex. Few polymorphisms were found in coding regions within a subspecies but many polymorphisms were observed between subspecies in noncoding regions. We describe a method based on a restriction enzyme polymorphism in polymerase chain reaction-amplified DNA, in which the presence or absence of one restriction site discriminates Cx. pipiens, Cx. quinquefasciatus, and their hybrids. This technique reliably discriminates mosquitoes from more than 30 worldwide strains or populations. Polymerase chain reaction amplification of specific alleles may also be a useful tool for characterizing specific alleles of each sibling taxon.

Acetylcholinesterase↗
PubMed1999

Acute lymphoblastic leukemia.

This article reviews the laboratory methodologies used to evaluate acute lymphoblastic leukemia (ALL) in children and their role in establishing a diagnosis and prognosis of this disease. These methodologies are: morphology, flow cytometry, cytogenetics, and molecular diagnostics. Additionally, immunophenotypic classifications of ALL and criteria for establishing a diagnosis of ALL independent of morphology are described.

Child↗
PubMed2002

[12S rRNA, cytochrome b and MDR1 gene DNA sequence and phylogenetic evolution of Muntiacus (M. muntjak, M. reevesi, M. crinifros)].

In the paper, 784 bp-DNA fragmensts of 12S rRNA and cytochrome b gene on Mitochondrial DNA and 728 bp-DNA fragments of MDR1 (multidrug resistance) gene from Muntiacus (M. muntjak, M. reevesi, M. crinifrons) were amplified and sequenced, while their phylogenetic relationships and classification were analysed. The molecular phylogenetic trees were constructed based on these combined DNA sequences, the results suggested that DIST is 0.042 between M. crinifrons and M. muntjak; DIST is 0.047 between M. crinifrons and M. reevesi; DIST is 0.055 between M. muntjak and M. reevesi, counted according to the evolution speed of 2.5% per million year, the divergent time between M. crinifrons and M. muntjak is 1.68 million year; the divergent time between M. crinifrons and M. reevesi is 1.88 million year; the divergent time between M. muntjak and M. reevesi is 2.2 million year; The conclusion is that the M. crinifrons and M. reevesi were diverged from an ancestor analogied with M. muntjak, M. nuntjak is the oldest species, M. crinifrons and M. reevesi are newer ones.

ATP Binding Cassette Transporter, Subfamily B, Mem↗
PubMed2003

[Carcinoma of the stomach].

Stomach cancer is one of the most common tumors in human pathology. More than 95% of all gastric malignancy are adenocarcinomas developed from epithelial cells of gastric mucosa. Still, this is highly lethal disease with five-year surveillance of 20%. This review explains most frequently used classifications of gastric cancers, molecular and cellular abnormalities in gastric cancer, chromosomal abnormalities, tumor suppressor genes, oncogenes and growth factors involved in gastric carcinogenesis.

Carcinoma↗
PubMed2005

Protein expression profiling identifies subclasses of breast cancer and predicts prognosis.

Breast cancer is a heterogeneous disease whose evolution is difficult to predict by using classic histoclinical prognostic factors. Prognostic classification can benefit from molecular analyses such as large-scale expression profiling. Using immunohistochemistry on tissue microarrays, we have monitored the expression of 26 selected proteins in more than 1,600 cancer samples from 552 consecutive patients with early breast cancer. Both an unsupervised approach and a new supervised method were used to analyze these profiles. Hierarchical clustering identified relevant clusters of coexpressed proteins and clusters of tumors. We delineated protein clusters associated with the estrogen receptor and with proliferation. Tumor clusters correlated with several histoclinical features of samples, including 5-year metastasis-free survival (MFS), and with the recently proposed pathophysiologic taxonomy of disease. The supervised method identified a set of 21 proteins whose combined expression significantly correlated to MFS in a learning set of 368 patients (P < 0.0001) and in a validation set of 184 patients (P < 0.0001). Among the 552 patients, the 5-year MFS was 90% for patients classified in the "good-prognosis class" and 61% for those classified in the "poor-prognosis class" (P < 0.0001). This difference remained significant when the molecular grouping was applied according to lymph node or estrogen receptor status, as well as the type of adjuvant systemic therapy. In multivariate analysis, the 21-protein set was the strongest independent predictor of clinical outcome. These results show that protein expression profiling may be a clinically useful approach to assess breast cancer heterogeneity and prognosis in stage I, II, or III disease.

Adult↗