Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Molecular Classification”

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 1,171 records · Page 65Linked to original sources
PubMed2005

Chemotaxonomic markers in Digitalideae (Plantaginaceae).

In a chemosystematic investigation of Digitalideae (Plantaginaceae), the water-soluble part of extracts of two species of Digitalis, two species of Isoplexis, as well as Erinus alpinus and Lafuentea rotundifolia were studied with regard to their content of main carbohydrates, iridoids and caffeoyl phenylethanoid glycosides (CPGs). Digitalis and Isoplexis contained sorbitol, cornoside and a number of other phenylethanoid glycosides including the new tyrosol beta-D-mannopyranoside, sceptroside but were found to lack iridoid glucosides. Erinus contained mainly glucose, the new 8,9-double bond iridoid, erinoside, and a number of known iridoid glucosides including two esters of 6-rhamnopyranosylcatalpol, as well as the CPG poliumoside. Finally, Lafuentea was characterized by the presence of glucose, aucubin and cryptamygin B but apparently lacked CPGs. The chemosystematic significance of the isolated compounds is discussed.

Carbohydrates↗
PubMed2004

Utility of plastid psaB gene sequences for investigating intrafamilial relationships within Orchidaceae.

DNA sequences of the plastid gene psaB were completed for 182 species of Orchidaceae (representing 150 different genera) and outgroup families in Asparagales. These data were analyzed using parsimony, and resulting trees were compared to a rbcL phylogeny of Orchidaceae for the same set of taxa after an additional 30 new rbcL sequences were added to a previously published matrix. The psaB tree topology is similar to the rbcL tree, although the psaB data contain less homoplasy and provide greater bootstrap support than rbcL alone. In combination, the two-gene tree recovers the five monophyletic subfamilial clades currently recognized in Orchidaceae, but fails to resolve the positions of Cypripedioideae and Vanilloideae. These new topologies help to clarify some of the anomalous results recovered when rbcL is analyzed alone. Both genes appear to be absent from the plastid genome of several achlorophyllous orchids, but are present in the form of presumably non-functional pseudogenes in Cyrtosia. This study is the first to document the utility of psaB sequences for phylogenetic studies of plants below the family level.

Base Sequence↗
PubMed2004

Assessing the passerine "Tapestry": phylogenetic relationships of the Muscicapoidea inferred from nuclear DNA sequences.

This study presents new comparative sequence data from the nuclear RAG-1 gene for an increased taxon sample in order to investigate phylogenetic relationships among a diverse songbird superfamily, the Muscicapoidea, which has variously included the waxwings, silky flycatchers, Palm Chat, dippers, starlings, mockingbirds, thrushes, chats, and Old World flycatchers. At the same time, our results provide a test of the often-cited relationships inferred from the phenetic studies of Sibley and Ahlquist [Phylogeny and Classification of Birds: A Study in Molecular Evolution. Yale University Press, New Haven, 1990] using DNA hybridization distances. Nuclear DNA sequences confirm the monophyly of the "core muscicapoid" group, as defined by Barker et al. [Proc. R. Soc. Lond. B 269 (2002) 295] and also support the sister-group relationship of the Sturnidae and Mimidae, on the one hand, and the large-bodied thrushes (Turdini)+the Old World flycatchers and robins, on the other. The results of the phylogenetic analysis allow preliminary inferences about muscicapoid biogeographic history.

Animals↗
PubMed2004

P elements in the saltans group of Drosophila: a new evaluation of their distribution and number of genomic insertion sites.

Few are studies on P elements that have addressed the saltans group. These studies had shown that species from the cordata and elliptica subgroups were devoid of any discernible P homologous sequences, while species from the parasaltans, sturtevanti, and saltans subgroups all contain P element sequences. Our analyses showed the presence of one to 15 P element insertion sites in species of the saltans group, including Drosophila neocordata and Drosophila emarginata (cordata and elliptica subgroups, respectively). From these species, only those from the parasaltans, sturtevanti, and saltans subgroups harbor canonical P elements and, only those of the last two subgroups seem to harbor putative full-sized elements. Due to the low similarity of the sequences found in D. neocordata and D. emarginata to those earlier described, we suggest that these sequences might be rudimental P element derivatives that were present in the ancestral of the subgenus Sophophora.

Animals↗
PubMed1998

Inherited carcinomas of the kidney.

Studies of families with inherited carcinomas have provided powerful tools to identify the genes involved in the pathogenesis of human cancers. In this review, we summarize the clinical, pathological, and genetic characteristics of the inherited carcinomas of the kidney. We emphasize the observation that different genes predispose to histologically different types of renal carcinoma. Hereditary papillary renal carcinoma, a recently described inherited disorder, is discussed in detail along with the predisposing gene, the MET protooncogene. The data support a classification of renal carcinomas based on molecular genetics.

Adenocarcinoma, Clear Cell↗
PubMed2001

New reciprocal translocation t(6;10) (q27;q11) associated with idiopathic myelofibrosis and eosinophilia.

Idiopathic myelofibrosis (IM), is a chronic myeloproliferative disorder (MPD) characterised by marrow fibrosis, extramedullary haematopoiesis and a leuco-erythroblastic picture of the peripheral blood. Cytogenetic data of IM is scarce: no specific karyotypic anomalies have been yet described. Trisomy 1q, del(13q), del(20q) and trisomy 8, appear in two-thirds of the cases with chromosome aberrations. We report on a 41-year-old patient diagnosed with IM associated with eosinophilia, bearing a novel translocation t(6;10)(q27;q11) as the sole chromosome anomaly. The patient, progressed to AML-M5a within 18 months from diagnosis. Recently new specific chromosomal translocations have been described in chronic MPD. These findings have allowed the classification of new syndromes with defined molecular abnormalities. The case we describe, because of the peculiar clinical features and the association with a previously unreported chromosomal translocation, might be a noteworthy addition.

Adult↗
PubMed1998

Characterization of atypical Aeromonas salmonicida by different methods.

Fifty two isolates of atypical Aeromonas salmonicida, recovered from a wide range of hosts and geographical locations, were heterogeneous in terms of molecular and phenotypic characteristics, and represented taxa which could not be accommodated by the current classification of four subspecies. Generally, there was incongruence between the molecular (PCR, RAPD and ribotyping) and phenotypic methods in terms of cluster membership. By PCR, 6 groups were described of which Group 1 encompassed 12 isolates including the type strain of A. salmonicida subsp. smithia. Group 2 accommodated 23 isolates including the reference cultures of subspecies achromogenes and masoucida. The named culture of Haemophilus piscium was recovered in Group 6. By ribotyping and RAPD, the reference cultures were recovered in separate groups. All methods pointed to the uniqueness of subspecies smithia. Most isolates contained 2-6 plasmids, of 2.3 to 150 kb in length. Nevertheless, all isolates possessed certain key characteristics, including Gram-negativity, and the absence of motility.

Aeromonas↗
PubMed2001

Congenital nephrotic syndromes.

Many acquired and familial renal diseases in man lead to kidney dysfunction and nephrotic syndrome. These diseases share a common pathological fate in the form of glomerular dysfunction and proteinuria. Classification of the disease is difficult because the onset of pathological appearance in congenital nephrotic syndrome (CNS) varies considerably. Recently, classification has been aided by applying molecular genetics to identify genes involved in the pathogenesis of proteinuria. Light has also been shed on the biology and mechanisms of glomerular filtration and the molecular pathogenesis of CNS.

Animals↗
PubMed1996

Optimized protein diagnosis in the autosomal recessive limb-girdle muscular dystrophies.

The genes for six forms of recessive muscular dystrophy have so far been identified, although more are certain to be revealed. Differential diagnosis on clinical grounds alone can be very difficult, so a classification system based on the underlying molecular defect has been introduced. Muscle biopsies are taken for routine diagnostic histopathology, and the various proteins implicated in muscular dystrophy can be analysed immunologically and the results used to indicate where to start searching for gene mutations. A flow diagram is presented which demonstrates how such protein analysis could be optimized.

Biopsy↗
PubMed2002

Thyroid hormone transporters: recent advances.

Thyroid hormones, being hydrophobic, were thought to enter target cell membranes by passive diffusion. However, recent studies have documented the existence of numerous organic anion transport systems, about half of which also transport thyroid hormones into (and possibly out of) a variety of target cells. Several of the genes encoding thyroid hormone transporters have been characterized by means of molecular approaches. Here, we discuss the classification of thyroid hormone transporters, with emphasis on how they are influenced by their ionic milieu and what their symported organic anions are.

Amino Acid Transport Systems↗
PubMed1997

Taxonomic description of Methanococcoides euhalobius and its transfer to the Methanohalophilus genus.

A sequence analysis of the 16S-rRNA of Methanococcoides euhalobius revealed that this organism was highly related to members of the genus Methanohalophilus. On the basis of sequence data, an oligonucleotide probe specific to Methanohalophilus species was designed. Hybridization studies with this probe confirmed close relationship of Methanococcoides euhalobius to Methanohalophilus species. Therefore, we propose that Methanococcoides euhalobius should be transferred to the genus Methanohalophilus as Methanohalophilus euhalobius.

Classification↗
PubMed2002

Functional and genomic implications of global gene expression profiles in cell lines from human hepatocellular cancer.

Global gene expression profiles in cancer have impacted both classification of tumors and definition of molecular pathways in neoplasia. To explore the possibility of employing human tumor cell lines to obtain information on the functional genomics of the early stages of tumorigenesis, we have characterized variation in gene-expression patterns in a cytogenetically well-defined series of cell lines derived from human hepatocellular carcinoma (HCC). Microarrays containing 6,720 sequence-verified human cDNAs were used in this study. Nineteen well-characterized HCC cell lines were analyzed, and a nontumorigenic liver-derived epithelial cell line (Chang) was used as a reference. Each sample was examined at least twice by switching fluorescent dyes, Cy-5 and Cy-3, and average values of 2 experiments on each sample were used for further analysis. Analysis of the clustered data revealed 2 distinctive subtypes of gene-expression patterns among the 19 cell lines, suggesting a degree of heterogeneity among the gene-expression profiles of cell lines. Remarkably, expression of alpha-fetoprotein (AFP) was highly correlated with the molecular subtypes of HCC. Although the 3 most distinctive gene-expression modules represented the signatures of 2 different subgroups of HCC, most of the cell lines shared many coexpressed genes. However, sets of coexpressed genes that are specific for the subtypes of HCC were identified. Furthermore, our results indicate that the comparison between gene-expression patterns and structural alterations in chromosomes is potentially useful in identifying genes critical in early stages of tumorigenesis. In conclusion, these results not only identified unrecognized subtypes of HCC, but also provided potential molecular markers for each subtype that can be useful for diagnostic and/or therapeutic purposes.

Carcinoma, Hepatocellular↗
PubMed1999

Distal myopathies.

Although muscle disease classically presents with proximal extremity weakness, some myopathic disorders, including several types of muscular dystrophy, result in predominantly, or exclusively, distal muscle involvement. Accurate diagnosis of these relatively uncommon conditions can be challenging for the clinician, because of both the unusual phenotype and the significant overlap in the clinical features of many of these entities. Advances in molecular genetics have permitted a tentative classification of these disorders and have led to the identification of the responsible gene lesion for several of these entities. This review summarizes current understanding of this interesting group of muscular dystrophies and briefly summarizes other myopathies that can present with distal weakness.

Atrophy↗
PubMed1994

rbcL gene sequences provide evidence for the evolutionary lineages of leptosporangiate ferns.

Pteriodophytes have a longer evolutionary history than any other vascular land plant and, therefore, have endured greater loss of phylogenetically informative information. This factor has resulted in substantial disagreements in evaluating characters and, thus, controversy in establishing a stable classification. To compare competing classifications, we obtained DNA sequences of a chloroplast gene. The sequence of 1206 nt of the large subunit of the ribulose-bisphosphate carboxylase gene (rbcL) was determined from 58 species, representing almost all families of leptosporangiate ferns. Phlogenetic trees were inferred by the neighbor-joining and the parsimony methods. The two methods produced almost identical phylogenetic trees that provided insights concerning major general evolutionary trends in the leptosporangiate ferns. Interesting findings were as follows: (i) two morphologically distinct heterosporous water ferns, Marsilea and Salvinia, are sister genera; (ii) the tree ferns (Cyatheaceae, Dicksoniaceae, and Metaxyaceae) are monophyletic; and (iii) polypodioids are distantly related to the gleichenioids in spite of the similarity of their exindusiate soral morphology and are close to the higher indusiate ferns. In addition, the affinities of several "problematic genera" were assessed.

Base Sequence↗
PubMed2004

Potential of genetic translational research in gastroenterology.

The concept that genetic variation underlies inter-individual differences in drug response and contributes to the risk of developing common, complex disorders is expanding rapidly. Consequently the interest in genetic translational research has increased. Polymorphic DNA markers, either microsatellites or single nucleotide polymorphisms (SNPs), are used to assess genetic identities and track genetic differences between individuals. Given their abundance and stability, SNPs hold great promise as markers for mapping disease susceptibility loci for common, complex disorders by association studies. For this purpose the development of inexpensive, accurate, high-throughput methods for scoring large numbers of SNPs from hundreds of patients and controls is critical. Furthermore, gene expression profiling using DNA microarrays is likely to become a useful diagnostic tool enabling classification of disease phenotype based on molecular basis of disease pathogenesis, revealing information that cannot be obtained by histological assessment. Moreover, identification of differentially expressed genes in affected versus control tissue or over time in affected tissue will lead to better understanding of the mechanisms underlying disease and ultimately to the development of more effective drug therapies. To illustrate the potential of genetic translational research, several examples in the field of gastroenterology are described.

Gastrointestinal Diseases↗
PubMedDate not supplied

Application of gene expression profiling for validating models of human breast cancer.

While classical histopathologic approaches are invaluable in classifying tumors and understanding aspects of cellular interactions, genomic approaches provide a means to molecularly dissect tumorigenesis. The relationship of gene expression to the development of neoplasia remains an area of intensive research. With the advent of large-scale genomic platforms, alterations in gene expression can be related to the morphological development of cancer. The feasibility of using large-scale genomic analysis platforms has dramatically changed the landscape of biological sciences, as cellular processes must be considered in the context of complex networks. Alterations in gene expression must now be understood in a systems approach in which the relationships between genes expression changes are studied by considering the interplay of multiple regulatory networks. Ultimately, such changes must be understood at the protein level. We have begun to apply this technology to determine changes in gene expression that differentiate various types of mammary cancers that arise in mouse models that have been initiated by different genetic alterations. Ultimately, a molecular catalogue of similarities and differences between rodent and human tumors can be created which will serve to validate or credential particular models for specific experimental purposes, such as preclinical testing. These approaches have led to new insights into molecular pathways involved in oncogenesis, new classifications of human breast cancer, and the identification of new genes that may be relevant to understanding and treating human cancer.

Animals↗
PubMed2004

Burkitt's lymphoma of the stomach: a case report with molecular cytogenetic analysis.

In 1974, a 28-year-old man presented with a 12 cm sized ulcerated tumor involving the middle third of the stomach, which was originally diagnosed as "lymphosarcoma". Clinical recurrence of the lymphoma resulted in rapidly progressing disease and the patient died 4 months after initial diagnosis. Retrospective work-up of the 29-year-old tumor blocks revealed the typical histologic appearance and phenotype (CD20, CD10, BCL-6 positive) of Burkitt's lymphoma (BL) with a proliferation rate of 95%. By fluorescence in situ hybridization (FISH). the tumor cells were shown to harbor an IGH-MYC fusion indicating the presence of the hallmark Burkitt-translocation t(8;14)(q24;q32). Considering the typical clinical features of BL requiring appropriate treatment regimes the case presented here highlights the importance of modern histopathologic and molecular cytogenetic techniques for the proper classification of such rare lymphomas presenting at atypical sites.

Adult↗
PubMed2005

Phenotypical enrichment strategies for microarray data analysis applied in a type II diabetes study.

Combining results from gene microarrays, clinical chemistry, and quantitative tissue histomorphology in an integrated bioinformatics setting enables prioritization of gene families as well as individual genes in a type II diabetes animal study. This new methodology takes advantage of a time-controlled mouse study as the animals progress from a normal phenotype to that of type II diabetes. Profiles from different levels of the biological hierarchy of unpooled entities provide an encompassing, system-wide view of biological changes. Here, phenotypic changes on the tissue-structural and physiological level are used as statistical covariants to enrich the gene expression analysis, suggesting correlative processes between gene expression and phenotype unlocked by multi-sample comparisons. We apply correlative and gene set enrichment procedures and compare the results to differential analysis to identify molecular markers. Evaluation based on ontological classifications proves changes in prioritization of disease-related genes that would have been overlooked by conventional gene expression analyses strategies.

Animals↗