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PubMed1993

BLH1 codes for a yeast thiol aminopeptidase, the equivalent of mammalian bleomycin hydrolase.

We have cloned the BLH1 gene of the yeast Saccharomyces cerevisiae coding for a peptidase with significant homology to rabbit bleomycin hydrolase. Bleomycin is a glycopeptide antibiotic used for the treatment of human cancers. The antitumor activity of the drug is limited by its metabolic inactivation caused by bleomycin hydrolase, a member of the cysteine protease family. The open reading frame of BLH1 consists of 1,449 base pairs encoding a 55.4-kDa protein consistent with the molecular mass found in sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The consensus sequence within the active site region of cysteine proteases is conserved in the yeast enzyme. Biochemical studies on the purified enzyme confirm its classification as a thiol protease. The nonvacuolar enzyme has a molecular mass of 220 kDa, suggesting a homotetrameric structure. It exhibits an aminopeptidase activity with broad substrate specificity. Biochemical and genetic linkage data give evidence that the BLH1 and the LAP3 (Trumbly, R. J., and Bradley, G. (1983) J. Bacteriol. 156, 36-48) encoded aminopeptidases are identical. Deletion of the BLH1 gene is not lethal under normal growth conditions. However, blh1 mutants show hypersensitivity to bleomycin, indicating that bleomycin hydrolase is able to inactivate bleomycin in vivo and to protect cells from bleomycin-induced toxicity.

Amino Acid Sequence↗
PubMed2003

Comparison of statistical methods for classification of ovarian cancer using mass spectrometry data.

MOTIVATION: Novel methods, both molecular and statistical, are urgently needed to take advantage of recent advances in biotechnology and the human genome project for disease diagnosis and prognosis. Mass spectrometry (MS) holds great promise for biomarker identification and genome-wide protein profiling. It has been demonstrated in the literature that biomarkers can be identified to distinguish normal individuals from cancer patients using MS data. Such progress is especially exciting for the detection of early-stage ovarian cancer patients. Although various statistical methods have been utilized to identify biomarkers from MS data, there has been no systematic comparison among these approaches in their relative ability to analyze MS data. RESULTS: We compare the performance of several classes of statistical methods for the classification of cancer based on MS spectra. These methods include: linear discriminant analysis, quadratic discriminant analysis, k-nearest neighbor classifier, bagging and boosting classification trees, support vector machine, and random forest (RF). The methods are applied to ovarian cancer and control serum samples from the National Ovarian Cancer Early Detection Program clinic at Northwestern University Hospital. We found that RF outperforms other methods in the analysis of MS data.

Algorithms↗
PubMed2000

Ribosomal DNA and resolution of branching order among the ascomycota: how many nucleotides are enough?

Molecular phylogenies for the fungi in the Ascomycota rely heavily on 18S rRNA gene sequences but this gene alone does not answer all questions about relationships. Particularly problematical are the relationships among the first ascomycetes to diverge, the Archiascomycetes, and the branching order among the basal filamentous ascomycetes, the Euascomycetes. Would more data resolve branching order? We used the jackknife and bootstrapping resampling approach that constitutes the "pattern of resolved nodes" method to address the relationship between number of variable sites in a DNA sequence alignment and support for taxonomic clusters. We graphed the effect of increasing sizes of subsamples of the 18S rRNA gene sequences on bootstrap support for nodes in the Ascomycota tree. Nodes responded differently to increasing data. Some nodes, those uniting the filamentous ascomycetes for example, would still have been well supported with only two thirds of the 18S rRNA gene. Other nodes, like the one uniting the Archiascomycetes as a monophyletic group, would require about double the number of variable sites available in the 18S gene for 95% neighbor-joining bootstrap support. Of the several groups emerging at the base of the filamentous ascomycetes, the Pezizales receive the most support as the first to diverge. Our analysis suggests that we would also need almost three times as much sequence data as that provided by the 18S gene to confirm the basal position for the Pezizales and more than seven times as much data to resolve the next group to diverge. If more data from other genes show the same pattern, the lack of resolution for the filamentous ascomycetes may indicate rapid radiation within this clade.

Ascomycota↗
PubMed2004

Molecular systematics and biogeography of the southern South american freshwater "crabs" Aegla (decapoda: Anomura: Aeglidae) using multiple heuristic tree search approaches.

Recently new heuristic genetic algorithms such as Treefinder and MetaGA have been developed to search for optimal trees in a maximum likelihood (ML) framework. In this study we combined these methods with other standard heuristic approaches such as ML and maximum parsimony hill-climbing searches and Bayesian inference coupled with Markov chain Monte Carlo techniques under homogeneous and mixed models of evolution to conduct an extensive phylogenetic analysis of the most abundant and widely distributed southern South American freshwater"crab,"the Aegla(Anomura: Aeglidae). A total of 167 samples representing 64 Aegla species and subspecies were sequenced for one nuclear (28S rDNA) and four mitochondrial (12S and 16S rDNA, COI, and COII) genes (5352 bp total). Additionally, six other anomuran species from the genera Munida,Pachycheles, and Uroptychus(Galatheoidea), Lithodes(Paguroidea), and Lomis(Lomisoidea) and the nuclear 18S rDNA gene (1964 bp) were included in preliminary analyses for rooting the Aegla tree. Nonsignificantly different phylogenetic hypotheses resulted from all the different heuristic methods used here, although the best scored topologies found under the ML hill-climbing, Bayesian, and MetaGA approaches showed considerably better likelihood scores (Delta> 54) than those found under the MP and Treefinder approaches. Our trees provided strong support for most of the recognized Aegla species except for A. cholchol,A. jarai,A. parana,A. marginata, A. platensis, and A. franciscana, which may actually represent multiple species. Geographically, the Aegla group was divided into a basal western clade (21 species and subspecies) composed of two subclades with overlapping distributions, and a more recent central-eastern clade (43 species) composed of three subclades with fairly well-recognized distributions. This result supports the Pacific-Origin Hypothesis postulated for the group; alternative hypotheses of Atlantic or multiple origins were significantly rejected by our analyses. Finally, we combined our phylogenetic results with previous hypotheses of South American paleodrainages since the Jurassic to propose a biogeographical framework of the Aegla radiation.

Animals↗
PubMedDate not supplied

Evolutionary history and higher order classification of AAA+ ATPases.

The AAA+ ATPases are enzymes containing a P-loop NTPase domain, and function as molecular chaperones, ATPase subunits of proteases, helicases or nucleic-acid-stimulated ATPases. All available sequences and structures of AAA+ protein domains were compared with the aim of identifying the definitive sequence and structure features of these domains and inferring the principal events in their evolution. An evolutionary classification of the AAA+ class was developed using standard phylogenetic methods, analysis of shared sequence and structural signatures, and similarity-based clustering. This analysis resulted in the identification of 26 major families within the AAA+ ATPase class. We also describe the position of the AAA+ ATPases with respect to the RecA/F1, helicase superfamilies I/II, PilT, and ABC classes of P-loop NTPases. The AAA+ class appears to have undergone an early radiation into the clamp-loader, DnaA/Orc/Cdc6, classic AAA, and "pre-sensor 1 beta-hairpin" (PS1BH) clades. Within the PS1BH clade, chelatases, MoxR, YifB, McrB, Dynein-midasin, NtrC, and MCMs form a monophyletic assembly defined by a distinct insert in helix-2 of the conserved ATPase core, and additional helical segment between the core ATPase domain and the C-terminal alpha-helical bundle. At least 6 distinct AAA+ proteins, which represent the different major clades, are traceable to the last universal common ancestor (LUCA) of extant cellular life. Additionally, superfamily III helicases, which belong to the PS1BH assemblage, were probably present at this stage in virus-like "selfish" replicons. The next major radiation, at the base of the two prokaryotic kingdoms, bacteria and archaea, gave rise to several distinct chaperones, ATPase subunits of proteases, DNA helicases, and transcription factors. The third major radiation, at the outset of eukaryotic evolution, contributed to the origin of several eukaryote-specific adaptations related to nuclear and cytoskeletal functions. The new relationships and previously undetected domains reported here might provide new leads for investigating the biology of AAA+ ATPases.

Adenosine Triphosphatases↗
PubMed1999

Life: past, present and future.

Molecular methods of taxonomy and phylogeny have changed the way in which life on earth is viewed; they have allowed us to transition from a eukaryote-centric (five-kingdoms) view of the planet to one that is peculiarly prokarote-centric, containing three kingdoms, two of which are prokaryotic unicells. These prokaryotes are distinguished from their eukaryotic counterparts by their toughness, tenacity and metabolic diversity. Realization of these features has, in many ways, changed the way we feel about life on earth, about the nature of life past and about the possibility of finding life elsewhere. In essence, the limits of life on this planet have expanded to such a degree that our thoughts of both past and future life have been altered. The abilities of prokaryotes to withstand many extreme conditions has led to the term extremophiles, used to describe the organisms that thrive under conditions thought just a few years ago, to be inconsistent with life. Perhaps the most extensive adaptation to extreme conditions, however, is represented by the ability of many bacteria to survive nutrient conditions not compatible with eukaryotic life. Prokaryotes have evolved to use nearly every redox couple that is in abundance on earth, filling the metabolic niches left behind by the oxygen-using, carbon-eating eukaryotes. This metabolic plasticity leads to a common feature in physically stratified environments of layered microbial communities, chemical indicators of the metabolic diversity of the prokaryotes. Such 'metabolic extremophily' forms a backdrop by which we can view the energy flow of life on this planet, think about what the evolutionary past of the planet might have been, and plan ways to look for life elsewhere, using the knowledge of energy flow on earth.

Adaptation, Physiological↗
PubMedDate not supplied

SVM-based feature selection for characterization of focused compound collections.

Artificial neural networks, the support vector machine (SVM), and other machine learning methods for the classification of molecules are often considered as a "black box", since the molecular features that are most relevant for a given classifier are usually not presented in a human-interpretable form. We report on an SVM-based algorithm for the selection of relevant molecular features from a trained classifier that might be important for an understanding of ligand-receptor interactions. The original SVM approach was extended to allow for feature selection. The method was applied to characterize focused libraries of enzyme inhibitors. A comparison with classical Kolmogorov-Smirnov (KS)-based feature selection was performed. In most of the applications the SVM method showed sustained classification accuracy, thereby relying on a smaller number of molecular features than KS-based classifiers. In one case both methods produced comparable results. Limiting the calculation of descriptors to only the most relevant ones for a certain biological activity can also be used to speed up high-throughput virtual screening.

Algorithms↗
PubMedDate not supplied

Molecular evolution of H+-ATPases. I. Methanococcus and Sulfolobus are monophyletic with respect to eukaryotes and Eubacteria.

The classification of methanogenic bacteria as archaebacteria based on 16 s rRNA sequence analysis is currently in dispute. To provide an alternative molecular marker, the polymerase chain reaction technique was used to amplify a 930 bp fragment of Methanococcus thermolithotrophicus genomic DNA corresponding to the catalytic domain of the membrane H+-ATPase. The deduced amino acid sequence was 54-58% identical to the approximately 70 kDa subunits of Sulfolobus acidocaldarius and the eukaryotic vacuolar-type H+-ATPase, and only 29% identical to the beta subunit of the eubacterial-type F0F1-ATPases. Interestingly, a highly conserved aspartate residue in the phosphorylation domain of E1E2-ATPases (P-type) is conserved in the Methanococcus sequence, but is absent from all other known vacuolar and F0F1-ATPases. This suggests that the H+-ATPase of M. thermolithotrophicus, like that of M. voltae, may have a phosphorylated intermediate, despite belonging to the vacuolar-type class of proton pumps. Phylogenetic analysis using Felsenstein's maximum likelihood method and Lake's evolutionary parsimony method confirmed that the H+-ATPases of the two archaebacteria, Methanococcus and Sulfolobus, when compared to eukaryotic vacuolar-type ATPases and eubacterial F0F1-ATPases, form a monophyletic group.

Amino Acid Sequence↗
PubMed1997

Hirschsprung's disease as a neurochristopathy.

Recent molecular-genetic and histochemical studies of intestinal aganglionosis have confirmed the initial classification established by Bolande, who considered Hirschsprung's disease (HD) a neurocristopathy. This paper is a critical review of the results of molecular-genetic studies carried out from 1992 to date. In particular, the author focuses on the possible clinical impact of the identification of RET as a causative gene for HD.

Drosophila Proteins↗
PubMed2004

Molecular phylogeny of the antitropical genus Pseudolabrus (Perciformes: Labridae): evidence for a Southern Hemisphere origin.

The genus Pseudolabrus comprises 11 species of marine nearshore fishes which are antitropically distributed: two species occur in East Asia, the remaining nine species being distributed in the Southern Hemisphere, mainly in the temperate Pacific. The distributions of their closely allied genera, collectively called "pseudolabrines" are, however, restricted to the Australia-New Zealand region. The molecular phylogeny of six of the 11 Pseudolabrus species from both Hemispheres and four of the five other pseudolabrine genera was reconstructed from nucleotide sequence data from mitochondrial DNA 12S rRNA, tRNAVal, and 16S rRNA genes. Both parsimony and Bayesian analyses were performed. Results are not consistent with a previous phylogenetic hypothesis based on osteological data, particularly in the relationship between Pseudolabrus and Notolabrus, indicating a probable need for reviewing the status of Notolabrus (or the delimitations of both Pseudolabrus and Notolabrus). The two Northern Hemisphere species of Pseudolabrus were monophyletic and nested deep into the clade of the Southern Hemisphere pseudolabrines, which indicates that both pseudolabrines and Pseudolabrus originated in the Southern Hemisphere. A dispersal rather than vicariance explanation for the antitropical distribution of Pseudolabrus is more parsimonious given the number of dispersal events, extinctions, and evolutionary adaptations required under the phylogeny. Based on molecular clock calibrations, the transequatorial divergence was suggested to be early to mid Pliocene at the earliest.

Animals↗
PubMed1982

Molecular weight distribution, diffusibility and comparability of middle molecular fractions prepared from normal and uremic sera by different fractionation procedures.

Sephadex G-25 (SG-25) chromatography of normal and uremic (U) sera yielded three (A, B, C) optically active (280 nm) fractions. Only fraction B disclosed a substantial increase in uremia that could not be counteracted by routine hemodialysis. Although middle molecules (MM) might be included in all SG-25 fractions (B greater than C greater than A), none of them was exclusively composed of MM. Solutes in U fraction B and C were found to be (a) heat stable; (b) soluble in ethanol; (c) diffusible through a Visking membrane, and (d) adsorbed by activated charcoal. Solutes in U fraction B and C and those in a toxic ethanol U serum extract could be partially or entirely recovered in the same Dowex fractions which were obtained by Dowex chromatography of native U sera. Methodical pitfalls leading to misinterpretation of molecular weight data obtained by SG chromatography and to erroneous classification of MM are also thoroughly discussed in this paper.

Chemical Fractionation↗
PubMed2003

Classification of seizures and epilepsy.

The management of seizures and epilepsy begins with forming a differential diagnosis, making the diagnosis, and then classifying seizure type and epileptic syndrome. Classification guides treatment, including ancillary testing, management, prognosis, and if needed, selection of the appropriate antiepileptic drug (AED). Many AEDs are available, and certain seizure types or epilepsy syndromes respond to specific AEDs. The identification of the genetics, molecular basis, and pathophysiologic mechanisms of epilepsy has resulted from classification of specific epileptic syndromes. The classification system used by the International League Against Epilepsy is periodically revised. The proposed revision changes the classification emphasis from the anatomic origin of seizures (focal vs generalized) to seizure semiology (ie, the signs or clinical manifestations). Modified systems have been developed for specific circumstances (eg, neonatal seizures, infantile seizures, status epilepticus, and epilepsy surgery). This article reviews seizure and epilepsy classification, emphasizing new data.

Animals↗
PubMed2001

[Esophageal, gastric and colorectal tumors].

The new WHO-classification of the tumours of the digestive System replaces the "blue books", and are now dealt with completely in a single book. In addition to the histological features of the lesions, the new classification also contains information on epidemiology, aetiology, endoscopy, genetic susceptibility, molecular genetics, prognosis and predictive factors. The erstwhile mostly black-and-white histological photographs have at last again been replaced by numerous colour photographs and supplemented by endoscopic and macroscopic pictures. The changes to the individual tumour classifications are only few. The former classification of the malignant lymphomas of the gastrointestinal tract has now been replaced by the classification of these lesions that has long been in use. New additions are the gastrointestinal tract has long been in use. New additions are the gastrointestinal stroma tumours (GIST) and the gastrointestinal autonomic nerve tumour (GANT). To the epithelial tumours of the oesophagus have now been added the basaloid squamous cell tumours of the vermiform appendix and the colorectum have now been added the serrated adenoma and the small-cell carcinoma. The following new chapter have been included: adenocarcinoma of the oesophagogastric junction, secondary carcinomas of the stomach, secondary tumours of the small bowel and colon, the Peutz-Jeghers syndrome, juvenile polyposis, familial adenomatosis coli, and HNPCC. For the first time the intra-epithelial neoplasias in chronic inflammatory bowel disease have been differentiated, i.e. adenomas distinguished from the dysplasias, while the latter term has now been replaced by the term "intra-epithelial neoplasias". In comparison with the former "blue books", the new WHO-classification, prepared by presentatives of numerous disciplines--for the first time including clinicians--has taken on the character of a text book.

Colonic Neoplasms↗
PubMed1992

[Morphometric-stereological study of hippocampal long term potentiation with special consideration of the analysis of variance with two-way hierarchical classification].

Regarding the hippocampal formation and especially the external two thirds of it's dentate molecular layer a lot of possible morphological changes after long-term potentiation (LTP) have been described in literature. The present morphometric-stereological study of vesicles in axo-spino-dendritic synapses of the inner third of the molecular layer was done under the aspect of heterosynaptic influences following LTP. Because of the hierarchical link of the three analytic levels (test-group, animal, synapse), for statistical interpretation we used the analysis of variance with two-way hierarchical classification. Between the 3 groups (passive control, active control, LTP-group) we found no significant differences. Because of the great differences between the vesicles even within a single synapse we subsequently investigated the middle third of the molecular layer, i.e. the terminal area of the stimulated perforant path. No differences between the three groups we found here either. There was no confirmation for the expected greater homogenization of the synapses based on the uniform input. As a result of this study pure morphological studies without selective staining of specific population of synapses are considered inadvisable. Only with the help of selective staining in the area of the synapses possible differences between the groups may be found.

Analysis of Variance↗
PubMed1997

Clustering Molecular Sequences with Their Components.

Motivation: Several methods in genetic information have recently been developed to estimate classification of protein sequences through their sequence similarity. These methods are essential for understanding the function of predicted open reading frames (ORFs) and their molecular evolutionary processes. However, since many protein sequences consist of a number of independently evolved structural units (we refer to these units as components), the combinatorial nature of the components makes it difficult to classify the sequences. Results: This paper presents a new method for classifying uncharacterized protein sequences. As the measure of sequence similarity, we use similarity score computed by a method based on the Smith-Waterman local alignment algorithm. Here we introduce how this method cope when sequences have multi-component structure. This method was applied to predicted ORFs on the Escherichia coli genome and we discuss the algorithm and experimental results.

Journal Article↗
PubMed1996

A molecular perspective of the genetic relationships of G-protein coupled melatonin receptor subtypes.

Successful cloning of melatonin receptors from various target tissues in the past few years has increased our understanding of the molecular signal transduction mechanisms of G-protein coupled melatonin receptors, of which three subtypes (MEL-1A, MEL-1B, and MEL-1C) have been reported in different vertebrates. Based upon melatonin receptor sequences available in the Genbank database, we have performed phylogenetic analyses of the nucleotide and encoded amino acid sequences of G-protein-coupled melatonin receptors, and determined the range of amino acid identities between melatonin receptors of the same and different subtypes. Besides the three well-known subtypes, a potential novel subtype of MEL-1D, as exemplified by unique separation of Xenopus X2.0 sequence (Genbank accession No. U31826) from the others in the protein phylogenetic tree, possibly exists. In addition, one of the chicken brain melatonin receptor sequences has been identified as belonging to the MEL-1B subtype. Our analyses showed that melatonin receptors of the same subtype and different subtypes are likely to share > or = 75% and < 65% amino acid identities, respectively. Phylogenetic analysis based on amino acid comparisons will be needed to determine the subtype status of any pair of melatonin receptor sequences that exhibit > or = 65% to < 75% amino acid identity. Despite the usefulness of genetic relatedness in the subtype classification of G-protein-coupled melatonin receptors, functional correlation of molecular structure may ultimately prove the most comprehensive approach in melatonin receptor classification.

Amino Acid Sequence↗
PubMed1996

Renal cell carcinoma.

Renal cell carcinoma remains a challenge to clinical medicine, with curative therapy experienced by a minority of patients. Mounting evidence suggests that the biological response modifiers, which consistently produce durable responses in some patients, may not need to be given in the high doses that have been associated with considerable, even fatal, toxicity; low-dose regimens in combination with conventional chemotherapeutic agents are yielding comparable, and possibly superior, results. Molecular biologic techniques have now advanced to the point where better classification schemes and prognostic variables are being elucidated, which may allow better optimization of specific treatment programs by allowing better patient discrimination. Further, with a better understanding of the molecular mechanisms of renal carcinogenesis, new agents and approaches to the problem of advanced renal cell carcinoma can be developed.

Carcinoma, Renal Cell↗
PubMed2006

Treatment of adult acute lymphoblastic leukemia.

In the early 1980s, adult acute lymphoblastic leukemia (ALL) was a rarely curable disease with overall survival < 10%. After adapting combinations employed by pediatric groups, the outcome improved to 30-40%. A period of stagnation followed with improvement only in distinct subgroups. In the past 5 years, however, striking new developments have been noticeable. Progress has been made in molecular diagnostics of ALL. Improvements to standard therapy including stem cell transplantation (SCT) have occurred and a variety of new drugs for ALL are under evaluation. Rapid diagnosis and classification of ALL is increasingly important to identify prognostic factors and molecular genetic subsets that will be the focus of "targeted" therapies as we enter the era of subset specific treatment. In the following review we will discuss treatment of adult ALL (excluding elderly patients,(1) adolescents(2) and patients with Ph/BCR-ABL positive ALL(3)).

Adult↗