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PubMed1993

Molecular mechanism of inhibition of mammalian protein synthesis by some four-chain agglutinins. Proposal of an extended classification of plant ribosome-inactivating proteins (rRNA N-glycosidases).

The four chain agglutinins from Abrus precatorius, Viscum album and Ricinus communis promote depurination of the 28 S rRNA from rabbit reticulocyte ribosomes characteristic of the common ribosome-inactivating proteins (RIPs). These agglutinins inhibited mammalian protein synthesis at nanomolar concentrations but they do not affect plant protein synthesis under the same conditions. Therefore, they should also be considered as true RIPs but of a new class, the four-chain RIPs. An extended classification of RIPs is presented based on the former one from Stirpe et al. [Bio/technology 10 (1992) 405-412].

Animals↗

PubMed2004

Pathological and molecular biological aspects of the renal epithelial neoplasms, up-to-date.

Renal neoplasms are not necessarily high in frequency, but they are characteristic in their heterogeneity and occasional association with systemic familial tumor syndromes and phacomatoses (e.g. clear cell renal cell carcinoma and von Hippel-Lindau disease, Wilms tumor and aniridia, genitourinary malformation and mental retardation (so-called, WAGR syndrome), and angiomyolipoma and tuberous sclerosis). Physicians and pathologists should take note of these syndromes and associated renal neoplasms because they have provided important clues to elucidate the mechanism of tumorigenesis concerning cancer-suppressor genes. This review aims to present recent classification of renal parenchymal neoplasms based on their molecular biological characteristics, and future problems yet to be clarified.

Adenocarcinoma↗

PubMed2003

Lissencephaly and the molecular basis of neuronal migration.

Migration of post-mitotic neurons from the ventricular zone to the cortical plate during embryogenesis comprises one of the most critical stages in brain development. Deficiency of this process often results in major brain malformations, including human lissencephaly (smooth brain). Since discovery of the first genetic cause of lissencephaly, deletions of chromosome 17p13.3 in Miller-Dieker syndrome, rapid progress in our understanding of neuronal migration has been made based on advances in both brain imaging technology and molecular genetics. This progress has resulted in a new system of classification that began with pathological descriptions and has evolved to include patterns on brain imaging, causative genes and most recently the molecular pathways and proposed modes of migration involved. In this review, we summarize current knowledge regarding five genes that cause or contribute to human lissencephaly, including LIS1, 14-3-3 epsilon, DCX, RELN and ARX. Each of these is associated with a characteristic pattern of malformation that involves the cerebral cortex and sometimes other brain structures. Based on detailed genotype-phenotype analysis, we can now infer the most likely causative gene based on brain imaging and other clinical findings, and inversely are becoming able to predict clinical severity based on the specific mutations detected. We also hypothesize, for the first time, a relationship between the specific type of lissencephaly observed and deficiency of specific modes of neuronal migration.

1-Alkyl-2-acetylglycerophosphocholine Esterase↗

PubMed1993

Molecular genetics of neuroendocrine tumors.

Neuroendocrine tumors are a group of malignancies that arise from primitive neuroectodermal cells. There is, however, considerable variation in the location and clinical behavior of these tumors. They are often difficult to distinguish from other malignancies and difficult to classify. Recent advances in molecular genetics have attempted to resolve some issues regarding accurate diagnosis, classification into prognostic subgroups, and understanding of basic common mechanisms underlying the development of these tumors. Correlation of morphologic changes with molecular changes induced by some potential therapeutic differentiating agents may lead to more rational therapy for these malignancies.

Cell Adhesion Molecules, Neuronal↗

PubMed2001

Clinical importance of cytogenetics in acute myeloid leukaemia.

Acquired chromosome aberrations are present in the marrow of most patients with acute myeloid leukaemia (AML) at diagnosis. Cytogenetically, AML is a very heterogeneous disease with over 160 structural chromosome abnormalities observed recurrently to date. Molecular dissection of many reciprocal translocations and inversions has resulted in cloning of the genes involved in leukaemogenesis. Some recurrent aberrations and the resulting gene rearrangements, namely inv(16)/t(16;16) and CBFbeta- MYH11, t(8;21) and CBFA2-CBFA2T1, t(15;17) and PML-RARalpha, and rearrangements of band 11q23 and the MLL gene, are now used to help define distinct disease entities within AML in the new World Health Organization classification of haematological malignancies. Moreover, cytogenetic abnormalities, whether molecularly characterized or not, are among the most important, independent prognostic factors in AML, and are being used in the management of AML patients. This review presents current information on chromosome abnormalities in AML, and on associations between karyotype and clinical characteristics and outcome of AML patients.

Acute Disease↗

PubMed2005

How to best classify breast cancer: conventional and novel classifications (review).

Breast cancer is a complex disease and different classifications, mostly based on clinical and pathological features, have been used for guiding the management of patients. Most of them fail to reflect breast cancer heterogeneity, which could be the reason why the treatment fails in approximately 30% of cases. Emerging molecular studies based on gene expression profiling using DNA microarrays have defined new molecular subtypes of breast cancer associated with the cell-of-origin distinction. Thus, breast cancer has been divided into five subgroups with distinct biological features and clinical outcomes. We have tried here to confront the conventional existing classifications with this new molecular taxonomy. It is likely that using all types of classification together will help in the management of breast cancer.

Breast Neoplasms↗

PubMed2005

Molecular phylogenetics and biogeography of Lepus in Eastern Asia based on mitochondrial DNA sequences.

In spite of several classification attempts among taxa of the genus Lepus, phylogenetic relationships still remain poorly understood. Here, we present molecular genetic evidence that may resolve some of the current incongruities in the phylogeny of the leporids. The complete mitochondrial cytb, 12S genes, and parts of ND4 and control region fragments were sequenced to examine phylogenetic relationships among Chinese hare taxa and other leporids throughout the World using maximum parsimony, maximum likelihood, and Bayesian phylogenetic reconstruction approaches. Using reconstructed phylogenies, we observed that the Chinese hare is not a single monophyletic group as originally thought. Instead, the data infers that the genus Lepus is monophyletic with three unique species groups: North American, Eurasian, and African. Ancestral area analysis indicated that ancestral Lepus arose in North America and then dispersed into Eurasia via the Bering Land Bridge eventually extending to Africa. Brooks Parsimony analysis showed that dispersal events followed by subsequent speciation have occurred in other geographic areas as well and resulted in the rapid radiation and speciation of Lepus. A Bayesian relaxed molecular clock approach based on the continuous autocorrelation of evolutionary rates along branches estimated the divergence time between the three major groups within Lepus. The genus appears to have arisen approximately 10.76 MYA (+/-0.86 MYA), with most speciation events occurring during the Pliocene epoch (5.65+/-1.15 MYA approximately 1.12 +/- 0.47 MYA).

Animals↗

PubMed1988

DNA probes in diagnostic pathology.

Molecular pathology has become firmly established as a distinctive discipline in medicine. It has introduced radical changes in concepts of disease causation and in classification of disease states affecting humans and other organisms. In addition, molecular pathology represents a "new" diagnostic technology with many potentials that have been heretofore untapped. This overview provides a discussion of the use of DNA probes in the study of human diseases. The role of detectable genetic abnormalities in pathogenesis will be considered, as well as their possible impact on nosology and disease classification.

DNA↗

PubMed2006

Molecular phylogenetics of the spider infraorder Mygalomorphae using nuclear rRNA genes (18S and 28S): conflict and agreement with the current system of classification.

Mygalomorph spiders, which include the tarantulas, trapdoor spiders, and their kin, represent one of three main spider lineages. Mygalomorphs are currently classified into 15 families, comprising roughly 2500 species and 300 genera. The few published phylogenies of mygalomorph relationships are based exclusively on morphological data and reveal areas of both conflict and congruence, suggesting the need for additional phylogenetic research utilizing new character systems. As part of a larger combined evidence study of global mygalomorph relationships, we have gathered approximately 3.7 kb of rRNA data (18S and 28S) for a sample of 80 genera, representing all 15 mygalomorph families. Taxon sampling was particularly intensive across families that are questionable in composition-Cyrtaucheniidae and Nemesiidae. The following primary results are supported by both Bayesian and parsimony analyses of combined matrices representing multiple 28S alignments: (1) the Atypoidea, a clade that includes the families Atypidae, Antrodiaetidae, and Mecicobothriidae, is recovered as a basal lineage sister to all other mygalomorphs, (2) diplurids and hexathelids form a paraphyletic grade at the base of the non-atypoid clade, but neither family is monophyletic in any of our analyses, (3) a clade consisting of all sampled nemesiids, Microstigmata and the cyrtaucheniid genera Kiama, Acontius, and Fufius is consistently recovered, (4) other sampled cyrtaucheniids are fragmented across three separate clades, including a monophyletic North American Euctenizinae and a South African clade, (5) of the Domiothelina, only idiopids are consistently recovered as monophyletic; ctenizids are polyphyletic and migids are only weakly supported. The Domiothelina is not monophyletic. The molecular results we present are consistent with more recent hypotheses of mygalomorph relationship; however, additional work remains before mygalomorph classification can be formally reassessed with confidence-increased taxonomic sampling and the inclusion of additional character systems (more genes and morphology) are required.

Animals↗

PubMed2003

Placental mammal diversification and the Cretaceous-Tertiary boundary.

Competing hypotheses for the timing of the placental mammal radiation focus on whether extant placental orders originated and diversified before or after the Cretaceous-Tertiary (KT) boundary. Molecular studies that have addressed this issue suffer from single calibration points, unwarranted assumptions about the molecular clock, andor taxon sampling that lacks representatives of all placental orders. We investigated this problem using the largest available molecular data set for placental mammals, which includes segments of 19 nuclear and three mitochondrial genes for representatives of all extant placental orders. We used the ThorneKishino method, which permits simultaneous constraints from the fossil record and allows rates of molecular evolution to vary on different branches of a phylogenetic tree. Analyses that used different sets of fossil constraints, different priors for the base of Placentalia, and different data partitions all support interordinal divergences in the Cretaceous followed by intraordinal diversification mostly after the KT boundary. Four placental orders show intraordinal diversification that predates the KT boundary, but only by an average of 10 million years. In contrast to some molecular studies that date the rat-mouse split as old as 46 million years, our results show improved agreement with the fossil record and place this split at 16-23 million years. To test the hypothesis that molecular estimates of Cretaceous divergence times are an artifact of increased body size subsequent to the KT boundary, we also performed analyses with a "KT body size" taxon set. In these analyses, interordinal splits remained in the Cretaceous.

Animals↗

PubMed2001

Geometric nomenclature and classification of RNA base pairs.

Non-Watson-Crick base pairs mediate specific interactions responsible for RNA-RNA self-assembly and RNA-protein recognition. An unambiguous and descriptive nomenclature with well-defined and nonoverlapping parameters is needed to communicate concisely structural information about RNA base pairs. The definitions should reflect underlying molecular structures and interactions and, thus, facilitate automated annotation, classification, and comparison of new RNA structures. We propose a classification based on the observation that the planar edge-to-edge, hydrogen-bonding interactions between RNA bases involve one of three distinct edges: the Watson-Crick edge, the Hoogsteen edge, and the Sugar edge (which includes the 2'-OH and which has also been referred to as the Shallow-groove edge). Bases can interact in either of two orientations with respect to the glycosidic bonds, cis or trans relative to the hydrogen bonds. This gives rise to 12 basic geometric types with at least two H bonds connecting the bases. For each geometric type, the relative orientations of the strands can be easily deduced. High-resolution examples of 11 of the 12 geometries are presently available. Bifurcated pairs, in which a single exocyclic carbonyl or amino group of one base directly contacts the edge of a second base, and water-inserted pairs, in which single functional groups on each base interact directly, are intermediate between two of the standard geometries. The nomenclature facilitates the recognition of isosteric relationships among base pairs within each geometry, and thus facilitates the recognition of recurrent three-dimensional motifs from comparison of homologous sequences. Graphical conventions are proposed for displaying non-Watson-Crick interactions on a secondary structure diagram. The utility of the classification in homology modeling of RNA tertiary motifs is illustrated.

Base Pairing↗

PubMed1997

Acrocephalosyndactyly syndromes: a review.

Over the last quarter century, a revision has taken place in the classification of the acrocephalosyndactyly syndromes. This reflects the advances in molecular biology that have led to improved genetic mapping of these syndromes. In this review we provide an overview of these major acrocephalosyndactyly syndromes, including the current classification system. The craniofacial, neurological, cardiac, pulmonary, visceral, and extremity anomalies are discussed with special emphasis on hand anomalies. Hand reconstruction techniques, including specific surgical procedures, the timing of the surgical reconstruction, and postoperative therapy are discussed. The need for coordinated care of the multidisciplinary disorders of these patients cannot be overemphasized, especially in the perioperative period.

Acrocephalosyndactylia↗

PubMed2005

A unique activating mutation in JAK2 (V617F) is at the origin of polycythemia vera and allows a new classification of myeloproliferative diseases.

Myeloproliferative disorders (MPDs) are heterogeneous diseases that occur at the level of a multipotent hematopoietic stem cell. They are characterized by increased blood cell production related to cytokine hypersensitivity and virtually normal cell maturation. The molecular pathogenesis of the MPDs has been poorly understood, except for chronic myeloid leukemia (CML), where the Bcr-Abl fusion protein exhibits constitutive kinase activity. Since some rare MPDs are also related to a dysregulated kinase activity, a similar mechanism was thought to be likely responsible for the more frequent MPDs. We investigated the mechanisms of endogenous erythroid colony formation (EEC) by polycythemia vera (PV) erythroid progenitor cells and found that EEC formation was abolished by a pharmacological inhibitor of JAK2 as well as an siRNA against JAK2. JAK2 sequencing revealed a unique mutation in the JH2 domain leading to a V617F substitution in more than 80% of the PV samples. This mutation in the pseudokinase autoinhibitory domain results in constitutive kinase activity and induces cytokine hypersensitivity or independence of factor-dependent cell lines. Retroviral transduction of the mutant JAK2 into murine HSC leads to the development of an MPD with polycythemia. The same mutation was found in about 50% of patients with idiopathic myelofibrosis (IMF) and 30% of patients with essential thrombocythemia (ET). Using different approaches, four other teams have obtained similar results. The identification of the JAK2 mutation represents a major advance in our understanding of the molecular pathogenesis of MPDs that will likely permit a new classification of these diseases and the development of novel therapeutic approaches.

Amino Acid Substitution↗

PubMed2001

The core region of the coat protein gene is highly useful for establishing the provisional identification and classification of begomoviruses.

Polymerase chain reaction (PCR) was applied to detect and establish provisional identity of begomoviruses through amplification of a approximately 575 bp fragment of the begomoviral coat protein gene (CP), referred to as the 'core' region of the CP gene (core CP). The core CP fragment contains conserved and unique regions, and was hypothesized to constitute a sequence useful for begomovirus classification. Virus relationships were predicted by distance and parsimony analyses using the A component (bipartite viruses) or full genome (monopartite viruses), CP gene, core CP, or the 200 5'-nucleotides (nt) of the CP. Reconstructed trees and sequence divergence estimates yielded very similar conclusions for all sequence sets, while the CP 5'-200 nt was the best strain discriminator. Alignment of the core CP region for 52 field isolates with reference begomovirus sequences permitted provisional virus identification based on tree position and extent of sequence divergence. Geographic origin of field isolates was predictable based on phylogenetic separation of field isolates examined here. A 'closest match' or genus-level identification could be obtained for previously undescribed begomoviruses using the BLAST program to search a reference core CP database located at our website and/or in GenBank. Here, we describe an informative molecular marker that permits provisional begomovirus identification and classification using a begomoviral sequence that is smaller than the presently accepted, but less accessible CP sequence.

Capsid↗

PubMed1988

Molecular determinants for recognition of RU 24969 analogs at central 5-hydroxytryptamine recognition sites: use of a bilinear function and substituent volumes to describe steric fit.

The putative serotonin (5-HT) agonist RU 24969 [5-methoxy-3-1,2,3,6-tetrahydropyridin-4-yl)indole; 5-MeO-THPI] has been extensively used in the study and classification of 5-HT receptors. In order to study molecular determinants for recognition of THPIs at central 5-HT recognition sites, about 25 additional THPI derivatives were synthesized, incorporating, among others, 16 different indole-5-substituents and three different pyridine-N substituents in various combinations. Two saturated derivatives (piperidin-4-ylindoles) and two 2-methyl analogs were also included. Binding affinities at 5-HT1A, 5-HT2, and total 5-HT1 sites were obtained and the data were incorporated in quantitative structure-activity relationships (QSARs) using a combined linear free energy/molecular modeling approach. The QSAR analyses suggest distinct differences in the structural features that determine optimal potency at 5-HT1A sites versus those directing optimal potency for 5-HT2 sites. The parameter of the indole-5 substituent that almost exclusively determines potency for 5-HT1A sites is volume, the optimal size being about 24 cubic angstroms (calculated by fitting the activity versus volume data to a bilinear function). This is approximately the size of a carboxamide group. In contrast, at the 5-HT2 site both volume and hydrophobicity play major but opposing roles for the 5-substituent. A balance between the smallest possible volume and the greatest possible hydrophobicity is required for maximal 5-HT2 potency. Benzyl groups on the indole-1 or pyridyl-1 positions also favor potency at the 5-HT2 site (probably largely due to increased hydrophobic binding) while decreasing potency at the 5-HT1A site. A minor electronic contribution to the QSARs involving the charge on the indole 5-carbon is of opposite sign for 5-HT1A versus 5-HT2 sites and thus may also be useful for selective drug design. The data are consistent with the possibility that the indole and pyridyl rings are in a coplanar configuration when binding at both 5-HT1A and 5-HT2 sites, because the indole-2-methyl substituent, which provides a large energy barrier to the coplanar configuration, greatly reduces the potency of THPIs at both binding sites. Similarities in analog selectivity patterns suggest that the indolic portion of these compounds binds similarly to that of other indole derivatives such as tryptamines; thus, it is possible that optimally selective substituents predicted by these QSARs may be extrapolated to tryptamines and other indoles.

Animals↗

PubMed2002

The conceptual basis for a new classification of the coccidia.

At the joint meeting of the 8th International Coccidiosis Conference and the Annual Scientific Meeting of the Australian Society for Parasitology in Palm Cove, Australia, in July 2001, a Controversial Roundtable was held on 'New classification of coccidia'. The aim of this Roundtable was to stimulate and encourage discussion and debate on current classification schemes for the group of parasitic protozoa known as the eimeriid coccidia. In the past, such classifications have been based only on phenotypic characters such as morphology, ultrastructure, life cycles, and host specificity. However, over the past 10-15 years, molecular phylogenetic studies on taxa of the eimeriid coccidia have revealed that several of the families, subfamilies, and genera that have been erected based on non-molecular characters are paraphyletic. Therefore, this Roundtable was an important forum for initial discussions on how a new and more comprehensive classification of the eimeriid coccidia, which takes into consideration both phenotypic and molecular characters, can be devised. The stimulus came from invited speakers who gave introductions into selected areas of taxonomy and classification. Following these introductions, a more general discussion with the audience addressed potential steps that may be taken in future work. This review is the immediate outcome of the Roundtable. It describes advantages and disadvantages of the use of phenotypic or molecular characters as the base for taxonomic schemes for eimeriid coccidia. It gives specific examples for drawbacks of current classifications based only on phenotypic characters as well as potential pitfalls associated with the use of only molecular phylogenies. It addresses current controversies as well as rules of taxonomy and nomenclature relevant for the eimeriid coccidia. Finally, it recommends the establishment of an international group of scientists to meet on a regular basis, stimulate further discussions, and give direction on how the final goal, i.e. a proposal for a revised, and widely accepted, classification of the eimeriid coccidia, may be achieved.

Animals↗

PubMed1979

The multiple forms of alpha-D-mannosidase in human plasma.

The acidic alpha-D-mannosidase in human plasma closely resembles liver acidic alpha-D-mannosidase in its affinity for concanavalin A-Sepharose, molecular weight and resolution into multiple components on DEAE-cellulose. A combination of chromatography on concanavalin A-Sepharose and gel filtration on Sephadex G-200 and Sepharose 6B suggests that four forms of intermediate alpha-D-mannosidase, which differ either in their molecular weight of affinity for concanavalin A, exist in human plasma. A practical classification and nomenclature for the multiple forms of intermediate alpha-D-mannosidase in plasma based on molecular weight and affinity for concanavalin A is proposed. Multiple forms of intermediate alpha-D-mannosidase were also observed by ion-exchange chromatography on DEAE-cellulose, but there was not a simple correlation between these forms and those obtained with the other separation procedures. The form of intermediate alpha-D-mannosidase least abundant in plasma, approx. 7% of the activity, has very similar properties to the neutral alpha-D-mannosidase in human liver. In contrast, the other three forms of intermediate alpha-D-mannosidase, which account for over 90% of the activity, do not appear to be present in liver, except perhaps in trace amounts.

Carbohydrate Metabolism, Inborn Errors↗

PubMed2001

Comparative immunohistochemical study of endometrioid and serous papillary carcinoma of endometrium.

OBJECTIVE: The aim of this study was to determine whether immunohistochemical analysis of molecular parameters can provide an alternative method for classification of endometrial cancer cases according to their aggressiveness. METHODS: Sixty-four cases of endometrial carcinoma were assigned to three groups: group I--28 cases of endometrioid well and moderately differentiated (G1-G2) carcinoma; group II--14 cases of endometrioid poorly differentiated (G3) carcinoma; group III--22 cases of serous papillary endometrial cancer. Immunohistochemistry was used to determine the existence of estrogen receptors (ER), progesterone receptors (PR), and the expression of bcl-2, p53, HER-2/neu and Ki-67. RESULTS: There was a significant difference in the immunohistochemical profile of the studied molecular parameters comparing the three study groups. The endometrioid G1-G2 cases (group I) were characterized by increased immunoreactivity for ER and PR (85.7% and 78.6%, respectively), increased immunoreactivity for bcl-2 (42.8%) and low expression of p53 (14.3%) and HER-2/neu (14.3%). In contrast to group I cases, the serous papillary endometrial cancer cases (group III) were characterized by immunonegativity for ER, PR and bcl-2 and high immunoreactivity for p53 (81.8%) and HER-2/neu (45.4%). The endometrioid G3 cases (group II) demonstrated an intermediate immunoprofile, characterized by immunonegativity for ER, PR and HER-2/neu, low immunoreactivity for bcl-2 (7.1%) and high expression of p53 (57.1%). The expression of Ki-67 did not differ significantly comparing the different cases of endometrial cancer. CONCLUSION: This study provides evidence that the immunohistochemical analysis of endometrial carcinoma differentiates between different grades and histological types, thus being useful in the distinction of high risk cases.

Aged↗