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PubMed2007

Recent advances in high-throughput molecular marker identification for superficial and invasive bladder cancers.

Bladder cancer is the fifth most common neoplasm in industrialized countries. Due to frequent recurrences of the superficial form of this disease, bladder cancer ranks as one of the most common cancers. Despite the description of a large number of tumor markers for bladder cancers, none have individually contributed to the management of the disease. However, the development of high-throughput techniques for simultaneous assessment of a large number of markers has allowed classification of tumors into clinically relevant molecular subgroups beyond those possible by pathological classification. Here, we review the recent advances in high-throughput molecular marker identification for superficial and invasive bladder cancers.

Biomarkers, Tumor↗
PubMed1994

Molecular systematics of the living rhinoceros.

Classification of the living species of rhinoceros has been somewhat controversial. Traditionally, the two-horned rhinoceros, which includes the African (Diceros and Ceratotherium) and the Asian (Dicerorhinus) forms, has been included in one group separate from the one-horned rhinoceros (Rhinoceros). However, recently some authors have regarded the Asian species as a group separate from the African species, irrespective of the number of horns. Furthermore, others have split the living rhinoceros into three unrelated groups that include the African two-horned species in one group, the Asian two-horned rhinoceros in another group, and the Asian one-horned rhinoceros in a third group. We investigated the systematic relationships of the living rhinoceros using high-resolution restriction site mapping of the ribosomal genes of the mitochondrial DNA, and our results support the traditional subdivision of the living rhinoceros based on the number of horns. Few groups of mammals are more critically endangered than the rhinoceros, and the data obtained in this work should provide information relevant to their conservation.

Animals↗
PubMed2006

Phylogeny of Cephalobina (Nematoda): molecular evidence for recurrent evolution of probolae and incongruence with traditional classifications.

Nematodes of the suborder Cephalobina include an ecologically and morphologically diverse array of species that range from soil-dwelling microbivores to parasites of vertebrates and invertebrates. Despite a long history of study, certain of these microbivores (Cephaloboidea) present some of the most intractable problems in nematode systematics; the lack of an evolutionary framework for these taxa has prevented the identification of natural groups and inhibited understanding of soil biodiversity and nematode ecology. Phylogenetic analyses of ribosomal (LSU) sequence data from 53 taxa revealed strong support for monophyly of taxa representing the Cephaloboidea, but do not support the monophyly of most genera within this superfamily. Historically these genera have primarily been recognized based on variation in labial morphology, but molecular phylogenies show the same general labial (probolae) morphotype often results from recurrent similarity, a result consistent with the phenotypic plasticity of probolae previously observed for some species in ecological time. Phylogenetic analyses of LSU rDNA also recovered strong support for some other groups of cephalobs, including taxa representing most (but not all) Panagrolaimoidea. In addition to revealing homoplasy of probolae, molecular trees also imply other unexpected patterns of character evolution or polarity, including recurrent similarity of offset spermatheca presence, and representation of complex probolae as the ancestral condition within Cephaloboidea. For Cephalobidae, molecular trees do not support traditional genera as natural groups, but it remains untested if deconstructing probolae morphotypes or other structural features into finer component characters may reveal homologies that help delimit evolutionary lineages.

Animals↗
PubMed1993

Molecular characterization of positive-strand RNA viruses: pestiviruses and the porcine reproductive and respiratory syndrome virus (PRRSV).

Molecular characterization has become an important tool for the analysis of viruses including their classification. The manuscript focuses on the molecular analysis of two members of the genus pestivirus (hog cholera virus, HCV and bovine viral diarrhea virus, BVDV) and of the recently discovered porcine reproductive and respiratory syndrome virus (PRRSV). The first protein encoded within the single large pestivirus ORF is a nonstructural protein with autoproteolytic activity. The cleavage site between the protease and the capsid protein p14 has been predicted previously, but recent experimental data indicate that processing occurs at a different site. The capsid protein is followed by a putative internal signal sequence and three glycoproteins which are part of the virion envelope. According to a new proposal for the nomenclature of the structural proteins of pestiviruses they are termed C, E0, E1 and E2. The genomes of BVDV pairs isolated from animals which came down with mucosal disease were analyzed. The genomes from cytopathogenic (cp) BVD viruses may contain insertions highly homologous to cellular sequences. In addition, cp BVDV may differ from its non cytopathogenic (noncp) counterpart by mere rearrangement of viral sequences. The disease PRRS, which emerged a few years ago, is caused by a single strand RNA virus; the viral genome is of positive polarity and has a size of 15 kb. Data concerning morphology, morphogenesis and virion composition suggested already that PRRSV belongs to a group of so-called arteriviruses which comprises equine arteritis virus (EAV), lactate dehydrogenase elevating virus (LDV) and simian hemorrhagic fever virus (SHFV). This conclusion has now been confirmed by analysis of genome organization, gene expression strategy and by comparison of deduced protein sequences.

Amino Acid Sequence↗
PubMed2003

[Mucinous spindle cell carcinoma of the kidney. A molecular analysis].

The new WHO-classification of renal tumors includes new subtypes, one of which is the mucinous, tubular, and spindle cell carcinoma. Many of these tumors had been previously diagnosed as sarcomatoid carcinoma. There are areas of cord-like growth and spindle cell configuration, sometimes with a clear cell appearance. The cells have low-grade nuclear features. It has been postulated that these tumors are related to the loop of Henle. In this study, 21 tumors were immunohistochemically and genetically analyzed. The analysis showed complex genomic aberrations, but no chromosome 3p losses. Fluorescence in situ hybridization detected no von Hippel-Lindau gene deletions on chromosome 3p25, which are characteristic for clear cell renal carcinomas. These findings show that there is no genetic relationship to clear cell renal carcinomas. The results of the immunohistochemical analyses showed a complex immunophenotype, but could not prove a derivation from the loop of Henle. The prognosis of these tumors seems to be favorable.

Adenocarcinoma, Mucinous↗
PubMedDate not supplied

[Current approaches to classification of glomerulonephritis].

Using methods of molecular pathology, the authors showed that characteristics of inflammatory-reparative processes in the kidney glomeruli depends on both nature of etiologic agents and specific features of the affected zone histoarchitectonics. They believe that subdivision of glomerulopathies into inflammatory (glomerulonephritis) and non-inflammatory is justified even though it is somewhat arbitrary.

Glomerulonephritis↗
PubMed2004

The role of molecular studies in lymphoma diagnosis: a review.

Lymphoma classification is based on a multiparametric approach to diagnosis, in which clinical features, morphology, immunophenotype, karyotype and molecular characteristics are important to varying degrees. While in most cases, a diagnosis can be confidently established on the basis of morphology and immunophenotype alone, a small proportion of diagnostically difficult cases will rely on molecular studies to enable a definitive diagnosis. This review discusses the various molecular techniques available including Southern blotting (SB), polymerase chain reaction (PCR), fluorescence in situ hybridisation (FISH)--including multicolour-FISH/spectral karyotyping and comparative genomic hybridisation--and also gene expression profiling using cDNA microarray technology. Emphasis is given to the analysis of antigen receptor gene rearrangements and chromosomal translocations as they relate to lymphoma diagnosis and also in the setting of minimal residual disease (MRD) detection and monitoring. Laboratories performing these tests need to have expertise in these areas of testing, and there is a need for greater standardisation of molecular tests. It is important to know the sensitivity and specificity of each test as well as its limitations and the pitfalls in the interpretation of results. Above all, results of molecular testing should never be considered in isolation, and must always be interpreted in the context of clinical and other laboratory data.

Blotting, Southern↗
PubMed2026

"Updates on diagnostic and prognostic molecular biomarkers of CNS tumors".

The diagnosis and classification of central nervous system (CNS) tumors has undergone a paradigm shift over the past decade, evolving from a purely histology-based approach to an integrated framework that incorporates molecular and epigenetic features. This review summarizes recent updates in key genomic and epigenomic biomarkers across major CNS tumor categories, with a focus on their diagnostic, prognostic, and therapeutic implications. DNA methylation profiling has emerged as a valuable tool for tumor classification, subgrouping, and grading, complementing traditional histopathologic assessment. Across diffuse gliomas, newly characterized molecular alterations have refined grading criteria and clarified the boundaries between tumor types, including important caveats about the use of individual molecular features as sole diagnostic criteria. In ependymomas, medulloblastomas, atypical teratoid/rhabdoid tumors, meningiomas, pineal tumors, and embryonal tumors, methylation profiling now defines biologically and clinically meaningful subgroups that inform risk stratification and treatment selection. The emerging recognition of mismatch repair-deficient gliomas and fusion-driven tumor entities further underscores the expanding complexity of CNS tumor taxonomy. As molecular technologies continue to advance, the integration of genomic, epigenomic, histopathologic, and clinical data will be essential to improving diagnostic precision, guiding therapy, and ultimately enhancing patient outcomes.

Embryonal↗
PubMed2002

Agenesis and dysgenesis of the corpus callosum.

Agenesis and dysgenesis of the corpus callosum is a frequent anomaly that presents with a spectrum of clinical features and exhibits variable findings in neurological studies. Clinical signs and symptoms are the result of cerebral and extracerebral malformations associated with callosal dysgenesis. Callosal agenesis may be an isolated anomaly or may be syndromic as part of more extensive malformations, metabolic and genetic disorders. The advent of modern techniques and equipment for neuroimaging have allowed us to define with more precision the type and severity of the callosal dysgenesis and accompanying other cerebral malformations. Molecular genetic studies allow the recognition and confirmation of new syndromes that until now were incompletely defined. In the context of these new pathologic entities, a new classification is proposed that may prove to be more useful than the traditional single category, "agenesis of the corpus callosum" and can serve as a basis for a later, more detailed, etiologic classification that integrates morphology and molecular genetics.

Agenesis of Corpus Callosum↗
PubMed1994

Molecular taxonomy of the yeasts.

The term 'yeast' is often taken as a synonym for Saccharomyces cerevisiae, but the phylogenetic diversity of yeasts is illustrated by their assignment to two taxonomic classes of fungi, the ascomycetes and the basidiomycetes. Subdivision of taxa within their respective classes is usually made from comparisons of morphological and physiological features whose genetic basis is often unknown. Application of molecular comparisons to questions in yeast classification offers an unprecedented opportunity to re-evaluate current taxonomic schemes from the perspective of quantitative genetic differences. This review examines the impact of molecular comparisons, notably rRNA/rDNA sequence divergence, on the current phenotypically defined classification of yeasts. Principal findings include: 1) budding ascomycetous yeasts are monophyletic and represent a sister group to the filamentous ascomycetes, 2) fission yeasts are ancestral to budding and filamentous ascomycetes, 3) the molecular phylogeny of basidiomycetous yeasts is generally congruent with type of hyphal septum, presence or absence of teliospores in the sexual state, and occurrence of cellular xylose.

DNA, Ribosomal↗
PubMed1998

Experimental pathology and breast cancer genetics: new technologies.

The goal is to understand the critical events in tumour development and to apply this understanding to new approaches to diagnosis, prevention and treatment. It is clear that breast cancer is a heterogeneous disease at the molecular level, raising the possibility of a future functional classification based on mechanisms rather than morphology. These molecular phenotypes will also confer predictive value on the potential of the tumour to invade, metastasise and respond to or resist new therapeutic strategies. Studies of the genome in individuals are predicted also to enable the identification of polymorphisms that are associated with increased susceptibility to environmental factors, in addition to possibly explaining de novo variations in responses to drugs and radiation. The difficulty is how to identify which, of the approximately 30,000 genes expressed by a typical cancer cell alone or in combination, are the ones involved in these processes. The majority of breast cancers have such a multitude of molecular changes that it is difficult to distinguish between those that are critical to tumour progression and those that are epiphenomena of genetic instability and abnormalities in DNA repair. The identification of the earliest events in carcinogenesis must be the best hope, as it will then be possible to target the events that predispose to other secondary changes before they occur. Genomics and proteomics is the current hope to take us forward. This involves the application of a number of new technologies to facilitate the profiling of individual tumours, including laser-guided microdissection of microscopic lesions, comparative genomic hybridisation and loss of heterozygosity analysis of DNA using microarray technology to study DNA and expressed RNAs and protein profiling using 2D gel mass spectroscopy. With over 100,000 mRNAs and proteins to examine in complex tissues and in various combinations, there is obviously going to be a requirement for a large investment in computing power (bioinformatics) to facilitate the analysis of these data in relation to the clinical characteristics of the individual tumour and the patient.

Bacteriophages↗
PubMed2004

Characterization of sorption mechanisms of VOCs with organobentonites using a LSER approach.

To fully utilize the sorption traits of organobentonites to control volatile organic compounds (VOCs) pollution, the sorption mechanisms of VOCs with organobentonites need to be understood adequately. The sorption of VOCs as vapors to a typical organobentonite, modified with cetyltrimethylammonium bromide (CTMAB-bentonite), was characterized using a linear solvation energy relationship (LSER) of the type log Kc = c + rR2 + s pi2H + a sigma(alpha2)H + b sigma(beta2)H + l log L16. The fitted LSER equation, log Kc = 0.434 + 0.968R2 - 0.0886pi2H + 2.170sigma(alpha2)H + 1.611sigma(beta2)H + 0.417 log L16, was obtained by a multiple regression of the partition coefficients of 22 probe solutes against the solvation parameters of the solutes. The coefficients of the LSER equation show that CTMAB-bentonite is a sorbent with nonsignificant dipolarity/polarizability, interacts with solutes partly through pi-/n-electron pairs, behaves both as hydrogen-bond donor and hydrogen-bond acceptor, and can interact with solutes by cavity/dispersion interactions. The related terms in LSER suggest that the potential factors governing the sorption of VOCs onto CTMAB-bentonite are dispersion interactions, hydrogen-bond acidity interactions, hydrogen-bond basicity interactions, and pi-/n-electron interactions. The dispersion interaction is recognized to be the predominant parameter for most solutes, whereas the contributions of the other parameters depend on specific solutes. The derived LSER equation successfully predicted the VOC partition coefficients and the selectivity of CTMAB-bentonite for the VOCs. The relationship between LSER and adsorption/partition model was compared. The classification of sorption mechanisms by LSER goes on the molecular interaction types between sorbate and sorbent, and classification by adsorption/partition model goes on the property difference among various components of sorbent. The LSER approach coupled with inverse gas chromatography (IGC) is a comparatively simple and reliable tool to rapidly characterize the sorption mechanism of VOCs with solid sorbents such as CTMAB-bentonite, and may potentially be applied to the design of an organoclay sorbent for control of VOCs.

Adsorption↗
PubMed2003

A Bayesian molecular interaction library.

We describe a library of molecular fragments designed to model and predict non-bonded interactions between atoms. We apply the Bayesian approach, whereby prior knowledge and uncertainty of the mathematical model are incorporated into the estimated model and its parameters. The molecular interaction data are strengthened by narrowing the atom classification to 14 atom types, focusing on independent molecular contacts that lie within a short cutoff distance, and symmetrizing the interaction data for the molecular fragments. Furthermore, the location of atoms in contact with a molecular fragment are modeled by Gaussian mixture densities whose maximum a posteriori estimates are obtained by applying a version of the expectation-maximization algorithm that incorporates hyperparameters for the components of the Gaussian mixtures. A routine is introduced providing the hyperparameters and the initial values of the parameters of the Gaussian mixture densities. A model selection criterion, based on the concept of a 'minimum message length' is used to automatically select the optimal complexity of a mixture model and the most suitable orientation of a reference frame for a fragment in a coordinate system. The type of atom interacting with a molecular fragment is predicted by values of the posterior probability function and the accuracy of these predictions is evaluated by comparing the predicted atom type with the actual atom type seen in crystal structures. The fact that an atom will simultaneously interact with several molecular fragments forming a cohesive network of interactions is exploited by introducing two strategies that combine the predictions of atom types given by multiple fragments. The accuracy of these combined predictions is compared with those based on an individual fragment. Exhaustive validation analyses and qualitative examples (e.g., the ligand-binding domain of glutamate receptors) demonstrate that these improvements lead to effective modeling and prediction of molecular interactions.

Algorithms↗
PubMed1998

Unstable mutations and neurodegenerative disorders.

Trinucleotide repeat expansions are involved in an increasing number of neurodegenerative disorders. Eight disorders are caused by translated CAG expansions with sizes usually below 100-200 repeats. Expansions are observed in unrelated genes, and the threshold above which the disease becomes manifest varies according to the locus. There is a strong negative correlation between age at onset and the number of repeats. Direct molecular diagnosis, which is now possible, allows classification according to genotype, thereby multiplying the number of related disorders. Molecular analysis is also useful to diagnose disorders with variable and overlapping clinical features. Recent findings suggest that intranuclear inclusions are a characteristic of disorders with translated CAG expansions. Their formation might constitute an important step in the pathological process. Friedreich ataxia is the first disorder caused by a trinucleotide repeat expansion located within an intron. The clinical spectrum of the disease and its diagnostic criteria have been recently reevaluated in a large series of patients. Interestingly, Friedreich's ataxia is now thought to be associated with intramitochondrial iron accumulation. Frataxin, the protein that is mutated, might normally be responsible for mitochondrial iron homeostasis in tissues that are affected by the disease.

Friedreich Ataxia↗
PubMed2006

TOMOCOMD-CARDD descriptors-based virtual screening of tyrosinase inhibitors: evaluation of different classification model combinations using bond-based linear indices.

A new set of bond-level molecular descriptors (bond-based linear indices) are used here in QSAR (quantitative structure-activity relationship) studies of tyrosinase inhibitors, for finding functions that discriminate between the tyrosinase inhibitor compounds and inactive ones. A database of 246 compounds was collected for this study; all organic chemicals were reported as tyrosinase inhibitors; they had great structural diversity. This dataset can be considered as a helpful tool, not only for theoretical chemists but also for other researchers in this area. The set used as inactive has 412 drugs with other clinical uses. Twelve LDA-based QSAR models were obtained, the first six using the non-stochastic total and local bond-based linear indices as well as the last six ones, the stochastic molecular descriptors. The best two discriminant models computed using the non-stochastic and stochastic molecular descriptors (Eqs. , respectively) had globally good classifications of 98.95% and 89.75% in the training set, with high Matthews correlation coefficients (C) of 0.98 and 0.78. The external prediction sets had accuracies of 98.89% and 89.44%, and (C) values of 0.98 and 0.78, for models 7 and 13, respectively. A virtual screening of compounds reported in the literature with such activity was carried out, to prove the ability of present models to search for tyrosinase inhibitors, not included in the training or test set. At the end, the fitted discriminant functions were used in the selection/identification of new ethylsteroids isolated from herbal plants, looking for tyrosinase inhibitory activity. A good behavior is shown between the theoretical and experimental results on mushroom tyrosinase enzyme. It might be highlighted that all the compounds showed values under 10microM and that ES2 (IC(50)=1.25microM) showed higher activity in the inhibition against the enzyme than reference compounds kojic acid (IC(50)=16.67microM) and l-mimosine (IC(50)=3.68microM). In addition, a comparison with other established methods was carried to prove the adequate discriminatory performance of the molecular descriptors used here. The present algorithm provided useful clues that can be used to speed up in the identification of new tyrosinase inhibitor compounds.

Agaricales↗
PubMed1998

[Ehlers-Danlos syndromes: we are all concerned].

UNLABELLED: EHLERS-DANLOS SYNDROMES (EDS): A heterogeneous group of hereditary conditions having in common a molecular anomaly of the extracellular matrix comprise EDS. Clinical and genetic features are used for classification and in some cases the molecular anomaly can be demonstrated. Six main types are recognized and termed classic, hypermobile, vascular, cyphoscoliotic, arthrochalasic and dermatosparaxis. CLINICAL MANIFESTATIONS: Skin and joint signs predominate, visceral disease is fortunately rare. The skin is hyperelastic and heals poorly. Joint involvement may lead to luxations and early-onset osteoarthritis causing chronic pain. The prognosis is severe in certain types such as vascular EDS where arterial ruptures may be life-threatening. Patients with cyphoscoliotic EDS may become bedridden due to the scoliosis and muscular hypotrophy. Minor forms as well as rapidly fatal major forms often go undiagnosed or are identified late after a complication which could have been avoided. MANAGEMENT: A multidisciplinary approach is needed as certain interventions, technical procedures or explorations may have catastrophic consequences. The creation of an EDS association would be helpful in federating specialists and allow global management. The gravity of certain forms, the poorly understood epidemiology and the progressive nature of EDS point to the need for a national registry.

Ehlers-Danlos Syndrome↗
PubMed2006

Computational prediction of the chromosome-damaging potential of chemicals.

We report on the generation of computer-based models for the prediction of the chromosome-damaging potential of chemicals as assessed in the in vitro chromosome aberration (CA) test. On the basis of publicly available CA-test results of more than 650 chemical substances, half of which are drug-like compounds, we generated two different computational models. The first model was realized using the (Q)SAR tool MCASE. Results obtained with this model indicate a limited performance (53%) for the assessment of a chromosome-damaging potential (sensitivity), whereas CA-test negative compounds were correctly predicted with a specificity of 75%. The low sensitivity of this model might be explained by the fact that the underlying 2D-structural descriptors only describe part of the molecular mechanism leading to the induction of chromosome aberrations, that is, direct drug-DNA interactions. The second model was constructed with a more sophisticated machine learning approach and generated a classification model based on 14 molecular descriptors, which were obtained after feature selection. The performance of this model was superior to the MCASE model, primarily because of an improved sensitivity, suggesting that the more complex molecular descriptors in combination with statistical learning approaches are better suited to model the complex nature of mechanisms leading to a positive effect in the CA-test. An analysis of misclassified pharmaceuticals by this model showed that a large part of the false-negative predicted compounds were uniquely positive in the CA-test but lacked a genotoxic potential in other mutagenicity tests of the regulatory testing battery, suggesting that biologically nonsignificant mechanisms could be responsible for the observed positive CA-test result. Since such mechanisms are not amenable to modeling approaches it is suggested that a positive prediction made by the model reflects a biologically significant genotoxic potential. An integration of the machine-learning model as a screening tool in early discovery phases of drug development is proposed.

Chromosomes↗
PubMed2000

Molecular identification of main cellular lineages as a tool for the classification of gastric cancer.

Gastric carcinomas (GC) are heterogeneous tumors comprising variable amounts of cells of different lineage phenotype, including gastric mucous cells (surface--SMC or gland--GMC) and intestinal cells (IC). The evaluation of tumor behavior has classically depended on strictly morphological classifications of tumors. Microsatellite instability (MSI) is frequently detected in GC, but whether MSI affects all gastric cellular lineages or exclusively occurs in unique cellular lineages in GC is not known. The aims of this study were to test a combination of anti-mucin antibodies to classify gastric cancer into predominant cell lineage phenotype and to determine whether MSI in GC is associated with particular cellular tumor phenotypes. Fifty-five GC were immunophenotyped with antibodies specific for SMC, GMC, or IC. DNA was extracted from tumor and non-neoplastic gastric tissues and amplified with 5 microsatellite markers. A mixed cellular pattern was the most frequent phenotype of GC (61%) and was seen in both glandular (63%) and diffuse (58%)-type tumors. No significant difference in the rate of MSI was found in tumors with predominant gastric, intestinal or mixed phenotype. However, tumors with null or low-level expression of cellular lineage differentiation markers displayed MSI more frequently than tumors with high-level expression (40% v 20%). In conclusion, different gastric carcinoma cell lineage patterns can be easily identified with the 3 immunohistochemical markers used in this study. The 3 main cellular lineage components of gastric cancer can be similarly affected by microsatellite instability, consistent with the notion that MSI is an early event in gastric carcinogenesis.

Adult↗