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Cytogenetic data are now available in most bone and soft tissue sarcomas. The characteristic chromosomal rearrangements observed are of great importance for the diagnosis, the classification and the comprehension of these cancers at the molecular level.
Up-dating of diagnostics of hereditary platelet disorders has been done. Due to the development of laboratory techniques some of the thrombopathies are now well characterized at the molecular level, and it can be seen that the classification of these defects has greatly progressed. However, the most frequent inherited disorders of platelet function encountered fall into the class "platelet secretion defect" and remain incompletely defined. Evidence of storage pool deficiency should be considered in all patients with an unexplained prolongation of the bleeding time, even in the absence of the classical aggregation abnormalities.
Permanent congenital hypothyroidism in the Netherlands (incidence 1:3000) is caused for 70-80% by a- or dysgenesis of the thyroid gland, for about 15% by dyshormonogenesis and for 10-15% by hypothalamic-pituitary disturbances. The heredity of congenital hypothyroidism caused by dyshormonogenesis is mendelian in character and follows, with a few exceptions, an autosomal recessive pattern. The diagnosis of these inborn errors is based on a combination of imaging studies, plasma hormone and thyroglobulin concentrations, and the concentration of iodide and iodinated peptides in the urine. The contribution of molecular biology is becoming an important factor in the classification of hereditary congenital hypothyroidism.
A. baumannii is a multiresistant bacteria which is recognised as responsible for nosocomial infections and hospital outbreaks. The control of these outbreaks depends on the strain's typing and on the fight's policy against nosocomial infections. An outbreak of A. baumannii is occurred to patients who were hospitalized in Centre Hospitalier de Versailles. To investigate this outbreak, we have determined the biotype (Bouvet's method), the succeptibility pattern (disk diffusion and agar dilution results were analysed with the hierarchical classification and main component analysis) and the total DNA macrorestriction pattern (Pulse Field Gel Electrophoresis using SmaI restriction enzyme). A risk factors for A. baumannii acquisition were delineated in case-control study. During 2 years, 38 patients have been infected or colonized to A. baumannii. Thirty two patients were hospitalized in ICU. We studied 38 non repetitive clinical isolates and 9 strains of the patient's rooms. Four biotypes were defined by the Bouvet's typing method. Fourteen groups were obtained when succeptibility results were analysed with the hierarchical classification and 6 with the main composant analysis. The molecular typing permit us to define 4 epidemic and 6 sporadic strains. All the epidemic strains were isolated on ICU hospitalized patients. Our study has shown wide contamination in patient's rooms (Water tap, dry surfaces, patient's mattresses...). Environmental objects have been a major risk factor for A. baumannii acquisition. The control of this outbreak has been possible by application of hygienic measures (hands washing, isolment, meticulous cleaning of the ICU and environmental controls). No new case is occurred in the last year. Typing methods and case-control study are necessary to investigate cross-infections and take efficient measures against these outbreaks.
The Bayesian model-based approach to inferring hidden genetic population structures using multilocus molecular markers has become a popular tool within certain branches of biology. In particular, it has been shown that heterogeneous data arising from genetically dissimilar latent groups of individuals can be effectively modelled using an unsupervised classification formulation. However, most currently employed models ignore potential linkage within the employed molecular information, and can therefore lead to biased inferences under certain circumstances. Utilizing the general theory of graphical models, we develop a framework that accounts for dependences both within linked molecular marker loci and DNA sequence data. Due to a high level of sequence conservation among eukaryotic species, the latter aspect is particularly relevant for analyzing rapidly evolving microbial species. The advantages of incorporating the dependence due to linkage in the classification models are illustrated by analyses of both simulated data and real samples of Bacillus cereus.
Lignin is a complex polymer of phenylpropanoid subunits. It is an essential component of woody tissue, to which it imparts structural rigidity. Lignin is remarkably resistant to degradation by most microbes; nevertheless, a few species of white-rot fungi are able to catalyse its oxidation to CO2. Its biodegradation is of great ecological significance because, next to cellulose, lignin is the most abundant renewable polymer on Earth. The first step in lignin degradation is depolymerization, catalysed by the lignin peroxidase isozymes (ligninases). These isozymes are secreted, along with hydrogen peroxide (H2O2) by the fungus Phanerochaete chrysosporium Burds, under conditions of nutrient (nitrogen) limitation. Ligninases are not only important in lignin biodegradation, but are also potentially valuable in chemical waste disposal because of their ability to degrade environmental pollutants. We have undertaken the cloning of the ligninase genes to understand further their regulation and enzymology. We report here the isolation and characterization of a ligninase complementary DNA clone with a full-length insert. The cDNA sequence shows that the sequence of the mature ligninase is preceded by a 28-residue leader, and the mature protein is predicted to have a relative molecular mass of 37,000 (Mr 37K). Consistent with the classification of ligninase as a peroxidase certain residues thought to be essential for peroxidase activity can be identified and near these residues the ligninase shows homology with other known peroxidases. Our cDNA clone has also allowed us to show that expression of ligninase is regulated at the messenger RNA level.
The results of a quantitative structure-property relationship (QSPR) analysis of 127 different solvent scales and 774 solvents using the CODESSA PRO program are presented. QSPR models for each scale were constructed using only theoretical descriptors. The high quality of the models is reflected by the squared multiple correlation coefficients that range from 0.726 to 0.999; only 18 models have R2< 0.800. This enables direct theoretical calculation of predicted values for any scale and/or for any organic solvent, including those previously unmeasured. The molecular descriptors involved in the models are classified and discussed according to (i) the origin of their calculation (i.e., constitutional, geometric, charge-related, etc.) and (ii) the commonly accepted classification of physical interactions between the solute and solvent molecules in liquid (condensed) media. A reduced matrix 774 (solvents) x 100 (solvent scales) was selected for the principal component analysis (PCA) by taking into account only the solvent scales with more than 20 experimental data points. The first 5 principal components account for 75% of the total variance. The robustness of the PCA model obtained was validated by the comparison models development for restricted submatrices of data and with the results obtained for the full data set. The total variance accounted for by the first three PCs, for the submatrices with the same number of solvent scales but different numbers of solvents, varies from 68.2% to 59.0%. This demonstrates that the total variance described by the first 3 components is essentially stable as the number of solvents involved varies from 100 to 774. Subsequently, a matrix with 703 diverse solvents and 100 solvent scales was selected for the general classification of the solvents and scales according to the scores and loadings obtained from the PCA treatment. Classification of the theoretical molecular descriptors, derived from the chemical structure alone, according to their relevance to specific types of intermolecular interaction (cavity formation, electrostatic polarization, dispersion, and hydrogen bonding) in liquid media enables a more easily comprehensible physical interpretation of the QSPR of molecular properties in liquids and solutions. The reported QSPR models for solvent scales with theoretical molecular descriptors and the results of the PCA analysis are potentially of great practical importance, as they extend the applicability of correlations with empirical solvent scales to many previously unmeasured systems.
A neural network system has been developed for rapid and accurate classification of ribosomal RNA sequences according to phylogenetic relationship. The molecular sequences are encoded into neural input vectors using an n-gram hashing method. A SVD (singular value decomposition) method is used to compress and reduce the size of long and sparse n-gram input vectors. The neural networks used are three-layered, feed-forward networks that employ supervised learning paradigms, including the back-propagation algorithm and a modified counter-propagation algorithm. A pedagogical pattern selection strategy is used to reduce the training time. After trained with ribosomal RNA sequences of the RDP (Ribosomal Database Project) database, the system can classify query sequences into more than one hundred phylogenetic classes with a 100% accuracy at a rate of less than 0.3 CPU second per sequence on a workstation. When compared to other sequence similarity search methods, including Similarity Rank, Blast and Fasta, the neural network method has a higher classification accuracy at a speed of about an order of magnitude faster. The software tool will be made available to the biology community, and the system may be extended into a gene identification system for classifying indiscriminately sequenced DNA fragments.
The identification of genetic and biochemical changes allows a more conclusive characterization and classification of disease. Up to now this information is mostly obtained through in vitro analysis after resection or biopsy by immunohistopathology and molecular biology. There is a definite need for non-invasive detection and repeated monitoring of such changes in experimental research as well as in clinical trials. Therefore, it is necessary to develop radiological imaging techniques that not only visualize morphologic and physiologic alterations, but track genetic and biochemical processes. This short review reports some of the various ongoing research projects that address this problem and provide some very promising approaches.
A well-resolved rhizobial species phylogeny with 51 haplotypes was inferred from a combined atpD + recA data set using Bayesian inference with best-fit, gene-specific substitution models. Relatively dense taxon sampling for the genera Rhizobium and Mesorhizobium was achieved by generating atpD and recA sequences for six type and 24 reference strains not previously available in GenBank. This phylogeny was used to classify nine nodule isolates from Sesbania exasperata, S. punicea and S. sericea plants native to seasonally flooded areas of Venezuela, and compared with a PCR-RFLP analysis of rrs plus rrl genes and large maximum likelihood rrs and nifH phylogenies. We show that rrs phylogenies are particularly sensitive to strain choice due to the high levels of sequence mosaicism found at this locus. All analyses consistently identified the Sesbania isolates as Mesorhizobium plurifarium or Rhizobium huautlense. Host range experiments on ten legume species coupled with plasmid profiling uncovered potential novel biovarieties of both species. This study demonstrates the wide geographic and environmental distribution of M. plurifarium, that R. galegae and R. huautlense are sister lineages, and the synonymy of R. gallicum, R. mongolense and R. yanglingense. Complex and diverse phylogeographic, inheritance and host-association patterns were found for the symbiotic nifH locus. The results and the analytical approaches used herein are discussed in the context of rhizobial taxonomy and molecular systematics.
In order to establish the molecular phylogeny of the genus Rhizopus, three molecules of the ribosomal RNA-encoding DNA (rDNA), complete 18S, internal transcribed spacer (ITS)1-5.8S-ITS2, and 28S D1/D2 regions of all the species of the genus were sequenced. Phylogenetic trees showed three major clusters corresponding to the three groups in the current morphological taxonomy, microsporus-group, stolonifer-group, and R. oryzae. R. stolonifer var. lyococcos was clustered independently from the major clusters. R. schipperae clustered differently in all trees. Strains of R. sexualis had multiple ITS sequences. A. rouxii clustered with R. oryzae. These results indicate the possibility of molecular identification of species groups using rDNA sequencing. Reclassification of the genus might be appropriate.
BACKGROUND: The increased demand for markers for colorectal cancer (CRC) highlights the importance of investigating immune cells involved in CRC progression. This study aims to dissect the mast cells in CRC, characterize the role of mast cells in CRC development, coordinate molecular communication between mast cells and malignant cells, and construct and validate a prognostic classification model based on mast cell markers. METHODS: Single-cell transcriptome data of CRC patients were extracted from GSE146771 for cell classification and annotation. The malignant cells were identified by copykat and the communication between mast cells and malignant cells was analyzed by CellChat. Least absolute shrinkage and selection operator (LASSO) regression analysis and Cox regression analysis of mast cell markers were performed in the TCGA-COAD cohort to construct a prognostic classification model. qRT-PCR was performed to detect the mRNA expression of the molecules in the classification model in P815 and MC-9 cells. The co-culture experiment of MC38 and P815 cells were performed in 12-well transwell dish. Wound healing assay and Transwell assay were performed to detect cell migration and invasion. RESULTS: 10,186 high-quality cells in GSE146771 were annotated to 9 cell types. Six markers in mast cells (HDC, GATA2, ASAH1, BTBD19, TIMP1, FAM110A) were selected to construct a classification model. The high-risk score defined showed high infiltration of immunosuppressive cells, including endothelial cells, CAFs, Tregs and high angiogenesis and epithelial-mesenchymal transition (EMT) activities. In the model, HDC were abnormally low expressed in P815 cells, while BTBD19, FAM110A, GATA2, ASAH1 and TIMP1 showed excessive expression in P815 cells. Knockdown of GATA2 in the co-culture system of P815 and MC38 cells blocked cell migration and invasion. CONCLUSION: This study identified the cell types within CRC, elaborated the cellular functions of mast cells in CRC development and their molecular communication to coordinate malignant cells, and highlighted the molecular components and biological features that constitute promising prognostic classification model.
BACKGROUND AND AIM: Currently there are three different subsite classification systems for carcinomas in the region of the gastroesophaeal junction (GEJ), namely ICD-O, Munich and Liverpool. The aim of the present study was to compare clinicoepidemiological, pathological and molecular features of adenocarcinomas in the proximity of the GEJ, classified according to their position with respect to the GEJ initially, and then classified according to ICD-O, Munich and Liverpool classifications. METHODS: Forty-seven adenocarcinomas in the proximity of the GEJ were subdivided into groups 1 (exclusively within esophagus), 2 (mainly within esophagus but extending distally across GEJ), 3 (equally present in esophagus and stomach) or 4 (mainly in stomach but extending proximally across GEJ), and analysis of their clinicoepidemiological, pathological and molecular features was performed. Molecular characterization included loss of heterozygosity (LOH) and microsatellite instability analyses. RESULTS: Group 3 carcinomas were younger than other carcinomas in the proximity of the GEJ, but otherwise these carcinomas were similar in their clinicoepidemiological, pathological and molecular features. There were no significant differences between esophageal (groups 1 and 2) and gastric (groups 3 and 4) carcinomas as classified by ICD-O. Munich types I (groups 1 and 2), II (group 3) and III (group 4) carcinomas of the GEJ were also similar. LOH at the site of the Rb tumor suppressor gene and at 17p11.1-p12 was more common in GEJ (groups 2, 3 and 4) than lower third (group 1) esophageal carcinomas classified according to the Liverpool system. CONCLUSION: Overall, adenocarcinomas of the lower esophagus and adenocarcinomas involving the GEJ have similar clinicoepidemiological, pathological and molecular features no matter which subsite classification is used, adding further evidence that they represent the same disease.
OBJECTIVE--To clarify the nosological classification of late-onset Friedreich's ataxia (LOFA), ie, patients who have later onset of Friedreich's ataxia (FRDA), often after 25 years of age. DESIGN--Comparison of clinical examination data, nerve conduction studies, electronystagmographic recording, and magnetic resonance imaging of a family with LOFA with a group of patients with FRDA. Genetic linkage analysis was performed in the family with LOFA. SETTING--Referral center. PATIENTS--Thirteen patients satisfied classic diagnostic criteria of FRDA, and three patients from one family satisfied all diagnostic criteria of FRDA but with disease onset after 25 years. RESULTS--Results of nerve conduction studies, electronystagmographic recording, and magnetic resonance imaging in patients with LOFA closely corresponded to observations made in patients with FRDA. In addition, genetic linkage analysis using markers tightly linked to the FRDA locus on chromosome 9 showed that all affected members of the LOFA family, but not their unaffected siblings, had inherited identical paternal and maternal genotypes. CONCLUSIONS--Data suggest that LOFA may also result from mutation within the FRDA locus.
The dissection of cancer and the underlying molecular processes that are defective in cancer cells has become an important tool in the fight against this disease. DNA microarrays can provide detailed information of the expression pattern of thousands of genes in tumours. But how much of this data is useful and is some superfluous? Can array data be used to identify a handful of critical genes that will lead to a more-detailed taxonomy of tumours and can this or similar array data be used to predict clinical outcome? Primary tumours will give us the statistical power to draw these conclusions, but can cancer cell lines be used as models to point us in the right direction?
A classification of plants based on the chemical structures of their skin sensitizers is presented. A whole range of chemical structures of contact sensitizers exists in plants containing sesquiterpene lactones (Compositae, Frullania, Lauraceae etc.), tulipalin (Tulipa, Alstroemeria etc.), quinones (Primula and tropical woods), long chain phenols (Anacardiaceae, Ginkgoaceae) and miscellaneous structures such as aldehydes, ketones, terpene hydrocarbons etc. Knowledge of allergens in various plants allows prediction of cross-reactivity.
We present a molecular systematic investigation of relationships among family-group taxa of Membracidae, comprising nearly 3.5 kb of nucleotide sequence data from the nuclear genes elongation factor-1alpha (EF-1alpha: 958 bp) and 28S ribosomal DNA (28S rDNA: 2363 bp); data partitions are analyzed separately and in combination for 79 taxa. Analysis of the combined sequence data provided a better-resolved and more robust hypothesis of membracid phylogeny than did separate analyses of the individual genes. Results support the monophyly of the family Membracidae and indicate the presence of two major lineages (Centrotinae + Stegaspidinae + Centrodontinae and Darninae + Membracinae + Smiliinae). Within Membracidae, molecular data support the following assertions: (1) the previously unplaced genera Antillotolania and Deiroderes form a monophyletic group with Microcentrini; (2) Centrodontini and Nessorhinini are monophyletic clades that arise independently from within the Centrotinae; (3) Centrotinae is paraphyletic with respect to Centrodontinae; (4) the subfamily Membracinae is monophyletic and possibly allied with the darnine tribe Cymbomorphini; (5) the subfamily Darninae is paraphyletic; (6) the subfamily Smiliinae is paraphyletic, with molecular evidence indicating the exclusion of Micrutalini and perhaps Acutalini and Ceresini; and (7) Membracidae arose and diversified in the New World with multiple subsequent colonizations of the Old World. Our phylogenetic results suggest that morphology-based classifications of the Membracidae need to be reevaluated in light of emerging molecular evidence.
Genetic variation between geographically and temporally distinct isolates of dengue-1 (DEN-1) and dengue-4 (DEN-4) viruses was investigated. The nucleotide sequences of a fragment of the envelope protein gene encoding amino acids 28 to 87 of 35 DEN-1 isolates and 28 DEN-4 isolates were determined. Maximum nucleotide sequence variation was 6.9% and 4.9% for DEN-1 and DEN-4 viruses, respectively. Taking a divergence of 6% between the nucleotide sequences as the cut-off value, three genotype groups were defined for DEN-1 viruses, whereas only one was observed for DEN-4 viruses. Molecular analysis of isolates from the South Pacific permits the classification of the recent strains of DEN-1 (1988-1989 epidemics) into a genotype distinct from the genotype which comprises earlier strains. This observation suggests that the recent epidemics were due to the introduction of a new genotype rather than to the re-emergence of the earlier strain.