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At least 649 records · Page 36Linked to original sources
PubMed1996

Protamines of reptiles.

We have characterized for the first time the complete primary structure of the main protamine components of the sperm from four reptiles: Chrysemys picta (turtle), Elaphe obsoleta (snake), Anolis carolinensis (lizard), and Alligator mississipiensis (crocodilian). These species were chosen to represent one of each of the main phylogenetic branches of this taxonomic group. Comparison of these protamine sequences with those already available from other vertebrate groups allows us to define properly the chemical consensus composition of protamines and provides a unique insight into their molecular evolution and classification.

Alligators and Crocodiles↗
PubMed2001

A molecular phylogeny of the Octopoda (Mollusca: Cephalopoda) evaluated in light of morphological evidence.

In this paper we examine the phylogenetic relationships of the Octopoda utilizing molecular sequence data from the cytochrome c oxidase subunit I (COI) gene and compare results from analyses of molecular data with classifications and phylogenies based on previous morphological studies. Partial COI sequences (657 bp, excluding primers) were obtained from 28 species representing most of the diversity in the Order Octopoda, along with a sequence from the established sister taxon to the Octopoda, Vampyroteuthis infernalis. Our results exhibit a number of basic differences from inferences based on standard morphological data. We attempt to resolve these differences based on our confidence in various morphological features. An important finding is the failure of the molecular data to support the monophyly of the Octopodidae. This family contains over 90% of the species in the Suborder Incirrata and has always been difficult to define. Statistical tests constraining Octopodidae monophyly by use of parsimony and maximum-likelihood techniques suggest that all incirrates may be derived from octopodids.

Animals↗
PubMed2006

Microarrays in breast cancer research and clinical practice--the future lies ahead.

Molecular profiling for classification and prognostic purposes has demonstrated that the genetic signatures of tumors contain information regarding biological properties as well as clinical behavior. This review highlights the progress that has been made in the field of gene expression profiling of human breast cancer. Breast cancer has become one of the most intensely studied human malignancies in the genomic era; several hundred papers over the last few years have investigated various clinical and biological aspects of human breast cancer using high-throughput molecular profiling techniques. Given the grossly heterogeneous nature of the disease and the lack of robust conventional markers for disease prediction, prognosis, and response to treatment, the notion that a transcriptional profile comprising multiple genes, rather than any single gene or other parameter, will be more predictive of tumor behavior is both appealing and reasonable. Promising results have emerged from these studies, correlating gene expression profiles with prognosis, recurrence, metastatic potential, therapeutic response, as well as biological and functional aspects of the disease. Clearly, the integration of genomic approaches into the clinic lies in the near future, but prospective studies based on larger patient cohorts representing the whole spectrum of breast cancer, oncogenic pathway-based studies, attendant care in bioinformatic analyses and validation studies are needed before the full promise of gene expression profiling can be realized in the clinical setting.

Biomedical Research↗
PubMed1999

Muscular dystrophy: historical overview and classification in the genetic era.

Despite recent advances in molecular genetics, it has proven very difficult to arrive at an accurate and clinically useful classification of the muscular dystrophies. Much of this difficulty arises from confusion related to the term "muscular dystrophy" itself, as well as a general reluctance on the part of the neuromuscular community to abandon traditional, clinically based classifications. Nevertheless, advances in the understanding of the molecular defects of these disorders have permitted a foundation for classification based on molecular biology. This review presents a historical perspective on the classification of the muscular dystrophies, and furnishes the underpinnings of a genetic classification that can be used both at the bedside and in the research laboratory.

Classification↗
PubMed2005

Proteomic signatures for histological types of lung cancer.

We performed proteomic studies on lung cancer cells to elucidate the mechanisms that determine histological phenotype. Thirty lung cancer cell lines with three different histological backgrounds (squamous cell carcinoma, small cell lung carcinoma and adenocarcinoma) were subjected to two-dimensional difference gel electrophoresis (2-D DIGE) and grouped by multivariate analyses on the basis of their protein expression profiles. 2-D DIGE achieves more accurate quantification of protein expression by using highly sensitive fluorescence dyes to label the cysteine residues of proteins prior to two-dimensional polyacrylamide gel electrophoresis. We found that hierarchical clustering analysis and principal component analysis divided the cell lines according to their original histology. Spot ranking analysis using a support vector machine algorithm and unsupervised classification methods identified 32 protein spots essential for the classification. The proteins corresponding to the spots were identified by mass spectrometry. Next, lung cancer cells isolated from tumor tissue by laser microdissection were classified on the basis of the expression pattern of these 32 protein spots. Based on the expression profile of the 32 spots, the isolated cancer cells were categorized into three histological groups: the squamous cell carcinoma group, the adenocarcinoma group, and a group of carcinomas with other histological types. In conclusion, our results demonstrate the utility of quantitative proteomic analysis for molecular diagnosis and classification of lung cancer cells.

Adenocarcinoma↗
PubMed1994

Phylogenetic classification of human T cell leukaemia/lymphoma virus type I genotypes in five major molecular and geographical subtypes.

Proviral DNA was obtained from ex vivo peripheral blood mononuclear cells of 75 human T cell leukaemia/lymphoma virus type I (HTLV-I)-infected individuals who were either asymptomatic or had adult T cell leukaemia or tropical spastic paraparesis/HTLV-I-associated myelopathy. Amplified long terminal repeats (LTRs) were analysed for restriction fragment length polymorphisms (RFLPs). The results, together with previously published LTR data (a total of 180 specimens analysed), showed the presence of 12 different RFLP profiles with four major molecular subtypes. Furthermore, a fragment of 413 bp (nucleotides 22 to 434) of the U3/R region was sequenced for 12 new HTLV-I specimens originating from Central and West Africa (8 cases), Iran (1 case), Caribbean (2 cases) and Reunion Island (1 case). Phylogenetic analysis using three different techniques (maximum parsimony, neighbour-joining and UPGMA) comparing these 12 strains (including four new African HTLV-I variants) with the 30 published partial HTLV-I LTR sequences (nt 120 to 434) showed the existence of clusters of molecular variants in discrete geographical areas. The topology of the phylogenetic trees is thought to reflect HTLV-I evolution and the migrations of virally infected populations in the recent or distant past. Furthermore, there was a nearly perfect concordance between the clustering based on the LTR sequence homologies and the LTR RFLP subtypes suggesting that this rapid and simple technique is well suited to the investigation of HTLV-I molecular epidemiology. These results allow a new phylogenetic classification of HTLV-I genotypes into five major molecular subtypes: Cosmopolitan (C) subtype widespread all over the world, Japanese (J) subtype, West African (WA) subtype. Central African (CA) subtype and Melanesian (M) subtype.

Africa↗
PubMedDate not supplied

A new graph descriptor for molecules containing cycles. Application as screening criterion for searching molecular structures within large databases of organic compounds.

The search of molecular structures inside a large database of chemical compounds is a critical step for many computer programs used in several domains of chemistry. During the last years, the size of many chemical databases has dramatically increased, hence in the meantime, search engines needed to be more and more powerful. The speed and the efficiency of screening processes of the chemical compounds are thus essential. Looking forward for algorithms dedicated to structure and substructure search, we have developed a new graph descriptor for structures containing cycles in order to find efficient indexation and classification criteria of molecular structures. This graph descriptor can be used as a screening criteria for structure and substructure search in large databases of organic compounds.

Journal Article↗
PubMed1999

Broadsheet number 52: Molecular genetics of colorectal cancer.

The molecular genetics of colorectal cancer is presented in an order that ascends from the basic to the applied: molecular mechanisms, morphogenesis, classification and diagnosis. Major consideration is given to the nature of genetic instability and the role of this mechanism in driving neoplastic progression. It is shown how the fundamental principle of genetic instability cuts across applied research, tissue diagnosis and clinical management with respect to both sporadic and inherited forms of colorectal cancer.

Adenocarcinoma↗
PubMed1996

Ocular manifestations of genetic and developmental diseases.

Although ophthalmic involvement in developmental and genetic abnormalities has been recognized for centuries, it is only recently, due to new discoveries in molecular biology, that our classification and pathophysiology of congenital eye diseases have been advanced. In the next few years these advances will increasingly influence aspects of diagnosis classification, and therapy in ophthalmology. Tests for acquired and inherited diseases in opthalmology are being revolutionized by biotechnical innovations. The molecular genetics of ocular diseases is currently undergoing changes in classification due to intense investigations using advanced biotechnology. The potential for new treatment modalities, such as gene therapy, for molecular eye diseases, once thought to be pure fiction, is now a reality. This paper will outline recent changes in classification, organization, and general knowledge regarding inherited eye diseases.

Animals↗
PubMed2004

[Application of molecular biology techniques in the identification of pathogenic fungi and the diagnosis of fungal infection].

With the increasing incidence and mortality of fungal infection, the requirements for strict diagnostic approaches became a very urgent issue. Because of the traditional detective techniques, such as culture, gave poor diagnostic outcomes, the molecular biological techniques are expected to develop the potential diagnostic approaches. During the past decades, we have carried out serial studies on the molecular properties of pathogenic fungi, and we would like to review as following. Firstly, we applied several molecular tools in classification and identification of pathogenic fungi. We performed random amplification of polymorphic DNA (RAPD), restriction fragment length polymorphism (RFLP) and other techniques in studying the typing, to classify and identify the properties of Dermatophytes, Candida spp., Cryptococcus neoformans, Dematiaceous fungi, and Aspergillus spp. Interestingly, we found the same T. rubrum strain might infect different sites of the host, while a site-specificity displayed in T. mentagrophytes. This finding indicated the genetic discrepancies among the fungi. Beside, we also found that the E. dermatitis strains with different virulences possessed some discrepancies at gene level. We then developed a PCR-based molecular procedure to identify the novel species in Exophiala spp. As the applicable strategy, we also investigated the rDNA sequence properties in several fungi. And as a result, we submitted for the first time to GenBank the complete sequence of Aspergillus fumigatus rDNA/ITSI/ITSII, which provided the basis for designing the species-specific probes and for its further clinical applications. Secondly, we have tried to develop the molecular diagnostic approaches based on our DNA sequence data which were used for identification studies previously. By analyzing the DNA sequence of Aspergillus fumigatus rDNA/ITSI/ITSII, we developed a nested PCR method to detect Aspergillus fumigatus genes. Our preliminary results indicated that this PCR-based molecular approach has great importance in the diagnosis of invasive aspergillosis. We also designed the species-specific probes and then established several in situ hybridization procedures. We found these hybridization methods could get the positive rate up to 81% (13/16), which suggests that these methods have potential diagnostic value for invasive candidiasis and aspergillosis. Based on our experiences, we would conclude that the molecular biological techniques possess great value to investigate the biological properties of pathogenic fungi, and we are looking forward to see more and more molecular tools will be used in the pathogenic mechanisms of fungal infections and antifungal activity studies.

Aspergillosis↗
PubMed2002

[New aspects of molecular biology diagnosis. Array technology and expression profile for characterization of rheumatic diseases].

Increasing availability of high throughput technologies, exponentially growing information about the human genome and gene expression, and the growing global network of databases on systematic biomedical information will change our view on inflammatory rheumatic diseases in a revolutionary way. Several research laboratories have already generated initial extensive datasets on gene expression analysis. Application of this technique has demonstrated that in addition to a precise analysis, verification and validation of the results also on the level of cell populations, a meticulous characterization of the patients according to current conventional clinical, laboratory, imaging and histological standards is essential. For functional interpretation, in vitro tests, animal models and therapeutic studies will provide further information. Bioinformatic structuring and development is needed for the large amounts of data. After an initial genome-wide screening, the objective is to identify those genes, which will allow characterization of the disease, classification according to molecular pathophysiology, evaluation of the prognosis and prediction of the correct and most potent therapeutic regimen. Derived from the improved knowledge about the molecular mechanisms, new and--as to expect--the crucial approaches for an effective therapy against chronic inflammation, organ destruction and pathological immune response in rheumatic diseases will emerge.

Autoantibodies↗
PubMed1997

Cladistic analysis of Tospovirus using molecular characters.

The genus Tospovirus was thought to be composed only of the tomato spotted wilt virus (TSWV), but now at least four Tospovirus species have been proposed based on serological and molecular data. A classification of tospoviruses has been proposed taking into account global similarities of the N gene and N protein sequences of 7 isolates of Tospovirus. Because phylogenetic analyses based on global similarities can lead to classifications which do not mirror the genealogy of the group, we have employed a cladistic analysis using parsimony of this genus with RNA sequences of 450 nucleotides of the N gene from 14 new Argentinean isolates and 4 previously described isolates. Representatives of the Bunyaviridae family, Rift Valley Fever Virus (Phlebovirus) and Bunyamwera (Bunyavirus), were used as the outgroup in separate analyses.

Argentina↗
PubMed2003

Predicting the genotoxicity of polycyclic aromatic compounds from molecular structure with different classifiers.

Classification models were developed to provide accurate prediction of genotoxicity of 277 polycyclic aromatic compounds (PACs) directly from their molecular structures. Numerical descriptors encoding the topological, geometric, electronic, and polar surface area properties of the compounds were calculated to represent the structural information. Each compound's genotoxicity was represented with IMAX (maximal SOS induction factor) values measured by the SOS Chromotest in the presence and absence of S9 rat liver homogenate. The compounds' class identity was determined by a cutoff IMAX value of 1.25-compounds with IMAX > 1.25 in either test were classified as genotoxic, and the ones with IMAX < or = 1.25 were nongenotoxic. Several binary classification models were generated to predict genotoxicity: k-nearest neighbor (k-NN), linear discriminant analysis, and probabilistic neural network. The study showed k-NN to provide the highest predictive ability among the three classifiers with a training set classification rate of 93.5%. A consensus model was also developed that incorporated the three classifiers and correctly predicted 81.2% of the 277 compounds. It also provided a higher prediction rate on the genotoxic class than any other single model.

Animals↗
PubMed2005

Comparative sequence analysis of the hexon gene in the entire spectrum of human adenovirus serotypes: phylogenetic, taxonomic, and clinical implications.

The adenovirus (AdV) hexon constitutes the major virus capsid protein. The epitopes located on the hexon protein are targets of neutralizing antibodies in vivo, serve in the recognition by cytotoxic T cells, and provide the basis for the classification of adenoviruses into the 51 serotypes known to date. We have sequenced the entire hexon gene from human serotypes with incomplete or no sequence information available (n = 34) and performed a comparative analysis of all sequences. The overall sequence divergence between the 51 human serotypes ranged from 0.7 to 25.4% at the protein level. The sequence information has been exploited to assess the phylogeny of the adenovirus family, and protein distances between the six AdV species (A to F) and among individual serotypes within each species were calculated. The analysis revealed that the differences among serotypes within individual species range from 0.3 to 5.4% in the conserved regions (765 amino acids [aa]) and from 1.5 to 59.6% in the variable regions (154 to 221 aa). Serotypes of different species showed an expectedly greater divergence both in the conserved (5.9 to 12.3%) and variable (49.0 to 74.7%) regions. Construction of a phylogenetic tree revealed three major clades comprising the species B+D+E, A+F, and C, respectively. For serotypes 50 and 51, the original assignment to species B and D, respectively, is not in accordance with the hexon DNA and protein sequence data, which placed serotype 50 within species D and serotype 51 within species B. Moreover, the hexon gene of serotype 16, a member of species B, was identified as the product of recombination between sequences of species B and E. In addition to providing a basis for improved molecular diagnostics and classification, the elucidation of the complete hexon gene sequence in all AdV serotypes yields information on putative epitopes for virus recognition, which may have important implications for future treatment strategies permitting efficient targeting of any AdV serotype.

Adenovirus Infections, Human↗
PubMed1994

[Male pseudohermaphroditism].

Male pseudohermaphroditism (MPH) is a complex variety of sexual differentiation disorders characterized by deficiency of masculinization of the internal and/or external genital organs in the presence of testicular development as the male gonad. This condition is caused by embryonic failure in the processes of male sexual development, which is a sequence of mechanisms originating from the genetic sex determination triggered by the SRY gene on the Y chromosome, followed by genital sex differentiation influenced by the fetal testis. Resulting phenotypical features of MPH vary from complete female to mostly normal but with some ambiguity in the maleness. Pubertal changes are also important factors related to etiology. Recent elucidation of detailed mechanisms of male differentiation and its derangements has been achieved in the era of molecular genetics. Classical classification of MPH, mainly based on anatomical and endocrinological findings obviously needs to subject to a complete revision. The newest version of MPH classification is reviewed and discussed in relation to etiological backgrounds of each type of the disorder. Main etiological factors are: failure of the SRY and its related genes involved in the testis determination; failure of anti-mülerian hormone (AMH) for normal involution of the female duct system; disordered production or function of androgen receptors essential for the fetal differentiation of the male genital organs; 5 alpha-reductase deficiency syndrome; defective responsiveness of the testis to gonadotropin due to Leydig cell agenesis; various types of enzyme defects involved in testicular androgen biosynthesis; fetal testicular dysgenesis syndromes occurring at various stages of embryogenesis; and other less clearly defined entities of MPH. Implications are that other types of sexual differentiation disorders than MPH, such as true hermaphroditism, gonadal dysgenesis and some other disorders that have been considered to be distinct entities, may have close linkage to MPH through dysgenetic process of gonadal development with subsequent degeneration and/or tumorigenesis. Molecular basis of these probably related disorders should be elucidated in the near future and some clues to preventive measures for these genetically determined malformations are awaited.

3-Oxo-5-alpha-Steroid 4-Dehydrogenase↗
PubMed2002

Amino acid sequence of the alpha- and beta-globin chains of the Hiroo sea snake (Laticauda laticaudata).

We determined the hemoglobin complete amino acid sequences of the Hiroo sea snake (Laticaudia laticuada) from the intact globin chain, enzymatically digested fragments, and chemical cleavage fragments to analyze molecular evolution for classification of the sea snake. The Hiroo sea snake has two hemoglobin components, Hb-I and Hb-II, which contain different alpha- and beta-chains, respectively. This is the first report of the complete primary structure of a snake hemoglobin. The sequences were compared with those of other reptilian hemoglobins. Amino acid replacements at positions critical for structure and physiological role of hemoglobin were loosely conserved. The requirements for binding of ATP and of diphosphoglycerate as allosteric effectors at beta-globins seemed to be fullfilled.

Adenosine Triphosphate↗
PubMed1997

The Heidelberg classification of renal cell tumours.

This paper presents the conclusions of a workshop entitled 'Impact of Molecular Genetics on the Classification of Renal Cell Tumours', which was held in Heidelberg in October 1996. The focus on 'renal cell tumours' excludes any discussion of Wilms' tumour and its variants, or of tumours metastatic to the kidneys. The proposed classification subdivides renal cell tumours into benign and malignant parenchymal neoplasms and, where possible, limits each subcategory to the most commonly documented genetic abnormalities. Benign tumours are subclassified into metanephric adenoma and adenofibroma, papillary renal cell adenoma, and renal oncocytoma. Malignant tumours are subclassified into common or conventional renal cell carcinoma; papillary renal cell carcinoma; chromophobe renal cell carcinoma; collecting duct carcinoma, with medullary carcinoma of the kidney; and renal cell carcinoma, unclassified. This classification is based on current genetic knowledge, correlates with recognizable histological findings, and is applicable to routine diagnostic practice.

Humans↗
PubMedDate not supplied

Classification of some active compounds and their inactive analogues using two three-dimensional molecular descriptors derived from computation of three-dimensional convex hulls for structures theoretically generated for them.

Two three-dimensional (3D) molecular descriptors are used to classify 73 protease inhibitors against the human immunodeficiency virus type 1 (HIV-1). X-ray structures of these HIV-1 protease bound inhibitors are used as templates to generate the most probable bioactive conformations of the inhibitors. A convex hull computation algorithm is applied to each structure generated. The frequency of atoms lying on the vertexes of each hull is counted. Vertexes of the same atomic charge state are then gathered together as a set of commonly exposed groups for all the structures generated. The first 3D descriptor is computed as the maximum molecular path length among any three distinct commonly exposed groups, while the second 3D one is computed as the maximum molecular path length among any three atoms of nonconvex hull vertexes. We find that the 73 HIV-1 protease inhibitors can be classified by the first 3D descriptor into two groups, which agrees with the result of visual classification using the activity data as a criterion for these compounds. The classification scheme is then used to classify a database of 427 active trypsin inhibitors and their inactive analogues. The structures of these compounds are generated theoretically from steps of energy minimization and molecular dynamics. Classification for all these compounds is performed using the SYBYL hierarchical clustering method on the first 3D descriptor and then the second 3D one computed. It is found that some inactive analogues are completely separated from the active inhibitors at the first stage of classification using the first 3D descriptor. Most of the highly active inhibitors are classified into a cluster at the second stage of classification using the second 3D descriptor. Finally, most of these highly active inhibitors are separated from all the accompanying inactive analogues in the cluster through a structural alignment process using a set of commonly exposed groups determined for them.

Algorithms↗