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At least 415 records · Page 23Linked to original sources
PubMed1999

Molecular characterization and classification of Stylosanthes mexicana, S. macrocarpa, S. seabrana and S. fruticosa by DNA sequence analysis of two chloroplast regions.

The trnL (UAA) intron and trnL (UAA) - trnF (GAA) intergenic spacer region from the diploid species Stylosanthes mexicana, S. macrocarpa and S. seabrana and the tetraploid species S. fruticosa were amplified by polymerase chain reaction and subjected to direct DNA sequencing. Comparison of these chloroplast regions with previously determined DNA sequences of 19 Stylosanthes species revealed a close relationship with a clade containing the diploid species S. hamata, S. calcicola, and the tetraploid species S. scabra. The results were used to infer relationships between the diploid species of this clade, in relation to the alloploid species S. scabra and S. fruticosa.

Base Sequence↗
PubMed2006

Molecular characterization and classification of a clip domain containing peptidase from the ectoparasite Lepeophtheirus salmonis (Copepoda, Crustacea).

Clip domain containing serine peptidases (CSPs) include one or more N-terminal clip domain(s) and a C-terminal serine peptidase domain that shares traits with both chymotrypsin and trypsin. CSPs are found in arthropods and are involved in embryonic patterning, immune responses and blood clotting. Among crustaceans only one CSP, which activates prophenoloxidase in crayfish, have previously been reported. We here present LsCSP1, the first CSP found in copepods. LsCSP1 is expressed in the subcuticular tissue and the transcription appears to be upregulated during development. In conjunction with previous studies of CSPs, this study suggests that LsCSP1 may play a role in the immune responses of L. salmonis. Phylogenetic and structural analyses indicate that the CSPs and catalytically inactive CSP homologs (CSPHs) constitute a monophyletic lineage.

Amino Acid Sequence↗
PubMed2000

Conserved structural features in class I major fimbrial subunits (Pilin) in gram-negative bacteria. Molecular basis of classification in seven subfamilies and identification of intrasubfamily sequence signature motifs which might Be implicated in quaternary structure.

Type 1 and P-pili are prototype members of Class I fimbriae produced by Gram-negative bacteria. Despite common structural characteristics, the low level of amino acid sequence conservation among the Class I major fimbrial subunits (pilins) indicates considerable evolutionary distance between members of this superfamily. We highlight here structural relatedness between Class I pilins from their two-dimensional sequence analysis using hydrophobic cluster analysis (HCA) and secondary structure predictions (PHD program). We present evidence that all members of the Class I pilin family have clear structural relatedness and suggest that classification based on phylogenetic analysis of Class I pilins into seven subfamilies correlates with differences in structural properties of the amino acid sequences. Using a sensitive alignment process (HCA), we identified 29 residues in topohydrophobic positions which probably play a prominent role in folding. The most striking aspects that distinguish the different pilin subfamilies are (i) large variation in the length of the loops connecting the structurally conserved regions and (ii) intrasubfamily sequence signature motifs located on regions predicted to be in the beta-conformation. We suggest that these "intrasubfamily sequence signature motifs" are part of interactive surfaces which participate in subunit-subunit interactions. These motifs prove highly useful in characterizing and classifying new Class I fimbriae that have not yet been described and whose sequence diverges appreciably from those of characterized groups. (After the submission of our manuscript, the experimental structure of Class I pilus subunits was published. In light of these actual pilin structures, a comparison has been made between the predicted results and the crystal structure in the Note Added in Proof.)

Amino Acid Motifs↗
PubMed2003

Development, characterization, and lethal effect of monoclonal antibodies against hemocytes in an adult female tick, Ornithodoros moubata (Acari: Argasidae).

In the present study, 19 monoclonal antibodies (mAbs) against adult Ornithodoros moubata hemocytes were established, and the reactivity of the hemocytes to these mAbs was examined by an indirect fluorescent antibody test (IFAT), Western blot and immunoprecipitation analyses. It was shown that the reactivities of the hemocytes to the mAbs varied among morphologically similar hemocyte types, and most mAbs produced in the present study showed the multiple band reactivity. However, the presence of shared epitopes among peptide subunits of the same protein or entirely different proteins are not common, so their reactivity could not be explained in detail. These results suggest that there are morphologically similar but functionally differentiated hemocytes. Therefore, in addition to morphological classification, the molecular-based classification of the hemocytes is also required. In order to assess the lethal effect of blood meal containing each mAb, artificial feeding was performed. The OmHC 31 showed the strongest lethal effect on adult female O. moubata. In conclusion, anti-hemocyte mAbs produced in this study are useful not only for the immunological classification of hemocytes but also for the immunological control of the tick.

Animals↗
PubMed2004

Towards a molecular identification and classification system of lepidopteran-specific baculoviruses.

Virus genomics provides novel approaches for virus identification and classification. Based on the comparative analyses of sequenced lepidopteran-specific baculovirus genomes, degenerate oligonucleotides were developed that allow the specific amplification of several regions of the genome using polymerase chain reaction (PCR) followed by DNA sequencing. The DNA sequences within the coding regions of three highly conserved genes, namely polyhedrin/granulin (polh/gran), late expression factor 8 (lef-8), and late expression factor 9 (lef-9), were targeted for amplification. The oligonucleotides were tested on viral DNAs isolated from historical field samples, and amplification products were generated from 12 isolated nucleopolyhedrovirus (NPV) and 8 granulovirus (GV) DNAs. The PCR products were cloned or directly sequenced, and phylogenetic trees were inferred from individual and combined data sets of these three genes and compared to a phylogeny, which includes 22 baculoviruses using a combined data set of 30 core genes. This method allows a fast and reliable detection and identification of lepidopteran-specific NPVs and GVs. Furthermore, a strong correlation of the base composition of these three genome areas with that of the complete virus genome was observed and used to predict the base composition of uncharacterized baculovirus genomes. These analyses suggested that GVs have a significantly higher AT content than NPVs.

Animals↗
PubMed2004

PDBLIG: classification of small molecular protein binding in the Protein Data Bank.

It is known that proteins can adopt different folds while sharing similar features for recognition of similar substrates or ligands, for example, in the binding sites of enzyme cofactors such as ATP. On the other hand, proteins that have highly flexible binding sites or belong to large and diverse protein families can bind structurally dissimilar ligands, as, for example, in the case of the matrix metalloprotease family. We have developed a database, PDBLIG, that classifies protein domains and ligands. The information stored includes each protein's function, domain class(es), which ligand(s) it binds, and so on. The database can provide valuable knowledge for drug discovery, supporting the answering of questions such as whether the same drug molecule can bind different target protein families and whether these families are related functionally or structurally, which ligand classes (such as metabolites or organic molecules) bind to a particular protein family and whether the ligands are druglike, and which target families bind a wide variety of ligands and whether different ligands are associated with different subfamilies.

Binding Sites↗
PubMed1970

Comparative allostery of 3-deoxy-D-arabino-heptulosonate-7-phosphate synthetase as a molecular basis for classification.

The allosteric pattern of control for 3-deoxy-d-arabino-heptulosonate 7-phosphate (DAHP) synthetase has previously been shown to be strongly conserved among the member species of a given genus in bacteria. The implications of this finding as a procedural tool of bacterial phylogeny were pursued by a study of two organisms, Sporosarcina ureae and Aeromonas formicans, the taxonomic positions of which have been historically controversial. S. ureae has characteristics of both Bacillaceae and Micrococcaceae, and A. formicans has characteristics of both Enterobacteriaceae and pseudomonads. Since the patterns of control for DAHP synthetase in all four of these microbial groups are different from one another but internally homogeneous within each group, the results obtained from the two test organisms were unambiguous. It was concluded that S. ureae is properly classified within Bacillaceae, probably deserving generic rank, and that A. formicans belongs with the family Enterobacteriaceae.

Aeromonas↗
PubMed2005

Toward an integrated clinical, molecular and serological classification of inflammatory bowel disease: report of a Working Party of the 2005 Montreal World Congress of Gastroenterology.

The discovery of a series of genetic and serological markers associated with disease susceptibility and phenotype in inflammatory bowel disease has led to the prospect of an integrated classification system involving clinical, serological and genetic parameters. The Working Party has reviewed current clinical classification systems in Crohn's disease, ulcerative colitis and indeterminate colitis, and provided recommendations for clinical classification in practice. Progress with respect to integrating serological and genetic markers has been examined in detail, and the implications are discussed. While an integrated system is not proposed for clinical use at present, the introduction of a widely acceptable clinical subclassification is strongly advocated, which would allow detailed correlations among serotype, genotype and clinical phenotype to be examined and confirmed in independent cohorts of patients and, thereby, provide a vital foundation for future work.

Biomarkers↗
PubMed1992

Chronic granulomatous disease: diagnosis and classification at the molecular level.

Chronic granulomatous disease (CGD) is caused by the failure of phagocytes to produce microbicidal derivatives of molecular oxygen, such as hydrogen peroxide. It is one of the best characterized of the phagocyte disorders and represents an important consideration in the differential diagnosis of recurrent infections. The clinical, biochemical, and molecular genetic aspects of CGD are reviewed in this context in this article.

Amino Acid Sequence↗
PubMed1995

Molecular mechanism and classification of von Willebrand disease.

The characterization of mutations in von Willebrand disease provides useful insight into the synthesis, structure, and function of von Willebrand factor. This growing body of information has prompted a reclassification of vWD types that is intended to reflect distinct pathophysiologic mechanisms. Despite this apparent progress, many aspects of vWF biology and pathophysiology remain poorly understood. These include the mechanism by which binding of vWF to platelets is induced at sites of vascular injury, and the factors that influence the likelihood of bleeding symptoms in patients with vWD type 1.

Alleles↗
PubMed2006

Classification of the hydrogen-bonding species in a series of novel hydrazide based azobenzene derivatives investigated by two-dimensional correlation infrared spectroscopy and molecular modeling.

Classification of hydrogen-bonding species in a series of novel hydrazide modified p-methoxyazobenzene derivatives, 4-{n-[4-(4-methoxy-phenylazo)-phenoxy]-alkoxy}-benzoic acid hydrazide (Dn, n = 3, 6, 10) are performed in the present study. Temperature-dependent infrared (IR) spectra of Dn have been measured to investigate the thermal stability of the weak intermolecular interactions, such as hydrogen bonding among hydrazide moieties, pi-pi stacking among aromatic groups, and hydrophobic interaction between alkyl chains. In order to reveal the hydrogen bonding formed between NH, NH2, and CONH groups efficiently, two-dimensional (2D) correlation spectra have been constructed in the thermal sensitive spectral regions of (a) 3500-3100 cm(-1) and (b) 1700-1450 cm(-1), separately, and it have also been constructed between these two spectral regions. Based on the experimental data, the ab initio computational models have been developed to the proposed patterns of hydrogen bonding related to intermolecular interactions in Dn. The intermolecular hydrogen bondings and molecular alignments patterns result from both the experimental data and the computational models are performed for D3, D6, and D10, respectively, in the present study.

Azo Compounds↗
PubMed2006

Classification of renal neoplasms based on molecular signatures.

PURPOSE: Gene expression microarray studies have demonstrated distinct molecular signatures for different types of renal neoplasms based on overall gene expression patterns. However, in most of these studies the investigators used renal tumors with defined histology. We analyzed a test set of renal tumors in double-blind fashion using recently established molecular profiles of renal tumors as benchmarks. MATERIALS AND METHODS: A total of 16 consecutive nephrectomies performed for neoplasms at a single urological service were subjected to gene expression profiling using cDNA chips containing 21,632 genes. Analysis was clustered with our previously established molecular profiles of 91 histologically defined kidney neoplasms and comparative genomic microarray analysis while blinded to tumor histology and clinical information. RESULTS: With molecular analysis 9, 4, 2 and 1 tumors were classified as clear cell, papillary RCC, chromophobe RCC, and renal oncocytoma, respectively. Histopathological evaluation was concordant in 14 tumors. One of the 2 tumors with a discrepancy between molecular and pathological diagnoses was composed of oncocytoma and high grade clear cell RCC, and the other was chromophobe RCC that histologically mimicked papillary RCC. CONCLUSIONS: We report the feasibility of the molecular diagnosis and classification of unknown renal neoplasms. Molecular diagnosis appears to be reliable and comparable to the standard of urological pathology. This molecular method may be a potentially useful test for establishing an accurate diagnosis that can impact clinical management.

Carcinoma, Renal Cell↗