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Functional Classification (functional + classification)
Selected AbstractsQuantification of upper extremity function and range of motion in children with cerebral palsyDEVELOPMENTAL MEDICINE & CHILD NEUROLOGY, Issue 12 2008L Andrew Koman MD This study evaluated the hypothesis that upper extremity function and range of motion can be quantified reliably in children with cerebral palsy (CP) in a busy clinical setting. The specific aim was to determine the inter- and intrarater reliability of a modified House Functional Classification (MHC) system to evaluate upper extremity function and a standardized instrument to document upper extremity range of motion (Upper Extremity Rating Scale [UERS]). Sixty-five children with CP (43 males, 22 females, mean age 9y 2mo, SD 4y 1mo) with spasticity involving the upper extremity (quadriplegia n=22; hemiplegia n=36; diplegia n=7; Gross Motor Functional Classification System Levels I n=41, II n=6, III n=3, IV n=5, V n=10) were evaluated independently by occupational therapists and orthopedic surgeons using both instruments at several visits. Inter- and intrarater reliability were determined for both instruments by calculating measures of agreement (weighted kappa values and intraclass correlation coefficients [ICCs]). Interrater agreement (ICC=0.94) and intrarater agreement (ICC=0.96) on the MHC were good to excellent. Similarly, inter-rater agreement (kappa 0.66,0.81) and intrarater agreement (kappa 0.64,0.88) on the UERS was either good or excellent. The MHC and the UERS provide standardized, reliable, reproducible, and efficient instruments that can be used by occupational therapists and orthopedic surgeons to evaluate the upper extremities of children with CP. [source] Functional Classification of Protein Kinase Binding Sites Using CavbaseCHEMMEDCHEM, Issue 10 2007Daniel Kuhn Dr. Abstract Increasingly, drug-discovery processes focus on complete gene families. Tools for analyzing similarities and differences across protein families are important for the understanding of key functional features of proteins. Herein we present a method for classifying protein families on the basis of the properties of their active sites. We have developed Cavbase, a method for describing and comparing protein binding pockets, and show its application to the functional classification of the binding pockets of the protein family of protein kinases. A diverse set of kinase cavities is mutually compared and analyzed in terms of recurring functional recognition patterns in the active sites. We are able to propose a relevant classification based on the binding motifs in the active sites. The obtained classification provides a novel perspective on functional properties across protein space. The classification of the MAP and the c-Abl kinases is analyzed in detail, showing a clear separation of the respective kinase subfamilies. Remarkable cross-relations among protein kinases are detected, in contrast to sequence-based classifications, which are not able to detect these relations. Furthermore, our classification is able to highlight features important in the optimization of protein kinase inhibitors. Using small-molecule inhibition data we could rationalize cross-reactivities between unrelated kinases which become apparent in the structural comparison of their binding sites. This procedure helps in the identification of other possible kinase targets that behave similarly in "binding pocket space" to the kinase under consideration. [source] Expressed sequence tag analysis of the diapausing queen of the bumblebee Bombus ignitusENTOMOLOGICAL RESEARCH, Issue 4 2006Yeon-Ju KIM Abstract We constructed a full-length cDNA library from diapausing queens of the bumblebee Bombus ignitus. A total of 480 randomly selected clones was sequenced by single-run 5,-end sequencing. Of these, there were 437 high quality clones, 23 poor quality clones and 20 read-fail clones. Each high quality clone sequence was searched against a public protein database. The most frequently found matching genes were ribosomal proteins (12.5%), p10 (3.58%), cytochrome P450 monooxygenase (3.13%) and sensory appendage protein (2.9%). Sequence similarity analysis between bumblebees and other insect species showed that 72 out of 437 (16.5%) bumblebee expressed sequence tags (EST) matched sequences of Apis mellifera, with matches to Drosophila melanogaster (6.6%), Caenorhabditis briggsae (6.2%), Lysiphlebus testaceipes (4.8%), Periplaneta americana (3.7%) and Anopheles gambiae (3.4%) following, suggesting that sequence similarity of bumblebee EST is closest to that of A. mellifera. Functional classification of EST based on Gene Ontology showed that most genes found by sequencing are associated with physiological processes in the bumblebee. The results of sequencing and analysis of our 437 cDNA demonstrated that high-throughput EST sequencing and data analysis are powerful means for identifying novel genes and for expression profiling. Our bumblebee EST collection could be a useful platform for further studies of gene expression in diapausing bumblebees. [source] Generation and analysis of 5318 expressed sequence tags from the filamentous sporophyte of Porphyra haitanensis (Rhodophyta),JOURNAL OF PHYCOLOGY, Issue 6 2007Fan Xiaolei Porphyra haitanensis T. J. Chang et B. F. Zheng (Bangiales, Rhodophyta) is cultivated in China and widely consumed in Asia. To gain more insight into its physiological and biochemical properties, we generated 5318 expressed sequence tags (ESTs) from the sporophyte of P. haitanensis, and upon assembling into a nonredundant set, 2535 sequences were obtained, among which only 32.2% (816) shared certain similarity with published sequences (Nr and KOG). Functional classification of such ESTs revealed that most of the transcripts were related to its conservative biological metabolism, and P. haitanensis most likely possesses cyanide-resistant respiration and a C4-like carbon-fixation pathway, both of which have never been reported in a rhodophyte before. Twenty-eight percent of the nonredundant gene clusters exhibited significant similarity to those from P. yezoensis Ueda sporophytes, and 16 genes up-regulated in P. yezoensis sporophytes were also expressed abundantly in P. haitanensis. Codon usage analysis indicated that exposure to high GC pressure might occur during evolution of P. haitanensis. These findings represent the most extensive collection of ESTs from P. haitanensis to date, and all the ESTs in this study have been submitted to GenBank (accession nos. DN604790,DN608469, EG016226,EG018540). [source] Can Functional Traits Predict Ecological Interactions?BIOTROPICA, Issue 3 2010A Case Study Using Rain forest Frugivores, Plants in Australia ABSTRACT In rain forest, the large numbers of species of fleshy-fruited plants and frugivorous animals result in a large number of potential fruit,frugivore interactions, which are challenging to survey in the field. Yet, knowledge of these relationships is needed to predict consequences of changes in the frugivore assemblage for seed dispersal. In the absence of comprehensive dietary information, it may be possible to delineate between frugivores that disperse different plants using ,functional traits,' or morphological and behavioral attributes of frugivores that interact with differences in salient characteristics of plant species. Here we use data on the consumption of 244 Australian rain forest plant species by 38 bird species to test for associations between patterns of frugivory and birds': (1) degree of frugivory, (2) gape width, and (3) seed treatment (seed crushing or seed dispersing). Degree of frugivory and gape width explain 74 percent of the variation in the sizes of fruits consumed by frugivorous birds. Among birds that consume a substantial dietary proportion of fruit, birds with wider gapes consume larger fruits. In contrast, this relationship was not shown by birds for which fruit is only a minor dietary component. Degree of frugivory and gape width, together with seed treatment, also strongly predict the overall taxonomic composition and diversity of plants consumed by bird species. Functional classifications of frugivore species may prove useful in developing a predictive understanding of fruit,frugivore interactions in other rain forest regions where detailed dietary information is not available for most frugivores. [source] Phenotypic classification of human CD8+ T,cells reflecting their function: inverse correlation between quantitative expression of CD27 and cytotoxic effector functionEUROPEAN JOURNAL OF IMMUNOLOGY, Issue 4 2004Hiroko Tomiyama Abstract Phenotypic classification of human CD8+ T,cells using three cell surface markers, CD27, CD28 and CD45RA, was recently suggested to be useful for identification of naive, memory and effector CD8+ T,cells. However, it still remains unclear whether such classification precisely reflects functional classification of CD8+ T,cells. To clarify this, we characterized each CD27CD28CD45RA subset of total and human cytomegalovirus (HCMV)-specific CD8+ T,cells by analyzing the expression of perforin and two chemokine receptors, CCR5 and CCR7, as well as their function. An inverse correlation between perforin and CD27 expression was found in all four CD28CD45RA subsets. Therefore, to achieve a phenotypic classification of CD8+ T,cells that moreprecisely reflects their function, the CD27+ subset was divided into CD27low and CD27high subsets based on the expression level of CD27. Functional and flow cytometric analyses of CD27CD28CD45RA subsets showed that this phenotypic classification reflects functional classification of CD8+ T,cells. HCMV-specific CD8+ T,cells from healthy HCMV-seropositive individuals were predominantly found in effector and memory/effector subsets, indicating that HCMV-specific effector CD8+ T,cells are actively induced by HCMV replication in healthy HCMV carriers. Phenotypic analyses of CD8+ T,cells using this classification will enable the characterization of antigen-specific CD8+ T,cells. [source] Analysis of the sugar-binding specificity of mannose-binding-type Jacalin-related lectins by frontal affinity chromatography , an approach to functional classificationFEBS JOURNAL, Issue 6 2008Sachiko Nakamura-Tsuruta The Jacalin-related lectin (JRL) family comprises galactose-binding-type (gJRLs) and mannose-binding-type (mJRLs) lectins. Although the documented occurrence of gJRLs is confined to the family Moraceae, mJRLs are widespread in the plant kingdom. A detailed comparison of sugar-binding specificity was made by frontal affinity chromatography to corroborate the structure,function relationships of the extended mJRL subfamily. Eight mJRLs covering a broad taxonomic range were used: Artocarpin from Artocarpus integrifolia (jackfruit, Moraceae), BanLec from Musa acuminata (banana, Musaceae), Calsepa from Calystegia sepium (hedge bindweed, Convolvulaceae), CCA from Castanea crenata (Japanese chestnut, Fagaceae), Conarva from Convolvulus arvensis (bindweed, Convolvulaceae), CRLL from Cycas revoluta (King Sago palm tree, Cycadaceae), Heltuba from Helianthus tuberosus (Jerusalem artichoke, Asteraceae) and MornigaM from Morus nigra (black mulberry, Moraceae). The result using 103 pyridylaminated glycans clearly divided the mJRLs into two major groups, each of which was further divided into two subgroups based on the preference for high-mannose-type N-glycans. This criterion also applied to the binding preference for complex-type N-glycans. Notably, the result of cluster analysis of the amino acid sequences clearly corresponded to the above specificity classification. Thus, marked correlation between the sugar-binding specificity of mJRLs and their phylogeny should shed light on the functional significance of JRLs. [source] Multienzyme Profiling of Thermophilic Microorganisms with a Substrate Cocktail AssayADVANCED SYNTHESIS & CATALYSIS (PREVIOUSLY: JOURNAL FUER PRAKTISCHE CHEMIE), Issue 7-8 2005Renaud Sicard Abstract Labeled substrates for 16 different catalytic activities were combined into a cocktail reagent for multienzyme functional profiling, called PHENOZYMTM. The assay involves a single reaction followed by determination of substrate consumption by HPLC-analysis. The method allows a rapid identification of multiple enzyme activities, and is compatible with a diversity of growth media and reaction conditions (pH, temperature). The PHENOZYMTM cocktail was used to analyze the activity of 16 enzyme activities in a series of microbial strains, including thermophilic microorganisms. The functional profiles were used for a functional classification of the different microbial strains tested by hierarchical cluster analysis. The resulting "phylo-enzymatic" tree revealed associations consistent with the known phylogenetic classification of the strains. The influence of the culture medium on the enzyme activity profiles was also apparent. [source] Using grey dynamic modeling and pseudo amino acid composition to predict protein structural classesJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 12 2008Xuan Xiao Abstract Using the pseudo amino acid (PseAA) composition to represent the sample of a protein can incorporate a considerable amount of sequence pattern information so as to improve the prediction quality for its structural or functional classification. However, how to optimally formulate the PseAA composition is an important problem yet to be solved. In this article the grey modeling approach is introduced that is particularly efficient in coping with complicated systems such as the one consisting of many proteins with different sequence orders and lengths. On the basis of the grey model, four coefficients derived from each of the protein sequences concerned are adopted for its PseAA components. The PseAA composition thus formulated is called the "grey-PseAA" composition that can catch the essence of a protein sequence and better reflect its overall pattern. In our study we have demonstrated that introduction of the grey-PseAA composition can remarkably enhance the success rates in predicting the protein structural class. It is anticipated that the concept of grey-PseAA composition can be also used to predict many other protein attributes, such as subcellular localization, membrane protein type, enzyme functional class, GPCR type, protease type, among many others. © 2008 Wiley Periodicals, Inc. J Comput Chem 2008. [source] Fast and automated functional classification with MED-SuMo: An application on purine-binding proteinsPROTEIN SCIENCE, Issue 4 2010Olivia Doppelt-Azeroual Abstract Ligand,protein interactions are essential for biological processes, and precise characterization of protein binding sites is crucial to understand protein functions. MED-SuMo is a powerful technology to localize similar local regions on protein surfaces. Its heuristic is based on a 3D representation of macromolecules using specific surface chemical features associating chemical characteristics with geometrical properties. MED-SMA is an automated and fast method to classify binding sites. It is based on MED-SuMo technology, which builds a similarity graph, and it uses the Markov Clustering algorithm. Purine binding sites are well studied as drug targets. Here, purine binding sites of the Protein DataBank (PDB) are classified. Proteins potentially inhibited or activated through the same mechanism are gathered. Results are analyzed according to PROSITE annotations and to carefully refined functional annotations extracted from the PDB. As expected, binding sites associated with related mechanisms are gathered, for example, the Small GTPases. Nevertheless, protein kinases from different Kinome families are also found together, for example, Aurora-A and CDK2 proteins which are inhibited by the same drugs. Representative examples of different clusters are presented. The effectiveness of the MED-SMA approach is demonstrated as it gathers binding sites of proteins with similar structure-activity relationships. Moreover, an efficient new protocol associates structures absent of cocrystallized ligands to the purine clusters enabling those structures to be associated with a specific binding mechanism. Applications of this classification by binding mode similarity include target-based drug design and prediction of cross-reactivity and therefore potential toxic side effects. [source] Novel identification of expressed genes and functional classification of hypothetical proteins from Neisseria meningitidis serogroup APROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 18 2007Giulia Bernardini Abstract To implement the 2-DE database of serogroup A Neisseria meningitidis (MenA) and improve its potential of investigation in bacterial biology, cell extracts were separated by tricine-SDS-PAGE and 131 novel proteins were identified by ,LC-ESI-IT-MS/MS. These identifications extended to 404, the number of MenA gene expression products characterized at the proteome level, approximately covering 20% of the total ORFs predicted from genome sequence. This technical approach was particularly useful in ascertaining expression of ribosomal as well as hypothetical proteins. Particular attention was paid to functional characterization of hypothetical proteins by means of software analyses and database searches. [source] A hierarchical analysis of transcriptome alterations in intrauterine growth restriction (IUGR) reveals common pathophysiological pathways in mammals,THE JOURNAL OF PATHOLOGY, Issue 3 2007C Buffat Abstract Intra-uterine growth restriction (IUGR) is a frequent disease, affecting up to 10% of human pregnancies and responsible for increased perinatal morbidity and mortality. Moreover, low birth weight is an important cause of the metabolic syndrome in the adult. Protein depletion during the gestation of rat females has been widely used as a model for human IUGR. By transcriptome analysis of control and protein-deprived rat placentas, we were able to identify 2543 transcripts modified more than 2.5 fold (1347 induced and 1196 repressed). Automatic functional classification enabled us to identify clusters of induced genes affecting chromosome structure, transcription, intracellular transport, protein modifications and apoptosis. In particular, we suggest the existence of a complex balance regulating apoptosis. Among repressed genes, we noted several groups of genes involved in immunity, signalling and degradation of noxious chemicals. These observations suggest that IUGR placentas have a decreased resistance to external aggression. The promoters of the most induced and most repressed genes were contrasted for their composition in putative transcription factor binding sites. There was an over-representation of Znfinger (ZNF) proteins and Pdx1 (pancreatic and duodenal homeobox protein 1) putative binding sites. Consistently, Pdx1 and a high proportion of ZNF genes were induced at the transcriptional level. A similar analysis of ZNF promoters showed an increased presence of putative binding sites for the Tata box binding protein (Tbp). Consistently again, we showed that the Tbp and TBP-associated factors (Tafs) were up-regulated in IUGR placentas. Also, samples of human IUGR and control placentas showed that human orthologous ZNFs and PDX1 were transcriptionnally induced, especially in non-vascular IUGR. Immunohistochemistry revealed increased expression of PDX1 in IUGR human placentas. In conclusion, our approach permitted the proposition of hypotheses on a hierarchy of gene inductions/repressions leading to massive transcriptional alterations in the IUGR placenta, in humans and in rodents. Copyright © 2007 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd. [source] Typology in Mediterranean transitional waters: new challenges and perspectivesAQUATIC CONSERVATION: MARINE AND FRESHWATER ECOSYSTEMS, Issue 5 2006A. Basset Abstract 1.Transitional waters are ecotones between terrestrial, freshwater and marine ecosystems, being characterized by high spatial heterogeneity and temporal variability. 2.The EU Water Framework Directive (WFD) posed to the scientific community the challenge to classify these ecosystems into a small number of types, while retaining a functional classification of ecosystem types. 3.A niche theory approach is proposed to identify the limiting forcing factors organizing biological quality elements, i.e. the limiting niche dimensions. 4.The analysis of a macro-invertebrate dataset from published papers on 36 Italian lagoons suggested a two-level typological classification of Mediterranean lagoons. 5.Basic ecological theories, such as niche and island biogeography theories, have fundamental implications for the process of developing a typological classification for all aquatic ecosystems, as required by the WFD. Copyright © 2006 John Wiley & Sons, Ltd. [source] Functional Classification of Protein Kinase Binding Sites Using CavbaseCHEMMEDCHEM, Issue 10 2007Daniel Kuhn Dr. Abstract Increasingly, drug-discovery processes focus on complete gene families. Tools for analyzing similarities and differences across protein families are important for the understanding of key functional features of proteins. Herein we present a method for classifying protein families on the basis of the properties of their active sites. We have developed Cavbase, a method for describing and comparing protein binding pockets, and show its application to the functional classification of the binding pockets of the protein family of protein kinases. A diverse set of kinase cavities is mutually compared and analyzed in terms of recurring functional recognition patterns in the active sites. We are able to propose a relevant classification based on the binding motifs in the active sites. The obtained classification provides a novel perspective on functional properties across protein space. The classification of the MAP and the c-Abl kinases is analyzed in detail, showing a clear separation of the respective kinase subfamilies. Remarkable cross-relations among protein kinases are detected, in contrast to sequence-based classifications, which are not able to detect these relations. Furthermore, our classification is able to highlight features important in the optimization of protein kinase inhibitors. Using small-molecule inhibition data we could rationalize cross-reactivities between unrelated kinases which become apparent in the structural comparison of their binding sites. This procedure helps in the identification of other possible kinase targets that behave similarly in "binding pocket space" to the kinase under consideration. [source] | ||||||||||||||||