Protein fold recognition score functions: Unusual construction strategies

We describe two ways of optimizing score functions for protein sequence to structure threading. The first method adjusts parameters to improve sequence to structure alignment. The second adjusts parameters so as to improve a score function's ability to rank alignments calculated in the first score function. Unlike those functions known as knowledge-based force fields, the resulting parameter sets do not rely on Boltzmann statistics, have no claim to representing free energies and are purely constructions for recognizing protein folds. The methods give a small improvement, but suggest that functions can be profitably optimized for very specific aspects of protein fold recognition, Proteins 1999;36:454-461. (C) 1999 Wiley-Liss, Inc.

Effects of habitat modification in mangroves on the structure of mollusc and crab assemblages

The abundance and species richness of mollusc and crab assemblages were examined in a subtropical mangrove forest in Moreton Bay, Queensland, Australia, which has been disturbed and damaged by the construction of a wooden boardwalk and a path. Sections of the forest immediately adjacent to the boardwalk and path were compared with reference areas to determine whether changes to the small-scale structural complexity within the forest affected the benthic fauna. The disturbed area was characterised by having 65-80% fewer pneumatophores, significantly fewer species and individuals of molluscs, but significantly more species and individuals of crabs than the reference areas. The abundance of mangrove pneumatophores and the attached epiphytic algae were manipulated at two sites to determine whether observed differences in these features could account for the differences in the assemblage of molluscs in the disturbed area of the forest compared with reference areas. Five experimental treatments were used: undisturbed controls, pneumatophore removals (abundance reduced by ca. 65%), epiphytic algal removals (algae removed from ca. 65% of pneumatophores), pneumatophore disturbance controls and algal disturbance controls. The experimental reduction of the abundance of mangrove pneumatophores and the associated epiphytic algae led to significant declines (by as much as 83%) in the number of molluscs utilising the substratum in the modified plots. There was no significant difference in the abundance of molluscs in the pneumatophore and algal removal plots suggesting any effect was primarily related to removal of the epiphytic algae from the surface of the pneumatophores. The responses by the biota to the changes in the physical environment demonstrate that even relatively small-scale modifications to the physical structure of subtropical mangrove forests can lead to significant effects on the diversity and abundance of macrobenthic organisms in these habitats. Such modifications have the potential to cause cascading effects at higher trophic levels with a deterioration in the value of these habitats as nursery and feeding grounds. Future efforts at conservation of these estuarine environments must focus on the prevention or reduction of modifications to the physical structure and integrity of the system, rather than just on the prevention of loss of entire patches of habitat. (C) 2000 Elsevier Science B.V. All rights reserved.

Construction and validation of a Bovine Innate Immune Microarray

Background: Microarray transcript profiling has the potential to illuminate the molecular processes that are involved in the responses of cattle to disease challenges. This knowledge may allow the development of strategies that exploit these genes to enhance resistance to disease in an individual or animal population. Results: The Bovine Innate Immune Microarray developed in this study consists of 1480 characterised genes identified by literature searches, 31 positive and negative control elements and 5376 cDNAs derived from subtracted and normalised libraries. The cDNA libraries were produced from 'challenged' bovine epithelial and leukocyte cells. The microarray was found to have a limit of detection of 1 pg/mu g of total RNA and a mean slide-to-slide correlation co-efficient of 0.88. The profiles of differentially expressed genes from Concanavalin A ( ConA) stimulated bovine peripheral blood lymphocytes were determined. Three distinct profiles highlighted 19 genes that were rapidly up-regulated within 30 minutes and returned to basal levels by 24 h; 76 genes that were upregulated between 2 - 8 hours and sustained high levels of expression until 24 h and 10 genes that were down-regulated. Quantitative real-time RT-PCR on selected genes was used to confirm the results from the microarray analysis. The results indicate that there is a dynamic process involving gene activation and regulatory mechanisms re-establishing homeostasis in the ConA activated lymphocytes. The Bovine Innate Immune Microarray was also used to determine the cross-species hybridisation capabilities of an ovine PBL sample. Conclusion: The Bovine Innate Immune Microarray has been developed which contains a set of well-characterised genes and anonymous cDNAs from a number of different bovine cell types. The microarray can be used to determine the gene expression profiles underlying innate immune responses in cattle and sheep.

On the construction of integrable closed chains with quantum supersymmetry

We present a general prescription for the construction of integrable one-dimensional systems with closed boundary conditions and quantum supersymmetry.

Construction of a 1-Mb restriction-mapped cosmid contig containing the candidate region for the familial mediterranean fever locus (MEFV) on chromosome 16p13.3

In this paper we describe the assembly and restriction map of a 1.05-Mb cosmid contig spanning the candidate region for familial Mediterranean fever (FMF), a recessively inherited disorder of inflammation localized to 16p13.3. Using a combination of cosmid walking and screening for P1, PAC, BAG, and YAC clones, we have generated a contig of genomic clones spanning similar to 1050 kb that contains the FMF critical region. The map consists of 179 cosmid, 15 P1, 10 PAC, 3 BAG, and 17 YAC clones, anchored by 27 STS markers. Eight additional STSs have been developed from the similar to 700 kb immediately centromeric to this genomic region. Five of the 35 STSs are microsatellites that have not been previously reported. NotI and EcoRI mapping of the overlapping cosmids, hybridization of restriction fragments from cosmids to one another, and STS analyses have been used to validate the assembly of the contig. Our contig totally subsumes the 250-kb interval recently reported, by founder haplotype analysis, to contain the FMF gene. Thus, our high-resolution clone map provides an ideal resource for transcriptional mapping toward the eventual identification of this disease gene. (C) 1997 Academic Press.

Bioinformatics construction of the human cell surfaceome

Cell surface proteins are excellent targets for diagnostic and therapeutic interventions. By using bioinformatics tools, we generated a catalog of 3,702 transmembrane proteins located at the surface of human cells (human cell surfaceome). We explored the genetic diversity of the human cell surfaceome at different levels, including the distribution of polymorphisms, conservation among eukaryotic species, and patterns of gene expression. By integrating expression information from a variety of sources, we were able to identify surfaceome genes with a restricted expression in normal tissues and/or differential expression in tumors, important characteristics for putative tumor targets. A high-throughput and efficient quantitative real-time PCR approach was used to validate 593 surfaceome genes selected on the basis of their expression pattern in normal and tumor samples. A number of candidates were identified as potential diagnostic and therapeutic targets for colorectal tumors and glioblastoma. Several candidate genes were also identified as coding for cell surface cancer/testis antigens. The human cell surfaceome will serve as a reference for further studies aimed at characterizing tumor targets at the surface of human cells.

Construction and Validation of the Brazilian Questionario de Respostas Socialmente Habilidosas Segundo Relato de Professores (QRSH-PR)

Behavioral problems in preschool children are one of the most frequent motives for seeking psychological care by parents and caregivers. Instruments are considered necessary, created from a Social Skills Training theoretical-practical perspective, which may systematically assist the identification of social skills and behavioral deficits. helping professionals in the prevention and/or reduction of behavioral problems. The purpose of this study was to test the psychometric validity and reliability of an instrument for evaluation of Socially Skilled Responses. from a teacher`s perspective (QRSH-PR). For this purpose, 260 preschool children were evaluated. differentiated in subgroups without and without behavioral difficulties, based on the Child Behavior Scale (Escala de Comportamento Infantil/ECI-Professor). Studies were conducted for construct. discrimination. concurrent and predictive validity. The Cronbach Alpha was calculated to evaluate internal consistency. The obtained results pointed to positive indicators in reference to construct, discrimination, and predictive validity, and even for good internal consistency. indicating that the items consistently measure the construct of social skills, and differentiated children with and without behavioral problems. The questionnaire is considered to be gauged for evaluation of socially skilled responses from preschool children. and applicable in educational and clinical environments.