Relationship between global structural parameters and Enzyme Commission hierarchy: Implications for function prediction

In protein databases there is a substantial number of proteins structurally determined but without function annotation. Understanding the relationship between function and structure can be useful to predict function on a large scale. We have analyzed the similarities in global physicochemical parameters for a set of enzymes which were classified according to the four Enzyme Commission (EC) hierarchical levels. Using relevance theory we introduced a distance between proteins in the space of physicochemical characteristics. This was done by minimizing a cost function of the metric tensor built to reflect the EC classification system. Using an unsupervised clustering method on a set of 1025 enzymes, we obtained no relevant clustering formation compatible with EC classification. The distance distributions between enzymes from the same EC group and from different EC groups were compared by histograms. Such analysis was also performed using sequence alignment similarity as a distance. Our results suggest that global structure parameters are not sufficient to segregate enzymes according to EC hierarchy. This indicates that features essential for function are rather local than global. Consequently, methods for predicting function based on global attributes should not obtain high accuracy in main EC classes prediction without relying on similarities between enzymes from training and validation datasets. Furthermore, these results are consistent with a substantial number of studies suggesting that function evolves fundamentally by recruitment, i.e., a same protein motif or fold can be used to perform different enzymatic functions and a few specific amino acids (AAs) are actually responsible for enzyme activity. These essential amino acids should belong to active sites and an effective method for predicting function should be able to recognize them. (C) 2012 Elsevier Ltd. All rights reserved.

CARBON MARKET AND INSTITUTIONS: OPPORTUNITIES IN THE SEARCH OF A NEW MODEL FOR DEVELOPMENT

Seeking alternatives for the economic system to face the several crises it has gone through lately (electrical power, cultural, financing and technological) brought about a new market involving the Kyoto Protocol signatory countries: the carbon market. The present article aims at assessing the carbon market institutional issue in Brazil by identifying the risks and opportunities inherent to the institutional agent characteristics and to that market rules. The research methodology was bibliographic and based on the analysis of the Securities and Exchange Commission of Brazil (Comissao de Valores Mobiliarios and Bolsa Mercantil de Valores) contents. Its theoretical basis rests on concepts of the institution and the new institutional economy. The results show that in spite of the risks and institutional problems it involves, the carbon market is promising due to the opportunities create by new technologies and energies developed to achieve and sustain the capitalist system new cycle, addressed to produce a clean development.

Consolidation of international guidelines for the management of canine populations in urban areas and proposal of performance indicators

Consolidation of international guidelines for the management of canine populations in urban areas and proposal of performance indicators The objective of this study is to propose a generic program for the management of urban canine populations with suggestion of performance indicators. The following international guidelines on canine population management were revised and consolidated: World Health Organization, World Organisation for Animal Health, World Society for the Protection of Animals, International Companion Animal Management Coalition, and the Food and Agriculture Organization. Management programs should cover: situation diagnosis, including estimates of population size; social participation with involvement of various sectors in the planning and execution of strategies; educational actions to promote humane values, animal welfare, community health, and responsible ownership (through purchase or adoption); environmental and waste management to eliminate sources of food and shelter; registration and identification of animals; animal health care, reproductive control; prevention and control of zoonoses; control of animal commerce; management of animal behavior and adequate solutions for abandoned animals; and laws regulating responsible ownership, prevention of abandonment and zoonoses. To monitor these actions, four groups of indicators are suggested: animal population indicators, human/animal interaction indicators, public service indicators, and zoonosis indicators. The management of stray canine populations requires political, sanitary, ethologic, ecologic, and humanitarian strategies that are socially acceptable and environmentally sustainable. Such measures must also include the control of zoonoses such as rabies and leishmaniasis, considering the concept of "one health," which benefits both the animals and people in the community.

Microcollinearity between autopolyploid sugarcane and diploid sorghum genomes

Abstract Background Sugarcane (Saccharum spp.) has become an increasingly important crop for its leading role in biofuel production. The high sugar content species S. officinarum is an octoploid without known diploid or tetraploid progenitors. Commercial sugarcane cultivars are hybrids between S. officinarum and wild species S. spontaneum with ploidy at ~12×. The complex autopolyploid sugarcane genome has not been characterized at the DNA sequence level. Results The microsynteny between sugarcane and sorghum was assessed by comparing 454 pyrosequences of 20 sugarcane bacterial artificial chromosomes (BACs) with sorghum sequences. These 20 BACs were selected by hybridization of 1961 single copy sorghum overgo probes to the sugarcane BAC library with one sugarcane BAC corresponding to each of the 20 sorghum chromosome arms. The genic regions of the sugarcane BACs shared an average of 95.2% sequence identity with sorghum, and the sorghum genome was used as a template to order sequence contigs covering 78.2% of the 20 BAC sequences. About 53.1% of the sugarcane BAC sequences are aligned with sorghum sequence. The unaligned regions contain non-coding and repetitive sequences. Within the aligned sequences, 209 genes were annotated in sugarcane and 202 in sorghum. Seventeen genes appeared to be sugarcane-specific and all validated by sugarcane ESTs, while 12 appeared sorghum-specific but only one validated by sorghum ESTs. Twelve of the 17 sugarcane-specific genes have no match in the non-redundant protein database in GenBank, perhaps encoding proteins for sugarcane-specific processes. The sorghum orthologous regions appeared to have expanded relative to sugarcane, mostly by the increase of retrotransposons. Conclusions The sugarcane and sorghum genomes are mostly collinear in the genic regions, and the sorghum genome can be used as a template for assembling much of the genic DNA of the autopolyploid sugarcane genome. The comparable gene density between sugarcane BACs and corresponding sorghum sequences defied the notion that polyploidy species might have faster pace of gene loss due to the redundancy of multiple alleles at each locus.

Biomechanical in vitro evaluation of three stable internal fixation techniques used in sagittal osteotomy of the mandibular ramus: a study in sheep mandibles

Among the osteotomies performed in orthognathic surgery, the sagittal osteotomy of the mandibular ramus (SOMR) is the most common, allowing a great range of movements and stable internal fixation (SIF), therefore eliminating the need of maxillomandibular block in the postoperative period. Objectives: The purpose of this study was to evaluate the biomechanical resistance of three national systems used for SIF in SOMR in sheep mandibles. Material and methods: The study was performed in 30 sheep hemi-mandibles randomly divided into 3 experimental groups, each containing 10 hemi-mandibles. The samples were measured to avoid discrepancies and then subjected to SOMR with 5-mm advancement. In group I, 2.0x12 mm screws were used for fixation, inserted in an inverted "L" pattern (inverted "L" group). In group II, fixation was performed with two 2.0x12 mm screws, positioned in a linear pattern and a 4-hole straight miniplate and four 2.0x6.0 mm monocortical screws (hybrid group). In group III, fixation was performed with two-hole straight miniplates and eight 2.0x6.0 mm monocortical screws (mini plate group). All materials used for SIF were supplied by Osteosin - SIN. The hemimandibles were subjected to vertical linear load test by Kratos K2000MP mechanical testing unit for loading registration and displacement. Results: All groups showed similar resistance during mechanical test for loading and displacement, with no statistically significant differences between groups according to analysis of variance. Conclusion: These results indicate that the three techniques of fixation are equally effective for clinical fixation of SOMR.

Signature of the scattering between dark sectors in large scale cosmic microwave background anisotropies

We study the interaction between dark sectors by considering the momentum transfer caused by the dark matter scattering elastically within the dark energy fluid. Describing the dark scattering analogy to the Thomson scattering which couples baryons and photons, we examine the impact of the dark scattering in CMB observations. Performing global fitting with the latest observational data, we find that for a dark energy equation of state w < -1, the CMB gives tight constraints on dark matter-dark energy elastic scattering. Assuming a dark matter particle of proton mass, we derive an elastic scattering cross section of sigma(D) < 3.295 x 10(-10)sigma(T) where sigma(T) is the cross section of Thomson scattering. For w > -1, however, the constraints are poor. For w = -1, sigma(D) can formally take any value.