Histological biomarkers and biometric data on trahira Hoplias malabaricus (Pisces, Characiformes, Erythrinidae): a bioindicator species in the Mearim river, Brazilian Amazon.

The objective of this study was to evaluate the levels of environmental contamination in a protected area in the Brazilian Amazon. For this, two areas were chosen along the Mearim River: the reference area (A1) and the potentially contaminated area (A2), where water samples were collected, for physicochemical and microbiological analyses, as well as specimens of Hoplias malabaricus, for the evaluation of biometric data and incidence of branchial lesions. The physicochemical analyzes of the water from both areas showed contamination (low levels of dissolved oxygen, tubidity and high iron concentrations, especially in A2). The microbiological analyzes showed that all water samples showed total coliform values higher than those acceptable by CONAMA and WHO (with higher values in A2), in addition to E. coli values higher than those allowed by legislation in A2. Regarding biometric data, male and female fishes were significantly longer and heavier in A1 during the dry and rain seasons and the gonadosomatic index also showed higher values in A1 than in A2 in both seasons. H. malabaricus showed gill lesions of minimal to moderate pathological importance in A1 and A2, indicating that specimens from both areas of the Mearim River showed biological responses to contamination. The observed changes in the water quality, bimetic parameters and the histological analyzes of the specimens of H. malabaricus directly reflect on the quality and health of the fishes in the Mearim River, and point to the urgent need for prevention and remediation of contamination in these ecosystems.

Biomarcadores enzimáticos e histológicos em brânquias de Ucides cordatus (Linnaeus, 1763) (Crustacea, Brachyura, Ucididae) indicativos de impactos ambientais em uma região portuária do nordeste do Brasil / [Enzymatic and histological biomarkers in Ucides cordatus (Linnaeus, 1763) (Crustacea, Brachyura, Ucididae) gills indicative of environmental impacts in a port region of northeastern Brazil]

Objetivou-se neste estudo analisar biomarcadores histológicos e bioquímicos em brânquias de U. cordatus indicativos de impactos na Baía de São Marcos. Caranguejos foram coletados em quatro áreas na Baía de São Marcos: A1= Ilha dos Caranguejos (com baixo impacto); A2= Coqueiro, A3= Porto Grande, A4= Cajueiro (áreas potencialmente impactadas). Mediram-se os dados biométricos de cada exemplar de caranguejo. Amostras de brânquias foram submetidas à técnica histológica padrão e homogeneizadas em tampão fosfato, e o sobrenadante foi utilizado para análise das enzimas glutationa-S-transferase (GST) e catalase (CAT). A biometria indicou que os caranguejos de A1 são significativamente (P<0,05) maiores e mais pesados do que os caranguejos das áreas A2, A3 e A4. As alterações branquiais (rompimento das células pilastras, deformação do canal marginal, deslocamento da cutícula e necrose) foram significativamente (P˂0,05) mais frequentes em caranguejos de A2, A3 e A4 do que nos caranguejos de A1. As atividades enzimáticas da GST e CAT nos caranguejos apresentaram diferença significativa (P<0,05) entre as áreas de coletas, com padrão similar ao observado para as alterações branquiais. Os biomarcadores analisados mostraram que os caranguejos estão sob diferentes níveis de impactos (A4>A3>A2>A1) ao longo da Baía de São Marcos.(AU)

The objective of this study was to analyze histological and biochemical biomarkers in U. cordatus gills indicative of impacts in São Marcos Bay. Crabs were collected from four areas in São Marcos Bay: A1=Ilha dos Caranguejos (with low impact); A2=Coqueiro, A3=Porto Grande, A4=Cajueiro (potentially impacted areas). The biometric data of each specimen was measured. Gill samples were submitted to standard histological technique and homogenized in phosphate buffer, and the supernatant was used for analysis of glutathione S-transferase (GST) and catalase (CAT) enzyme activity. Biometric data indicated that crabs found in A1 are significantly (P<0.05) larger and heavier than crabs found in A2, A3 and A4 areas. Gill alterations (rupture of pilaster cells, Dilation of the marginal channel, Cuticle Rupture and necrosis) were significantly (P˂0.05) more frequent in the crabs in A2, A3 and A4 than crabs in A1. The enzymatic activities of GST and CAT showed significant difference (P<0.05) between the sampling areas, similar to that observed for gill alterations. The biomarkers analyzed showed that the crabs are under different impact levels (A4> A3> A2> A1) along the São Marcos Bay.(AU)

Biology of Corythucha gossypii Fabricius, 1794 (Hemiptera: Tingidae) in Ricinus communis at different temperatures and thermal requirements / Biologia de Corythucha gossypii Fabricius, 1794 (Hemiptera: Tingidae) em Ricinus communis em diferentes temperaturas e exigências térmicas

Abstract We studied the biology of Corythucha gossypii in Ricinus communis under different temperatures in climatic chambers adjusted at 20, 23, 25, and 28 °C, 60 ± 10% relative humidity, and a 12-h photoperiod. The development period and viability of eggs, the development period and survival rate of nymphs, and egg-adult cycle of C. gossypii as well as the adult longevity and fecundity were estimated. The thermal requirements (K) and temperature-base (Tb) were estimated for each of the immature stages and for the eggs-adults period. The duration of the eggs and nymphs phases and the egg-adult cycle of the C. gossypii on castor bean leaves at 20-28 °C were 7.6-17 days, 10.2-27.5 days, and 16.9-44.5 days, respectively. The lower temperature inhibited the oviposition of C. gossypii, whereas the higher temperatures were most favorable for its development. The municipalities of the Bahia state of Brumado, Irecê, Itaberaba, Jacobina, and Senhor do Bonfim were estimated to have a high potential for the population growth of C. gossypii. However, a greater number of generations per year of C. gossypii were observed in the municipalities of Brumado and Itaberaba.

Resumo Estudamos a biologia de Corythucha gossypii em Ricinus communis sob diferentes temperaturas em câmaras climatizadas ajustadas as temperaturas de 20, 23, 25 e 28 °C, umidade relativa de 60 ± 10% e fotoperíodo de 12 horas. O período de desenvolvimento e a viabilidade dos ovos, o período de desenvolvimento e a taxa de sobrevivência de ninfas e do ciclo de ovo-adulto de C. gossypii, bem como a longevidade dos adultos e fecundidade foram estimados. As exigências térmicas (K) e as temperaturas-bases (Tb) foram estimadas para cada um dos estádios imaturos e para o ciclo de ovo-adulto. A duração das fases de ovos e ninfas e do ciclo de ovo a adulto de C. gossypii em folhas de mamona a 20-28 °C foram de 7,6-17 dias, 10,2-27,5 dias e 16,9-44,5 dias, respectivamente. A temperatura mais baixa inibiu a oviposição de C. gossypii , enquanto as temperaturas mais altas foram favoráveis ao seu desenvolvimento. Os municípios do estado da Bahia de Brumado, Irecê, Itaberaba, Jacobina e Senhor do Bonfim foram estimados para ter um alto potencial para o crescimento populacional de C. gossypii. No entanto, o maior número de gerações por ano de C. gossypii foi observado nos municípios de Brumado e Itaberaba.

Biology of Corythucha gossypii Fabricius, 1794 (Hemiptera: Tingidae) in Ricinus communis at different temperatures and thermal requirements.

We studied the biology of Corythucha gossypii in Ricinus communis under different temperatures in climatic chambers adjusted at 20, 23, 25, and 28 °C, 60 ± 10% relative humidity, and a 12-h photoperiod. The development period and viability of eggs, the development period and survival rate of nymphs, and egg-adult cycle of C. gossypii as well as the adult longevity and fecundity were estimated. The thermal requirements (K) and temperature-base (Tb) were estimated for each of the immature stages and for the eggs-adults period. The duration of the eggs and nymphs phases and the egg-adult cycle of the C. gossypii on castor bean leaves at 20-28 °C were 7.6-17 days, 10.2-27.5 days, and 16.9-44.5 days, respectively. The lower temperature inhibited the oviposition of C. gossypii, whereas the higher temperatures were most favorable for its development. The municipalities of the Bahia state of Brumado, Irecê, Itaberaba, Jacobina, and Senhor do Bonfim were estimated to have a high potential for the population growth of C. gossypii. However, a greater number of generations per year of C. gossypii were observed in the municipalities of Brumado and Itaberaba.

Genetic and non-genetic factors that increase the risk of non-syndromic cleft lip and/or palate development.

OBJECTIVES: We investigated the relationship between non-syndromic cleft lip/palate (NSCLP) and polymorphisms in methylenetetrahydrofolate reductase (MTHFR), methionine synthase (MTR), methionine synthase reductase (MTRR), and RFC1, as well as the corresponding interactions with environmental factors. SUBJECTS AND METHODS: One hundred and forty NSCLP patients and their mothers, as well as 175 control individuals and their mothers, were recruited. Information regarding smoking and alcohol consumption was recorded. Blood samples were obtained in order to measure serum folate and cobalamin, as well as, plasma total homocysteine concentrations and to extract DNA. Polymorphisms in MTHFR(677C>T and 1298A>C), MTR(2756A>G), MTR(66A>G), and RFC1(80A>G) were analyzed by PCR-restriction fragment length polymorphism. RESULTS: Among the patients, 59.5% had cleft lip and palate, 22.0% had cleft palate, and 18.5% had cleft lip only. Maternal alcohol consumption and reduced folic acid concentrations in both children and mothers (P < 0.001 and P = 0.003, respectively) were risk factors for NSCLP. Patients and their mothers carrying the MTHFR 667T allele showed lower serum folate than CC (P = 0.011 and P = 0.030, respectively). Mothers who carried the MTHFR 1298C allele exhibited increased risk of having a child with NSCLP, after adjusting for alcohol consumption (OR: 1.75, 95% CI: 1.03-2.99, P = 0.038). CONCLUSIONS: Reduced folic acid levels, alcohol consumption, and the MTHFR 677T and 1298C alleles may have contributed to NSCLP development in this sample population from Rio Grande do Norte.

Tumor necrosis factor beta (TNF-ß) NcoI polymorphism is associated with multiple sclerosis in Caucasian patients from Southern Brazil independently from HLA-DRB1.

This study evaluated the association of tumor necrosis factor beta (TNF-ß) NcoI polymorphism with the presence of multiple sclerosis (MS), disability, and HLA-DRB1 alleles in 208 Brazilian MS patients. As controls, 147 healthy individuals were included. The disability was evaluated at baseline and 5-year follow-up using the Expanded Disability Status Scale (EDSS). The TNF-ß genotypes were determined using PCR and restriction fragment length polymorphism and serum TNF-α level was determined using enzyme-linked immunosorbent assay. Among the MS patients, 166 (79.8 %) were white, 39 (18.7 %) were brown, and three (1.4 %) were Asian descents (those were excluded from the further analysis). Among the 205 MS patients, 149 (72.6 %) presented remitting-relapsing MS. The baseline and 5-year follow-up EDSS ranged from 0.0 to 3.0 and from 1.0 to 5.7, respectively. The TNFB2/B2 genotype was associated with the presence of MS among the white patients (p = 0.0443). Brown patients presented higher disability (p = 0.0234) and higher TNF-α levels (p = 0.0463) than white patients. White and brown patients carrying TNFB2/B2 genotype exhibited higher TNF-α levels (p = 0.0354 and p = 0.0309, respectively) than those with other geotypes. Association between TNF-ß NcoI genotypes and HLA-DRB1 alleles was not observed among the MS patients (p > 0.05). Taken together, TNFB2 allele was associated with the presence of MS independently of HLA-DRB1 in white patients and the TNFB2/B2 genotype was associated with increased TNF-α levels in white and brown patients, which could be an important genetic factor candidate for the susceptibility and pathogenesis of MS.

Hypertension is associated with serologically active disease in patients with systemic lupus erythematosus: role of increased Th1/Th2 ratio and oxidative stress.

OBJECTIVES: To determine whether disease activity verified by laboratorial parameters is associated with a higher frequency of hypertension in patients with systemic lupus erythematosus (SLE) without renal impairment and to investigate factors that could influence this hypertension. METHOD: This study included 102 controls, 70 patients with inactive SLE, and 53 patients with active SLE without renal impairment. We evaluated T helper type 1 (Th1)/Th2 lineage cytokines, nitric oxide (NO), insulin resistance (IR), and oxidative stress. RESULTS: Patients with active SLE had a higher probability of developing hypertension compared to controls [odds ratio (OR) 3.833, 95% confidence interval (CI) 1.806-8.137, p < 0.0003] and patients with inactive SLE (OR 2.215, 95% CI 1.032-4.752, p = 0.0394). Active SLE patients had a higher interleukin (IL)-12/IL-4 ratio (p < 0.05) than both controls and inactive SLE patients. Protein oxidation was significantly higher in patients with active SLE than in the control group and in patients with inactive SLE (p < 0.01 and p < 0.05, respectively). Multivariate analysis revealed an association between the presence of hypertension and he levels of glucose (p = 0.0276), insulin (p = 0.0498), hydroperoxides (p = 0.0221), IFN-γ (p = 0.0494), IL-17 (p = 0.0272), IL-12/IL-10 (p = 0.0373), IFN-γ/IL-10 (p = 0.0142), IFN-γ/IL-4 (p = 0.0320), and adiponectin (p = 0.0433). CONCLUSIONS: Patients with active SLE without renal impairment had an increased frequency of high blood pressure (43.4%) compared with patients with inactive SLE (25.7%) and controls (16.7%). Hypertension was associated with serologically active disease and was influenced by an increased Th1/Th2 ratio and oxidative stress.

Relationship between iron metabolism, oxidative stress, and insulin resistance in patients with systemic lupus erythematosus.

OBJECTIVE: The aim of the present study was to assess oxidative stress and iron metabolism in systemic lupus erythematosus (SLE) patients with and without insulin resistance (IR). METHOD: This study included 236 subjects (125 controls and 111 SLE patients). Patients with SLE were divided in two groups: with (n = 72) or without (n = 39) IR. RESULTS: SLE patients with IR showed higher advanced oxidation protein product (AOPP) levels (p = 0.030) and gamma-glutamyltransferase (GGT) levels (p = 0.001) and lower sulfhydryl groups of proteins (p = 0.0002) and total radical-trapping antioxidant parameter (TRAP) corrected by uric acid (UA) levels (p = 0.04) when compared to SLE patients without IR. However, SLE patients with IR presented lower serum 8-isoprostane (p = 0.05) and carbonyl protein levels (p = 0.04) when compared to SLE patients without IR. Serum ferritin levels were significantly higher in SLE patients (p = 0.0006) than in controls, and SLE patients with IR presented higher serum ferritin levels (p = 0.01) than SLE patients without IR. Patients with SLE showed that IR was inversely correlated to TRAP/UA (r = -0.2724, p = 0.0008) and serum ferritin was positively correlated to AOPP (r = 0.2870, p = 0.004). CONCLUSIONS: This study found that oxidative stress was higher in the group of SLE patients with IR, and increased ferritin, whether caused by the inflammatory process per se or hyperinsulinaemia, can favour the redox process. In addition, the preset data reinforce the need to measure oxidative stress with several methodologies with different assumptions.

Decreased oxidant profile and increased antioxidant capacity in naturally postmenopausal women.

Recent works have shown a dual side of estrogens, and research on the relationship between oxidative stress and menopausal status remains unclear and has produced controversial results. In this work, we aimed to evaluate by sensitive methods the oxidant and antioxidant changes that develop after natural menopause. Thirty premenopausal and 28 naturally postmenopausal women volunteered for this study. Blood was collected and plasma used. 17-OH estradiol levels in plasma were estimated. Plasma levels of advanced oxidation protein products (AOPP), lipid peroxidation products (such as hydroperoxides and malondialdehyde (MDA)), and nitrites were measured, and total radical antioxidant parameter testing was performed to determine the oxidant and antioxidant profiles, respectively. Estrogen levels were significantly increased (p < 0.02) in premenopausal women (54.28 ± 9.34 pg/mL) as compared with postmenopausal women (18.10 ± 1.49 pg/mL). Postmenopausal women had lower levels of lipid hydroperoxide oxidation (p < 0.0001), lipid hydroperoxide levels evaluated by the area under the curve (AUC; 1,366,000 ± 179,400 AUC; p < 0.01), and hydroperoxides as measured by the ferrous oxidation-xylenol orange method (31.48 ± 2.7 µM; p < 0.0001). The MDA levels did not differ between pre- and postmenopausal women whether measured by thiobarbituric acid-reactive substances or high-performance liquid chromatography assays. No differences in AOPP and nitrite levels were observed between pre- and postmenopausal women. Postmenopausal women also exhibited a higher total radical antioxidant level (0.89 ± 0.08 µM Trolox; p < 0.0001). Postmenopausal women demonstrated lower levels of oxidative damage and a higher antioxidant capacity than premenopausal women.

MSX1 gene polymorphisms in non-syndromic cleft lip and/or palate.

OBJECTIVE: The aim of this study was to investigate the contribution of 6 polymorphic variants of the MSX1 gene in non-syndromic cleft lip and/or palate (NSCL/P). METHODS: Three hundred and fifty-eight individuals (158 NSCL/P cases and 200 controls) were genotyped by TaqMan allelic discrimination using predesigned SNP assays. Statistical analyses were conducted using the software spss 15.0 and the r statistical suite. Haplotype block structure and haplotype frequencies were determined using the Haploview. A P-value of 0.05 and confidence interval of 95% were used for all of statistical tests. RESULTS: The patients with non-syndromic cleft lip and/or palate were characterized by similar distribution of MSX1 genotypes and allele in comparison to subjects without oral clefts (P > 0.05). Two haplotype blocks were constructed with polymorphisms of MSX1 gene and haplotypes formed showed a similar frequency in patients with and without oral clefts. CONCLUSIONS: The present study provides no evidence that MSX1 polymorphisms (rs3775261, rs1042484, rs12532, rs6446693, rs4464513 and rs1907998) play a major role in NSCL/P.

The influence of vibrissal somatosensory processing in rat superior colliculus on prey capture.

The lateral part of intermediate layer of superior colliculus (SCl) is a critical substrate for successful predation by rats. Hunting-evoked expression of the activity marker Fos is concentrated in SCl while prey capture in rats with NMDA lesions in SCl is impaired. Particularly affected are rapid orienting and stereotyped sequences of actions associated with predation of fast moving prey. Such deficits are consistent with the view that the deep layers of SC are important for sensory guidance of movement. Although much of the relevant evidence involves visual control of movement, less is known about movement guidance by somatosensory input from vibrissae. Indeed, our impression is that prey contact with whiskers is a likely stimulus to trigger predation. Moreover, SCl receives whisker and orofacial somatosensory information directly from trigeminal complex, and indirectly from zona incerta, parvicelular reticular formation and somatosensory barrel cortex. To better understand sensory guidance of predation by vibrissal information we investigated prey capture by rats after whisker removal and the role of superior colliculus (SC) by comparing Fos expression after hunting with and without whiskers. Rats were allowed to hunt cockroaches, after which their whiskers were removed. Two days later they were allowed to hunt cockroaches again. Without whiskers the rats were less able to retain the cockroaches after capture and less able to pursue them in the event of the cockroach escaping. The predatory behaviour of rats with re-grown whiskers returned to normal. In parallel, Fos expression in SCl induced by predation was significantly reduced in whiskerless animals. We conclude that whiskers contribute to the efficiency of rat prey capture and that the loss of vibrissal input to SCl, as reflected by reduced Fos expression, could play a critical role in predatory deficits of whiskerless rats.

Antifungal activity of tri- and tetra-thioureido amino derivatives against different Candida species.

The in vitro antifungal activity of six thioureido substituted amines (P1-P6) was evaluated against Candida species, including Candida albicans, C. glabrata, C. krusei and C. parapsilosis. These tri- and tetra-thioureido amino derivatives with different methylation levels were synthesised through easy synthetic routes to evaluate their antifungal properties against Candida species. Among all studied derivatives, the tri-(2-thioureido-ethyl)-amine (P1) was the most active compound inhibiting C. albicans and C. glabrata at a concentration of 0.49 µg ml(-1); P3, the N,N',N'',N'''-hexamethyl-derivative, also showed inhibitory activity against C. albicans and C. glabrata, but in higher concentrations (250 µg ml(-1) ). The N,N',N'',N'''-tetramethylated amine (P5) only inhibited the growth of C. glabrata, but its corresponding N,N',N'',N'''-octamethyl derivative (P6) was also active against C. glabrata (125 µg ml(-1)) and it was the only compound active against C. parapsilosis. P2 and P4 showed no significant antifungal activity. The structure-activity relationship of the thioureido-substituted derivatives indicates that the molecular branching and the alkylation levels can influence the antifungal activity. This study demonstrated that thioureido derivatives exhibited significant antifungal activity against Candida species and that they can be considered as a very promising bioactive lead compound to develop novel antifungal agents.

Sting_RDB: a relational database of structural parameters for protein analysis with support for data warehousing and data mining.

An effective strategy for managing protein databases is to provide mechanisms to transform raw data into consistent, accurate and reliable information. Such mechanisms will greatly reduce operational inefficiencies and improve one's ability to better handle scientific objectives and interpret the research results. To achieve this challenging goal for the STING project, we introduce Sting_RDB, a relational database of structural parameters for protein analysis with support for data warehousing and data mining. In this article, we highlight the main features of Sting_RDB and show how a user can explore it for efficient and biologically relevant queries. Considering its importance for molecular biologists, effort has been made to advance Sting_RDB toward data quality assessment. To the best of our knowledge, Sting_RDB is one of the most comprehensive data repositories for protein analysis, now also capable of providing its users with a data quality indicator. This paper differs from our previous study in many aspects. First, we introduce Sting_RDB, a relational database with mechanisms for efficient and relevant queries using SQL. Sting_rdb evolved from the earlier, text (flat file)-based database, in which data consistency and integrity was not guaranteed. Second, we provide support for data warehousing and mining. Third, the data quality indicator was introduced. Finally and probably most importantly, complex queries that could not be posed on a text-based database, are now easily implemented. Further details are accessible at the Sting_RDB demo web page: http://www.cbi.cnptia.embrapa.br/StingRDB.

Sting_RDB: a relational database of structural parameters for protein analysis with support for data warehousing and data mining

An effective strategy for managing protein databases is to provide mechanisms to transform raw data into consistent, accurate and reliable information. Such mechanisms will greatly reduce operational inefficiencies and improve one’s ability to better handle scientific objectives and interpret the research results. To achieve this challenging goal for the STING project, we introduce Sting_RDB, a relational database of structural parameters for protein analysis with support for data warehousing and data mining. In this article, we highlight the main features of Sting_RDB and show how a user can explore it for efficient and biologically relevant queries. Considering its importance for molecular biologists, effort has been made to advance Sting_RDB toward data quality assessment. To the best of our knowledge, Sting_RDB is one of the most comprehensive data repositories for protein analysis, now also capable of providing its users with a data quality indicator. This paper differs from our previous study in many aspects. First, we introduce Sting_RDB, a relational database with mechanisms for efficient and relevant queries using SQL. Sting_rdb evolved from the earlier, text (flat file)-based database, in which data consistency and integrity was not guaranteed. Second, we provide support for data warehousing and mining. Third, the data quality indicator was introduced. Finally and probably most importantly, complex queries that could not be posed on a text-based database, are now easily implemented. Further details are accessible at the Sting_RDB demo web page: http://www.cbi.cnptia.embrapa.br/StingRDB.

The Star STING server: a multiplatform environment for protein structure analysis.

Star STING is the latest version of the STING suite of programs and corresponding database. We report on five important aspects of this package that have acquired some new characteristics, designed to add key advantages to the whole suite: 1) availability for most popular platforms and browsers, 2) introduction of the STING_DB quality assessment, 3) improvement in algorithms for calculation of three STING parameters, 4) introduction of five new STING modules, and 5) expansion of the existing modules. Star STING is freely accessible at: http://sms.cbi.cnptia.embrapa.br/SMS/, http://trantor.bioc.columbia.edu/SMS, http://www.es.embnet.org/SMS/, http://gibk26.bse.kyutech.ac.jp/SMS/ and http://www.ar.embnet.org/SMS.

Predicting enzyme class from protein structure using Bayesian classification

Predicting enzyme class from protein structure parameters is a challenging problem in protein analysis. We developed a method to predict enzyme class that combines the strengths of statistical and data-mining methods. This method has a strong mathematical foundation and is simple to implement, achieving an accuracy of 45%. A comparison with the methods found in the literature designed to predict enzyme class showed that our method outperforms the existing methods.

Building multiple sequence alignments with a flavor of HSSP alignments

Homology-derived secondary structure of proteins (HSSP) is a well-known database of multiple sequence alignments (MSAs) which merges information of protein sequences and their three-dimensional structures. It is available for all proteins whose structure is deposited in the PDB. It is also used by STING and (Java)Protein Dossier to calculate and present relative entropy as a measure of the degree of conservation for each residue of proteins whose structure has been solved and deposited in the PDB. However, if the STING and (Java)Protein Dossier are to provide support for analysis of protein structures modeled in computers or being experimentally solved but not yet deposited in the PDB, then we need a new method for building alignments having a flavor of HSSP alignments (myMSAr). The present study describes a new method and its corresponding databank (SH2QS--database of sequences homologue to the query [structure-having] sequence). Our main interest in making myMSAr was to measure the degree of residue conservation for a given query sequence, regardless of whether it has a corresponding structure deposited in the PDB. In this study, we compare the measurement of residue conservation provided by corresponding alignments produced by HSSP and SH2QS. As a case study, we also present two biologically relevant examples, the first one highlighting the equivalence of analysis of the degree of residue conservation by using HSSP or SH2QS alignments, and the second one presenting the degree of residue conservation for a structure modeled in a computer, which , as a consequence, does not have an alignment reported by HSSP.

PDB-Metrics: a web tool for exploring the PDB contents

PDB-Metrics (http://sms.cbi.cnptia.embrapa.br/SMS/pdb_metrics/index.html) is a component of the Diamond STING suite of programs for the analysis of protein sequence, structure and function. It summarizes the characteristics of the collection of protein structure descriptions deposited in the Protein Data Bank (PDB) and provides a Web interface to search and browse the PDB, using a variety of alternative criteria. PDB-Metrics is a powerful tool for bioinformaticians to examine the data span in the PDB from several perspectives. Although other Web sites offer some similar resources to explore the PDB contents, PDB-Metrics is among those with the most complete set of such facilities, integrated into a single Web site. This program has been developed using SQLite, a C library that provides all the query facilities of a database management system

The Star STING server: a multiplatform environment for protein structure analysis

Star STING is the latest version of the STING suite of programs and corresponding database. We report on five important aspects of this package that have acquired some new characteristics, designed to add key advantages to the whole suite: 1) availability for most popular platforms and browsers, 2) introduction of the STING_DB quality assessment, 3) improvement in algorithms for calculation of three STING parameters, 4) introduction of five new STING modules, and 5) expansion of the existing modules. Star STING is freely accessible at: http://sms.cbi.cnptia.embrapa.br/SMS/, http://trantor.bioc.columbia.edu/SMS, http://www.es.embnet.org/SMS/, http://gibk26.bse.kyutech.ac.jp/SMS/ and http://www.ar.embnet.org/SMS.

A clinical study of glass ionomer cement.

The aim of this investigation was to compare the clinical performance of a glass ionomer cement (GIC) with a composite resin when used for direct bonding of standard edgewise orthodontic brackets. Fourteen patients (10 females, four males), in whom 242 teeth were bonded with brackets, were divided into two groups: GIC (121 teeth) and composite (121 teeth). The brackets were allocated to alternate quadrants and first-time failures were recorded over a period of 24 months. Data were analysed statistically (non-parametric chi-squared test). The results demonstrated a significantly lower unpreviewed debonding index (UDI) (15.7 per cent) for the composite than for the GIC (28.1 per cent) (P = 0.042). The use of heavy archwires was largely responsible for this difference. No difference was observed when light and medium archwires were used. GIC may be a viable alternative to composite for use with light archwires and with limited treatment objectives.