AMYPdb: a database dedicated to amyloid precursor proteins.

BACKGROUND: Misfolding and aggregation of proteins into ordered fibrillar structures is associated with a number of severe pathologies, including Alzheimer's disease, prion diseases, and type II diabetes. The rapid accumulation of knowledge about the sequences and structures of these proteins allows using of in silico methods to investigate the molecular mechanisms of their abnormal conformational changes and assembly. However, such an approach requires the collection of accurate data, which are inconveniently dispersed among several generalist databases. RESULTS: We therefore created a free online knowledge database (AMYPdb) dedicated to amyloid precursor proteins and we have performed large scale sequence analysis of the included data. Currently, AMYPdb integrates data on 31 families, including 1,705 proteins from nearly 600 organisms. It displays links to more than 2,300 bibliographic references and 1,200 3D-structures. A Wiki system is available to insert data into the database, providing a sharing and collaboration environment. We generated and analyzed 3,621 amino acid sequence patterns, reporting highly specific patterns for each amyloid family, along with patterns likely to be involved in protein misfolding and aggregation. CONCLUSION: AMYPdb is a comprehensive online database aiming at the centralization of bioinformatic data regarding all amyloid proteins and their precursors. Our sequence pattern discovery and analysis approach unveiled protein regions of significant interest. AMYPdb is freely accessible 1.

APC2 Cullin protein and APC11 RING protein comprise the minimal ubiquitin ligase module of the anaphase-promoting complex.

In mitosis, the anaphase-promoting complex (APC) regulates the onset of sister-chromatid separation and exit from mitosis by mediating the ubiquitination and degradation of the securin protein and mitotic cyclins. With the use of a baculoviral expression system, we have reconstituted the ubiquitin ligase activity of human APC. In combination with Ubc4 or UbcH10, a heterodimeric complex of APC2 and APC11 is sufficient to catalyze the ubiquitination of human securin and cyclin B1. However, the minimal APC2/11 ubiquitin ligase module does not possess substrate specificity, because it also ubiquitinates the destruction box deletion mutants of securin and cyclin B1. Both APC11 and UbcH10 bind to the C-terminal cullin homology domain of APC2, whereas Ubc4 interacts with APC11 directly. Zn(2+)-binding and mutagenesis experiments indicate that APC11 binds Zn(2+) at a 1:3 M ratio. Unlike the two Zn(2+) ions of the canonical RING-finger motif, the third Zn(2+) ion of APC11 is not essential for its ligase activity. Surprisingly, with Ubc4 as the E2 enzyme, Zn(2+) ions alone are sufficient to catalyze the ubiquitination of cyclin B1. Therefore, the Zn(2+) ions of the RING finger family of ubiquitin ligases may be directly involved in catalysis.

The value of short amino acid sequence matches for prediction of protein allergenicity.

Typically, genetically engineered crops contain traits encoded by one or a few newly expressed proteins. The allergenicity assessment of newly expressed proteins is an important component in the safety evaluation of genetically engineered plants. One aspect of this assessment involves sequence searches that compare the amino acid sequence of the protein to all known allergens. Analyses are performed to determine the potential for immunologically based cross-reactivity where IgE directed against a known allergen could bind to the protein and elicit a clinical reaction in sensitized individuals. Bioinformatic searches are designed to detect global sequence similarity and short contiguous amino acid sequence identity. It has been suggested that potential allergen cross-reactivity may be predicted by identifying matches as short as six to eight contiguous amino acids between the protein of interest and a known allergen. A series of analyses were performed, and match probabilities were calculated for different size peptides to determine if there was a scientifically justified search window size that identified allergen sequence characteristics. Four probability modeling methods were tested: (1) a mock protein and a mock allergen database, (2) a mock protein and genuine allergen database, (3) a genuine allergen and genuine protein database, and (4) a genuine allergen and genuine protein database combined with a correction for repeating peptides. These analyses indicated that searches for short amino acid sequence matches of eight amino acids or fewer to identify proteins as potential cross-reactive allergens is a product of chance and adds little value to allergy assessments for newly expressed proteins.

Avaliação dos estudantes de enfermagem sobre a aprendizagem com a simulação clínica / Evaluación de los estudiantes de enfermería sobre el aprendizaje con la simulación clínica / Evaluation of nursing students about learning with clinical simulation

RESUMO Objetivo: descrever as contribuições da simulação clínica para aprendizagem de atributos cognitivos e procedimentais, por meio do debriefing, na perspectiva dos estudantes de enfermagem. Método: estudo descritivo exploratório. Participaram 20 estudantes de Graduação em Enfermagem de uma universidade do interior paulista. Na coleta de dados, realizada na etapa do debriefing, foi registrada a percepção do aluno sobre a simulação, aspectos positivos e o que poderia ser feito de forma diferente. Os relatos foram agrupados em categorias temáticas centrais, segundo referencial de análise de conteúdo de Bardin (2011), analisadas por meio de estatística descritiva. Resultados: identificada valorização da aprendizagem ativa, crítica e reflexiva (47,5%) em decorrência da aproximação à realidade assistencial (20,3%), manifestação dos sentimentos vivenciados durante a simulação (16,9%) e composição do cenário (15,3%). Conclusão: a simulação clínica seguida do debriefing favorece a compreensão da relação entre ação e resultados alcançados na aprendizagem. .

RESUMEN Objetivo: describir las contribuciones de simulación clínica para aprender atributos cognitivos y de procedimiento, a través de debriefing, desde la perspectiva de los estudiantes de enfermería. Método: estudio exploratorio descriptivo. 20 estudiantes participaron en el Pregrado en Enfermería de una universidad de São Paulo. Durante la recolección de datos, que se aplicó durante el debriefing, fue grabado en la percepción de los estudiantes de la simulación, los aspectos positivos y lo que podría hacerse de otra manera. Los informes de los estudiantes se agrupan de acuerdo a los temas centrales, según el referencial de análisis de contenido de Bardin (2011) y analizados mediante estadística descriptiva. Resultados: identificado la mejora de aprendizaje activo, crítico y reflexivo (47,5%) debido a la aproximación a la realidad en la atención de enfermería (20,3%), un resultado de la composición del escenario (16,9%), lo que favorece el desarrollo de sentimientos experimentados durante la simulación (15,3%). Conclusión: la simulación clínica seguida de debriefing favorece la comprensión de la relación entre la acción y los resultados obtenidos en el aprendizaje. .

ABSTRACT Objective: to describe the contributions of clinical simulation for learning cognitive and procedural attributes through debriefi ng, from the perspective of nursing students. Method: descriptive exploratory study. Twenty nursing undergraduate students from a university in the interior of the state of São Paulo participated in this study. Data collection was performed at the debriefi ng stage. Student’s perceptions about the simulation, positive aspects and what they could have done differently were registered. The students’ statements were grouped according to the central themes and the framework of Bardin’s content analysis (2011) and were analyzed using descriptive statistics. Results: enhancement of active, critical and refl ective learning (47.5%) was identifi ed due to the closeness to reality in nursing care (20.3%), manifestation of feelings experienced during the simulation (15.3%) and composition of the scenario (15.3%). Conclusion: the clinical simulation followed by debriefi ng promotes the understanding of the link between action and achievements in learning. .

Phylogenetic analysis of human group C rotavirus circulating in Brazil reveals a potential unique NSP4 genetic variant and high similarity with Asian strains

Group C rotaviruses (RVC) cause gastroenteritis in humans and animals worldwide, and the evidence for a possible zoonotic role has been recently provided. To gain information on the genetic diversity and relationships between human and animal RVC, we sequenced the VP4, VP7, and NSP4 genes of 12, 19, and 15 human strains, respectively, detected in São Paulo state during historical (1988 and 1993) and recent (2007 and 2008) Brazilian rotavirus surveillance. All RVC strains analyzed in the present study grouped into human genotype (G4-P[2]-E2), and did not show any evidence of animal ancestry. Phylogenetic analysis showed that RVC samples detected in 1988 and 1993 clustered together with strains from distinct continents, indicating that historical RVC strains circulating in São Paulo were closely related to those strains circulating worldwide. All three genes (VP7, VP4 and NSP4) of São Paulo RVC strains isolated in 2007-2008 exhibited close phylogenetic relationship with human RVC strains isolated in China and Japan, suggesting that they are genetically linked, and that a gene flow could be occurring between this Asian countries and Brazil. We identified two distinct clusters in the NSP4 phylogenetic tree. One cluster formed exclusively by human Brazilian strains detected in 1997 and 2003-2004 in Rio de Janeiro, Bahia, and Rio Grande do Sul states (Subgroup II) previously described in a different study, that displayed low sequence identities to other human strains formerly published, and to the Brazilian RVC strains (Subgroup I) characterized in the present study. These data suggests the circulation of two genetic profiles of the NSP4 gene in Brazil. High sequence diversity in NSP4 gene was previously reported in Asia, and additional diversity in NSP4 RVC strains spreading in the world should be expected. More in-depth molecular and epidemiological analysis of human RVC throughout the world will be needed to understand their diversity and clarify their evolution, as well as to develop classifications schemes.

Autonomia do graduando em enfermagem na (re)construção do conhecimento mediado pela aprendizagem baseada em problemas / Autonomy of nursing undergraduate student in the (re)construction of knowledge mediated by problem-based learning / La autonomía del estudiante de enfermería en la (re)construcción del conocimiento mediada por el aprendizaje basado en problemas

Estudo qualitativo, método Bricolagem, que objetivou analisar como a Aprendizagem Baseada em Problemas (ABP) promove o desenvolvimento da autonomia do aluno no processo de aprender a aprender. Os sujeitos foram 16 alunos e dois tutores envolvidos na disciplina. A coleta dos dados combinou entrevista semiestruturada, observação participante, registro em portfólios, fichas de avaliação, e gravação em áudio das tutorias. A análise dos dados seguiu estratégias de interpretação definidas pelas autoras: leituras iniciais e aprofundada; construção e reunião de mapas de significados; elaboração, descrição e análise de categorias empíricas, à luz do referencial teórico. A ABP favorece a (re)construção de conhecimentos pela utilização de saberes e experiências prévias, que são compartilhados no pequeno grupo; pelo processo de teorização; e pela via do conhecimento pertinente - aquele passível de aplicação à prática. Concluímos que a ABP estimula o aprendizado contínuo, desenvolvendo no aluno autonomia no processo de aprender a aprender.

This is a qualitative study, using the ‘Do it yourself’ method, which aimed to analyze how Problem-Based Learning (PBL) promotes the development of learner’s autonomy in the process of learning to learn. The subjects were 16 students and two tutors involved in the discipline. Data collection techniques combined semi-structured interviews, participant observation, log in portfolios, evaluation forms, and audio recording of the tutorials. Data analysis followed interpretation strategies defined by the authors: initial and in depth readings; construction and assembly of meanings’ maps; development, description and analysis of empirical categories, in the light of the theoretical framework. The PBL favors the (re)construction of knowledge by the use of prior knowledge and experiences that are shared in small group; through the process of theorization; and by means of relevant knowledge - one that can be applied to practice. We conclude that PBL encourages continuous learning, developing in the student the autonomy in the process of learning to learn.

Estudio cualitativo, con método Bricolage, que tuvo como objetivo analizar cómo el Aprendizaje Basado en Problemas (ABP) promueve el desarrollo de la autonomía del alumno en el proceso de aprender a aprender. Los sujetos fueron 16 alumnos y dos tutores que participan en la disciplina. Para recolección de datos se combinaran entrevistas estructuradas, observación participante, registro en portfolios, formularios de evaluación y grabación de audio de los tutoriales. El análisis de los datos siguió las estrategias de interpretación definidos por los autores: lecturas iniciales y profundadas; construcción y montaje de mapas de significados; el desarrollo, descripción y análisis de categorías empíricas, a la luz de lo referencial teórico. El ABP favorece la construcción de conocimientos mediante el uso de saberes y experiencias que se comparten en grupos pequeños, a través del proceso de teorización, y por medio de los conocimientos pertinentes - uno que se puede aplicar a la práctica. Llegamos a la conclusión que el ABP promueve el aprendizaje continuo, el desarrollo de los estudiantes, la autonomía en el proceso de aprender a aprender.

Identification of novel bradykinin-potentiating peptides and C-type natriuretic peptide from Lachesis muta venom

The generation of expressed sequence tags (ESTs) from the pit-viper snake Lachesis muta venom glands allowed us to identify two cDNA isoforms which encode the precursors for bradykinin-potentiating peptides (BPPs) and a C-type natriuretic peptide (CNP). The sequence data derived from these cDNAs combined with the venom peptides identification using MALDI-TOF mass spectrometry analysis predicted that these molecules are the precursor protein isoforms that are further processed to produce five novel BPPs and a CNP. They were identified directly in crude venom using MALDI-TOF. The BPPs sequences were further confirmed by MALDI-TOF/TOF de novo sequencing, and an unusual BPP with a residue of tryptophan at the N-terminus (usually it is pyroglutamate) was identified. The putative processing steps required to form the mature BPPs and CNP seem to be similar to those proposed for the ones found in the venom of Bothrops jararaca and Glodyus blomhoffi.