The CATH Hierarchy Revisited-Structural Divergence in Domain Superfamilies and the Continuity of Fold Space

This paper explores the structural continuum in CATH and the extent to which superfamilies adopt distinct folds. Although most superfamilies are structurally conserved, in some of the most highly populated superfamilies (4% of all superfamilies) there is considerable structural divergence. While relatives share a similar fold in the evolutionary conserved core, diverse elaborations to this core can result in significant differences in the global structures. Applying similar protocols to examine the extent to which structural overlaps occur between different fold groups, it appears this effect is confined to just a few architectures and is largely due to small, recurring super-secondary motifs (e.g., alpha beta-motifs, alpha-hairpins). Although 24% of superfamilies overlap with superfamilies having different folds, only 14% of nonredundant structures in CATH are involved in overlaps. Nevertheless, the existence of these overlaps suggests that, in some regions of structure space, the fold universe should be seen as more continuous.

Ligand induced interaction of thyroid hormone receptor beta with its coregulators

Thyroid hormones exert most of their physiological effects through two thyroid hormone receptor (TR) subtypes, TR alpha and TR beta, which associate with many transcriptional coregulators to mediate activation or repression of target genes. The search for selective TR beta ligands has been stimulated by the finding that several pharmacological actions mediated by TR beta might be beneficial in medical conditions such as obesity, hypercholesterolemia and diabetes. Here, we present a new methodology which employs surface plasmon resonance to investigate the interactions between TR beta ligand binding domain (LBD) complexes and peptides derived from the nuclear receptor interaction motifs of two of its coregulators, SRC2 and DAX1. The effect of several TR beta ligands, including the TR beta selective agonist GC-I and the TR beta selective antagonist NH-3, were investigated. We also determined the kinetic rate constants for the interaction of TR beta-T3 with both coregulators, and accessed the thermodynamic parameters for the interaction with DAX1. Our findings Suggest that flexibility plays an important role in the interaction between the receptor and its coregulators. and point out important aspects of experimental design that should be addressed when using TR beta LBD and its agonists. Furthermore, the methodology described here may be useful for the identification of new TR beta ligands. (C) 2008 Elsevier Ltd. All rights reserved.

Structural stability and reversible unfolding of recombinant porcine S100A12

Porcine S100A12 is a member of the S100 proteins, family of small acidic calcium-binding proteins characterized by the presence of two EF-hand motifs. These proteins are involved in many cellular events such as the regulation of protein phosphorylation, enzymatic activity, protein-protein interaction, Ca(2+) homeostasis, inflammatory processes and intermediate filament polymerization. In addition, members of this family bind Zn(2+) or Ca(2+) with cooperative effect on binding. In this study, the gene sequence encoding porcine S100A12 was obtained by the synthetic gene approach using E. coli codon bias. Additionally, we report a thermodynamic study of the recombinant S100A12 using circular dichroism, fluorescence and isothermal titration calorimetry. The results of urea and temperature induced unfolding and refolding processes indicated a reversible two-state process. Also, the ANS fluorescence studies showed that in presence of divalent ions the protein exposes hydrophobic sites which could facilitate the interaction with other proteins and trigger the physiological responses. (c) 2008 Elsevier B.V. All rights reserved.

The defensive functions of plant inhibitors are not restricted to insect enzyme inhibition

Three plant proteinase inhibitors BbKI (kallikrein inhibitor) and BbCI (cruzipain inhibitor) from Bauhinia bouhinioides, and a BrTI (trypsin inhibitor) from B. rufa, were examined for other effects in Callosobruchus maculatus development; of these only BrTI affected bruchid emergence. BrTI and BbKI share 81% identities in their primary sequences and the major differences between them are the regions comprising the RGD and RGE motifs in BrTI. These sequences were shown to be essential for BrTI insecticidal activity, since a modified BbKI [that is a recombinant form (BbKIm) with some amino acid residues replaced by those found in BrTI sequence] also strongly inhibited insect development. By using synthetic peptides related to the BrTI sequence, YLEAPVARGDGGLA-NH(2) (RGE) and IVYYPDRGETGL-NH(2) (RGE), it was found that the peptide with an RGE sequence was able to block normal development of C. maculatus larvae (ED(50) 0.16% and LD(50) 0.09%), this being even more effective than the native protein. (C) 2009 Elsevier Ltd. All rights reserved.

Network genealogy of 195-bp satellite DNA supports the superimposed hybridization hypothesis of Trypanosoma cruzi evolutionary pattern

Trypanosoma cruzi is highly diverse genetically and has been partitioned into six discrete typing units (DTUs), recently re-named T. cruzi I-VI. Although T. cruzi reproduces predominantly by binary division, accumulating evidence indicates that particular DTUs are the result of hybridization events. Two major scenarios for the origin of the hybrid lineages have been proposed. It is accepted widely that the most heterozygous TcV and TcVI DTUs are the result of genetic exchange between TcII and TcIII strains. On the other hand, the participation of a TcI parental in the current genome structure of these hybrid strains is a matter of debate. Here, sequences of the T. cruzi-specific 195-bp satellite DNA of TcI, TcII, Tat, TcV, and TcVI strains have been used for inferring network genealogies. The resulting genealogy showed a high degree of reticulation, which is consistent with more than one event of hybridization between the Tc DTUs. The data also strongly suggest that Tat is a hybrid with two distinct sets of satellite sequences, and that genetic exchange between TcI and TcII parentals occurred within the pedigree of the TcV and TcVI DTUs. Although satellite DNAs belong to the fast-evolving portion of eukaryotic genomes, in >100 satellite units of nine T. cruzi strains we found regions that display 100% identity. No DTU-specific consensus motifs were identified, inferring species-wide conservation. (C) 2010 Elsevier B.V. All rights reserved.

Structure, Dynamics, and RNA Interaction Analysis of the Human SBDS Protein

Shwachman-Bodian-Diamond syndrome is an autosomal recessive genetic syndrome with pleiotropic phenotypes, including pancreatic deficiencies, bone marrow dysfunctions with increased risk of myelodysplasia or leukemia, and skeletal abnormalities. This syndrome has been associated with mutations in the SBDS gene, which encodes a conserved protein showing orthologs in Archaea and eukaryotes. The Shwachman-Bodian-Diamond syndrome pleiotropic phenotypes may be an indication of different cell type requirements for a fully functional SBDS protein. RNA-binding activity has been predicted for archaeal and yeast SBDS orthologs, with the latter also being implicated in ribosome biogenesis. However, full-length SBDS orthologs function in a species-specific manner, indicating that the knowledge obtained from model systems may be of limited use in understanding major unresolved issues regarding SBDS function, namely, the effect of mutations in human SBDS on its biochemical function and the specificity of RNA interaction. We determined the solution structure and backbone dynamics of the human SBDS protein and describe its RNA binding site using NMR spectroscopy. Similarly to the crystal structures of Archaea, the overall structure of human SBDS comprises three well-folded domains. However, significant conformational exchange was observed in NMR dynamics experiments for the flexible linker between the N-terminal domain and the central domain, and these experiments also reflect the relative motions of the domains. RNA titrations monitored by heteronuclear correlation experiments and chemical shift mapping analysis identified a classic RNA binding site at the N-terminal FYSH (fungal, Yhr087wp, Shwachman) domain that concentrates most of the mutations described for the human SBDS. (C) 2010 Elsevier Ltd. All rights reserved.

Development of secondary palate requires strict regulation of ECM remodeling: sequential distribution of RECK, MMP-2, MMP-3, and MMP-9

We have evaluated RECK (reversion-inducing-cysteine-rich protein with Kazal motifs), MMP-2 (matrix metalloproteinase-2), MMP-3, and MMP-9 involvement during palate development in mice by using various techniques. Immunohistochemical features revealed the distribution of RECK, MMP-2, and MMP-3 in the mesenchymal tissue and in the midline epithelial seam at embryonic day 13 (E13), MMPs-2, -3, and -9 being particularly expressed at E14 and E14.5. In contrast, RECK was weakly immunostained at these times. Involvement of MMPs was validated by measuring not only their protein expression, but also their activity (zymograms). In situ hybridization signal (ISH) for RECK transcript was distributed in mesenchymal and epithelial regions within palatal shelves at all periods evaluated. Importantly, the results from ISH analysis were in accord with those obtained by real-time polymerase chain reaction. The expression of RECK was found to be temporally regulated, which suggested possible roles in palatal ontogeny. Taken together, our results clearly show that remodeling of the extracellular matrix is finely modulated during secondary palate development and occurs in a sequential manner.

Overexpression of Nrp/b (nuclear restrict protein in brain) suppresses the malignant phenotype in the C6/ST1 glioma cell line

Upon searching for glucocorticoid-regulated cDNA sequences associated with the transformed to normal phenotypic reversion of C6/ST1 rat glioma cells, we identified Nrp/b (nuclear restrict protein in brain) as a novel rat gene. Here we report on the identification and functional characterization of the complete sequence encoding the rat NRP/B protein. The cloned cDNA presented a 1767 nucleotides open-reading frame encoding a 589 aminoacids residues sequence containing a BTB/POZ (broad complex Tramtrack bric-a-brac/Pox virus and zinc finger) domain in its N-terminal region and kelch motifs in its C-terminal region. Sequence analysis indicates that the rat Nrp/b displays a high level of identity with the equivalent gene orthologs from other organisms. Among rat tissues, Nrp/b expression is more pronounced in brain tissue. We show that overexpression of the Nrp/b cDNA in C6/ST1 cells suppresses anchorage independence in vitro and tumorigenicity in vivo, altering their malignant nature towards a more benign phenotype. Therefore, Nrp/b may be postulated as a novel tumor suppressorgene, with possible relevance for glioblastoma therapy. (C) 2009 Elsevier Ltd. All rights reserved.

Etniska stereotyper på film : med utgångspunkt i amerikansk film med ryska motiv (2008-2011)

Filmmediet idag är den mest populära formen av masskultur. Med sin världstäckande genomslagskraft och sitt stereotypa porträtterande av verklighet, påverkar filmen världsåskådningen för människor runtom i världen. Ett brinnande ämne i amerikansk film har alltid varit Ryssland, på grund av de politiska motsättningarna och den historiska rivaliteten med USA. Studiens syfte är att undersöka hur Ryssland porträtteras i amerikanska filmer från perioden för presidenterna Dmitrij Medvedevs respektive Barack Obamas första mandatperiod. Frågeställningen för uppsatsen är: hur ser stereotypa föreställningar om Ryssland ut i amerikansk film 2008-2011? Trettiotal filmer med ryska motiv valdes ut för undersökningen och analyserades utifrån de visuella och sociala aspekterna. Resultatet visar på att det förekommer tre skikt av stereotyper om Ryssland: de eviga, som har existerat i hundratals år och spridits av resenärer; stereotyper från epoken för det kalla kriget; och stereotyper om det moderna Ryssland inspirerade av medias nyhetsrapporteringar.

La thématique de l’eau dans l’œuvre de Marguerite Duras

The aim of this thematic study is to examine how the water motif is used in Marguerite Duras’s literary work. The study shows that water has multiple functions in these texts: it is linked to major themes and creates an enigmatic atmosphere by its association with the unknown, the inexplicable and the unconscious. The strong presence of water in Duras’s texts is striking. References to the water element can be found in several titles throughout her career, from early works such as Un barrage contre le Pacifique (1950) to La mer écrite (1996), published just after her death. Almost all of her fiction take place near water – and the rain or the sound of waves serve as leitmotifs in specific novels. The water motif can play a metonymic as well as a metaphoric role in the texts and it sometimes takes on human or animalistic characteristics (Chapter 4). Several emblematic Durassian characters (e.g. the beggar-woman, Anne-Marie Stretter and Lol V. Stein) have a close relationship to water (Chapter 5). The water motif is linked to many major Durassian themes, and illustrates themes with positive connotations, for example, creation, fecundity, maternity, liberty and desire, as well as themes with negative connotations such as destruction and death (Chapter 6). A close reading of three novels, La vie tranquille (1944), L’après-midi de Monsieur Andesmas (1962) and La maladie de la mort (1982), shows that the realism of the first novel is replaced by intriguing evocations of the sea and the pond in the second text, motifs which resist straightforward interpretation. The enigmatic feeling persists in the last novel, in which the sea illustrates the overall sombre mood of the story (Chapter 7). Finally, the role of the water element in psychoanalytic theory is discussed (Chapter 8), and a parallel is drawn between the Jungian concept of the mother archetype and the water motif in Duras’s texts. The suggestion is made in this last chapter that water is used to illustrate an oriental influence (Taoist or Buddhist) of some of the female characters in Duras’s work.

Supply chain turbulence: the impact of a mid-range event in multi-tier, multi-dimension supply chains

Nota: A autora agradece à Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) pela concessão de bolsa de estudos para o desenvolvimento deste projeto de pesquisa.

Geografia da dominação: um estudo sobre a organização espacial da terra do sal (Macau-RN)

This work aims to understand the spatial organization in the Town of Macau, State of Rio Grande do Norte, Brazil. This approach focus on bringing back the history of the town, the main personages responsible for the construction of this place, denominated "social agents", as well as its social processes and the spatial forms derived from them. As the personages and their practices were identified, it was found out the existence of a driving force for structuring, interlocking, and maintaining the actions carried out by the social agents during the time. Such actions were materialized in the urban space: "the social segregation". The social segregation takes place as a specific geography of domination. The outcome of those owning the best areas" and ways of accessibility in the urban space, varies from the enrichment by property valorization, because of the concentration of public investments of infrastructure, to the comfort of easily reaching all the daily needs related to the displacements in the urban space. In the latter case, such facility has contributed to improve life quality. While one takes advantage of the location in the urban space, others are negatively affected by the same process. This research identified the salina worker as the weakest element of this social structure, occupying the urban periphery of the town of Macau. Such area is characterized by the lack of services and urban equipment in opposition to the center of the town, the locus of elite. This way, it is established the most known segregation pattern: center x periphery, in which the space acts as a mechanism of segregation

Estudo do genoma do vírus causador da mionecrose infecciosa em camarões e desenvolvimento de métodos para detecção de diferentes variantes

Shrimp farming is one of the activities that contribute most to the growth of global aquaculture. However, this business has undergone significant economic losses due to the onset of viral diseases such as Infectious Myonecrosis (IMN). The IMN is already widespread throughout Northeastern Brazil and affects other countries such as Indonesia, Thailand and China. The main symptom of disease is myonecrosis, which consists of necrosis of striated muscles of the abdomen and cephalothorax of shrimp. The IMN is caused by infectious myonecrosis virus (IMNV), a non-enveloped virus which has protrusions along its capsid. The viral genome consists of a single molecule of double-stranded RNA and has two Open Reading Frames (ORFs). The ORF1 encodes the major capsid protein (MCP) and a potential RNA binding protein (RBP). ORF2 encodes a probable RNA-dependent RNA polymerase (RdRp) and classifies IMNV in Totiviridae family. Thus, the objective of this research was study the IMNV complete genome and encoded proteins in order to develop a system differentiate virus isolates based on polymorphisms presence. The phylogenetic relationship among some totivirus was investigated and showed a new group to IMNV within Totiviridae family. Two new genomes were sequenced, analyzed and compared to two other genomes already deposited in GenBank. The new genomes were more similar to each other than those already described. Conserved and variable regions of the genome were identified through similarity graphs and alignments using the four IMNV sequences. This analyze allowed mapping of polymorphic sites and revealed that the most variable region of the genome is in the first half of ORF1, which coincides with the regions that possibly encode the viral protrusion, while the most stable regions of the genome were found in conserved domains of proteins that interact with RNA. Moreover, secondary structures were predicted for all proteins using various softwares and protein structural models were calculated using threading and ab initio modeling approaches. From these analyses was possible to observe that the IMNV proteins have motifs and shapes similar to proteins of other totiviruses and new possible protein functions have been proposed. The genome and proteins study was essential for development of a PCR-based detection system able to discriminate the four IMNV isolates based on the presence of polymorphic sites

Umbelliferone induces changes in the structure and pharmacological activities of Bn IV, a phospholipase A(2) isoform isolated from Bothrops neuwiedi

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Temperatura e tipo de preparo na conservação de produto minimamente processado de abacaxi-'Pérola'

O presente trabalho teve como objetivo avaliar o efeito do tipo de preparo (rodelas e metades) e da temperatura de armazenamento (3ºC, 6ºC e 9ºC) na conservação de produto minimamente processado de abacaxi-'Pérola'. Os frutos, depois de selecionados, lavados e desinfectados com cloro, foram armazenados por 12 horas a 10ºC, antes de serem processados sob condições higiênicas, embalados em contentores de polietileno tereftalatado (rodelas) ou bandeja de isopor recoberta com filme de cloreto de polivinila esticável (metades) e armazenados por até 12 dias. Os produtos foram avaliados quanto à evolução da atmosfera interna na embalagem, respiração, quantidade de suco drenado e evolução da massa fresca e da aparência. Foram testadas, durante o período de armazenamento, a aceitabilidade pelos consumidores, no início do experimento e enquanto a aparência e a análise microbiológica permitiram. A presença de bactérias mesofílicas e coliformes totais e fecais foi avaliada a cada três dias. Durante o armazenamento, a porcentagem de O2 nas embalagens apresentou decréscimo, enquanto a de CO2 aumentou até 20% para as metades e até 1,86% para as rodelas. A intensidade dos cortes no preparo teve influência direta na respiração, assim como nas perdas de suco e de massa fresca. A temperatura influenciou na respiração e foi fator limitante à vida de prateleira do produto, pois os produtos armazenados a 9ºC, conservaram-se por 6 dias, enquanto os mantidos a 3ºC e 6ºC, por até 9 dias.