Modeling the peptide-T cell receptor interaction by the comparative molecular similarity indices analysis-soft independent modeling of class analogy technique

A set of 38 epitopes and 183 non-epitopes, which bind to alleles of the HLA-A3 supertype, was subjected to a combination of comparative molecular similarity indices analysis (CoMSIA) and soft independent modeling of class analogy (SIMCA). During the process of T cell recognition, T cell receptors (TCR) interact with the central section of the bound nonamer peptide; thus only positions 4−8 were considered in the study. The derived model distinguished 82% of the epitopes and 73% of the non-epitopes after cross-validation in five groups. The overall preference from the model is for polar amino acids with high electron density and the ability to form hydrogen bonds. These so-called “aggressive” amino acids are flanked by small-sized residues, which enable such residues to protrude from the binding cleft and take an active role in TCR-mediated T cell recognition. Combinations of “aggressive” and “passive” amino acids in the middle part of epitopes constitute a putative TCR binding motif

Histidine hydrogen bonding in MHC at pH 5 and pH 7 modeled by molecular docking and molecular dynamics simulations

Hydrogen bonds play important roles in maintaining the structure of proteins and in the formation of most biomolecular protein-ligand complexes. All amino acids can act as hydrogen bond donors and acceptors. Among amino acids, Histidine is unique, as it can exist in neutral or positively charged forms within the physiological pH range of 5.0 to 7.0. Histidine can thus interact with other aromatic residues as well as forming hydrogen bonds with polar and charged residues. The ability of His to exchange a proton lies at the heart of many important functional biomolecular interactions, including immunological ones. By using molecular docking and molecular dynamics simulation, we examine the influence of His protonation/deprotonation on peptide binding affinity to MHC class II proteins from locus HLA-DP. Peptide-MHC interaction underlies the adaptive cellular immune response, upon which the next generation of commercially-important vaccines will depend. Consistent with experiment, we find that peptides containing protonated His residues bind better to HLA-DP proteins than those with unprotonated His. Enhanced binding at pH 5.0 is due, in part, to additional hydrogen bonds formed between peptide His+ and DP proteins. In acidic endosomes, protein His79β is predominantly protonated. As a result, the peptide binding cleft narrows in the vicinity of His79β, which stabilizes the peptide - HLA-DP protein complex. © 2014 Bentham Science Publishers.

Functional astrocyte-neuron lactate shuttle in a human stem cell derived neuronal network

The development of stem cell-derived neuronal networks will promote experimental system development for drug screening, toxicological testing and disease modelling, providing that they mirror closely the functional competencies of their in vivo counterparts. The NT2 cell line is one of the best documented embryocarcinoma cell lines, and can be differentiated into neurons and astrocytes. Great focus has also been placed on defining the electrophysiological properties of these cells, and more recently we have investigated the functional properties of their associated astrocytes. We now show for the first time in a human stem cell derived co-culture model that these cultures are also metabolically competent and demonstrate a functional astrocyte neuron lactate shuttle (ANLS). The ANLS hypothesis proposes that during neuronal activity, glutamate released into the synaptic cleft is taken up by astrocytes and triggers glucose uptake which is converted into lactate and released via monocarboxylate transporters for neuronal use. Using mixed cultures of NT2 derived neurons and astrocytes we have shown that these cells modulate their glucose uptake in response to glutamate, an effect that was blocked by cytochalasin B and ouabain. Additionally we demonstrate that in response to increased neuronal activity and under hypoglycaemic conditions, co-cultures modulate glycogen turnover and increase lactate production. Similar results were also shown following treatment with glutamate, potassium, Isoproterenol and dbcAMP. Together these results demonstrate for the first time a functional ANLS in a human stem cell derived co-culture.

A nasalidade no dialeto quilombola do Norte de Minas: uma análise contrastiva baseada em corpus

This research investigated the nasality of vowels in the spontaneous speech of inhabitants of the quilombola communities of Brejo dos Crioulos and Poções (MG). As a theoretical framework, we based on the assumptions of Phonetics and Phonology, in renowned scholars on the investigation of nasality (CAGLIARI, 1977; CÂMARA JR., 1984, 2013; BISOL, 2013; ABAURRE; PAGOTTO, 1996; SILVA, 2015), with subsidies of the Corpus Linguistics. Its general goal was to investigate the occurrence of nasality, in the dialect of these quilombola communities, and their linguistic behavior, considering the linguistic factors that can interfere in the phenomenon. Specifically it was aimed to a) detect the occurrence of nasalized vowels with the help of the resources that the Corpus Linguistics provides (Praat and WorldSmith Tolls); b) discriminate the different types of occurring contexts of nasalized vowels; c) make quantitative and qualitative analyzes of the nasalized vowels in the study corpus; d) describe and analyze the behavior of nasalized vowels and; e) contrast the values of F1 and F2 of the oral and nasalized vowels. It was hypothesized that the nasality happens because it is conditioned by the nasal segment following the nasalized vowel - phonological process of “assimilation” - its position as the primary stress and grammatical category. It was believed that the quilombolas communities of Brejo dos Crioulos and Poções produce nasalized vowels in their speech and this linguistic phenomenon is favored by the adjacent presence of consonants or nasal vowels. Furthermore, it was hypothesized that the values of F1 and F2 of oral and nasalized vowels in these communities are distinct. The following research questions were elaborated: (i) is the presence of nasalized vowels in the speech of these quilombola communities conditioned to the presence of a nasal sound segment? (ii) does the nasal sound segment following the nasalized vowel favor the occurrence of the nasality phenomenon? is there a difference between the values of F1 and F2 of the oral and nasalized vowels in both quilombola communities considered? To compose our corpus, 24 interviews recordings were used (12 female speakers and 12 male speakers), a total of 24 participants. It was found that the following nasal sound segment tends to condition the nasalized vowel. In general, it assimilates the lowering of the soft palate of nasal consonant segment immediately following, but there are cases of nasal vowel segment - regressive assimilation; the stressed syllable tends to favor the nasality, but it occurs in pretonic and postonic position as well; F1 and F2 values of oral and nasalized vowels in the quilombola communities of Poções and Brejo dos Crioulos are distinct: the group of Brejo dos Crioulos tends to produce the F1 of oral and nasalized vowels more lowered than the group of Poções and the F2, in a more anterior position. The nasality tends to occur in verbs and nouns, although it is not specific to a grammatical category. This research found cases of spurious nasalization, confirming previous studies. In turn, it revealed cases of lexical items with favorable context for nasalization, but with its non-occurrence. This last case, considered as the lowering of the uniform soft palate in PB, presented pronounced vowels without the soft palate lowering. That is, it was detected variation in the phenomenon of nasalization in PB. With this work, it was promoted the discussion about nasality, in order to contribute to the linguistic studies about the functioning of Brazilian Portuguese in this geographical context.

Structural and Biochemical Dissection of the Trehalose Biosynthetic Complex in Pathogenic Fungi

Trehalose is a non-reducing disaccharide essential for pathogenic fungal survival and virulence. The biosynthesis of trehalose requires the trehalose-6-phosphate synthase, Tps1, and trehalose-6-phosphate phosphatase, Tps2. More importantly, the trehalose biosynthetic pathway is absent in mammals, conferring this pathway as an ideal target for antifungal drug design. However, lack of germane biochemical and structural information hinders antifungal drug design against these targets.

In this dissertation, macromolecular X-ray crystallography and biochemical assays were employed to understand the structures and functions of proteins involved in the trehalose biosynthetic pathway. I report here the first eukaryotic Tps1 structures from Candida albicans (C. albicans) and Aspergillus fumigatus (A. fumigatus) with substrates or substrate analogs. These structures reveal the key residues involved in substrate binding and catalysis. Subsequent enzymatic assays and cellular assays highlight the significance of these key Tps1 residues in enzyme function and fungal stress response. The Tps1 structure captured in its transition-state with a non-hydrolysable inhibitor demonstrates that Tps1 adopts an “internal return like” mechanism for catalysis. Furthermore, disruption of the trehalose biosynthetic complex formation through abolishing Tps1 dimerization reveals that complex formation has regulatory function in addition to trehalose production, providing additional targets for antifungal drug intervention.

I also present here the structure of the Tps2 N-terminal domain (Tps2NTD) from C. albicans, which may be involved in the proper formation of the trehalose biosynthetic complex. Deletion of the Tps2NTD results in a temperature sensitive phenotype. Further, I describe in this dissertation the structures of the Tps2 phosphatase domain (Tps2PD) from C. albicans, A. fumigatus and Cryptococcus neoformans (C. neoformans) in multiple conformational states. The structures of the C. albicans Tps2PD -BeF3-trehalose complex and C. neoformans Tps2PD(D24N)-T6P complex reveal extensive interactions between both glucose moieties of the trehalose involving all eight hydroxyl groups and multiple residues of both the cap and core domains of Tps2PD. These structures also reveal that steric hindrance is a key underlying factor for the exquisite substrate specificity of Tps2PD. In addition, the structures of Tps2PD in the open conformation provide direct visualization of the conformational changes of this domain that are effected by substrate binding and product release.

Last, I present the structure of the C. albicans trehalose synthase regulatory protein (Tps3) pseudo-phosphatase domain (Tps3PPD) structure. Tps3PPD adopts a haloacid dehydrogenase superfamily (HADSF) phosphatase fold with a core Rossmann-fold domain and a α/β fold cap domain. Despite lack of phosphatase activity, the cleft between the Tps3PPD core domain and cap domain presents a binding pocket for a yet uncharacterized ligand. Identification of this ligand could reveal the cellular function of Tps3 and any interconnection of the trehalose biosynthetic pathway with other cellular metabolic pathways.

Combined, these structures together with significant biochemical analyses advance our understanding of the proteins responsible for trehalose biosynthesis. These structures are ready to be exploited to rationally design or optimize inhibitors of the trehalose biosynthetic pathway enzymes. Hence, the work described in this thesis has laid the groundwork for the design of Tps1 and Tps2 specific inhibitors, which ultimately could lead to novel therapeutics to treat fungal infections.

Lesões orais com potencial de malignização: análise clínica e morfológica de 205 casos

Silveira , E. J. D. et al. Lesões orais com potencial de malignização: análise clínica e morfológica de 205 casos. J. Bras. Patol. Med. Lab., v. 45, n. 3, p. 233-238, jun 2009. ISBN 1676-2444.

A cocaína e suas manifestações orofaciais

A cocaína é uma droga com ação estimulante no sistema nervoso central, extraída e refinada a partir da planta de coca (Erythroxylum coca). É característica por induzir o consumidor a um estado de hipervigilância reduzindo ao mesmo tempo, o cansaço e a fadiga. Este pó branco, cristalino, de sabor amargo, possui também um efeito anestésico local e vasoconstritor. As formas de apresentação mais comuns da droga são o cloridrato de cocaína e a cocaína crack. Esta droga destaca-se por ser o estimulante mais consumido na Europa com cerca de 3,4 milhões de consumidores estimados no ano de 2014. A prevalência do consumo desta droga em Portugal aumentou 0,3% de 2001, para 2012 na população geral (15-64 anos). Os estudos mais recentes em populações escolares (entre 2010 e 2011) evidenciaram, de um modo geral, o aumento da prevalência de consumo nesta população. Os efeitos adversos resultantes, tanto a nível físico como psíquico, são vários, sendo as manifestações orofaciais as que mais interferem na Qualidade de vida do toxicómano. As manifestações mais frequentes são as perfurações do septo nasal e palatino, bruxismo, gengivite, erosão dentária, xerostomia, cárie, lesões brancas atípicas e cefaleias em salva, tendo o Médico Dentista um papel importante no diagnóstico e tratamento destas lesões. A legislação, ao nível Europeu, sobre drogas procura uma uniformização das medidas aplicadas nos países membros, baseando-se no equilíbrio entre as sanções e o tratamento. Apesar das convenções das Nações Unidas sobre drogas limitarem o consumo de estupefacientes e substâncias psicotrópicas exclusivamente para fins médicos e científicos, cabe aos países signatários a liberdade de decisão das políticas a adoptar em matérias de infrações penais como a posse e o consumo ilegal.

Lesões orais com potencial de malignização: análise clínica e morfológica de 205 casos

Silveira , E. J. D. et al. Lesões orais com potencial de malignização: análise clínica e morfológica de 205 casos. J. Bras. Patol. Med. Lab., v. 45, n. 3, p. 233-238, jun 2009. ISBN 1676-2444.

Assessment and Life-Cycle Analysis of Recycled Materials for Sustainable Highway

Recycled materials replacing part of virgin materials in highway applications has shown great benefits to the society and environment. Beneficial use of recycled materials can save landfill places, sparse natural resources, and energy consumed in milling and hauling virgin materials. Low price of recycled materials is favorable to cost-saving in pavement projects. Considering the availability of recycled materials in the State of Maryland (MD), four abundant recycled materials, recycled concrete aggregate (RCA), recycled asphalt pavement (RAP), foundry sand (FS), and dredged materials (DM), were studied. A survey was conducted to collect the information of current usage of the four recycled materials in States’ Department of Transportation (DOTs). Based on literature review, mechanical and environmental properties, recommendations, and suggested test standards were investigated separately for the four recycled materials in different applications. Constrains in using these materials were further studied in order to provide recommendations for the development of related MD specifications. To measure social and environmental benefits from using recycled materials, life-cycle assessment was carried out with life-cycle analysis (LCA) program, PaLATE, and green highway rating system, BEST-in-Highway. The survey results indicated the wide use of RAP and RCA in hot mix asphalt (HMA) and graded aggregate base (GAB) respectively, while FS and DM are less used in field. Environmental concerns are less, but the possibly low quality and some adverse mechanical characteristics may hinder the widely use of these recycled materials. Technical documents and current specifications provided by State DOTs are good references to the usage of these materials in MD. Literature review showed consistent results with the survey. Studies from experimental research or site tests showed satisfactory performance of these materials in highway applications, when the substitution rate, gradation, temperature, moisture, or usage of additives, etc. meet some requirements. The results from LCA revealed significant cost savings in using recycled materials. Energy and water consumption, gas emission, and hazardous waste generation generally showed reductions to some degree. Use of new recycled technologies will contribute to more sustainable highways.

A Staggered Decameric Assembly of Human C-Reactive Protein Stabilized by Zinc Ions Revealed by X-ray Crystallography

International audience

Trèlat's beads as oral manifestations in patients with HIV/TB

Tuberculosis (TB) is a contagious infectious disease caused by Mycobacterium tuberculosis (Koch's bacillus). Co-infection with human immunodeficiency virus (HIV) and TB has reached a significant importance as a public health problem and this association has been recognized as the most significant event that changed "the balance between man and Koch's bacillus" in the last century, and has a large contribution to the risk for disease spreading. Tuberculosis has two main standard categories of clinical manifestations: primary and secondary. Primary TB is responsible for the initial infection with lungs being the involved organ. Oral lesions are observed as a secondary TB clinical manifestation with most frequent sites being hard and soft palate, tongue, lips, gums, tonsils, and salivary glands. A case of classical TB lesions in the oral cavity is reported, and the importance of a correct diagnosis through careful history taking is emphasized. Treatment selection needs to be done assertively, with great determination and building a link between patient and treatment protocol, in order to promote patient's adherence.

Brachycephalic obstructive airway syndrome : a review with six clinical cases

Dissertação de Mestrado Integrado em Medicina Veterinária

Étude du rôle de la membrane basale spécialisée dans la maturation de l'émail

Les cellules épithéliales qui produisent l’émail, les améloblastes, sont séparées de l'émail au niveau de la zone de maturation par une membrane basale spécialisée (MBS) enrichie en laminine 332 (LM-332). Cette protéine hétérotrimérique (composée des chaînes α3, ß3 et γ2) assure l'intégrité structurelle des membranes basales (MB) et influence divers processus cellulaires épithéliaux tels que l'adhésion et la différenciation cellulaire. Des modèles de souris « knockout » (KO), où les gènes codant pour LM-332 ont été supprimés, meurent peu après la naissance. Néanmoins, ce phénotype létal peut être contourné en substituant chez la souris le gène produisant la chaîne γ2 de la laminine (LAMC2) par sa forme humaine, sous le contrôle de l’expression du promoteur-rtTA, de la cytokératine 14, inductible par la prise de doxycycline (Dox) - (Tet-on). Le but de ce projet est d’examiner si l’utilisation de cette protéine humaine chez la souris a un effet sur la structuration de la MBS ainsi que sur la maturation de l'émail. La phase de maturation de l’organe de l’émail chez la souris transgénique a été sévèrement altérée par rapport à une souris normale (WT). La MBS n’est plus visible, une matrice dystrophique s’est formée dans la couche d'émail dans la phase de maturation, et la présence d’une matrice résiduelle de l'émail est observée durant la phase tardive de maturation. Des micro-analyses tomographiques ont révélé une usure excessive des surfaces occlusales des molaires, un écroulement de l'émail sur les pointes des incisives et une hypominéralisation de l'émail. Cependant, aucune altération structurale due à cette recombinaison transgénique n’a été observée dans d'autres sites épithéliaux, tels que la peau, le palais et la langue. Ces résultats indiquent que, bien que ce modèle de souris humanisée soit capable de rétablir ses fonctions dans divers tissus épithéliaux, il est incapable de soutenir la structuration d'une MBS à l'interface entre les améloblastes et l’émail en maturation. Cet échec peut être lié à la composition spécifique de la MBS dans la phase de maturation et supporte l’hypothèse que la MBS est essentielle pour la maturation adéquate de l'émail.

Étude du rôle de la membrane basale spécialisée dans la maturation de l'émail

Les cellules épithéliales qui produisent l’émail, les améloblastes, sont séparées de l'émail au niveau de la zone de maturation par une membrane basale spécialisée (MBS) enrichie en laminine 332 (LM-332). Cette protéine hétérotrimérique (composée des chaînes α3, ß3 et γ2) assure l'intégrité structurelle des membranes basales (MB) et influence divers processus cellulaires épithéliaux tels que l'adhésion et la différenciation cellulaire. Des modèles de souris « knockout » (KO), où les gènes codant pour LM-332 ont été supprimés, meurent peu après la naissance. Néanmoins, ce phénotype létal peut être contourné en substituant chez la souris le gène produisant la chaîne γ2 de la laminine (LAMC2) par sa forme humaine, sous le contrôle de l’expression du promoteur-rtTA, de la cytokératine 14, inductible par la prise de doxycycline (Dox) - (Tet-on). Le but de ce projet est d’examiner si l’utilisation de cette protéine humaine chez la souris a un effet sur la structuration de la MBS ainsi que sur la maturation de l'émail. La phase de maturation de l’organe de l’émail chez la souris transgénique a été sévèrement altérée par rapport à une souris normale (WT). La MBS n’est plus visible, une matrice dystrophique s’est formée dans la couche d'émail dans la phase de maturation, et la présence d’une matrice résiduelle de l'émail est observée durant la phase tardive de maturation. Des micro-analyses tomographiques ont révélé une usure excessive des surfaces occlusales des molaires, un écroulement de l'émail sur les pointes des incisives et une hypominéralisation de l'émail. Cependant, aucune altération structurale due à cette recombinaison transgénique n’a été observée dans d'autres sites épithéliaux, tels que la peau, le palais et la langue. Ces résultats indiquent que, bien que ce modèle de souris humanisée soit capable de rétablir ses fonctions dans divers tissus épithéliaux, il est incapable de soutenir la structuration d'une MBS à l'interface entre les améloblastes et l’émail en maturation. Cet échec peut être lié à la composition spécifique de la MBS dans la phase de maturation et supporte l’hypothèse que la MBS est essentielle pour la maturation adéquate de l'émail.

Effet du climat viticole sur la perception sensorielle du vin: éléments méthodologiques pour une modélisation au niveau mondial.

Summary The objective of this study was to develop a methodology capable of modeling the effect of viticultural climate on wine sensory characteristics. The climate was defined by the Géoviticulture Multicriteria Climatic Classification System (Tonietto and Carbonneau, 2004), based on the Heliothermal index (HI), Cool Night index (CI) and Dryness index (DI). The sensory wine description was made according with the methodology established by Zanus and Tonietto (2007). In this study we focused on the 5 principal wine producing regions of Brazil: Serra Gaúcha, Serra do Sudeste, Campanha (Meridional and Central), Planalto Catarinense and Vale do Submédio São Francisco. The results from Principal Component Analysis (PCA) show the HI and CI opposed to the DI. High HI values were associated to a lower perception of acidity, as well as to a lower perception of concentration (palate) and persistence by mouth. For the red wines, high HI values were positively associated with alcohol (palate), conversely to the DI index, which showed high values related to the perception of tanins and acidity. The higher the CI, the lower were the color intensity, tanins, concentration and persistence by mouth. It may be concluded that viticultural climate - expressed by the HI, CI and DI indexes ? adequately explained much of the sensory differences of the wines made in different regions. The methodology proposed and the enlargement of the database it will maybe open the possibility of modeling the part of wine sensory characteristics as dependent variables of the viticultural climate, as defined by the Géoviticulture MCC System. Keywords: viticultural climate, modeling, wine, tipicity.