Protein Microarray: "Theory" to "Real Practice"

Fueled by ever-growing genomic information and rapid developments of proteomics–the large scale analysis of proteins and mapping its functional role has become one of the most important disciplines for characterizing complex cell function. For building functional linkages between the biomolecules, and for providing insight into the mechanisms of biological processes, last decade witnessed the exploration of combinatorial and chip technology for the detection of bimolecules in a high throughput and spatially addressable fashion. Among the various techniques developed, the protein chip technology has been rapid. Recently we demonstrated a new platform called “Spacially addressable protein array” (SAPA) to profile the ligand receptor interactions. To optimize the platform, the present study investigated various parameters such as the surface chemistry and role of additives for achieving high density and high-throughput detection with minimal nonspecific protein adsorption. In summary the present poster will address some of the critical challenges in protein micro array technology and the process of fine tuning to achieve the optimum system for solving real biological problems.

Extensional rheology and stability of gas cell walls in bread doughs at elevated temperatures in relation to breadmaking performance

The rheological properties of gas cell walls in bread doughs are considered to be important in relation to their stability and gas retention during proof and baking. Large deformation rheological properties of gas cell walls were measured using biaxial extension for a number of doughs of varying breadmaking quality at constant strain rate and elevated temperatures of 25-60degreesC. Strain hardening and failure strain of cell walls both decreased with temperature, with cell walls in good breadmaking doughs remaining stable and retaining their strain hardening properties at higher temperatures (60degreesC), while the cell walls of poor breadmaking doughs became unstable at lower temperatures (45-50degreesC) and had lower strain hardening. Strain hardening measured at 50degreesC gave good correlations with baking volume, with the best correlations achieved between rheological measurements and baking tests that used similar mixing conditions. As predicted by the considered failure criterion, a strain hardening value of I defines a region below which gas cell walls become unstable, and discriminates well between the baking quality of a range of commercial flour blends of varying quality. This indicates that the stability of gas cell walls during baking is strongly related to strain hardening properties, and that extensional rheological measurements can be used as indicators of baking quality.

Rheology and the breadmaking process

The applications of rheology to the main processes encountered during breadmaking (mixing, sheeting, fermentation and baking) are reviewed. The most commonly used rheological test methods and their relationships to product functionality are reviewed. It is shown that the most commonly used method for rheological testing of doughs, shear oscillation dynamic rheology, is generally used under deformation conditions inappropriate for breadmaking and shows little relationship with end-use performance. The frequency range used in conventional shear oscillation tests is limited to the plateau region, which is insensitive to changes in the HMW glutenin polymers thought to be responsible for variations in baking quality. The appropriate deformation conditions can be accessed either by long-time creep or relaxation measurements, or by large deformation extensional measurements at low strain rates and elevated temperatures. Molecular size and structure of the gluten polymers that make up the major structural components of wheat are related to their rheological properties via modern polymer rheology concepts. Interactions between polymer chain entanglements and branching are seen to be the key mechanisms determining the rheology of HMW polymers. Recent work confirms the observation that the dynamic shear plateau modulus is essentially independent of variations in MW of glutens amongst wheat varieties of varying baking performance and also that it is not the size of the soluble glutenin polymers, but the secondary structural and rheological properties of the insoluble polymer fraction that are mainly responsible for variations in baking performance. Extensional strain hardening has been shown to be a sensitive indicator of entanglements and long-chain branching in HMW polymers, and is well related to baking performance of bread doughs. The Considere failure criterion for instability in extension of polymers defines a region below which bubble walls become unstable, and predicts that when strain hardening falls below a value of around 1, bubble walls are no longer stable and coalesce rapidly, resulting in loss of gas retention and lower volume and texture. Strain hardening in doughs has been shown to reach this value at increasingly higher temperatures for better breadmaking varieties and is directly related to bubble stability and baking performance. (C) 2003 Elsevier Ltd. All rights reserved.

The physics of baking: rheological and polymer molecular structure-function relationships in breadmaking

Molecular size and structure of the gluten polymers that make up the major structural components of wheat are related to their rheological properties via modem polymer rheology concepts. Interactions between polymer chain entanglements and branching are seen to be the key mechanisms determining the rheology of HMW polymers. Recent work confirms the observation that dynamic shear plateau modulus is essentially independent of variations in MW amongst wheat varieties of varying baking performance and is not related to variations in baking performance, and that it is not the size of the soluble glutenin polymers, but the structural and rheological properties of the insoluble polymer fraction that are mainly responsible for variations in baking performance. The rheological properties of gas cell walls in bread doughs are considered to be important in relation to their stability and gas retention during proof and baking, in particular their extensional strain hardening properties. Large deformation rheological properties of gas cell walls were measured using biaxial extension for a number of doughs of varying breadmaking quality at constant strain rate and elevated temperatures in the range 25-60 degrees C. Strain hardening and failure strain of cell walls were both seen to decrease with temperature, with cell walls in good breadmaking doughs remaining stable and retaining their strain hardening properties to higher temperatures (60 degrees C), whilst the cell walls of poor breadmaking doughs became unstable at lower temperatures (45-50 degrees C) and had lower strain hardening. Strain hardening measured at 50 degrees C gave good correlations with baking volume, with the best correlations achieved between those rheological measurements and baking tests which used similar mixing conditions. As predicted by the Considere failure criterion, a strain hardening value of I defines a region below which gas cell walls become unstable, and discriminates well between the baking quality of a range of commercial flour blends of varying quality. This indicates that the stability of gas cell walls during baking is strongly related to their strain hardening properties, and that extensional rheological measurements can be used as predictors of baking quality. (C) 2004 Elsevier B.V. All rights reserved.

The physics of baking: rheological and polymer molecular structure-function relationships in breadmaking

Molecular size and structure of the gluten polymers that make up the major structural components of wheat are related to their rheological properties via modern polymer rheology concepts. Interactions between polymer chain entanglements and branching are seen to be the key mechanisms determining the rheology of HMW polymers. Recent work confirms the observation that dynamic shear plateau modulus is essentially independent of variations in MW amongst wheat varieties of varying baking performance and is not related to variations in baking performance, and that it is not the size of the soluble glutenin polymers, but the structural and rheological properties of the insoluble polymer fraction that are mainly responsible for variations in baking performance. The rheological properties of gas cell walls in bread doughs are considered to be important in relation to their stability and gas retention during proof and baking, in particular their extensional strain hardening properties. Large deformation rheological properties of gas cell walls were measured using biaxial extension for a number of doughs of varying breadmaking quality at constant strain rate and elevated temperatures in the range 25oC to 60oC. Strain hardening and failure strain of cell walls were both seen to decrease with temperature, with cell walls in good breadmaking doughs remaining stable and retaining their strain hardening properties to higher temperatures (60oC), whilst the cell walls of poor breadmaking doughs became unstable at lower temperatures (45oC to 50oC) and had lower strain hardening. Strain hardening measured at 50oC gave good correlations with baking volume, with the best correlations achieved between those rheological measurements and baking tests which used similar mixing conditions. As predicted by the Considere failure criterion, a strain hardening value of 1 defines a region below which gas cell walls become unstable, and discriminates well between the baking quality of a range of commercial flour blends of varying quality. This indicates that the stability of gas cell walls during baking is strongly related to their strain hardening properties, and that extensional rheological measurements can be used as predictors of baking quality.

On the threshold of adulthood: a new approach for the use of maturation indicators to assess puberty in adolescents from medieval England

Objectives: This study provides the first large scale analysis of the age at which adolescents in medieval England entered and completed the pubertal growth spurt. This new method has implications for expanding our knowledge of adolescent maturation across different time periods and regions. Methods: In total, 994 adolescent skeletons (10-25 years) from four urban sites in medieval England (AD 900-1550) were analysed for evidence of pubertal stage using new osteological techniques developed from the clinical literature (i.e. hamate hook development, CVM, canine mineralisation, iliac crest ossification, radial fusion). Results: Adolescents began puberty at a similar age to modern children at around 10-12 years, but the onset of menarche in girls was delayed by up to 3 years, occurring around 15 for most in the study sample and 17 years for females living in London. Modern European males usually complete their maturation by 16-18 years; medieval males took longer with the deceleration stage of the growth spurt extending as late as 21 years. Conclusions: This research provides the first attempt to directly assess the age of pubertal development in adolescents during the tenth to seventeenth centuries. Poor diet, infections, and physical exertion may have contributed to delayed development in the medieval adolescents, particularly for those living in the city of London. This study sheds new light on the nature of adolescence in the medieval period, highlighting an extended period of physical and social transition.

In silico identification and characterization of protein-ligand binding sites

Protein–ligand binding site prediction methods aim to predict, from amino acid sequence, protein–ligand interactions, putative ligands, and ligand binding site residues using either sequence information, structural information, or a combination of both. In silico characterization of protein–ligand interactions has become extremely important to help determine a protein’s functionality, as in vivo-based functional elucidation is unable to keep pace with the current growth of sequence databases. Additionally, in vitro biochemical functional elucidation is time-consuming, costly, and may not be feasible for large-scale analysis, such as drug discovery. Thus, in silico prediction of protein–ligand interactions must be utilized to aid in functional elucidation. Here, we briefly discuss protein function prediction, prediction of protein–ligand interactions, the Critical Assessment of Techniques for Protein Structure Prediction (CASP) and the Continuous Automated EvaluatiOn (CAMEO) competitions, along with their role in shaping the field. We also discuss, in detail, our cutting-edge web-server method, FunFOLD for the structurally informed prediction of protein–ligand interactions. Furthermore, we provide a step-by-step guide on using the FunFOLD web server and FunFOLD3 downloadable application, along with some real world examples, where the FunFOLD methods have been used to aid functional elucidation.

Algoritmos de agrupamento aplicados a dados de expressão gênica de câncer: um estudo comparativo

The use of clustering methods for the discovery of cancer subtypes has drawn a great deal of attention in the scientific community. While bioinformaticians have proposed new clustering methods that take advantage of characteristics of the gene expression data, the medical community has a preference for using classic clustering methods. There have been no studies thus far performing a large-scale evaluation of different clustering methods in this context. This work presents the first large-scale analysis of seven different clustering methods and four proximity measures for the analysis of 35 cancer gene expression data sets. Results reveal that the finite mixture of Gaussians, followed closely by k-means, exhibited the best performance in terms of recovering the true structure of the data sets. These methods also exhibited, on average, the smallest difference between the actual number of classes in the data sets and the best number of clusters as indicated by our validation criteria. Furthermore, hierarchical methods, which have been widely used by the medical community, exhibited a poorer recovery performance than that of the other methods evaluated. Moreover, as a stable basis for the assessment and comparison of different clustering methods for cancer gene expression data, this study provides a common group of data sets (benchmark data sets) to be shared among researchers and used for comparisons with new methods

Integração de métodos geofísicos na modelagem crustal da Bacia de Santos

A Bacia de Santos é uma bacia de margem passiva gerada durante o Neocomiano, associado com o evento de ruptura do Supercontinente de Gondwana. A espessura da seção sedimentar pode alcançar 15 km, incluindo a seqüência rifte, e foi depositada sobre uma crosta afinada cuja espessura original era de cerca de 35 km. Foi realizada uma modelagem crustal em 8 linhas, aproximadamente perpendiculares ao mergulho deposicional da bacia, objetivando o reconhecimento da geometria da fase rifte e a estimativa do estiramento crustal. Foram utilizados durante a modelagem quatro horizontes sísmicos em profundidade, mapas magnético e gravimétrico além de dados da profundidade do embasamento magnético. Foi reconhecido um pronunciado estiramento crustal em toda a bacia (fatores de estiramento crustal variando entre 1.2 e 3.1), evidenciando ampla acomodação da deformação. Os resultados da modelagem necessitaram, ainda, de espessas e contínuas camadas de rochas vulcânicas para ajuste do modelo. Estas cunhas de rochas vulcânicas, limitadas lateralmente por falhas normais, são feições comuns em bacias rifte. Os resultados da modelagem foram confrontados com dados da profundidade do embasamento magnético, obtidos anteriormente, e evidenciaram forte correlação, sobretudo nas áreas rasas da bacia.

Determinação de fósforo microbiano: comparação entre métodos e coberturas florestais

Muitos trabalhos mostram a importância da biomassa microbiana do solo (BMS), principalmente como fonte/dreno de C e de N em plantações florestais; contudo, são escassos os trabalhos relacionados ao fósforo microbiano (PBM), sobretudo aqueles relativos aos métodos de determinação do PBM nesses ecossistemas. O presente trabalho foi realizado com o objetivo de avaliar métodos de determinação do PBM em solo com diferentes coberturas vegetais. O trabalho consistiu da análise de amostras de Latossolo Vermelho-Amarelo distrófico muito argiloso (LVAd) localizado no município de Viçosa (MG), coletadas nas profundidades de 0 a 5 e 5 a 10 cm, em áreas com as seguintes coberturas vegetais: pínus (Pinus taeda), eucalipto (Eucalyptus grandis) e floresta nativa. Para determinação do P microbiano, foram empregados os métodos fumigação-extração (FE), irradiação com micro-ondas-extração (IE) e irradiação com micro-ondas-extração com membrana de troca aniônica (EMTA). em termos gerais, menores teores de PBM foram obtidos com o método irradiação-extração. Considerando a cobertura vegetal, foi detectada diferença significativa entre os três métodos sob floresta de eucalipto e floresta nativa, principalmente na camada superficial. Sob pínus, apenas o método IE diferiu dos demais, na camada subsuperficial. Menores coeficientes de variação (CV) foram obtidos com o FE, retratando maior precisão do método. Entretanto, o método IE mostrou-se, em termos operacionais, o mais adequado à determinação do PBM quando se tem maior número de amostras. Com relação às coberturas vegetais, a grande variabilidade observada nos CVs obtidos para cada cobertura, nos três métodos testados, inviabiliza a escolha de um único método que apresente maior precisão na avaliação do PBM.

Rough turning of titanium alloy (6Al-4V)

Metal machining is the complex process due the used cutting parameters. In metal cutting process, materials of workpiece differ widely in their ability to deform plastically, to fracture and to sustain tensile stresses. Moreover, the material involved in the process has a great influence in these operations. The Ti-6Al-4V alloy is very used in the aeronautical industry, mainly in the manufacture of engines, has very important properties such the mechanical and corrosion resistance in high te mperatures. The turning of the Ti-Al-4V alloy is very difficult due the rapid tool wear. Such behavior result of the its low thermal conductivity in addition the high reactivity with the cutting tool. The formed chip is segmented and regions of the large deformation named shear bands plows formed. The machinability of the cutting process can be evaluated by several measures including power consume, machined surface quality, tool wear, tool life, microstructure and morphology of the obtained chip. This paper studies the effect of cutting parameters, speed and feed rates, in the tool wear and chip properties using uncoating cemented carbide tool. Microe-structural characterization of the chip and tool wear was performed using scanning electron microscopy (SEM) and Light Optical Mcroscopy (LOM).

A atividade pesqueira nas ilhas do entorno de Belém

O Estuário Amazônico é uma região com condições propícias de produtividade, tornando a área favorável a pesca. As ilhas do Combu, Ilha das Onças e Mosqueiro, alvo deste estudo, fazem parte do Estuário Amazônico e a pesca é uma atividade praticada constantemente pelos moradores dessas ilhas. Baseando-se nessas informações, o objetivo do presente estudo foi descrever e comparar as diferentes modalidades de pesca das ilhas do Combu, Ilha das Onças e Mosqueiro, identificando os atributos que mais contribuem para a formação dos sistemas de produção, para o posterior acompanhamento das pescarias nas ilhas do entorno de Belém, considerando as dimensões econômica, social, ecológica e tecnológica. Deste modo espera-se auxiliar a geração de subsídios para a formulação de políticas públicas para o setor pesqueiro. Variáveis descritivas e numéricas considerando as diferentes dimensões foram utilizadas com a finalidade de descrever os sistemas de produção pesqueira de forma que tornassem comparativos tanto os sistemas quanto as ilhas estudadas. Para a análise estatística comparativa foram utilizadas apenas as variáveis numéricas (médias e porcentagens), provenientes tanto de dados coletados em campo quanto da pesquisa em dados secundários. Análise multivariada de agrupamento e ordenação (MDS), comparando os sistemas foi aplicada visando identificar os agrupamentos e as possíveis causas da semelhança entre os sistemas de pesca por ilha. Na ilha do Combu foram identificados os sistemas de matapi, emalhe consumo, tapagem, espinhel anzol médio e espinhel anzol grande. Na ilha das Onças foram observados os sistemas de matapi, emalhe consumo, emalhe comercial, tapagem, espinhel anzol médio e espinhel anzol grande. Em Mosqueiro identificou-se a pesca de matapi, emalhe comercial, espinhel anzol médio e espinhel anzol grande. As análises dos sistemas em todas as dimensões mostraram que a ilha de Mosqueiro se diferencia das demais ilhas estudadas. Quando analisadas por dimensão separadamente o sistema matapi, tapagem e emalhe consumo das ilhas do Combu e Ilha das Onças se mostraram muito similares. Entretanto os sistemas observados em Mosqueiro se diferenciam principalmente na dimensão econômica. Com base nos resultados observados pode-se afirmar que a pesca nas ilhas do Combu e Ilha das Onças é de subsistência e a atividade principal é o extrativismo vegetal enquanto em Mosqueiro a pesca caracteriza-se principalmente como comercial. Apesar da pesca nas ilhas do Combu e Ilha das Onças servirem apenas para subsistência representam importante fonte de alimento e renda extra para os moradores. Em Mosqueiro a pesca tem importância econômica elevada, porém as áreas de pesca são exploradas também por pescadores de outros locais do Estado sem que existam iniciativas de manejo por parte dos governantes.

Influência da mesa na resistência ao cisalhamento de lajes nervuradas unidirecionais de concreto armado

A resistência ao cisalhamento de lajes nervuradas unidirecionais de concreto armado sem armadura transversal em suas nervuras é avaliada através de seu comportamento estrutural ao cisalhamento. Para quantificar a participação da altura da mesa e da mesa colaborante na resistência característica ao cisalhamento, foram confeccionados 8 painéis de lajes nervuradas unidirecionais de concreto armado com variações da altura das mesas, visando avaliar as recomendações das normas NBR 6118 (2007), ACI 318 (2011) e EUROCODE 2 (2002) no que se refere ao desempenho das lajes nervuradas unidirecionais de concreto armado ao cisalhamento. As lajes, simplesmente apoiadas nas bordas, apresentaram-se em dois grupos, buscando abranger os limites prescritos pela norma brasileira: o primeiro com 4 lajes de (2000 x 1300) mm² com distância entre os eixos de nervuras de 610 mm e o segundo com 4 lajes de (2000 x 2000) mm² com distância entre eixos de nervuras de 960 mm, sendo que houve uma variação da altura da mesa de 30, 50, 80 e 100 mm. A armadura de flexão foi mantida constante em todos os casos e a armadura de cisalhamento foi suprimida, para que todas as lajes tivessem rupturas por cisalhamento. As lajes apresentaram aumento da resistência com o aumento da altura da mesa, indicado pelo considerável ganho de contribuição do concreto na resistência ao cisalhamento, bem como a grande deformação das armaduras longitudinais e de distribuição, e pelos elevados valores das flechas. Portanto, no cálculo de resistência ao cisalhamento de lajes nervuradas, poderia ser repensada a falta da utilização da altura da mesa como variável, visto que sua contribuição à resistência ao cisalhamento é real.

Modulation of HJURP (Holliday Junction-Recognizing Protein) Levels Is Correlated with Glioblastoma Cells Survival

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Mechanisms of cell senescence: p21 and DNA damage response in aging and longevity

Theory of aging postulates that aging is a remodeling process where the body of survivors progressively adapts to internal and external damaging agents they are exposed to during several decades. Thus , stress response and adaptation mechanisms play a fundamental role in the aging process where the capability of adaptating effects, certainly, also is related the lifespan of each individual. A key gene linking aging to stress response is indeed p21, an induction of cyclin-dependent kinase inhibitor which triggers cell growth arrest associated with senescence and damage response and notably is involved in the up-regulation of multiple genes that have been associated with senescence or implicated in age-related . This PhD thesis project that has been performed in collaboration with the Roninson Lab at Ordway Research Institute in Albany, NY had two main aims: -the testing the hypothesis that p21 polymorphisms are involved in longevity -Evaluating age-associated differences in gene expression and transcriptional response to p21 and DNA damage In the first project, trough PCR-sequencing and Sequenom strategies, we we found out that there are about 30 polymorphic variants in the p21 gene. In addition, we found an haplotpype located in -5kb region of the p21 promoter whose frequency is ~ 2 fold higher in centenarians than in the general population (Large-scale analysis of haplotype frequencies is currently in progress). Functional studies I carried out on the promoter highilighted that the ―centenarian‖ haplotype doesn’t affect the basal p21 promoter activity or its response to p53. However, there are many other possible physiological conditions in which the centenarian allele of the p21 promoter may potentially show a different response (IL6, IFN,progesterone, vitamin E, Vitamin D etc). In the second part, project #2, trough Microarrays we seeked to evaluate the differences in gene expression between centenarians, elderly, young in dermal fibroblast cultures and their response to p21 and DNA damage. Microarray analysis of gene expression in dermal fibroblast cultures of individuals of different ages yielded a tentative "centenarian signature". A subset of genes that were up- or downregulated in centenarians showed the same response to ectopic expression of p21, yielding a putative "p21-centenarian" signature. Trough RQ-PCR (as well Microarrays studies whose analysis is in progress) we tested the DNA damage response of the p21-centenarian signature genes showing a correlation stress/aging in additional sets of young and old samples treated with p21-inducing drug doxorubicin thus finding for a subset of of them , a response to stress age-related.