The powerful high pressure tool for protein conformational studies

The pressure behavior of proteins may be summarized as a the pressure-induced disordering of their structures. This thermodynamic parameter has effects on proteins that are similar but not identical to those induced by temperature, the other thermodynamic parameter. Of particular importance are the intermolecular interactions that follow partial protein unfolding and that give rise to the formation of fibrils. Because some proteins do not form fibrils under pressure, these observations can be related to the shape of the stability diagram. Weak interactions which are differently affected by hydrostatic pressure or temperature play a determinant role in protein stability. Pressure acts on the 2º, 3º and 4º structures of proteins which are maintained by electrostatic and hydrophobic interactions and by hydrogen bonds. We present some typical examples of how pressure affects the tertiary structure of proteins (the case of prion proteins), induces unfolding (ataxin), is a convenient tool to study enzyme dissociation (enolase), and provides arguments to understand the role of the partial volume of an enzyme (butyrylcholinesterase). This approach may have important implications for the understanding of the basic mechanism of protein diseases and for the development of preventive and therapeutic measures.

The GATO gene annotation tool for research laboratories

Large-scale genome projects have generated a rapidly increasing number of DNA sequences. Therefore, development of computational methods to rapidly analyze these sequences is essential for progress in genomic research. Here we present an automatic annotation system for preliminary analysis of DNA sequences. The gene annotation tool (GATO) is a Bioinformatics pipeline designed to facilitate routine functional annotation and easy access to annotated genes. It was designed in view of the frequent need of genomic researchers to access data pertaining to a common set of genes. In the GATO system, annotation is generated by querying some of the Web-accessible resources and the information is stored in a local database, which keeps a record of all previous annotation results. GATO may be accessed from everywhere through the internet or may be run locally if a large number of sequences are going to be annotated. It is implemented in PHP and Perl and may be run on any suitable Web server. Usually, installation and application of annotation systems require experience and are time consuming, but GATO is simple and practical, allowing anyone with basic skills in informatics to access it without any special training. GATO can be downloaded at [http://mariwork.iq.usp.br/gato/]. Minimum computer free space required is 2 MB.

FANCD2 Western blot as a diagnostic tool for Brazilian patients with Fanconi anemia

Fanconi anemia is a rare hereditary disease showing genetic heterogeneity due to a variety of mutations in genes involved in DNA repair pathways, which may lead to different clinical manifestations. Phenotypic variability makes diagnosis difficult based only on clinical manifestations, therefore laboratory tests are necessary. New advances in molecular pathogenesis of this disease led researchers to develop a diagnostic test based on Western blot for FANCD2. The objective of the present study was to determine the efficacy of this method for the diagnosis of 84 Brazilian patients with Fanconi anemia, all of whom tested positive for the diepoxybutane test, and 98 healthy controls. The FANCD2 monoubiquitinated isoform (FANCDS+/FANCD2L-) was not detected in 77 patients (91.7%). In 2 patients (2.4%), there was an absence of both the monoubiquitinated and the non-ubiquitinated proteins (FANCD2S-/FANCD2L-) and 5 patients (5.9%) had both isoforms (FANCD2S+/FANCD2L+). This last phenotype suggests downstream subtypes or mosaicism. All controls were diepoxybutane negative and were also negative on the FANCD2 Western blot. The Western blot for FANCD2 presented a sensitivity of 94% (79/84) and specificity of 100% (98/98). This method was confirmed as an efficient approach to screen Brazilian patients with deleterious mutations on FANCD2 (FANCD2S-/FANCD2L-) or other upstream genes of the FA/BRCA pathway (FANCDS+/FANCD2L-), to confirm the chromosome breakage test and to classify patients according to the level of FA/BRCA pathway defects. However, patients showing both FANCD2 isoforms (FANCD2S+/FANCD2L+) require additional studies to confirm mutations on downstream Fanconi anemia genes or the presence of mosaicism.

The effects of stretching on the flexibility, muscle performance and functionality of institutionalized older women

Stretching has been widely used to increase the range of motion. We assessed the effects of a stretching program on muscle-tendon length, flexibility, torque, and activities of daily living of institutionalized older women. Inclusion/exclusion criteria were according to Mini-Mental State Examination (MMSE) (>13), Barthel Index (>13) and Lysholm Scoring Scale (>84). Seventeen 67 ± 9 year-old elderly women from a nursing home were divided into 2 groups at random: the control group (CG, N = 9) participated in enjoyable cultural activities; the stretching group (SG, N = 8) performed active stretching of hamstrings, 4 bouts of 1 min each. Both groups were supervised three times per week over a period of 8 weeks. Peak torque was assessed by an isokinetic method. Both groups were evaluated by a photogrammetric method to assess muscle-tendon length of uni- and biarticular hip flexors and hamstring flexibility. All measurements were analyzed before and after 8 weeks by two-way ANOVA with the level of significance set at 5%. Hamstring flexibility increased by 30% in the SG group compared to pre-training (76.5 ± 13.0° vs 59.5 ± 9.0°, P = 0.0002) and by 9.2% compared to the CG group (76.5 ± 13.0° vs 64.0 ± 12.0°, P = 0.0018). Muscle-tendon lengths of hip biarticular flexor muscles (124 ± 6.8° vs 118.3 ± 7.6°, 5.0 ± 7.0%, P = 0.031) and eccentric knee extensor peak torque were decreased in the CG group compared to pre-test values (-49.4 ± 16.8 vs -60.5 ± 18.9 Nm, -15.7 ± 20%, P = 0.048). The stretching program was sufficient to increase hamstring flexibility and a lack of stretching can cause reduction of muscle performance.

Cell cycle synchronization and BrdU incorporation as a tool to study the possible selective elimination of ErbB1 gene in the micronuclei in A549 cells

Lung cancer often exhibits molecular changes, such as the overexpression of the ErbB1 gene that encodes epidermal growth factor receptor (EGFR). ErbB1 amplification and mutation are associated with tumor aggressiveness and low response to therapy. The aim of the present study was to design a schedule to synchronize the cell cycle of A549 cell line (a non-small cell lung cancer) and to analyze the possible association between the micronuclei (MNs) and the extrusion of ErbB1 gene extra-copies. After double blocking, by the process of fetal bovine serum deprivation and vincristine treatment, MNs formation was monitored with 5-bromo-2-deoxyuridine (BrdU) incorporation, which is an S-phase marker. Statistical analyses allowed us to infer that MNs may arise both in mitosis as well as in interphase. The MNs were able to replicate their DNA and this process seemed to be non-synchronous with the main cell nuclei. The presence of ErbB1 gene in the MNs was evaluated by fluorescent in situ hybridization (FISH). ErbB1 sequences were detected in the MNs, but a relation between the MNs formation and extrusion of amplified ErbB1could not be established. The present study sought to elucidate the meaning of MNs formation and its association with the elimination of oncogenes or other amplified sequences from the tumor cells.

Automated static image analysis as a novel tool in describing the physical properties of dietary fiber

Abstract The growing interest in the usage of dietary fiber in food has caused the need to provide precise tools for describing its physical properties. This research examined two dietary fibers from oats and beets, respectively, in variable particle sizes. The application of automated static image analysis for describing the hydration properties and particle size distribution of dietary fiber was analyzed. Conventional tests for water holding capacity (WHC) were conducted. The particles were measured at two points: dry and after water soaking. The most significant water holding capacity (7.00 g water/g solid) was achieved by the smaller sized oat fiber. Conversely, the water holding capacity was highest (4.20 g water/g solid) in larger sized beet fiber. There was evidence for water absorption increasing with a decrease in particle size in regards to the same fiber source. Very strong correlations were drawn between particle shape parameters, such as fiber length, straightness, width and hydration properties measured conventionally. The regression analysis provided the opportunity to estimate whether the automated static image analysis method could be an efficient tool in describing the hydration properties of dietary fiber. The application of the method was validated using mathematical model which was verified in comparison to conventional WHC measurement results.

Optimization and functionality of millet supplemented pasta

Abstract Millets are having superior nutritional qualities and health benefits; hence they can be used for supplementation of pasta. Pasta was prepared using composite flour (CF) of durum wheat semolina (96%) and carrot pomace (4%) supplemented with finger millet flour (FMF, 0-20g), pearl millet flour (PMF, 0-30g) and carboxy methyl cellulose (CMC, 2-4g). Second order polynomial described the effect of FMF, PMF and CMC on lightness, firmness, gruel loss and overall acceptability of extruded pasta products. Results indicate that an increasing proportion of finger and pearl millet flour had signed (p≤0.05) negative effect on lightness, firmness, gruel loss and overall acceptability. However, CMC addition showed significant (p≤0. 05) positive effect on firmness, overall acceptability and negative effect on gruel loss of cooked pasta samples. Numeric optimization results showed that optimum values for extruded pasta were 20g FMF, 12g PMF and 4g CMC per 100g of CF and 34ml water with 0.981 desirability. The pasta developed is nutritionally rich as it contains protein (10.16g), fat (6g), dietary fiber (16.71g), calcium (4.23mg), iron (3.99mg) and zinc (1.682mg) per 100g.

A Project Portfolio Tool for Forecasting Small Projects Profitability

The case company in this study is a large industrial engineering company whose business is largely based on delivering a wide-range of engineering projects. The aim of this study is to create and develop a fairly simple Excel-based tool for the sales department. The tool’s main function is to estimate and visualize the profitability of various small projects. The study also aims to find out other possible and more long-term solutions for tackling the problem in the future. The study is highly constructive and descriptive as it focuses on the development task and in the creation of a new operating model. The developed tool focuses on estimating the profitability of the small orders of the selected project portfolio currently on the bidding-phase (prospects) and will help the case company in the monthly reporting of sales figures. The tool will analyse the profitability of a certain project by calculating its fixed and variable costs, then further the gross margin and operating profit. The bidding phase of small project is a phase that has not been covered fully by the existing tools within the case company. The project portfolio tool can be taken into use immediately within the case company and it will provide fairly accurate estimate of the profitability figures of the recently sold small projects.

Review of investment strategy, portfolio management, and scorecard based portfolio selection tool for direct property investments in Finland

The lack of research of private real estate is a well-known problem. Earlier studies have mostly concentrated on the USA or the UK. Therefore, this master thesis offers more information about the performance and risk associated with private real estate investments in Nordic countries, but especially in Finland. The structure of this master thesis is divided into two independent sections based on the research questions. In first section, database analysis is performed to assess risk-return ratio of direct real estate investment for Nordic countries. Risk-return ratios are also assessed for different property sectors and economic regions. Finally, review of diversification strategies based on property sectors and economic regions is performed. However, standard deviation itself is not usually sufficient method to evaluate riskiness of private real estate. There is demand for more explicit assessment of property risk. One solution is property risk scoring. In second section risk scorecard based tool is built to make different real estate comparable in terms of risk. In order to do this, nine real estate professionals were interviewed to enhance the structure of theory-based risk scorecard and to assess weights for different risk factors.

Citizens against the State: the riddle of high impact, low functionality courts in Brazil

The Brazilian federal judiciary offers an interesting riddle to scholars of judicial politics and policy change. While the courts have played a major policy role over the past two decades, constraining and altering federal policy across a range of subjects, the court system has simultaneously been labeled "dysfunctional." This paper investigates this riddle: a system plagued by major systemic flaws in its day-to-day operations, which nonetheless still manages to exert a powerful influence on public policy in Brazil. I adopt a new institutional perspective, focusing on how the institutional and normative structure within which judges and other legal actors operate affects policy outcomes.