Gene Expression Complex Networks: Synthesis, Identification, and Analysis

Thanks to recent advances in molecular biology, allied to an ever increasing amount of experimental data, the functional state of thousands of genes can now be extracted simultaneously by using methods such as cDNA microarrays and RNA-Seq. Particularly important related investigations are the modeling and identification of gene regulatory networks from expression data sets. Such a knowledge is fundamental for many applications, such as disease treatment, therapeutic intervention strategies and drugs design, as well as for planning high-throughput new experiments. Methods have been developed for gene networks modeling and identification from expression profiles. However, an important open problem regards how to validate such approaches and its results. This work presents an objective approach for validation of gene network modeling and identification which comprises the following three main aspects: (1) Artificial Gene Networks (AGNs) model generation through theoretical models of complex networks, which is used to simulate temporal expression data; (2) a computational method for gene network identification from the simulated data, which is founded on a feature selection approach where a target gene is fixed and the expression profile is observed for all other genes in order to identify a relevant subset of predictors; and (3) validation of the identified AGN-based network through comparison with the original network. The proposed framework allows several types of AGNs to be generated and used in order to simulate temporal expression data. The results of the network identification method can then be compared to the original network in order to estimate its properties and accuracy. Some of the most important theoretical models of complex networks have been assessed: the uniformly-random Erdos-Renyi (ER), the small-world Watts-Strogatz (WS), the scale-free Barabasi-Albert (BA), and geographical networks (GG). The experimental results indicate that the inference method was sensitive to average degree k variation, decreasing its network recovery rate with the increase of k. The signal size was important for the inference method to get better accuracy in the network identification rate, presenting very good results with small expression profiles. However, the adopted inference method was not sensible to recognize distinct structures of interaction among genes, presenting a similar behavior when applied to different network topologies. In summary, the proposed framework, though simple, was adequate for the validation of the inferred networks by identifying some properties of the evaluated method, which can be extended to other inference methods.

A new correlation between electronic parameters and glass forming ability of metallic alloys

A quantitative correlation between the glass forming ability and the electronic parameters of metallic alloys is presented. It is found that the critical cooling rate for glass formation (R(c)) correlates well with the average work function difference (Delta phi) and the average electron density difference (Delta n(ws)(1/3)) among the constituent elements of the investigated alloys. A correlation coefficient (R(2)) of 0.77 was found for 68 alloys in 30 metallic systems, which is better than the previous proposed correlation between the glass forming ability and the average Pauling electronegativity difference.

Detection of Sourgrass (Digitaria insularis) Biotypes Resistant to Glyphosate in Brazil

Sourgrass is a perennial weed infesting annual and perennial crops in Brazil. Three biotypes (R1, R2, and R3) of sourgrass suspected to be glyphosate-resistant (R) and another one (S) from a natural area without glyphosate application, in Brazil, were tested for resistance to glyphosate based on screening, dose-response, and shikimic acid assays. Both screening and dose-response assays confirmed glyphosate resistance in the three sourgrass biotypes. Dose-response assay indicated a resistance factor of 2.3 for biotype RI and 3.9 for biotypes R2 and R3. The hypothesis of a glyphosate resistance was corroborated on the basis of shikimic acid accumulation, where the S biotype accumulated 3.3, 5.0, and 5.7 times more shikimic acid than biotypes R1, R2, and R3, respectively, 168 h after treatment with 157.50 g ae ha(-1) of glyphosate. There were no differences in contact angle of spray droplets on leaves and spray retention, indicating that differential capture of herbicide by leaves was not responsible for resistance in these biotypes. The results confirmed resistance of sourgrass to glyphosate in Brazil.

Retention of the Enzymatic Activity and Product Properties During Spray Drying of Pineapple Stem Extract in Presence of Maltodextrin

The aim of this work was to investigate the effects of drying parameters on the retention of the enzymatic activity and on the physical properties of spray-dried pineapple stem extract. A Box and Behnken experimental design was used to investigate the effects of the processing parameters on the product properties. The parameters studied were the inlet temperature of drying gas (Tgi), the feed flow rate of the pineapple extract relative to evaporative capacity of the system (Ws /Wmax), and the concentration of maltodextrin added to the extract (MD). Significant effects of the processing parameters on the retention of the proteolytic activity of the powdered extract were observed. High processing temperatures lead to a product with a smaller moisture content, particle size, and lower agglomerating tendency. A product with insignificant losses of the proteolytic activity ( 10%) and low moisture content (less than 6.5%) is obtained at selected conditions.

Stabilization of Endophytic Fungus Cercospora kikuchii Lipase by Spray Drying in the Presence of Maltodextrin and beta-Cyclodextrin

In this study the effects of spray-drying conditions on the retention of enzyme activity of lipase produced by the endophytic fungus Cercospora kikuchii have been investigated. Drying runs were carried out in a bench-top spray dryer with a concurrent flow regime. The influence of the variables inlet temperature of drying gas, Tgi (86.4 to 153.6 degrees C); mass flow rate of the enzymatic extract fed to the dryer, Ws (2.63 to 9.36g/min); and concentration of the drying adjuvant added to the extract, ADJ (1.95 to 12.05%), on the spray-drying performance and on product quality was evaluated through experimental planning and regression analysis. The use of maltodextrin, as a stabilizing agent, slightly improved the retention of enzyme activity compared to -cyclodextrin. Statistical optimization of the experimental results allowed the determination of the processing conditions that maximized the retention of the enzymatic activity (RAE), namely, concentration of drying adjuvants of 12.05%, inlet temperature of the drying gas of 153.6 degrees C, and flow rate of the enzymatic extract fed to the dryer of 9.36g/min for the both drying adjuvants investigated.

Stability Testing of Spray- and Spouted Bed-Dried Extracts of Passiflora alata

The aim of this research was to perform a stability testing of spray- and spouted bed-dried extracts of Passiflora alata Dryander (Passion flower) under stress storage conditions. Spouted bed- and spray-dried extracts were characterized by determination of the average particle diameter (dP), apparent moisture content (XP), total flavonoid content (TF), and vitexin content. Smaller and more irregular particles were generated by the spouted bed system due to a higher attrition rate (surface erosion) inside the dryer. The SB dryer resulted in an end product with higher concentration of flavonoids (approximate to 10%) and lower moisture content (1.6%, dry basis) than the spray dryer, even with both dryers working at similar inlet drying air temperature and ratio between the extract feed flow rate to drying air flow rate (Ws/Wg). Samples of the spouted bed- and spray-dried extracts were stored at two different temperatures (34 and 45 degrees C) and two different relative humidities (52 and 63% RH for 34 degrees C; 52 and 60% RH for 45 degrees C) in order to perform the stability testing. The dried extracts were stored for 28 days and were analyzed every 4 days. The flavonoid vitexin served as the marker compound, which was assayed during the storage period. Results revealed shelf lives ranging from 9 to 184 days, depending on the drying process and storage conditions.

Identification of novel mutations of the WFS1 gene in Brazilian patients with Wolfram syndrome

Objective: Wolfram syndrome (WS) is a rare, progressive, neurodegenerative disorder with an autosomal recessive pattern of inheritance. The gene for WS, WFS1, was identified on chromosome 4p16 and most WS patients carry mutations in this gene. However. some studies have provided evidence for genetic heterogeneity and the genotype-phenotype relationships are not clear. Our aim was to ascertain the spectrum of WFS1 mutations in Brazilian patients with WS and to examine the phenotype-genotype relationships in these patients. Design and methods: Clinical characterization and analyses of the WFS1. gene were performed in 27 Brazilian patients with WS from 19 families. Results: We identified 15 different mutations in the WFS1 gene in 26 patients, among which nine are novel. All mutations occurred in exon 8, except for one missense mutation which was located in exon 5. Although we did not find any clear phenotype-genotype relationship in patients with mutations in exon 8, the homozygous missense mutation in exon 5 was associated with a mild phenotype: onset of diabetes mellitus and optic atrophy during adulthood with good metabolic control being achieved with low doses of sulfonylurea Conclusions: Our data show that WFS1 is the major gene involved in WS in Brazilian patients and most mutations are concentrated in exon 8. Also, our study increases the spectrum of WFS1 mutations. Although no clear phenotype-genotype relationship was found for mutations in exon 8, a mild phenotype was associated with a homozygous missense mutation in exon 5.

WRN Cys1367Arg SNP is not associated with risk and prognosis of gliomas in Southeast Brazil

Werner syndrome (WS) is a premature aging disorder characterized by early onset of symptoms related to normal aging and by a high predisposition to various types of cancer, including gliomas. WS is caused by inherited recessive mutations in the WRN gene, which encodes a helicase considered a caretaker of the genome. Aiming to study the role of WRN Cys1367Arg in glioma susceptibility and oncologic prognosis of patients, we investigated the genotype distribution of this single nucleotide polymorphism in 94 glioma patients and 100 healthy subjects. Comparisons of genotype distributions and allele frequencies did not reveal any significant difference between the groups. Overall and disease-free survival rates were calculated, but no statistically significant difference was observed. Our data suggest that WRN Cys1367Arg SNP is not involved either in susceptibility to developing gliomas or in patient survival, at least in the Brazilian population.

Genetic associations between carcass traits measured by real-time ultrasound and scrotal circumference and growth traits in Nelore cattle

The aim of the present study was to evaluate the genetic correlations among real-time ultrasound carcass, BW, and scrotal circumference (SC) traits in Nelore cattle. Carcass traits, measured by real-time ultrasound of the live animal, were recorded from 2002 to 2004 on 10 farms across 6 Brazilian states on 2,590 males and females ranging in age from 450 to 599 d. Ultrasound records of LM area (LMA) and backfat thickness (BF) were obtained from cross-sectional images between the 12th and 13th ribs, and rump fat thickness (RF) was measured between the hook and pin bones over the junction between gluteus medius and biceps femoris muscles. Also, BW (n = 22,778) and SC ( n = 5,695) were recorded on animals born between 1998 and 2003. The BW traits were 120, 210, 365, 450, and 550-d standardized BW (W120, W210, W365, W450, and W550), plus BW (WS) and hip height (HH) on the ultrasound scanning date. The SC traits were 365-, 450-, and 550-d standardized SC (SC365, SC450, and SC550). For the BW and SC traits, the database used was from the Nelore Breeding Program-Nelore Brazil. The genetic parameters were estimated with multivariate animal models and REML. Estimated genetic correlations between LMA and other traits were 0.06 (BF), -0.04 ( RF), 0.05 (HH), 0.58 (WS), 0.53 (W120), 0.62 (W210), 0.67 (W365), 0.64 ( W450 and W550), 0.28 (SC365), 0.24 (SC450), and 0.00 ( SC550). Estimated genetic correlations between BF and with other traits were 0.74 ( RF), -0.32 (HH), 0.19 (WS), -0.03 (W120), -0.10 (W210), 0.04 (W365), 0.01 (W450), 0.06 ( W550), 0.17 (SC365 and SC450), and -0.19 (SC550). Estimated genetic correlations between RF and other traits were -0.41 (HH), -0.09 (WS), -0.13 ( W120), -0.09 ( W210), -0.01 ( W365), 0.02 (W450), 0.03 (W550), 0.05 ( SC365), 0.11 ( SC450), and -0.18 (SC550). These estimates indicate that selection for carcass traits measured by real-time ultrasound should not cause antagonism in the genetic improvement of SC and BW traits. Also, selection to increase HH might decrease subcutaneous fat as correlated response. Therefore, to obtain animals suited to specific tropical production systems, carcass, BW, and SC traits should be considered in selection programs.

Bond durability in erbium:yttrium-aluminum-garnet laser-irradiated enamel

This study sought to evaluate the influence of thermocycling and water storage on the microtensile bond strength of composite resin bonded to erbium:yttrium-aluminum-garnet (Er:YAG)-irradiated and bur-prepared enamel. Eighty bovine incisors were selected and sectioned. Specimens were ground to produce a flat enamel surface. Samples were randomly assigned according to cavity preparation device: (I) Er:YAG laser and (II) high-speed turbine, and were subsequently restored with composite resin. They were subdivided according to the duration of water storage (WS)/number of thermocycles (TCs): 24 h WS/no TCs; 7 days WS/500 TCs; 1 month WS/2,000 TCs; 6 months WS/12,000 TCs. The teeth were sectioned into 1.0 mm(2)-thick slabs and subjected to tensile stress in a universal testing machine. Data were submitted to two-way analysis of variance (ANOVA) and Tukey`s test at a 0.05 significance level. The different periods of water storage and thermocycling did not influence the microtensile bond strength (A mu TBS) values in the Er:YAG laser-prepared groups. In bur-prepared enamel, the group submitted to 12,000 TCs/6 months` WS (IID) showed a significant decrease in bond strength values when compared to the group stored in water for 24 h and not submitted to thermocycling (IIA), but values were statistically similar to those obtained in all Er:YAG laser groups and in the bur- prepared groups degraded with 500 TCs/1 week WS (IIB) or 2,000 TCs/1 month WS (IIC). It may be concluded that adhesion of an etch-and-rinse adhesive to Er:YAG laser-irradiated enamel was not affected by the methods used to simulate degradation of the adhesive interface and was similar to adhesion in the bur-prepared groups in all periods of water storage and thermocycling.

Adhesion to Er : YAG laser-prepared dentin after long-term water storage and thermocycling

This in vitro study evaluated the microtensile bond strength of a resin composite to Er:YAG-prepared dentin after long-term storage and thermocycling. Eighty bovine incisors were selected and their roots removed. The crowns were ground to expose superficial dentin. The samples were randomly divided according to cavity preparation method (I-Er:YAG laser and II-carbide bur). Subsequently, an etch & rinse adhesive system was applied and the samples were restored with a resin composite. The samples were subdivided according to time of water storage (WS)/number of thermocycles (TC) performed: A) 24 hours WS/no TC; B) 7 days WS/500 TC; C) 1 month WS/2,000 TC; D) 6 months WS/12,000 TC. The teeth were sectioned in sticks with a cross-sectional area of 1.0-mm(2), which were loaded in tension in a universal testing machine. The data were subjected to two-way ANOVA, Scheffe and Fisher`s tests at a 5% level. In general, the bur-prepared group displayed higher microtensile bond strength values than the laser-treated group. Based on one-month water storage and 2,000 thermocycles, the performance of the tested adhesive system to Er:YAG-laser irradiated dentin was negatively affected (Group IC), while adhesion of the bur-prepared group decreased only within six months of water storage combined with 12,000 thermocycles (Group IID). It may be concluded that adhesion to the Er:YAG laser cavity preparation was more affected by the methods used for simulating degradation of the adhesive interface.