Bias in the prediction of genetic gain due to mass and half-sib selection in random mating populations

The prediction of gains from selection allows the comparison of breeding methods and selection strategies, although these estimates may be biased. The objective of this study was to investigate the extent of such bias in predicting genetic gain. For this, we simulated 10 cycles of a hypothetical breeding program that involved seven traits, three population classes, three experimental conditions and two breeding methods (mass and half-sib selection). Each combination of trait, population, heritability, method and cycle was repeated 10 times. The predicted gains were biased, even when the genetic parameters were estimated without error. Gain from selection in both genders is twice the gain from selection in a single gender only in the absence of dominance. The use of genotypic variance or broad sense heritability in the predictions represented an additional source of bias. Predictions based on additive variance and narrow sense heritability were equivalent, as were predictions based on genotypic variance and broad sense heritability. The predictions based on mass and family selection were suitable for comparing selection strategies, whereas those based on selection within progenies showed the largest bias and lower association with the realized gain.     

Effect of COX-2 inhibitor after TNBS-induced colitis in wistar rats

Inflammatory bowel disease (IBD) is a common chronic gastrointestinal disorder characterized by alternating periods of remission and active intestinal inflammation. Some studies suggest that antiinflammatory drugs are a promising alternative for treatment of the disease. Thus, this study aimed to evaluate the effect of lumiracoxib, a selective-cyclooxygenase-2 (COX-2) inhibitor, on 2,4,6-trinitrobenzene sulfonic acid (TNBS)-induced experimental colitis. Wistar rats (n = 25) were randomized into four groups, as follows: Group (1) Sham group: sham induced-colitis rats; Group (2) TNBS group: nontreated induced-colitis rats; Group (3) Lumiracoxib control group; and Group (4) Lumiracoxib-treated induced-colitis rats. Our results showed that rats from groups 2 and 4 presented similar histopathological damage and macroscopic injury in the distal colon as depicted by significant statistically differences (P < 0.01; P < 0.05) compared to the other two groups. Weak expression of COX-2 mRNA was detected in normal colon cells, while higher levels of COX-2 mRNA were detected in group 2 and group 4. Therapy with lumiracoxib reduced COX-2 expression by 20–30%, but it was still higher and statistically significant compared to data obtained from the lumiracoxib control group. Treatment with the selective COX-2 inhibitor lumiracoxib did not reduce inflammation-associated colonic injury in TNBS-induced experimental colitis. Thus, the use of COX-2 inhibitors for treating IBD should be considered with caution and warrants further experimental investigation to elucidate their applicability.     

No mutations found in exon 2 of gene p16CDKN2A during rat tongue carcinogenesis induced by 4-nitroquinoline-1-oxide

The medium-term tongue carcinogenesis assay is a useful model for studying oral squamous cell carcinomas phase by phase. The present study aimed to investigate mutations in exon 2 of gene p16CDKN2A during rat tongue carcinogenesis induced by 4-nitroquinoline 1-oxide (4NQO) using direct DNA-sequencing method. A total of 30 male Wistar rats were treated with 4-nitroquinoline 1-oxide (4NQO) in drinking water for 4, 12, and 20 weeks at 50 ppm dose. Ten animals were used as negative control. No histopathological changes in tongue epithelia were observed among controls or in the group treated for 4 weeks with 4NQO. Following 12-week treatment, hyperplasia and epithelial dysplasia were found in mild and moderate forms. At 20 weeks, the tongue presented moderate and/or severe oral dysplasia and squamous cell carcinoma, with squamous cell carcinoma in the majority of animals. No mutations were found in any experimental period evaluated that corresponded to normal oral mucosa, hyperplasia, dysplasia and squamous cell carcinomas. Taken together, our results suggest that p16CDKN2A mutations in exon 2 are not involved in the multistep tongue carcinogenesis of Wistar rats induced by 4NQO.     

Evaluation of holocellulase production by plant-degrading fungi grown on agro-industrial residues

Agaricus brasiliensis CS1, Pleurotus ostreatus H1 and Aspergillus flavus produced holocellulases when grown in solid and submerged liquid cultures containing agro-industrial residues, including sugar cane bagasse and dirty cotton residue, as substrates. These isolates proved to be efficient producers of holocellulases under the conditions used in this screening. Bromatological analysis of agro-industrial residues showed differences in protein, fiber, hemicellulose, cellulose and lignin content. Maximal holocellulase activity (hemicellulase, cellulase and pectinase) was obtained using solid-state cultivation with 10% substrate concentration. In this case, remarkably high levels of xylanase and polygalacturonase activity (4,008 and 4,548 IU/l, respectively) were produced by A. flavus when grown in media containing corn residue, followed by P. ostreatus H1 with IU/l values of 1,900 and 3,965 when cultivated on 5% and 10% sugar cane bagasse, respectively. A. brasiliensis CS1 showed the highest reducing sugar yield (11.640 mg/ml) when grown on medium containing sugar cane bagasse. A. brasiliensis was also the most efficient producer of protein, except when cultivated on dirty cotton residue, which induced maximal production in A. flavus. Comparison of enzymatic hydrolysis of sugar cane bagasse and dirty cotton residue by crude extracts of A. brasiliensis CS1, P. ostreatus H1 and A. flavus showed that the best reducing sugar yield was achieved using sugar cane bagasse as a substrate.     

Biological and structural characterization of the Mycobacterium smegmatis nitroreductase NfnB,and its role in benzothiazinone resistance

Tuberculosis is still a leading cause of death in developing countries, for which there is an urgent need for new pharmacological agents. The synthesis of the novel antimycobacterial drug class of benzothiazinones (BTZs) and the identification of their cellular target as DprE1 (Rv3790), a component of the decaprenylphosphoryl‐β‐d ‐ribose 2′‐epimerase complex, have been reported recently. Here, we describe the identification and characterization of a novel resistance mechanism to BTZ in Mycobacterium smegmatis. The overexpression of the nitroreductase NfnB leads to the inactivation of the drug by reduction of a critical nitro‐group to an amino‐group. The direct involvement of NfnB in the inactivation of the lead compound BTZ043 was demonstrated by enzymology, microbiological assays and gene knockout experiments. We also report the crystal structure of NfnB in complex with the essential cofactor flavin mononucleotide, and show that a common amino acid stretch between NfnB and DprE1 is likely to be essential for the interaction with BTZ. We performed docking analysis of NfnB‐BTZ in order to understand their interaction and the mechanism of nitroreduction. Although Mycobacterium tuberculosis seems to lack nitroreductases able to inactivate these drugs, our findings are valuable for the design of new BTZ molecules, which may be more effective in vivo.     

CGDEase, a Pseudomonas fluorescens protein of the PLC/APase superfamily with CDP-ethanolamine and (dihexanoyl)glycerophosphoethanolamine hydrolase activity induced by osmoprotectants under phosphate-deficient conditions

A novel enzyme, induced by choline, ethanolamine, glycine betaine or dimethylglycine, was released at low temperature and phosphate from Pseudomonas fluorescens (CECT 7229) suspensions at low cell densities. It is a CDP-ethanolamine pyrophosphatase/(dihexanoyl)glycerophosphoethanolamine phosphodiesterase (CGDEase) less active on choline derivatives, and inactive on long-chain phospholipids, CDP-glycerol and other NDP-X compounds. The reaction pattern was typical of phospholipase C (PLC), as either phosphoethanolamine or phosphocholine was produced. Peptide-mass analyses, gene cloning and expression provided a molecular identity for CGDEase. Bioinformatic studies assigned it to the PLC branch of the phospholipase C/acid phosphatase (PLC/APase) superfamily, revealed an irregular phylogenetic distribution of close CGDEase relatives, and suggested their genes are not in operons or conserved contexts. A theoretical CGDEase structure was supported by mutagenesis of two predicted active-site residues, which yielded essentially inactive mutants. Biological relevance is supported by comparisons with CGDEase relatives, induction by osmoprotectants (not by osmotic stress itself) and repression by micromolar phosphate. The low bacterial density requirement was related to phosphate liberation from lysed bacteria in denser populations, rather than to a classical quorum-sensing effect. The results fit better a CGDEase role in phosphate scavenging than in osmoprotection.     

Redox-sensitive prosurvival and proapoptotic protein expression in the myocardial remodeling post-infarction in rats

In this study, we investigated the oxidative stress influence in some prosurvival and proapoptotic proteins after myocardial infarction (MI). Male Wistar rats were divided in two groups: Sham-operated (control) and MI. MI was induced by left coronary artery occlusion. 28-days after surgery, echocardiographic, morphometric, and hemodynamic parameters were evaluated. Redox status (reduced to oxidized glutathione ratio, GSH/GSSG) and hydrogen peroxide levels (H₂O₂) were measured in heart tissue. The p-ERK/ERK, p-Akt/Akt, p-mTOR/mTOR and p-GSK-3β/GSK-3β ratios, as well as apoptosis-inducing factor (AIF) myocardial protein expression were quantified by Western blot. MI group showed an increase in cardiac hypertrophy (23%) associated with a decrease in ejection fraction (38%) and increase in left ventricular end-diastolic pressure (82%) when compared to control, characterizing ventricular dysfunction. Redox status imbalance was seen in MI animals, as evidenced by the decrease in the GSH/GSSG ratio (30%) and increased levels of H₂O₂ (45%). This group also showed an increase in the ERK phosphorylation and a reduction of Akt and mTOR phosphorylation when compared to control. Moreover, we showed a reduction in the GSK-3β phosphorylation and an increase in AIF protein expression in MI group. Taken together, our results show increased H₂O₂ levels and cellular redox imbalance associated to a higher p-ERK and AIF immunocontent, which would contribute to a maladaptive hypertrophy phenotype.     

Estimation of the Initial Viral Growth Rate and Basic Reproductive Number during Acute HIV-1 Infection

During primary infection, the number of HIV-1 particles in plasma increases rapidly, reaches a peak, and then declines until it reaches a set point level. Understanding the kinetics of primary infection, and its effect on the establishment of chronic infection, is important in defining the early pathogenesis of HIV. We studied the viral dynamics of very early HIV-1 infection in 47 subjects identified through plasma donation screening. We calculated how fast the viral load increases and how variable this parameter is among individuals. We also estimated the basic reproductive ratio, the number of new infected cells generated by an infectious cell at the start of infection when target cells are not limiting. The initial viral doubling time had a median of 0.65 days with an interquartile range of 0.56 to 0.91 days. The median basic reproductive ratio was 8.0 with an interquartile range of 4.9 to 11. In 15 patients, we also observed the postpeak decay of plasma virus and found that the virus decay occurred at a median rate of 0.60 day⁻¹, corresponding to a half-life of 1.2 days. The median peak viral load was 5.8 log₁₀ HIV-1 RNA copies/ml, and it was reached 14 days after the virus was quantifiable with an assay, with a lower limit of detection of 50 copies/ml. These results characterize the early plasma viral dynamics in acute HIV infection better than it has been possible thus far. They also better define the challenge that the immune response (or therapeutic intervention) has to overcome to defeat HIV at this early stage.During primary infection, the number of human immunodeficiency virus type 1 (HIV-1) particles in plasma increases rapidly, reaches a peak, and then declines until it reaches a set point level (i.e., a quasi-steady state) (3, 26). Often, the peak in viral load coincides with the first appearance of an acquired immune response. Thus, early HIV infection can be seen as a race between the immune system and the virus (4). It has been suggested, based on the macaque model with simian immunodeficiency virus (SIV) infection, that early viral expansion is somewhat homogeneous across subjects, but the viral load set point varies by orders of magnitude (14). However, studies with SIV also suggest that the early events during viral expansion, i.e., before the peak, are important in defining the viral load set point later in infection (14).Thus, improved knowledge of the very early expansion of HIV-1 will be beneficial for our understanding of primary infection and its effect on the establishment of chronic infection. Moreover, if the immune system primed by a vaccine could respond quickly enough to HIV, perhaps it would be possible to prevent infection. However, all but the recombinant canarypox-gp120 vaccine, used in the RV144 trial in Thailand (23), have failed to provide protection, and the immune response generated by T-cell-based vaccines has been described as “too little, too late” (1, 5, 24). Here, we characterize the early events in infection and the prepeak expansion of HIV-1 to better understand the biology of infection.We examine longitudinal viral load data from 47 frequent plasma donors who became HIV positive during the course of their plasma donations. Thus, this data set includes samples in which virus was absent or below the limit of detection of the assay used, as well as viral loads at very early times postexposure with HIV. From this data, we quantify the rate of viral expansion during primary HIV infection. Previously, Fiebig et al. (8, 9) analyzed some aspects of early viral load expansion, the existence of viral blips, and the timing of HIV-1 marker expression, defining the stages for early infection (9). Here, we extend these analyses to characterize in detail the expansion of the virus and its basic reproductive ratio, R₀. In the context of host viral dynamics, R₀ is a measure of whether a virus can establish infection (12). It specifically measures how many cells a single infected cell will infect when there is no target cell limitation. If R₀ is less than 1, on average an infected cell will infect less than 1 susceptible cell, and the infection will die out. If R₀ is greater than 1, on average an infected cell will infect more than 1 susceptible cell, and generally the infection will spread (25).R₀ for HIV infection in humans has been estimated previously in smaller data sets. Little et al. (15) used both viral load and CD4⁺ T-cell count data to find R₀ for four individuals whose infection was identified within a couple of weeks of exposure. Stafford et al. (27) estimated R₀ from viral load data obtained from 10 primary infection patients, again identified within a few weeks of infection. Our work differs from these previous studies in that we analyzed a much larger number of patients and the viral load data that we analyzed encompassed the earliest stages of infection, in most cases before the viral load was even detectable. By contrast, both Little et al. (15) and Stafford et al. (27) analyzed data obtained primarily near or after the peak in viral load.     

Genetic damage in multiple organs of acutely exercised rats

The aim of this study was to investigate the effects of acute exercise on genomic damage in an animal model. Male adult Wistar rats were divided into the following groups: control and acute exercised (experimental). For this purpose, 15 animals were accustomed to running on a rodent treadmill for 15 min per day for 5 days (10–20 m min^?1; 08 grade). After 4 days at rest, active animals ran on the treadmill (22 m min^?1, 58 grade) till exhaustion. Cells from peripheral blood, liver, heart, and brain were collected after 0, 2, and 6 h after exercise. The results showed that acute exercise was able to induce genetic damage in peripheral blood cells after 2 and 6 h of exercise, whereas liver pointed out genetic damage for all periods evaluated. No genetic damage was induced either in brain or in heart cells. In conclusion, our results suggest that acute exercise could contribute to the genetic damage in peripheral blood and liver cells. It seems that liver is a sensitive organ to the genotoxic insult after acute exercise. Copyright © 2010 John Wiley & Sons, Ltd.