The generation and utilization of a cancer-oriented representation of the human transcriptome by using expressed sequence tags

Whereas genome sequencing defines the genetic potential of an organism, transcript sequencing defines the utilization of this potential and links the genome with most areas of biology. To exploit the information within the human genome in the fight against cancer, we have deposited some two million expressed sequence tags (ESTs) from human tumors and their corresponding normal tissues in the public databases. The data currently define approximate to23,500 genes, of which only approximate to1,250 are still represented only by ESTs. Examination of the EST coverage of known cancer-related (CR) genes reveals that <1% do not have corresponding ESTs, indicating that the representation of genes associated with commonly studied tumors is high. The careful recording of the origin of all ESTs we have produced has enabled detailed definition of where the genes they represent are expressed in the human body. More than 100,000 ESTs are available for seven tissues, indicating a surprising variability of gene usage that has led to the discovery of a significant number of genes with restricted expression, and that may thus be therapeutically useful. The ESTs also reveal novel nonsynonymous germline variants (although the one-pass nature of the data necessitates careful validation) and many alternatively spliced transcripts. Although widely exploited by the scientific community, vindicating our totally open source policy, the EST data generated still provide extensive information that remains to be systematically explored, and that may further facilitate progress toward both the understanding and treatment of human cancers.

Influence of domestic sewage leakage on the collapse of tropical soils

In the studied region, 35% of the soil collapses are related to leakage from sewage ducts. The paper describes the soils from this part of Brazil and a series of laboratory tests undertaken using water and domestic sewage fluid as the wetting agents. It is considered that the presence of soaps and detergents as recorded by the sodium concentration facilitates the densification of the soils and hence has a major effect on the surface settlement/collapse.

Population biology and habitat utilization of the stone crab Menippe nodifrons in the Ubatuba region, São Paulo, Brazil

The aim of the current study was to evaluate a population of Menippe nodiffons in a reef of sabellariid worms, Phragmatopoma lapidosa, with regard to recruitment, population structure and sex ratio. Sampling was carried out each other month from September 1994 up to and including July 1995, on the rocky shores of the Tenorio beach, São Paulo, Brazil. It resulted in 183 individuals, whose average carapace width in this biotope was 9.1 +/- 5.6 m. The animals were grouped in nine size classes and the frequency distribution showed that 80% occupied the three first classes. This means that the polychaete worm colonies are of great importance for the establishment of individuals in the first juvenile stages.

Utilization of epiphytes by birds in a Brazilian Atlantic Forest

Epiphytes constitute a great part of the vegetation biomass in Neotropical forests, offering a large variety of resources to birds. Despite their structural and ecological importance, few studies investigated the use of epiphytes by birds in the Neotropical region. We studied the bird species that exploit vascular epiphytes (and hemi-epiphytes) in an Atlantic forest site in southeastern Brazil. The resources exploited, seasonal variation in the use of epiphytes, the frequency of foraging and selectivity in epiphytes, and the relationship between the use of epiphytes and the participation in mixed-species bird flocks were investigated. After 360 h of observations along trails crossing the forest, 24 bird species (12 families) were recorded in a total of 74 events of epiphyte exploitation. Thamnophilidae (four species), Trochiliclae, Thraupidae and Furnariidae (three species) were the richest bird families in our sample, while Furnariidae and Dendrocolaptidae were the more frequently recorded families. Plants in the Bromeliaceae and Araceae families were the most abundant and more frequently exploited epiphytes. Nectar, water, nest material and invertebrates were the most frequently exploited resources, mainly from Bromeliaceae. None of the species for which we had enough data revealed to be a frequent user of epiphytes for foraging or selective to any epiphyte group. The White-eyed Foliage-gleaner (Automolus leucophthalmus; Furnariidae), a common participant of understory mixed-species flocks, exploited epiphytes more frequently when associated with mixed-species flocks. The utilization of epiphytes was opportunistic for most of the bird species recorded and occurred throughout the year with no seasonal variation.

Tannery sludge compost amendment rates on soil microbial biomass of two different soils

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Effect of different tannery sludge compost amendment rates on growth, biomass accumulation and yield responses of Capsicum plants

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Fecal Sterols in Estuarine Sediments as Markers of Sewage Contamination in the Cubatao Area, São Paulo, Brazil

Sterol biomarkers serve as an alternative method for detecting sewage pollution. Sterols were extracted from samples of surface sediment collected in Cubato (the Vila dos Pescadores and Vila Esperan double dagger a communities) and quantified using GC-MS after Soxhlet extraction, cleanup, and derivatization. Fecal contamination was evaluated based on the concentration of coprostanol and the ratio of the selected sterols. The most abundant sterol was cholestanol, followed by coprostanol. The concentrations of coprostanol in surface sediments ranged from a minimum of 4.21 mu g g(-1) dry sediment (Vila dos Pescadores station) to a maximum of 8.32 mu g g(-1) dry sediment (Vila Esperan double dagger a station). A coprostanol concentration of about 10 mu g g(-1) was found, indicating areas of high sewage contamination. Coprostanol levels at sewage stations were higher than in other Brazilian coastal areas, which may be attributed to the fraction of the population without sanitation services.

Growth, nodulation and nitrogen fixation of cowpea in soils amended with composted tannery sludge

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Subgingival utilization of a 1% chlorhexidine collagen gel for the treatment of periodontal pockets. A clinical and microbiological study.

This study evaluates the effect of subgingival irrigation with a 1% chlorhexidine collagen gel in periodontal pockets as an adjunct procedure to scaling and root planing (SRP). Thirty-seven sites with probing depth (PD) of 5-7 mm and BANA positive in 6 patients with chronic periodontal disease were selected. Sites were assigned to different treatment groups consisting of SRP only (group 1), SRP + irrigation with collagen gel (group 2), or SRP + irrigation with collagen gel containing 1% chlorhexidine (group 3). Subgingival irrigation was performed after initial SRP and at 7, 14 and 21 days. Clinical measurements including PD, plaque index (PI), gingival index (GI), gingival recession (GI), bleeding on probing (BOP) and clinical attachment level (CAL) were performed at the selected sites at baseline, 60 and 90 days and the BANA test was performed on plaque samples from the same sites at baseline and 90 days. There was an improvement in clinical parameters in all groups with a significantly greater decrease in GI and bleeding in the chlorhexidine group. There was a greater reduction of BANA positive sites in groups 2 and 3. The authors concluded that 1% chlorhexidine collagen gel is a promising adjunct to SRP in the treatment of adult periodontitis.

Genetic diversity in Colletotrichum gloeosporioides from Stylosanthes spp. at Centers of origin and utilization

Using molecular markers, this work compares the genetic diversity in Colletotrichum gloeosporioides infecting species of the tropical forage legume Stylosanthes at the center of origin in Brazil and Colombia with that of Australia, China, and India, where Srylosanthes spp. have been introduced for commercial use. There was extensive diversity in the pathogen population from Brazil, Colombia, China, and India. The Australian pathogen population was least diverse probably due to its geographical isolation and effective quarantine. The extensive diversity in China and India means that threats from exotic pathogen races to Stylosanthes pastures can potentially come from countries outside the South American center of origin. In Brazil and India, both with native Stylosanthes populations, a high level of genetic differentiation in the pathogen population was associated with sites where native or naturalized host population was widely distributed. There was limited genetic diversity at germplasm evaluation sites, with a large proportion of isolates having identical haplotypes. This contrasts recent pathogenicity results for 78 of the Brazilian isolates that show hot spots of complex races are more common around research stations where host germplasm are tested, but few are found at sites containing wild host populations. For a pathogen in which the same races arise convergently from different genetic backgrounds, this study highlights the importance of using both virulence and selectively neutral markers to understand pathogen population structure.

Modeling metabolizable energy utilization in broiler breeder pullets

The objective of this study was to determine models for ME requirements for broiler breeder pullets using the factorial method. The influence of the temperature on maintenance ME requirements was determined by experiments conducted in three environmental rooms with temperature kept constant at 15, 22, and 30°C, using the comparative slaughter technique. The energy requirements for weight gain were determined based on the body energy content and efficiency of energy utilization for weight gain. Two ME requirement models for each age were developed using the coefficients for maintenance and weight gain. The models for 3 to 8 wk were ME = W 0.75 (186.52 - 1.94T) + 2.47WG, and ME = W 0.75 (174 - 1.88T) + 2.83WG; for 9 to 14 wk, ME = W 0.75 (186.52 - 1.94T) + 2.69WG, and ME = W 0.75 (174 - 1.88T) + 2.50WG; and 15 to 20 wk, ME = W 0.75 (186.52 - 1.94T) + 2.76WG, and ME = W 0.75 (174 - 1.88T) + 3.24WG. In these equations, W is BW (kg), T is temperature (°C), and WG is daily weight gain (g). These models were compared to the breeder's recommendations in a feeding trial from 5 to 20 wk of age. Models 1 and 2 provided energy intakes that promoted BW smaller than the breeder's recommendation. However, all breeder pullets had weights above the standard recommendation. Model 2 gave the smallest ME intake and BW close to the standard recommendation and provided the best prediction of ME requirements.

Utilization of fish protein hydrolysate in prepared diets for pacu, Piaractus mesopotamicus, larvae

Growth and survival rates of pacu, Piaractus mesopotamicus, larvae fed prepared diets containing different animal protein sources were evaluated. Four diets with the same level of crude protein (CP) (36%) and calories (4.02 kcal gross energy/g of diet) were fed to the larvae. Diets were formulated to contain one of four protein sources: (1) fish meal (FM), (2) tilapia residue silage (TS), (3) protein hydrolysate from tilapia residue (HT), and (4) eviscerated tilapia residue (HET). Larvae were fed Artemia nauplii for six days, prior to the start of the study, and the prepared diet was supplied from day 7 until the study concluded. Variance analysis showed no significant differences (P > 0.05) for survival rates and larval final lengths among treatments. However, final average weights were significantly different (P < 0.05 for larvae fed FM and HT. Average survival rates were relatively high and ranged from 68.1% to 73.9%. After the live food was replaced by prepared diets, no larval growth was observed for any treatment. Fish protein hydrolysate (HT and HET) and fish silage showed potential to be used as ingredients in the diet of pacu larvae. However, hydrolysate inclusion levels, processing methods to minimize nutrient lixiviation, and the best moment to replace live food with an inert diet (weaning) need further investigation. © 2003 by The Haworth Press, Inc. All rights reserved.

Water-soluble extract of Coleus barbatus modulates weight gain, energy utilization and lipid metabolism in secondary biliary cirrhosis: an experimental study in young rats.

PURPOSE: To test if a water extract of Coleus barbatus (WEB) has any effect on weight gain, food energy utilization and lipid metabolism in young rats with obstructive cholestasis. METHODS: Forty 21 day old (P21) Wistar rats, in groups of 10, were submitted to one of the following treatments: a sham operation with daily water or WEB administration, double ligature and resection of the bile duct with daily water or WEB administration. At P49 they were submitted for euthanasia when the following were determined: ingested feed (IF), energy utilization (EU) and weight gain (WG) from P29 to P49, together with total serum cholesterol (TC) and triacylglycerol (TG) concentrations, liver wet weight (LWW) and fat content (LFC). Two Way ANOVA and the S.N.K. test for paired comparisons were employed to study the effects of cholestasis and those of WEB and their interactions (p < or = 0.05). RESULTS: Cholestasis, independently of WEB, and WEB, independently of cholestasis both reduced IF, EU, and WG but there was no significant interaction between the two factors. Cholestasis, independently of WEB, increased LWW, LFC, the TC and TG The WEB, independently of cholestasis, reduced these values, and there was a significant interaction between the two factors; such that these effects were more accentuated in animals with cholestasis. CONCLUSION: The WEB reduced IF, WG, and EU, both in the presence and absence of cholestasis in the same proportion. It also partially inhibited the increase in LWW, LFC, TC and TG caused by cholestasis.

Modeling energy utilization and growth parameter description for broiler chickens

Two experiments were conducted to develop and evaluate a model to estimate ME requirements and determine Gompertz growth parameters for broilers. The first experiment was conducted to determine maintenance energy requirements and the efficiencies of energy utilization for fat and protein deposition. Maintenance ME (ME m) requirements were estimated to be 157.8, 112.1, and 127.2 kcal of ME/kg 0.75 per day for broilers at 13, 23, and 32°C, respectively. Environmental temperature (T) had a quadratic effect on maintenance requirements (ME m = 307.87 - 15.63T + 0.3105T 2; r 2= 0.93). Energy requirements for fat and protein deposition were estimated to be 13.52 and 12.59 kcal of ME/g, respectively. Based on these coefficients, a model was developed to calculate daily ME requirements: ME = BW 0.75 (307.87 - 15.63T + 0.3105 T 2) + 13.52 G f + 12.59 G p. This model considers live BW, the effects of environmental temperature, and fractional fat (G f) and protein (G p) deposition. The second experiment was carried out to estimate the growth parameters of Ross broilers and to collect data to evaluate the ME requirement model proposed. Live BW, empty feather-free carcass, weight of the feathers, and carcass chemical compositions were analyzed until 16 wk of age. Parameters of Gompertz curves for each component were estimated. Males had higher growth potential and higher capacity to deposit nutrients than females, except for fat deposition. Data of BW and body composition collected in this experiment were fitted into the energy model proposed herein and the equations described by Emmans (1989) and Chwalibog (1991). The daily ME requirements estimated by the model determined in this study were closer to the ME intake observed in this trial compared with other models. ©2005 Poultry Science Association, Inc.