Identification of suitable internal control genes for expression studies in Coffea arabica under different experimental conditions

Background: Quantitative data from gene expression experiments are often normalized by transcription levels of reference or housekeeping genes. An inherent assumption for their use is that the expression of these genes is highly uniform in living organisms during various phases of development, in different cell types and under diverse environmental conditions. To date, the validation of reference genes in plants has received very little attention and suitable reference genes have not been defined for a great number of crop species including Coffea arabica. The aim of the research reported herein was to compare the relative expression of a set of potential reference genes across different types of tissue/organ samples of coffee. We also validated the expression profiles of the selected reference genes at various stages of development and under a specific biotic stress.Results: The expression levels of five frequently used housekeeping genes (reference genes), namely alcohol dehydrogenase (adh), 14-3-3, polyubiquitin (poly), beta-actin (actin) and glyceraldehyde-3-phosphate dehydrogenase (gapdh) was assessed by quantitative real-time RT-PCR over a set of five tissue/organ samples (root, stem, leaf, flower, and fruits) of Coffea arabica plants. In addition to these commonly used internal controls, three other genes encoding a cysteine proteinase (cys), a caffeine synthase (ccs) and the 60S ribosomal protein L7 (rpl7) were also tested. Their stability and suitability as reference genes were validated by geNorm, NormFinder and BestKeeper programs. The obtained results revealed significantly variable expression levels of all reference genes analyzed, with the exception of gapdh, which showed no significant changes in expression among the investigated experimental conditions.Conclusion: Our data suggests that the expression of housekeeping genes is not completely stable in coffee. Based on our results, gapdh, followed by 14-3-3 and rpl7 were found to be homogeneously expressed and are therefore adequate for normalization purposes, showing equivalent transcript levels in different tissue/ organ samples. Gapdh is therefore the recommended reference gene for measuring gene expression in Coffea arabica. Its use will enable more accurate and reliable normalization of tissue/organ-specific gene expression studies in this important cherry crop plant.

Laboratory Assessment of two Active Ingredients for Control of Coptotermes gestroi (Isoptera: Rhinotermitidae)

The subterranean termite Coptotermes gestroi Wasmann (Isoptera: Rhinotermitidae) is a pest of major economic importance in urban environments of southeastern Brazil. Compared to using pesticides for termite control, termite bait products target termites more specifically and also address environmental contamination issues. In this point of view, we performed two different bioassays ill order to evaluate the efficacy of boric acid and fipronil against different populations of C. gestroi. The results showed that concentration between 2000 and 3000 ppm of boric acid caused approximately 100 percent mortality ill termites. Concentrations between 0.01 and 0.0001 ppm of fipronil resulted in 100% termite mortality after 2 wk exposure. The data displayed a fast mortality of termites contaminated with fipronil, even with small concentrations, and therefore it is riot a Suitable product to be used ill baits against C gestroi. The present Study showed a delayed toxicity of boric acid against the subterranean termite C gestroi which suggests a need for further field tests.

Analytical Methods Employed at Quality Control of Fuel Ethanol

The existence of organic and inorganic contaminants present in both fossil and biomass fuels and the fact that they can provide undesirable effects (environmental problems, corrosion processes, lead to storage instability, and others) implies a rigorous quality control of these fuels, although these contaminants make up a small part of the final fuel composition. Considering the rising importance of fuel ethanol in the worldwide panorama, this review aims at reporting the use of successful alternative analytical methods in the monitoring of organic and inorganic contaminants at trace levels, used to determine and to quantify these substances in fuel ethanol and also presenting all official norms for quality control of fuel ethanol employed by ABNT (Brazilian Association of Technical Norms), ASTM (American Society for Testing and Materials), and ECS (European Committee for Standardization).

Environmental color affects Nile tilapia reproduction

We investigated the effects of environmental color on the reproductive behavior of Nile tilapia, Oreochromis niloticus. Two environmental colors were tested by covering the aquarium (60 x 60 x 40 cm) with white (12 groups) or blue (13 groups) cellophane and observing reproductive behavior in groups of 2 males (10.27 ± 0.45 cm) and 3 females (10.78 ± 0.45 cm) each. After assignment to the respective environmental color (similar luminosity = 100 to 120 Lux), the animals were observed until reproduction (identified by eggs in the female's mouth) or up to 10 days after the first nest building. Photoperiod was from 6:00 h to 18:00 h every day. Food was offered in excess once a day and water quality was similar among aquaria. Daily observations were made at 8:00, 11:00, 14:00 and 17:00 h regarding: a) latency to the first nest, b) number of nests, c) gravel weight removed (the male excavates the nest in the bottom of the aquarium), d) nest area, and e) mouthbrooding incubation (indication of reproduction). The proportion of reproducing fish was significantly higher (6 of 13) in the group exposed to the blue color compared the group exposed to the white color (1 of 12; Goodman's test of proportions). Moreover, males under blue light removed significantly larger masses of gravel (blue = 310.70 ± 343.50 g > white = 130.38 ± 102.70 g; P = 0.01) and constructed wider nests (blue = 207.93 ± 207.80 cm² > white = 97.68 ± 70.64 cm²; P = 0.03) than the control (white). The other parameters did not differ significantly between light conditions. We concluded that reproduction in the presence of blue light was more frequent and intense than in the presence of white light.

Assessment of aquatic plants in the reservoirs of AES-Tiete and development of an integrated control model for the most important species

The general objective of this work was to develop a monitoring and management model for aquatic plants that could be used in reservoir cascades in Brazil, using the reservoirs of AES-Tiete as a study case. The investigations were carried out at the reservoirs of Barra-Bonita, Bariri, Ibitinga, Promissao, and Nova-Avanhandava, located in the Tiete River Basin; Agua Vermelha, located in the Grande River Basin; Caconde, Limoeiro, and Euclides da Cunha, which are part of the Pardo River Basin; and the Mogi-Guacu reservoir, which belongs to the Mogi-Guacu River basin. The main products of this work were: development of techniques using satellite-generated images for monitoring and planning aquatic plant control; planning and construction of a boat to move floating plant masses and an airboat equipped with a DGPS navigation and application flow control system. Results allowed to conclude that the occurrence of all types of aquatic plants is directly associated with sedimentation process and, consequently, with nutrient and light availability. Reservoirs placed at the beginning of cascades are more subject to sedimentation and occurrence of marginal, floating and emerged plants, and are the priority when it comes to controlling these plants, since they provide a supply of weeds for the other reservoirs. Reservoirs placed downstream show smaller amounts of water-suspended solids, with greater transmission of light and occurrence of submerged plants.

Effect of doses of fungicides and plant resistance activators on the control of Rhizoctonia foliar blight of soybean, and on Rhizoctonia solani AG1-IA in vitro development

Rhizoctonia foliar blight (RFB) of soybean [Glycine max (L.) Merrill] occurs in many tropical and subtropical regions, causing yield reductions of up to 70% and in Brazil, up to 60%. The disease is caused by Rhizoetonia solani AG1-IA and AG1-IB, and by AG2-3 in Japan. RFB occurs in the North, Northeast and Mid-west regions of Brazil. Chemical control remains the only effective method of controlling RFB, but its efficiency depends upon environmental conditions. In this study, 18 fungicides, salicylic acid (SA) and acibenzolar-s-methyl (ASM) were evaluated on R. solani AG1-IA in vitro, by mycelial growth rating and estimating effective concentration for 50% (EC 50) and 90% (EC 90) inhibition of mycelial growth, and in vivo by reduction of disease severity on soybean plants in greenhouse conditions. Mycelial growth was strongly inhibited by the fungicides pyraclostrobin + boscalid and fludioxonil. Preventive fungicide applications were the most effective. Strobilurins were more efficient both in preventive and curative applications. Best results with plant resistance activators were obtained with SA (2.5 mM) sprayed at 20 d before inoculation and with ASM (12.5 mg a.i. l(-1)) 10 d before inoculation. (c) 2005 Elsevier Ltd. All rights reserved.

Immunoassays for pesticide analysis in environmental and food matrices

Immunochemical methods have increased considerably in the past years, and many examples of small and large scale studies have demonstrated the reliability of the immunotechniques for control and monitoring gf contaminant residues in different kinds of samples. Application of the immunoassay (IA) methods in pesticide residue control is an area with enormous potential for growth. The most extensively studied IA is the enzyme-linked absorbent assay (ELISA), but several other approaches, that include radioimmunoassay and immunoaffinity chromatography, have been also developed recently. In comparison with classical analytical methods, IA methods offer the possibility of highly sensitive, relatively vapid, and cost-effective measurements. This paper introduces the general IAs used until now, focusing on their use in pesticide analysis, and discussing briefly the effects of interferences from solvent residues or matrix components on the IA performance. Numerous immunochemical methods commonly used for pesticide determination in different samples such as food, crop and environmental samples are presented.

Acclimation of broiler chickens to chronic high environmental temperature

The present study was conducted to evaluate the zootechnical parameters and age related changes in physiological responses of broiler chickens exposed to hot environment from early age onwards. The broiler chickens were exposed to high temperature (30 degreesC) at 15 d of age and maintained to Day 38 or maintained under thermoneutral environment (control).No significant decrease in feed consumption (FC) and body weight (BW) gain was observed in high temperature group after 7 d of exposure, but in the subsequent period, heat exposure lowered BW and FC, compared to control group. However, the weight gain was not significantly changed after 24 d of exposure, and the feed efficiency was not affected throughout the experimental period.The venous pCO(2) pressure was only significantly decreased by temperature after 24 d of heat exposure. The glucose, non-esterified fatty acid (NEFA), triglyceride (TG), glucose, lipid peroxidation (LPO), creatine kinase (CK), and corticosterone were not influenced by the temperature treatment. The significant decrease in uric acid and increase in lactate concentration due to high temperature were observed respectively at 28 and 35 d of age. The concentrations of triiodothyronine (T-3) and thyroxine (T-4) were changed oppositely at 28 d of age, as T-3 was decreased and T-4 was elevated by high temperature. However, the concentration of T-4 in plasma was decreased whereas T-3 was not changed at 38 d of age. The relationships between the blood parameters were changed due to the temperature treatment, suggesting that not only absolute values but also their interrelationships have to be considered when studying the effects of a particular treatment on physiological functioning.These results suggest the growth and physiological responses of broiler chickens, exposed to high temperature from early age onwards, differed at different stages of acclimation. The process of heat acclimation is related to the mode of heat exposure imposed and is not only reflected in the changes in the absolute concentrations, but also in the correlations among the blood indices.

Diagnosis and environmental planning for Paranagud - PR - Brazil

The main goal of this study was to identify and analyse environmental problems related to human occupation at the south part of the city of Paranagua PR, Brazil, aiming the diagnosis and conceptual evaluation of landscape use. For landscape use assessments and degradation diagnosis purposes, the environment was classified considering mainly geological and geomorphologic characteristics, such as declivity and sediment origin. The identification of potential environmental impacts was made by aerial photographs, Landsat-TM images, photographic records, surface sediment samples, water-column samples, and mainly observation visits to each classified unit. Surface sediment samples were taken with a Petit-Ponar sampler, in 13 station located in Paranagua Bay. In order to characterize the contamination level on sediments, the concentration of the following elements were analysed: arsenic (As), copper (Cu), cadmium (Cd), nickel (Ni), lead (Ph) e zinc (Zn). For the extraction of these elements, samples were treated with HCl 0.1N for 12 hours. This method has the advantage of determining contaminants which are weakly bind to the sediment, thus more available to the system. Analysis were performed by atomic absorption spectroscopy. According to the adopted criteria, sectors were classified as hills, mangroves, continental sediments and beach ridges urban and port industrial. Water quality and concentrations of metallic elements were determined at three sectors one control and two with the influence of urban and port/industrial activities, respectively the major upland impacts found were: deforestation due to disordered occupation, and solid waste emission through domestic and industrial sewage. The diagnosis of the actual situation was used as a basis for a management plan, once it allows the identification of impacts, and consequent environmental irregularities. Based on this considerations, suggestions for land use and management were presented, which offers a better approach for recuperation and protection of the studied ecosystem.

Environmental implications of soil remediation using the Fenton process

This work evaluates some collateral effects caused by the application of the Fenton process to 1,1-bis(4-chlorophenyl)-2,2,2-trichloroethane (DDT) and diesel degradation in soil. While about 80% of the diesel and 75% of the DDT present in the soil were degraded in a slurry system, the dissolved organic carbon (DOC) in the slurry filtrate increased from 80 to 880 mg l(-1) after 64 h of reaction and the DDT concentration increased from 12 to 50 mu g l(-1). Experiments of diesel degradation conducted on silica evidenced that soluble compounds were also formed during diesel oxidation. Furthermore, significant increase in metal concentrations was also observed in the slurry filtrate after the Fenton treatment when compared to the control experiment leading to excessive concentrations of Cr, Ni, Cu and Mn according to the limits imposed for water. Moreover, 80% of the organic matter naturally present in the soil was degraded and a drastic volatilization of DDT and 2,2-bis(4-chlorophenyl)-1,1-dichloroethylene was observed. Despite the high percentages of diesel and DDT degradation in soil, the potential overall benefits of its application must be evaluated beforehand taking into account the metal and target compounds dissolution and the volatilization of contaminants when the process is applied. (c) 2007 Elsevier Ltd. All rights reserved.

The application of biochemical responses to assess environmental quality of tropical estuaries: field surveys

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Study of environmental burden of lead in children using teeth as bioindicator

The south region of São Paulo city hosts the Guarapiranga dam, responsible for water supply to 25% of the city population. Their surroundings have been subject to intense and irregular occupation by people from very low socioeconomics classes. Measurements undertaken on sediment and particulate materials in the dam revealed concentrations of lead. copper, zinc and cadmium above internationally accepted limits. Epidemiological and toxicological studies undertaken by the World Health Organization in individuals exhibiting lead concentrations in blood, near or below the maximum recommended (10 mu g dl(-1)), surprisingly revealed that toxic effects are more intense in individuals belonging to low socioeconomics classes. Motivated by these facts, we aimed at the investigation of chronic incorporation of lead. as well as the use of our BIOKINETICS code, which is based on an accepted ICRP biokinetics model for lead, in order to extrapolate the results from teeth to other organs. The focus of our data taking was children from poor families, living in a small, restrict and allegedly contaminated area in São Paulo city. Thus, a total of 74 human teeth were collected. The average concentration of lead in teeth of children 5 to 10 years old was determined by means of a high-resolution inductively coupled plasma mass spectrometer (ICP-MS). For standardization of the measurements, an animal bone certified material (H-Animal Bone), from the International Atomic Energy Agency, was analyzed. The amount of lead in children living in the surroundings of the dam, was approximately 40% higher than those from the control region, and the average lead concentration was equal to 1.3 mu g g(-1) approximately. Grouping the results in terms of gender, tooth type and condition, it was concluded that a carious molar of boys is a much more efficient contamination pathway for lead, resulting in concentrations 70% higher than in the control region. We also inferred the average concentrations of lead in other organs of these children, by making use of our BIOKINETIC code. (C) 2008 Elsevier Ltd. All rights reserved.

Polymorphisms of DNA repair genes XRCC1 and XRCC3, interaction with environmental exposure and risk of chronic gastritis and grastic cancer

Aim: To evaluate the association between polymorphisms XRCC1 Arg194Trp and Arg399Gln and XRCC3 Thr241Met and the risk for chronic gastritis and gastric cancer, in a Southeastern Brazilian population. Methods: Genotyping by PCR-RFLP was carried out on 202 patients with chronic gastritis (CG) and 160 patients with gastric cancer (GC), matched to 202 (C1) and 150 (C2) controls, respectively. Results: No differences were observed among the studied groups with regard to the genotype distribution of XRCC1 codons 194 and 399 and of XRCC3 codon 241. However, the combined analyses of the three variant alleles (194Trp, 399Gln and 241Met) showed an increased risk for chronic gastritis when compared to the GC group. Moreover, an interaction between the polymorphic alleles and demographic and environmental factors was observed in the CG and GC groups. XRCC1 194Trp was associated with smoking in the CG group, while the variant alleles XRCC1 399Gln and XRCC3 241Met were related with gender, smoking, drinking and H pylori infection in the CG and GC groups. Conclusion: Our results showed no evidence of a rela-tionship between the polymorphisms XRCC1 Arg194Trp and Arg399Gln and XRCC3 Thr241Met and the risk of chronic gastritis and gastric cancer in the Brazilian population, but the combined effect of these variants may interact to increase the risk for chronic gastritis, considered a premalignant lesion. Our data also indicate a gene-environment interaction in the susceptibility to chronic gastritis and gastric cancer. © 2005 The WJG Press and Elsevier Inc. All rights reserved.