Determination of banana fruit susceptibility to post-harvest diseases: wound anthracnose, quiescent anthracnose and crown rot

Introduction. This protocol aims at ( a) evaluating the resistance to post-harvest diseases within different genotypes of bananas, and ( b) comparing different origins of bananas ( geographic origin, physiological stage, etc.) for their susceptibility to post-harvest diseases. The principle, key advantages, starting plant material, time required and expected results are presented. Materials and methods. Materials required and details of the twelve steps of the protocol ( fruit sampling and inoculum preparation, wound anthracnose resistance study, quiescent anthracnose resistance study and crown-rot resistance study) are described. Results. Typical symptoms of the different diseases are obtained after artificial inoculation.

Method for early quantification of quiescent infections of Colletotrichum musae on bananas

Introduction. This protocol aims at detecting and quantifying quiescent infections of Colletotrichum musae on bananas. The principle, key advantages, starting plant material, time required and expected results are presented. Materials and methods. The materials required and details of the three steps of the protocol (fruit sampling, fruit ripening and anthracnose lesion quantification) are described. Possible troubleshooting is discussed. Results. The protocol results in the quantification of anthracnose lesions on the fruits, which makes it possible to predict postharvest losses due to anthracnose (peel rot), and also to propose a better management of postharvest fungicide applications.

Measurement of fungicide efficacy on post-harvest diseases: wound anthracnose, quiescent anthracnose, crown rot

Introduction. This protocol aims at evaluating (a) the efficacy of new fungicides for the control of post-harvest diseases, (b) the efficacy of various application methods for the chemical control of post-harvest diseases, and (c) the quality of the fungicide solution during the same packing day where this solution is recycled. The principle, key advantages, starting plant material, time required and expected results are presented. Materials and methods. Materials required and details of the eighteen steps of the protocol (fruit sampling and inoculum preparation, wound anthracnose study, quiescent anthracnose study, and crown-rot study) are described. Results. Comparison between untreated control bananas and bananas treated with fungicide allows the calculation of the fungicide treatment efficacy.

ProbFAST: Probabilistic Functional Analysis System Tool

Background: The post-genomic era has brought new challenges regarding the understanding of the organization and function of the human genome. Many of these challenges are centered on the meaning of differential gene regulation under distinct biological conditions and can be performed by analyzing the Multiple Differential Expression (MDE) of genes associated with normal and abnormal biological processes. Currently MDE analyses are limited to usual methods of differential expression initially designed for paired analysis. Results: We proposed a web platform named ProbFAST for MDE analysis which uses Bayesian inference to identify key genes that are intuitively prioritized by means of probabilities. A simulated study revealed that our method gives a better performance when compared to other approaches and when applied to public expression data, we demonstrated its flexibility to obtain relevant genes biologically associated with normal and abnormal biological processes. Conclusions: ProbFAST is a free accessible web-based application that enables MDE analysis on a global scale. It offers an efficient methodological approach for MDE analysis of a set of genes that are turned on and off related to functional information during the evolution of a tumor or tissue differentiation. ProbFAST server can be accessed at http://gdm.fmrp.usp.br/probfast.

Spatio-Temporal Tracking and Phylodynamics of an Urban Dengue 3 Outbreak in Sao Paulo, Brazil

The dengue virus has a single-stranded positive-sense RNA genome of similar to 10.700 nucleotides with a single open reading frame that encodes three structural (C, prM, and E) and seven nonstructural (NS1, NS2A, NS2B, NS3, NS4A, NS4B, and NS5) proteins. It possesses four antigenically distinct serotypes (DENV 1-4). Many phylogenetic studies address particularities of the different serotypes using convenience samples that are not conducive to a spatio-temporal analysis in a single urban setting. We describe the pattern of spread of distinct lineages of DENV-3 circulating in Sao Jose do Rio Preto, Brazil, during 2006. Blood samples from patients presenting dengue-like symptoms were collected for DENV testing. We performed M-N-PCR using primers based on NS5 for virus detection and identification. The fragments were purified from PCR mixtures and sequenced. The positive dengue cases were geo-coded. To type the sequenced samples, 52 reference sequences were aligned. The dataset generated was used for iterative phylogenetic reconstruction with the maximum likelihood criterion. The best demographic model, the rate of growth, rate of evolutionary change, and Time to Most Recent Common Ancestor (TMRCA) were estimated. The basic reproductive rate during the epidemics was estimated. We obtained sequences from 82 patients among 174 blood samples. We were able to geo-code 46 sequences. The alignment generated a 399-nucleotide-long dataset with 134 taxa. The phylogenetic analysis indicated that all samples were of DENV-3 and related to strains circulating on the isle of Martinique in 2000-2001. Sixty DENV-3 from Sao Jose do Rio Preto formed a monophyletic group (lineage 1), closely related to the remaining 22 isolates (lineage 2). We assumed that these lineages appeared before 2006 in different occasions. By transforming the inferred exponential growth rates into the basic reproductive rate, we obtained values for lineage 1 of R(0) = 1.53 and values for lineage 2 of R(0) = 1.13. Under the exponential model, TMRCA of lineage 1 dated 1 year and lineage 2 dated 3.4 years before the last sampling. The possibility of inferring the spatio-temporal dynamics from genetic data has been generally little explored, and it may shed light on DENV circulation. The use of both geographic and temporally structured phylogenetic data provided a detailed view on the spread of at least two dengue viral strains in a populated urban area.

Genotoxic potential generated by biomass burning in the Brazilian Legal Amazon by Tradescantia micronucleus bioassay: a toxicity assessment study

Background: The Brazilian Amazon has suffered impacts from non-sustainable economic development, especially owing to the expansion of agricultural commodities into forest areas. The Tangara da Serra region, located in the southern of the Legal Amazon, is characterized by non-mechanized sugar cane production. In addition, it lies on the dispersion path of the pollution plume generated by biomass burning. The aim of this study was to assess the genotoxic potential of the atmosphere in the Tangara da Serra region, using Tradescantia pallida as in situ bioindicator. Methods: The study was conducted during the dry and rainy seasons, where the plants were exposed to two types of exposure, active and passive. Results: The results showed that in all the sampling seasons, irrespective of exposure type, there was an increase in micronucleus frequency, compared to control and that it was statistically significant in the dry season. A strong and significant relationship was also observed between the increase in micronucleus incidence and the rise in fine particulate matter, and hospital morbidity from respiratory diseases in children. Conclusions: Based on the results, we demonstrated that pollutants generated by biomass burning in the Brazilian Amazon can induce genetic damage in test plants that was more prominent during dry season, and correlated with the level of particulates and elevated respiratory morbidity.

Prevalence of diabetes mellitus and impaired glucose tolerance in a rural community of Angola

Background: To determine the prevalence of diabetes mellitus (DM) and impaired glucose tolerance (IGT) in a rural community (Bengo) of Angola. Methods: A random sample of 421 subjects aged 30 to 69 years (30% men and 70% women) was selected from three villages of Bengo province. This cross-sectional home survey was conducted using a sampling design of stage conglomerates. First, clinical and anthropometric data were obtained and fasting capillary glucose level was determined. Subjects who screened positive (fasting capillary glucose >= 100 mg/dl and < 200 mg/dl) and each sixth consecutive subject who screened negative (fasting capillary glucose < 100 mg/dl) were submitted to the second phase of survey, consisting of the 75 g oral glucose tolerance test. Data was analyzed by the use of SAS statistical software. Results: The prevalence rates of diabetes mellitus and IGT were 2.8% and 8.1%, respectively. The age group with the highest prevalence of diabetes was 60 to 69 years (42%). Impaired glucose tolerance prevalence was 38% in the 40 to 49 year age group and it increased with age, considering that the 50 to 59 and 60 to 69 year age groups as a whole represent 50% of all subjects with impaired glucose tolerance. The prevalence of diabetes mellitus did not differ significantly between men (3.2%) and women (2.7%) (p = 0.47). On the other hand, the prevalence of impaired glucose tolerance among women showed almost twice that found in men (9.1% vs. 5.6%, respectively). Overweight was present in 66.7% of the individuals with diabetes mellitus and 26.5% of individuals with impaired glucose tolerance showed overweight or obesity. Conclusions: Although the prevalence of diabetes mellitus was low, the prevalence of impaired glucose tolerance is considered to be within an intermediary range, suggesting a future increase in the frequency of diabetes in this population.

Esophageal Ulcer in Brazilian Patients with HIV: Prevalence and Comparative Analysis Among Diagnostic Methods

Esophageal ulcer (EU) represents an important comorbidity in AIDS. We evaluated the prevalence of EU, the accuracy of the endoscopic and histologic methods used to investigate viral EU in HIV-positive Brazilian patients and the numerical relevance of tissue sampling. A total of 399 HIV-positive patients underwent upper gastrointestinal (UGI) endoscopy. HIV-positive patients with EU determined by UGI endoscopy followed by biopsies were analyzed by the hematoxylin-eosin (HE) and immunohistochemical (IH) methods. EU was detected in 41 patients (mean age, 39.2 years; 23 males), with a prevalence of 10.27%. The median CD4 count was 49 cells/mm(3) (range, 1-361 cells/mm(3)) and the viral load was 58,869 copies per milliliter (range, 50-77,3290 copies per milliliter). UGI endoscopy detected 29 of 41 EU suggestive of cytomegalovirus (CMV) infection and 7 of 41 indicating herpes simplex virus (HSV) infection. HE histology confirmed 4 of 29 ulcers induced by CMV, 2 of 7 induced by HSV, and 1 of 7 induced by HSV plus CMV. IH for CMV and HSV confirmed the HE findings and detected one additional CMV-induced case. UGI endoscopy showed 100% sensitivity and 15% specificity for the diagnosis of EU due to CMV or HSV compared to HE and IH. HE proved to be an adequate method for etiologic evaluation, with 87% sensitivity and 100% specificity compared to IH. The number of samples did not influence the etiologic evaluation. The data support the importance of IH as a complementary method for HE in the diagnosis of EU of viral etiology.

LIFE CYCLE AND POPULATION STRUCTURE OF AEGLA PAULENSIS (DECAPODA: ANOMURA: AEGLIDAE)

We describe growth, longevity, sex ratio, reproductive period, and recruitment of Aegla paulensis from Jaragua Stale Park, Sao Paulo, Brazil (23 degrees 27'27.9 '' S; 46 degrees 45'32.3 '' W). The population was sampled monthly (September 2007 through August 2009) with the aid of traps. Over five thousand individuals were captured, sexed, measured (carapace length = CL) and inspected for reproductive traits (females only), and then released back to the sampling site. The pattern of the reproductive cycle was strongly seasonal (austral mid autumn through late winter), with a single recruitment pulse per year. The obtained von Bertalanffy growth equations were CL = 21.25[1-e(-0.041(t + 1.250))] and CL = 16.52[1-e(-0.049(t + 1.823))] for males and females, respectively. Males (mean CL +/- SD = 11.86 +/- 2.79 mm) attain larger sizes than females (mean CL +/- SD = 10.84 +/- 2.36 mm). Aegla paulensis reproduces twice during an estimated life span of 40.2 months for females and 33.9 months for males. Temporal variation of sex ratio showed a distinctive pattern characterized by a sequence of three distinct periods that repeated from one year to another, and which suggested that a behavioral component influence the proportion of sex in adult specimens sampled with traps during reproductive and non-reproductive periods.

CHARACTERIZATION OF THE TREE COMPONENT IN A SEMIDECIDUOUS FOREST IN THE ESPINHACO RANGE: A SUBSIDY TO CONSERVATION

This study was conducted in the Private Reserve Mata do Jambreiro (912 ha), localized in the Iron Quadrangle, Minas Gerais, southeastern portion of the Espinhaco Range, which is predominantly covered by semideciduous seasonal montane forest. Three topographically and physiognomic similar areas located within a continuum forest fragment, distant by 1.3 to 1.5 km were sampled by the point-quadrat method. In each area, 30 points were marked. Individuals with a minimum perimeter at the breast height (PBH) of 15 cm were sampled, totaling 111 species belonging to 40 families. The most representative family was Fabaceae, with 14.29% of the total number of species. Low floristic similarity (5.3% to 34.4%) was observed between the areas, pointing out the importance of distribution of sample units in continuous fragments. Shannon diversity index (H') found was 4.22 and Pielou equability (J) 0.894. Soil analysis showed some differences in chemical composition between the three studied areas and was an important component for the interpretation of the floristic variation found. The low floristic similarity observed here for close areas justify the requirement of more detailed inventories by Brazilian Environmental Agencies for the legal authorization procedures prior to the establishment of new enterprising projects. Also, the professionals that conduct rapid inventories, mainly the Environmental Consultants, should give more attention to this kind of floristic variation and to the methods used to inventory complex forests.

Evaluation of the carbon content of aerosols from the burning of biomass in the Brazilian Amazon using thermal, optical and thermal-optical analysis methods

Aerosol samples were collected at a pasture site in the Amazon Basin as part of the project LBA-SMOCC-2002 (Large-Scale Biosphere-Atmosphere Experiment in Amazonia - Smoke Aerosols, Clouds, Rainfall and Climate: Aerosols from Biomass Burning Perturb Global and Regional Climate). Sampling was conducted during the late dry season, when the aerosol composition was dominated by biomass burning emissions, especially in the submicron fraction. A 13-stage Dekati low-pressure impactor (DLPI) was used to collect particles with nominal aerodynamic diameters (D(p)) ranging from 0.03 to 0.10 mu m. Gravimetric analyses of the DLPI substrates and filters were performed to obtain aerosol mass concentrations. The concentrations of total, apparent elemental, and organic carbon (TC, EC(a), and OC) were determined using thermal and thermal-optical analysis (TOA) methods. A light transmission method (LTM) was used to determine the concentration of equivalent black carbon (BC(e)) or the absorbing fraction at 880 nm for the size-resolved samples. During the dry period, due to the pervasive presence of fires in the region upwind of the sampling site, concentrations of fine aerosols (D(p) < 2.5 mu m: average 59.8 mu g m(-3)) were higher than coarse aerosols (D(p) > 2.5 mu m: 4.1 mu g m(-3)). Carbonaceous matter, estimated as the sum of the particulate organic matter (i.e., OC x 1.8) plus BC(e), comprised more than 90% to the total aerosol mass. Concentrations of EC(a) (estimated by thermal analysis with a correction for charring) and BC(e) (estimated by LTM) averaged 5.2 +/- 1.3 and 3.1 +/- 0.8 mu g m(-3), respectively. The determination of EC was improved by extracting water-soluble organic material from the samples, which reduced the average light absorption Angstrom exponent of particles in the size range of 0.1 to 1.0 mu m from >2.0 to approximately 1.2. The size-resolved BC(e) measured by the LTM showed a clear maximum between 0.4 and 0.6 mu m in diameter. The concentrations of OC and BC(e) varied diurnally during the dry period, and this variation is related to diurnal changes in boundary layer thickness and in fire frequency.

Determination of post-mortem interval using in situ tissue optical fluorescence

In this study we have used fluorescence spectroscopy to determine the post-mortem interval. Conventional methods in forensic medicine involve tissue or body fluids sampling and laboratory tests, which are often time demanding and may depend on expensive analysis. The presented method consists in using time-dependent variations on the fluorescence spectrum and its correlation with the time elapsed after regular metabolic activity cessation. This new approach addresses unmet needs for post-mortem interval determination in forensic medicine, by providing rapid and in situ measurements that shows improved time resolution relative to existing methods. (C) 2009 Optical Society of America

INTERANNUAL VARIABILITY IN TROPICAL ESTUARINE COPEPOD ASSEMBLAGES OFF NORTHEASTERN BRAZIL

We studied copepod assemblage variability among years, seasons, and tidal states in the Mucuri River estuary (Bahia State, Brazil). Zooplankton samples were collected seasonally through five years (2002-2006) at three sampling stations, one of which was sampled over a complete tidal cycle (two ebb and two flood tides). Temperature, salinity, river flux, and rainfall data were collected. Winter and summer represented dry and wet seasons, respectively. Copepod abundances ranged from 40 to 63% of the total zooplankton assemblage and comprised 46 taxa, among which, common estuarine species such as Temora turbinata (first record for the studied area), Parvocalanus crassirostris, Acartia lilljeborgi, Oithona hebes were the most abundant (euryhaline species). Interannual and seasonal variations were most marked in stenohaline species, e.g.. Notodiaptomus sp. and Thermocyclops minutus; density variations of euryhaline species, which made up the majority of the abundant taxa, were most closely related to tides. Diversity and richness also followed an intertidal pattern of variation.

Estrutura populacional do camarão-branco Litopenaeus schmitti nas regiões estuarina e marinha da baixada santista, São Paulo, Brasil

The white-shrimp Litopenaeus schmitti distributes in West Atlantic Ocean, occurring along all Brazilian cost. Population structure in the Baixada Santista region was identified from samples obtained from artisanal and industrial fishery between June of 2005 and May of 2006. A total of 2.912 specimens were collected, being 2.138 females (1.008 in the estuary and 1.130 in the marine region) and 774 males ( 334 in the estuary and 440 in the marine region). Environmental parameters were annotated together the sampling, allowing to identify that water temperature influences directly the catches. Catches variations, length composition of samples by sex and gonadal maturation of females allowed to identify that: (i) estuary is used as a nursery area by individuals with small lengths, most young; (ii) marine region is used by larger individuals ( adults) and the spawning period extend from June to February, mainly between November and January. It was verified that estuarine fishery ( artisanal) focuses immature and in development individuals, with small lengths and, the marine fishery ( industrial) focuses adults during the whole year and, only in the summer, youngling from spawn. The length of first gonadal maturation of females was estimated in 15,8mm. These results and diagnoses must be considered in the management of L. schmitti fishery in Baixada Santista region.

Abundance of sedentary consumers and sessile organisms along the wave exposure gradient of subtropical rocky shores of the south-west Atlantic

Sedentary consumers play an important role on populations of prey and, hence, their patterns of abundance, distribution and coexistence on shores are important to evaluate their potential influence on ecosystem dynamics. Here, we aimed to describe their spatio-temporal distribution and abundance in relation to wave exposure in the intertidal rocky shores of the south-west Atlantic to provide a basis for further understanding of ecological processes in this system. The abundance and composition of the functional groups of sessile organisms and sedentary consumers were taken by sampling the intertidal of sheltered and moderately exposed shores during a period of one year. The sublittoral fringe of sheltered areas was dominated by macroalgae, while the low midlittoral was dominated by bare rock and barnacles. In contrast, filter-feeding animals prevailed at exposed shores, probably explaining the higher abundance of the predator Stramonita haemastoma at these locations. Limpets were more abundant at the midlittoral zone of all shores while sea urchins were exclusively found at the sublittoral fringe of moderately exposed shores, therefore, adding grazing pressure on these areas. The results showed patterns of coexistence, distribution and abundance of those organisms in this subtropical area, presumably as a result of wave action, competition and prey availability. It also brought insights on the influence of top-down and bottom-up processes in this area.