Evaluation of statistical and geostatistical models of digital soil properties mapping in tropical mountain regions

Soil properties have an enormous impact on economic and environmental aspects of agricultural production. Quantitative relationships between soil properties and the factors that influence their variability are the basis of digital soil mapping. The predictive models of soil properties evaluated in this work are statistical (multiple linear regression-MLR) and geostatistical (ordinary kriging and co-kriging). The study was conducted in the municipality of Bom Jardim, RJ, using a soil database with 208 sampling points. Predictive models were evaluated for sand, silt and clay fractions, pH in water and organic carbon at six depths according to the specifications of the consortium of digital soil mapping at the global level (GlobalSoilMap). Continuous covariates and categorical predictors were used and their contributions to the model assessed. Only the environmental covariates elevation, aspect, stream power index (SPI), soil wetness index (SWI), normalized difference vegetation index (NDVI), and b3/b2 band ratio were significantly correlated with soil properties. The predictive models had a mean coefficient of determination of 0.21. Best results were obtained with the geostatistical predictive models, where the highest coefficient of determination 0.43 was associated with sand properties between 60 to 100 cm deep. The use of a sparse data set of soil properties for digital mapping can explain only part of the spatial variation of these properties. The results may be related to the sampling density and the quantity and quality of the environmental covariates and predictive models used.

Genetics of leprosy reactions: an overview

Type-1 (T1R) and Type-2 (T2R) leprosy reactions (LR), which affect up to 50% of leprosy patients, are aggressive inflammatory episodes of sudden onset and highly variable incidence across populations. LR are often diagnosed concurrently with leprosy, but more frequently occur several months after treatment onset. It is not uncommon for leprosy patients to develop recurring reactional episodes; however, they rarely undergo both types of LR. Today, LR are the main cause of permanent disabilities associated with leprosy and represent a major challenge in the clinical management of leprosy patients. Although progress has been made in understanding the immunopathology of LR, the factors that cause a leprosy patient to suffer from LR are largely unknown. Given the impact that ethnic background has on the risk of developing LR, host genetic factors have long been suspected of contributing to LR. Indeed, polymorphisms in seven genes [Toll-like receptors (TLR)1, TLR2, nucleotide-binding oligomerisation domain containing 2, vitamin D receptor, natural resistance-associated macrophage protein 1, C4B and interleukin-6] have been found to be associated with one or more LR outcomes. The identification of host genetic markers with predictive value for LR would have a major impact on nerve damage control in leprosy. In this review, we present the recent advances achieved through genetic studies of LR.

Selecting statistical models to study the relationship between soybean yield and soil physical properties

Statistical models allow the representation of data sets and the estimation and/or prediction of the behavior of a given variable through its interaction with the other variables involved in a phenomenon. Among other different statistical models, are the autoregressive state-space models (ARSS) and the linear regression models (LR), which allow the quantification of the relationships among soil-plant-atmosphere system variables. To compare the quality of the ARSS and LR models for the modeling of the relationships between soybean yield and soil physical properties, Akaike's Information Criterion, which provides a coefficient for the selection of the best model, was used in this study. The data sets were sampled in a Rhodic Acrudox soil, along a spatial transect with 84 points spaced 3 m apart. At each sampling point, soybean samples were collected for yield quantification. At the same site, soil penetration resistance was also measured and soil samples were collected to measure soil bulk density in the 0-0.10 m and 0.10-0.20 m layers. Results showed autocorrelation and a cross correlation structure of soybean yield and soil penetration resistance data. Soil bulk density data, however, were only autocorrelated in the 0-0.10 m layer and not cross correlated with soybean yield. The results showed the higher efficiency of the autoregressive space-state models in relation to the equivalent simple and multiple linear regression models using Akaike's Information Criterion. The resulting values were comparatively lower than the values obtained by the regression models, for all combinations of explanatory variables.

Mating system in Myracrodruon urundeuva (Anarcadiaceae): implications for conservation genetics

The aims of this study were to investigate the mating system of a fragmented population of the dioecious tropical tree Myracrodruon urundeuva Allemão, using five microsatellite loci and the mixed mating and correlated mating models. The study was conducted in the Estação Ecológica de Paulo de Farias (436 ha), where the population occupies about 142 ha. The mating system was estimated using 514 open-pollinated offspring, collected from 30 seed-trees. Estimates of the multilocus outcrossing rate confirm that the species is dioecious (t m = 1.0). Low levels of mating among relatives were detected in the population (1 - t s = 0.020). The estimate of paternity correlation (r p(m)) indicated that offsprings were composed of mixtures of half-sibs and full-sibs, with the latter occurring at a low frequency (average of 0.148). The estimated coancestry coefficient within families (Θ = 0.147) was larger and the effective population size (Ne(v)) was lower (Ne(v) = 2.98) than expected in progenies from panmictic populations (Θ = 0.125, Ne(v) = 4, respectively). In terms of conservation, the results indicate that to retain an effective population size of 150, is necessary to collect seeds from at least 50 seed-trees.

A ação dos gens gametofíticos com referência especial ao milho

1) The first part deals with the different processes which may complicate Mendelian segregation and which may be classified into three groups, according to BRIEGER (1937b) : a) Instability of genes, b) Abnormal segregation due to distur- bances during the meiotic divisions, c) obscured segregation, after a perfectly normal meiosis, caused by elimination or during the gonophase (gametophyte in higher plants), or during zygophase (sporophyte). Without entering into detail, it is emphasized that all the above mentioned complications in the segregation of some genes may be caused by the action of other genes. Thus in maize, the instability of the Al factor is observed only when the gene dt is presente in the homozygous conditions (RHOADES 1938). In another case, still under observation in Piracicaba, an instability is observed in Mirabilis with regard to two pairs of alleles both controlling flower color. Several cases are known, especially in corn, where recessive genes, when homozigous, affect the course of meiosis, causing asynapsis (asyndesis) (BEADLE AND MC CLINTOCK 1928, BEADLE 1930), sticky chromosomes (BEADLE 1932), supermunmerary divisions (BEADLE 1931). The most extreme case of an obscured segregatiou is represented by the action of the S factors in self stetrile plants. An additional proof of EAST AND MANGELSDORF (1925) genetic formula of self sterility has been contributed by the studies on Jinked factors in Nicotina (BRIEGER AND MANGELSDORF (1926) and Antirrhinum (BRIEGER 1930, 1935), In cases of a incomplete competition and selection between pollen tubes, studies of linked indicator-genes are indispensable in the genetic analysis, since it is impossible to analyse the factors for gametophyte competition by direct aproach. 2) The flower structure of corn is explained, and stated that the particularites of floral biology make maize an excellent object for the study of gametophyte factors. Since only one pollen tube per ovule may accomplish fertilization, the competition is always extremely strong, as compared with other species possessing multi-ovulate ovaries. The lenght of the silk permitts the study of pollen tube competitions over a varying distance. Finally the genetic analysis of grains characters (endosperm and aleoron) simpliflen the experimental work considerably, by allowing the accumulation of large numbers for statistical treatment. 3) The four methods for analyzing the naturing of pollen tube competition are discussed, following BRIEGER (1930). Of these the first three are: a) polinization with a small number of pollen grains, b) polinization at different times and c) cut- ting the style after the faster tubes have passe dand before the slower tubes have reached the point where the stigma will be cut. d) The fourth method, alteration of the distatice over which competition takes place, has been applied largely in corn. The basic conceptions underlying this process, are illustrated in Fig. 3. While BRINK (1925) and MANGELSDORF (1929) applied pollen at different levels on the silks, the remaining authors (JONES, 1922, MANGELSDORF 1929, BRIEGER, at al. 1938) have used a different process. The pollen was applied as usual, after removing the main part of the silks, but the ears were divided transversally into halves or quarters before counting. The experiments showed generally an increase in the intensity of competition when there was increase of the distance over which they had to travel. Only MANGELSDORF found an interesting exception. When the distance became extreme, the initially slower tubes seemed to become finally the faster ones. 4) Methods of genetic and statistical analysis are discussed, following chiefly BRIEGER (1937a and 1937b). A formula is given to determine the intensity of ellimination in three point experiments. 5) The few facts are cited which give some indication about the physiological mechanism of gametophyte competition. They are four in number a) the growth rate depends-only on the action of gametophyte factors; b) there is an interaction between the conductive tissue of the stigma or style and the pollen tubes, mainly in self-sterile plants; c) after self-pollination necrosis starts in the tissue of the stigma, in some orchids after F. MÜLLER (1867); d) in pollon mixtures there is an inhibitory interaction between two types of pollen and the female tissue; Gossypium according to BALLS (1911), KEARNEY 1923, 1928, KEARNEY AND HARRISON (1924). A more complete discussion is found in BRIEGER 1930). 6) A list of the gametophyte factors so far localized in corn is given. CHROMOSOME IV Ga 1 : MANGELSDORF AND JONES (1925), EMERSON 1934). Ga 4 : BRIEGER (1945b). Sp 1 : MANGELSDORF (1931), SINGLETON AND MANGELSDORF (1940), BRIEGER (1945a). CHROMOSOME V Ga 2 : BRIEGER (1937a). CHROMOSOME VI BRIEGER, TIDBURY AND TSENG (1938) found indications of a gametophyte factor altering the segregation of yellow endosperm y1. CHROMOSOME IX Ga 3 : BRIEGER, TIDBURY AND TSENG (1938). While the competition in these six cases is essentially determined by one pair of factors, the degree of elimination may be variable, as shown for Ga2 (BRIEGER, 1937), for Ga4 (BRIEGER 1945a) and for Spl (SINGLETON AND MANGELSDORF 1940, BRIEGER 1945b). The action of a gametophyte factor altering the segregation of waxy (perhaps Ga3) is increased by the presence of the sul factor which thus acts as a modifier (BRINCK AND BURNHAM 1927). A polyfactorial case of gametophyte competition has been found by JONES (1922) and analysed by DEMEREC (1929) in rice pop corn which rejects the pollen tubes of other types of corn. Preference for selfing or for brothers-sister mating and partial elimination of other pollen tubes has been described by BRIEGER (1936). 7) HARLAND'S (1943) very ingenious idea is discussed to use pollen tube factors in applied genetics in order to build up an obstacle to natural crossing as a consequence of the rapid pollen tube growth after selfing. Unfortunately, HARLAND could not obtain the experimental proof of the praticability of his idea, during his experiments on selection for minor modifiers for pollen tube grouth in cotton. In maize it should be possible to employ gametophyte factors to build up lines with preference for crossing, though the method should hardly be of any practical advantage.

A population genetics study of Anopheles darlingi (Diptera: Culicidae) from Colombia based on random amplified polymorphic DNA-polymerase chain reaction and amplified fragment lenght polymorphism markers

The genetic variation and population structure of three populations of Anopheles darlingi from Colombia were studied using random amplified polymorphic markers (RAPDs) and amplified fragment length polymorphism markers (AFLPs). Six RAPD primers produced 46 polymorphic fragments, while two AFLP primer combinations produced 197 polymorphic fragments from 71 DNA samples. Both of the evaluated genetic markers showed the presence of gene flow, suggesting that Colombian An. darlingi populations are in panmixia. Average genetic diversity, estimated from observed heterozygosity, was 0.374 (RAPD) and 0.309 (AFLP). RAPD and AFLP markers showed little evidence of geographic separation between eastern and western populations; however, the F ST values showed high gene flow between the two western populations (RAPD: F ST = 0.029; Nm: 8.5; AFLP: F ST = 0.051; Nm: 4.7). According to molecular variance analysis (AMOVA), the genetic distance between populations was significant (RAPD:phiST = 0.084; AFLP:phiST = 0.229, P < 0.001). The F ST distances and AMOVAs using AFLP loci support the differentiation of the Guyana biogeographic province population from those of the Chocó-Magdalena. In this last region, Chocó and Córdoba populations showed the highest genetic flow.

A preliminary analysis of the population genetics and molecular phylogenetics of Onchocerca volvulus (Nematoda: Filarioidea) using nuclear ribosomal second internal transcribed spacer sequences

Nuclear internal transcribed spacer 2 (ITS2) rDNA sequences were used for a molecular phylogenetics analysis of five Onchocerca species. The sister species of the human parasite O. volvulus was found to be the cattle parasite O. ochengi and not O. gibsoni, contrary to chromosomal evidence. The genetic differentiation of two African populations (representing the two African strains) and a Brazilian population of O. volvulus was also studied. Phylogenetic and network reconstruction did not show any clustering of ITS2 alleles on geographic or strain grounds. Furthermore, population genetics tests showed no indication of population differentiation but suggested gene flow among the three populations.

Genetics of chloroquine-resistant malaria: a haplotypic view

The development and rapid spread of chloroquine resistance (CQR) in Plasmodium falciparum have triggered the identification of several genetic target(s) in the P. falciparum genome. In particular, mutations in the Pfcrt gene, specifically, K76T and mutations in three other amino acids in the region adjoining K76 (residues 72, 74, 75 and 76), are considered to be highly related to CQR. These various mutations form several different haplotypes and Pfcrt gene polymorphisms and the global distribution of the different CQR- Pfcrt haplotypes in endemic and non-endemic regions of P. falciparum malaria have been the subject of extensive study. Despite the fact that the Pfcrt gene is considered to be the primary CQR gene in P. falciparum , several studies have suggested that this may not be the case. Furthermore, there is a poor correlation between the evolutionary implications of the Pfcrt haplotypes and the inferred migration of CQR P. falciparum based on CQR epidemiological surveillance data. The present paper aims to clarify the existing knowledge on the genetic basis of the different CQR- Pfcrt haplotypes that are prevalent in worldwide populations based on the published literature and to analyse the data to generate hypotheses on the genetics and evolution of CQR malaria.

Construction and characterisation of a complete reverse genetics system of dengue virus type 3

Dengue virulence and fitness are important factors that determine disease outcome. However, dengue virus (DENV) molecular biology and pathogenesis are not completely elucidated. New insights on those mechanisms have been facilitated by the development of reverse genetic systems in the past decades. Unfortunately, instability of flavivirus genomes cloned in Escherichia coli has been a major problem in these systems. Here, we describe the development of a complete reverse genetics system, based on the construction of an infectious clone and replicon for a low passage DENV-3 genotype III of a clinical isolate. Both constructs were assembled into a newly designed yeast- E. coli shuttle vector by homologous recombination technique and propagated in yeast to prevent any possible genome instability in E. coli . RNA transcripts derived from the infectious clone are infectious upon transfection into BHK-21 cells even after repeated passages of the plasmid in yeast. Transcript-derived DENV-3 exhibited growth kinetics, focus formation size comparable to original DENV-3 in mosquito C6/36 cell culture. In vitro characterisation of DENV-3 replicon confirmed its identity and ability to replicate transiently in BHK-21 cells. The reverse genetics system reported here is a valuable tool that will facilitate further molecular studies in DENV replication, virus attenuation and pathogenesis.

When population and evolutionary genetics met behaviour

In this review, we analyse the impact of a population and evolutionary genetics approach on the study of insect behaviour. Our attention is focused on the model organism Drosophila melanogaster and several other insect species. In particular, we explore the relationship between rhythmic behaviours and the molecular evolution of clock and ion channel genes.

The three phases of the ensemble forecasting of niche models: geographic range and shifts in climatically suitable areas of Utetheisa ornatrix (Lepidoptera, Arctiidae)

Species' geographic ranges are usually considered as basic units in macroecology and biogeography, yet it is still difficult to measure them accurately for many reasons. About 20 years ago, researchers started using local data on species' occurrences to estimate broad scale ranges, thereby establishing the niche modeling approach. However, there are still many problems in model evaluation and application, and one of the solutions is to find a consensus solution among models derived from different mathematical and statistical models for niche modeling, climatic projections and variable combination, all of which are sources of uncertainty during niche modeling. In this paper, we discuss this approach of ensemble forecasting and propose that it can be divided into three phases with increasing levels of complexity. Phase I is the simple combination of maps to achieve a consensual and hopefully conservative solution. In Phase II, differences among the maps used are described by multivariate analyses, and Phase III consists of the quantitative evaluation of the relative magnitude of uncertainties from different sources and their mapping. To illustrate these developments, we analyzed the occurrence data of the tiger moth, Utetheisa ornatrix (Lepidoptera, Arctiidae), a Neotropical moth species, and modeled its geographic range in current and future climates.

Effects of genetics and environment on isoflavone content of soybean from different regions of Brazil

The effects of genetics and environmental factors on isoflavone content of soybean (Glycine max L.) cultivars grown in different locations in Brazil in 1993/94 were evaluated. Seeds of different cultivars were analised by high performance liquid chromatography (HPLC). In Rio Grande do Sul (RS), Paraná (PR), and Mato Grosso do Sul (MS) States, a significant difference in the isoflavone total content average of the cultivars IAS 5 and FT-Abyara (163.9, 116.4 and 79.5 mg/100 g, respectively) was observed. In general, IAS 5 contained higher isoflavone than FT-Abyara. Cultivars IAS 5 and FT-Abyara grown at Vacaria, RS (28°30' S latitude) with temperature average of 19°C, had the highest isoflavone concentrations (218.7 and 163.8 mg/100 g, respectively). In Palotina, PR (24°27' S latitude), where temperature average was 24°C, the isoflavone concentrations were 105.9 and 86.8 mg/100 g, respectively. The lowest isoflavone contents were observed for FT-Estrela and FT-Cristalina, (27.6 and 46.5 mg/100 g, repectively) at Rondonópolis, MT (16°20' S latitude), where the temperature was 27°C.

Genetics of resistance to the fungus Helminthosporium sativum in wheat: use of culture filtrates in tissue culture

Six wheat genotypes and their F1 and F2 generations were exposed to the action of Helminthosporium sativum culture filtrates to examine the genetics of hexaploid wheat resistance. The objective was to improve the efficiency of breeding programs by identifying the action and number of genes involved in the resistance. The varied response of the tested genotypes to the culture filtrates allowed division of the genotypes into four groups: resistant, moderately resistant, moderately susceptible and susceptible. This variability was detected in the progeny, suggesting that the parents have distinct genetic constitutions. Additive gene action predominated and genetic gain was shown to be possible through selection. The genetic control of the resistance trait seems to be complex because of the presence of gene interaction and the difficulty of eliminating the environmental effects. The inheritance seems to be oligogenic