Evaluation of algorithms used to order markers on genetic maps

When building genetic maps, it is necessary to choose from several marker ordering algorithms and criteria, and the choice is not always simple. In this study, we evaluate the efficiency of algorithms try (TRY), seriation (SER), rapid chain delineation (RCD), recombination counting and ordering (RECORD) and unidirectional growth (UG), as well as the criteria PARF (product of adjacent recombination fractions), SARF (sum of adjacent recombination fractions), SALOD (sum of adjacent LOD scores) and LHMC (likelihood through hidden Markov chains), used with the RIPPLE algorithm for error verification, in the construction of genetic linkage maps. A linkage map of a hypothetical diploid and monoecious plant species was simulated containing one linkage group and 21 markers with fixed distance of 3 cM between them. In all, 700 F(2) populations were randomly simulated with and 400 individuals with different combinations of dominant and co-dominant markers, as well as 10 and 20% of missing data. The simulations showed that, in the presence of co-dominant markers only, any combination of algorithm and criteria may be used, even for a reduced population size. In the case of a smaller proportion of dominant markers, any of the algorithms and criteria (except SALOD) investigated may be used. In the presence of high proportions of dominant markers and smaller samples (around 100), the probability of repulsion linkage increases between them and, in this case, use of the algorithms TRY and SER associated to RIPPLE with criterion LHMC would provide better results. Heredity (2009) 103, 494-502; doi:10.1038/hdy.2009.96; published online 29 July 2009

Generation and Analysis of Interaction Energy Maps of p-Substituted Benzoic Acid [(5-Nitro-thiophen-2-yl)-methylene]-Hydrazides Active against MRSA

In this preliminary study eighteen p-substituted benzoic acid [(5-nitro-thiophen-2-yl)-methylene]-hydrazides with antimicrobial activity were evaluated against multidrug-resistant Staphylococcus aureus, correlating the three-dimensional characteristics of the ligands with their respective bioactivities. The computer programs Sybyl and CORINA were used, respectively, for the design and three-dimensional conversion of the ligands. Molecular interaction fields were calculated using GRID program. Calculations using Volsurf resulted in a statistically consistent model with 48 structural descriptors showing that hydrophobicity is a fundamental property in the analyzed biological response.

Self-Organizing Maps as a New Tool for Classification of Plants at Lower Hierarchical Levels

A chemotaxonomic analysis is described of a database containing various types of compounds from the Heliantheae tribe (Asteraceae) using Self-Organizing Maps (SOM). The numbers of occurrences of 9 chemical classes in different taxa of the tribe were used as variables. The study shows that SOM applied to chemical data can contribute to differentiate genera, subtribes, and groups of subtribes (subtribe branches), as well as to tribal and subtribal classifications of Heliantheae, exhibiting a high hit percentage comparable to that of an expert performance, and in agreement with the previous tribe classification proposed by Stuessy.

KuhlmanniodendronFiaschi & Groppo, a new eastern Brazilian genus of Achariaceae sensu lato segregated from Carpotroche Endl. (formerly included in Flacourtiaceae)

Kuhlmanniodendron Fiaschi & Groppo, a new genus of the tribe Lindackerieae (Achariaceae sensu lato) is created to accommodate Carpotroche apterocarpa Kuhlm, a species previously described based on incomplete floriferous and fruiting material from the rainforests of Espirito Santo state, eastern Brazil. The genus is defined by a unique set of character states, including leaves with Clusia-like venation and scaly trichomes, flowers with glabrous stamen filaments and three free styles, and indehiscent fruits with a smooth surface (sometimes with vertical ribs when dried). A description and illustration are provided, with comments on geographical distribution, phenology and generic relationships, and an emended key to neotropical genera of Lindackerieae. (c) 2008 The Linnean Society of London.

A new species of Almeidea (Galipeinae, Galipeeae, Rutaceae) from Eastern Brazil

A new species of Almeidea (Rutaceae) belonging to the neotropical tribe Galipeeae (subtribe Galipeinae) is described and illustrated. This new species, Almeidea albiflora, is known so far only from a few collections made in small disturbed forest remnants in the vicinity of Cachoeiro de Itapemirim, in the state of Espirito Santo, and by a single collection from northern Rio de Janeiro state, both in the domain of the Atlantic Forest, Eastern Brazil. Diagnostic features, like white petals, sericeous ovary and distal secondary axes as long as the proximal ones are identified. Pollen morphology is also described, and brief discussions of the relationships of the new taxon to other species of Almeidea, as well as comments on its conservation status, are provided.

Phylogeography of the cactophilic species Drosophila gouveai: demographic events and divergence timing in dry vegetation enclaves in eastern Brazil

Aim The aim of this study was to assess the causal mechanisms underlying populational subdivision in Drosophila gouveai, a cactophilic species associated with xeric vegetation enclaves in eastern Brazil. A secondary aim was to investigate the genetic effects of Pleistocene climatic fluctuations on these environments. Location Dry vegetation enclaves within the limits of the Cerrado domain in eastern Brazil. Methods We determined the mitochondrial DNA haplotypes of 55 individuals (representing 12 populations) based on sequence data of a 483-bp fragment from the cytochrome c oxidase subunit II (COII) gene. Phylogenetic and coalescent analyses were used to test for the occurrence of demographic events and to infer the time of divergence amongst genetically independent groups. Results Our analyses revealed the existence of two divergent subclades (G1 and G2) plus an introgressed clade restricted to the southernmost range of D. gouveai. Subclades G1 and G2 displayed genetic footprints of range expansion and segregated geographical distributions in south-eastern and some central highland regions, east and west of the Parana River valley. Molecular dating indicated that the main demographic and diversification events occurred in the late to middle Pleistocene. Main conclusions The phylogeographical and genetic patterns observed for D. gouveai in this study are consistent with changes in the distribution of dry vegetation in eastern Brazil. All of the estimates obtained by molecular dating indicate that range expansion and isolation pre-dated the Last Glacial Maximum, occurring during the late to middle Pleistocene, and were probably triggered by climatic changes during the Pleistocene. The current patchy geographical distribution and population subdivision in D. gouveai is apparently closely linked to these past events.

Hepatitis D and B virus genotypes in chronically infected patients from the Eastern Amazon Basin

Hepatitis D virus (HDV) is a defective hepatotropic virus whose infectivity is dependent on hepatitis B virus (HBV). HDV super- or co-infiection leads to an increased risk of fulminant hepatitis or progression to severe chronic liver disease in HBV infected patients. The Brazilian Amazon Basin has been reported to be endemic for HBV and HDV, especially in the Western Amazon Basin. In this region, HDV infection is frequently associated with acute fulminant hepatitis with characteristic histologic features. HDV is classified into seven major clades (HDV-1 to HDV-7) and HBV is subdivided into eight genotypes (A-H). HDV and HBV genotypes have been shown to have a distinct geographic distribution. The aim of this study was to determine the HBV and HDV genotypes harbored by chronically infected patients from the Eastern Amazon Basin, Brazil. We studied 17 serum samples from HBV and HDV chronically infected patients admitted to a large public hospital (Santa Casa de Misericordia) at Belem, state of Para, Brazil, between 1994 and 2002. HDV-3 and HBV genotype A (subtype adw2) have been identified in all cases, in contrast to previous studies from other regions of the Amazon, where HBV genotype F has been found co-infecting patients that harbored HDV-3. The HDV-3/HBV-A co-infection suggests that there is not a specific interaction between HBV and HDV genotypes, and co-infection might merely reflect the most frequent genotypes found in a particular geographic area. The analysis of the carboxy-terminal region of the large hepatitis D antigen (L-HDAg), which interacts with the hepatitis B surface antigen (HBsAg) and is essential for HDV assembly, showed some diversity between the different isolates from the Eastern Amazon. This diversity is not observed among HDV-3 sequences from other South American regions. (C) 2008 Elsevier B.V. All rights reserved.

Timing of Dose Relative to Sexual Intercourse Attempt in Previous Sildenafil Citrate Users Treated with Tadalafil: A Geographical Comparison from a Single Arm, Open-Label Study

Introduction. Previous research has demonstrated that sildenafil citrate users alter dosing-sexual attempt behavior when switched to tadalafil. The impact of geography and culture on sexual behavior with phosphodiesterase type 5 (PDE5) inhibitor treatment has not been fully investigated. Aim. To describe and compare the changes in dosing-sexual attempt behavior with sildenafil citrate vs. tadalafil treatment across four distinct geographies: Asia, Australia/New Zealand (ANZ), Central Eastern Europe/Middle East (CEE/ME), and Latin America (LA). Methods. Data from a single-arm, open-label clinical trial conducted in 21 countries from November 2002 to May 2004 were used in this analysis. Men with erectile dysfunction and a history of >= 6-week prior sildenafil citrate use continued sildenafil citrate treatment for 4 weeks then switched to tadalafil for 8 weeks. Dosing instructions were provided. Main Outcomes Measures. Timing of dose and sexual intercourse was assessed through patient diaries for the final 4 weeks of each treatment period. Results. A total of 2,760 men were enrolled: Asia 15.8%; ANZ 29.4%; CEE/ME 19.7%; LA 35.1%. The median time from dosing to intercourse was significantly increased during tadalafil treatment across all geographical regions; however, the magnitude of increase differed significantly by geography (P < 0.0001). The Asian cohort demonstrated the shortest duration between dosing and sexual intercourse attempts (irrespective of drug), and altered sexual behavior the least upon switching to tadalafil. The ANZ cohort demonstrated the longest duration between dosing and sexual intercourse attempts (irrespective of drug), and altered sexual behavior the most upon switching to tadalafil. Conclusion. Men with a history of established sildenafil citrate use alter their dose-attempt behavior when treated with tadalafil irrespective of geography. However, the extent to which sexual behavior alters is not uniform across geographical regions, suggesting that dosing instructions and duration of drug effectiveness, in combination with personal and cultural preferences, may determine sexual behavior with PDE5 inhibitor use. Rubio-Aurioles E, Glina S, Abdo CHN, Hernandez-Serrano R, Rampazzo C, Sotomayor M, West TM, Gallagher GL, and Lenero E. Timing of dose relative to sexual intercourse attempt in previous sildenafil citrate users treated with tadalafil: A geographical comparison from a single arm, open-label study. J Sex Med 2009;6:2836-2850.

Hypomania: a transcultural perspective

This study examined the transcultural robustness of a screening instrument for hypomania, the Hypomania Checklist-32. first revised version(HCL-32 R1) It was carried out in 2606 patients from twelve countries in five geographic regions (Northern, Southern and Eastern Europe, South America and East Asia) In addition, GAMIAN Europe contributed data from its members Exploratory and confirmatory factor analyses were used to examine the transregional stability of the measurement properties of the HCL-32 R 1, including the influence of sex and age as covariates A cross cultures, a two-factor structure was confirmed the first factor (F 1) reflected the more positive aspects of hypomania (being more active, elated, self-confident, and cognitively, enhanced), the second factor (F2) reflected the more negative aspects (being irritable, impulsive, careless. more substance use). The measurement properties of the HCL-32 R1 were largely invariant across cultures Only few items showed transcultural differences in their relation to hypomania as measured by the test F2 was higher among men and in more severe manic syndromes, F1 was highest in North and East Europe and lowest in South America Vie scores decreased slightly with age The frequency of the 32 items showed remarkable similarities across geographic areas, with two exceptions. South Europeans had lower symptom frequencies in general and East Europeans higher rates of substance use These findings support the international applicability of the HCL-32 R1 as a screening instrument for hypomania

Ecological aspects of the free-living ticks (Acari: Ixodidae) on animal trails within Atlantic rainforest in south-eastern Brazil

In a recent ecological study of the ticks on animal trails within an area of Atlantic rainforest in south-eastern Brazil, Amblyomma aureolatum, A. brasiliense, A. incisum, A. ovale and Haemaphysalis juxtakochi were found questing on the vegetation. Most of the ticks recorded by a small, man-made dam on the forest border were A. dubitatum but a few A. brasiliense and A. cajennense, one A. incisum and one H. juxtakochi were also found. The seasonal activity of the ticks indicated that A. incisum and A. brasiliense had one generation/year. On the animal trails, most tick species and stages quested on the vegetation at a height of 30-40 cm above ground level. The questing larvae and adults of A. incisum tended to be found higher, however, with the greatest numbers recorded 40-50 cm (larvae) or 60-70 cm (adults) above ground level. Most of the adult ticks (81.1% -100%), nymphs (78.6%-100%) and larval clusters (100%) found on a forest trail remained questing at the same location over a 24-h period. Carbon-dioxide traps in the rainforest attracted, 50% of the ticks observed questing on the nearby vegetation and, curiously, the CO(2) traps set deep in the forest attracted far fewer ticks than similar traps set by the dam. The ecological relationships between the ticks, their hosts and the rainforest environment are discussed.

Rickettsia in Synanthropic and Domestic Animals and Their Hosts from Two Areas of Low Endemicity for Brazilian Spotted Fever in the Eastern Region of Minas Gerais, Brazil

The aim of this study was to understand the current epidemiology of rickettsial diseases in two rickettsial-endemic regions in Brazil. In the municipalities of Pingo D`Agua and Santa Cruz do Escalvado, among serum samples obtained from horses and dogs, reactivity by immunofluorescent assay against spotted fever group rickettsiae was verified. In some serum samples from opossums (Didelphis aurita) captured in Santa Cruz do Escalvado, serologic response against rickettsiae was also verified. Polymerase chain reaction identified rickettsiae only in ticks and fleas obtained in Santa Cruz do Escalvado. Rickettsiae in samples had 100% sequence homology with Rickettsia fells. These results highlight the importance of marsupials in maintenance of the sylvatic cycle of rickettsial disease and potential integration with the domestic cycle. Our data also support the importance of horses and dogs as sentinels in monitoring circulation of rickettsiae in an urban area.

Density of the Near Threatened jaguar Panthera onca in the caatinga of north-eastern Brazil

We report the first estimate of jaguar density in the semi-arid caatinga biome of north-eastern Brazil. During August-October 2007, in the Serra da Capivara National Park, we used camera traps to identify and count jaguars. Jaguar abundance and density were calculated using mark-recapture models. In a sampling effort of 1,249 camera-trap-nights we identified 12 adult jaguars and estimated an 2 abundance of 14 +/- 3.6 jaguars in an area of 524 km(2), i.e. a density of 2.67 +/- 1.00 jaguars per 100 km(2). This estimate is higher than in most other Brazilian biomes and indicates Serra da Capivara National Park as an important reserve for protecting jaguars in north-eastern Brazil.