Phylogeography of the tree Hymenaea stigonocarpa (Fabaceae: Caesalpinioideae) and the influence of quaternary climate changes in the Brazilian cerrado

BACKGROUND AND AIMS: Hymenaea stigonocarpa (Fabaceae: Caesalpinioideae) is an endemic tree from the Brazilian cerrado (savanna vegetation), a biome classified as a hotspot for conservation priority. This study investigates the phylogeographic structure of H. stigonocarpa, in order to understand the processes that have led to its current spatial genetic pattern. METHODS: The polymorphism level and spatial distribution of variants of the plastid non-coding region between the genes psbC and trnS were investigated in 175 individuals from 17 populations, covering the greater part of the total distribution of the species. Molecular diversity indices were calculated and intra-specific relationships were inferred by the construction of haplotype networks using the median-joining method. Genetic differentiation among populations and main geographical groups was evaluated using spatial analysis of molecular variance (SAMOVA). KEY RESULTS: Twenty-three different haplotypes were identified. The level of differentiation among the populations analysed was relatively high (F(ST) = 0.692). Phylogeographic analyses showed a clear association between the haplotype network and geographic distribution of populations, revealing three main geographical groups: western, central and eastern. SAMOVA corroborated this finding, indicating that most of the variation can be attributed to differences among these three groups (58.8 %), with little difference among populations within groups (F(SC) = 0.252). CONCLUSIONS: The subdivision of the geographic distribution of H. stigonocarpa populations into three genetically differentiated groups can be associated with Quaternary climatic changes. The data suggest that during glacial times H. stigonocarpa populations became extinct in most parts of the southern present-day cerrado area. Milder climatic conditions in the north and eastern portions of the cerrado resulted in maintenance of populations in these regions. Thus it is inferred that the most southern part of the present-day cerrado was re-colonized by different lineages from northern parts of this biome, after postglacial climate amelioration.     

Use of leukocytes as treatment for endometritis in mares experimentally infected with Streptococcus equi subsp. zooepidemicus

This study compared four treatments for bacterial endometritis in mares experimentally infected with Streptococcus zooepidemicus. Twenty-five mares were used, 20 resistant and five susceptible to endometritis. Mares would be in estrus when infected. Twenty-four hours after inoculation, clinical, bacteriological and cytological examinations were performed and repeated until the first occurrence: negative cytology and no Streptococcus growth or the seventh day post-infection. All mares showed clinical signs of endometritis and were assigned to one of the following treatments: (1) intrauterine infusion of fresh leukocytes; (2) intrauterine infusion of frozen-thawed leukocytes; (3) intrauterine infusion of lysed leukocytes; (4) intrauterine infusion of recombinant human interleukin-8 (rhIL-8); (5) control. Mares were submitted to all treatments, with at least a 14-day interval between treatments in a Latin square design. Treatment did not affect (P=0.121) time needed for resistant mares to eliminate bacteria. Time needed for elimination of bacteria was similar in susceptible mares treated with fresh and frozen leukocytes (P=0.333). Susceptible mares treated with frozen leukocytes also did not differ from those treated with lysed leukocytes (P=0.227) for time to eliminate bacteria, but were significantly different (P>0.02) from those treated with rhIL-8 and control. In resistant mares, physical clearance ability was probably the responsible for bacterial elimination. Intrauterine infusions in susceptible mares with viable or lysed leukocytes associated or not to opsonizing factors, reduced the time to elimination of bacteria. Infusions with bactericidal effect (functional neutrophils and granules) was likely effective and responsible for the more rapid elimination of bacteria in susceptible mares.     

Histoplasmosis as cause of penile ulcer in acquired immune deficiency syndrome (AIDS): three case reports

Background Histoplasma capsulatum is the causative agent of American histoplasmosis. The relationship between disseminated histoplasmosis and AIDS has been well established. Widespread hematogenous dissemination of Histoplasma capsulatum in HIV positive patients can cause a plethora of clinical manifestations; virtually any organic system can be affected. However, genital ulceration by H. capsulatum in patients with AIDS is a real challenge during investigation of the infection due to the great variety of differential diagnoses that are involved. Method The diagnosis was performed by histopathologic study; H. capsulatum was detected by silver staining (Grocott staining) and confirmed by immunocytochemistry. Results We report three cases of histoplasmosis in patients with AIDS, in which we observed genital ulcers, an unusual form of presentation of this disease. In one of these cases, the treatment resulted in total cure. Conclusion The cases reported herein are to illustrate the plurality of pathologies and clinical manifestations, which may affect immunocompromised patients. The correct diagnosis of fungal diseases in these patients following well established treatment will improve the prognosis.     

Seasonal variation of suicide in Brazil

Most of what is known about the seasonal variation in suicide rate originates from studies conducted in the northern hemisphere; very few studies have been done in the southern hemisphere. The purpose of the present study was to explore the possibility that in Brazil, the seasonal variation of suicides is a function of photoperiod. This was accomplished by analyzing monthly suicide data for a 12 yr period (1979 to 1990), within latitudes ranging from 2°N to 33°S. Single cosinor analyses with periods of 12 or 6 months were applied to time series of monthly total and suicidal deaths, separated by gender and state. Significant spring or early summer peaks of suicide were found only in the south of Brazil for both men and women, except for the latter in one state. These peaks did not coincide with those found for total deaths, which occurred in the autumn or winter in all areas. No significant six-month period was found. In the present study, the chance of a suicide was typically 10-17% higher during the peak period than during the other months of the year. Although this moderate seasonal effect might not be sufficient to justify planning large scale prophylactic interventions, those dealing with patients who have suicide ideation should be aware of this high risk time.     

RAD51AP1 mediates RAD51 activity through nucleosome interaction

RAD51-associated protein 1 (RAD51AP1) is a key protein in the homologous recombination (HR) DNA repair pathway. Loss of RAD51AP1 leads to defective HR, genome instability, and telomere erosion. RAD51AP1 physically interacts with the RAD51 recombinase and promotes RAD51-mediated capture of donor DNA, synaptic complex assembly, and displacement-loop formation when tested with nucleosome-free DNA substrates. In cells, however, DNA is packaged into chromatin, posing an additional barrier to the complexities of the HR reaction. In this study, we show that RAD51AP1 binds to nucleosome core particles (NCPs), the minimum basic unit of chromatin in which approximately two superhelical turns of 147 bp double-stranded DNA are wrapped around one histone octamer with no free DNA ends remaining. We identified a C-terminal region in RAD51AP1, including its previously mapped DNA-binding domain, as critical for mediating the association between RAD51AP1 and both the NCP and the histone octamer. Using in vitro surrogate assays of HR activity, we show that RAD51AP1 is capable of promoting duplex DNA capture and initiating joint-molecule formation with the NCP and chromatinized template DNA, respectively. Together, our results suggest that RAD51AP1 directly assists in the RAD51-mediated search for donor DNA in chromatin. We present a model, in which RAD51AP1 anchors the DNA template through affinity for its nucleosomes to the RAD51-ssDNA nucleoprotein filament.     

Integrating dark diversity and functional traits to enhance nature conservation of epiphytic lichens: a case study from Northern Italy

Biodiversity and Conservation - Mountains provide a timely opportunity to examine the potential effects of climate change on biodiversity. However, nature conservation in mountain areas have mostly...     

Fast Reconstruction of Compact Context-Specific Metabolic Network Models

Systemic approaches to the study of a biological cell or tissue rely increasingly on the use of context-specific metabolic network models. The reconstruction of such a model from high-throughput data can routinely involve large numbers of tests under different conditions and extensive parameter tuning, which calls for fast algorithms. We present fastcore, a generic algorithm for reconstructing context-specific metabolic network models from global genome-wide metabolic network models such as Recon X. fastcore takes as input a core set of reactions that are known to be active in the context of interest (e.g., cell or tissue), and it searches for a flux consistent subnetwork of the global network that contains all reactions from the core set and a minimal set of additional reactions. Our key observation is that a minimal consistent reconstruction can be defined via a set of sparse modes of the global network, and fastcore iteratively computes such a set via a series of linear programs. Experiments on liver data demonstrate speedups of several orders of magnitude, and significantly more compact reconstructions, over a rival method. Given its simplicity and its excellent performance, fastcore can form the backbone of many future metabolic network reconstruction algorithms.     

Plant size,flowering synchrony and edge effects: What,how and where they affect the reproductive success of a Neotropical tree species

Plant reproductive success is supposedly influenced by phenology and individual size, which may be modified under edge effects. We tested if reproductive success, estimated by fruit set, in Senefeldera verticillata (Euphorbiaceae) is related to flowering synchrony and tree size, including plant height and circumference at breast height. The study was carried out in the interior and in edges of clearings for gas pipelines and electric lines of a lowland rainforest in south‐eastern Brazil. Monthly observations were performed during one reproductive season, of 19 individuals that grew at edges of electric lines and gas pipelines and at forest interior. Reproductive success was significantly higher at forest interior than at gas pipeline area; there was no significant difference between gas pipeline and electric line areas or between forest interior and electric line area. In the forest edges, only plant height was positively related to plant reproductive success. This is probably related to crown exposure to sunlight, which enhances flower production. At forest interior, reproductive success was positively influenced by the synchrony of flowering activity among neighbouring individuals. In contrast, flowering synchrony based on phenophase intensity negatively impacted reproductive success. Senefeldera verticillata shows temporal dioecy and is mainly pollinated by small social bees, and the high degree of flowering synchrony at low intensity may increase the number of mating partners and therefore enhance its reproductive success. Inside the forest fragments, individuals with thicker trunks showed lower reproductive success, which may be related to a loss of reproductive capacity of older individuals. Our results evidenced the complexity of responses experienced by tropical plants subjected to forest fragmentation because of linear clearings.     

Fine-scale genetic structure of the threatened rosewood Dalbergia nigra from the Atlantic Forest: comparing saplings versus adults and small fragment versus continuous forest

Assessing the population genetic structure of threatened species is important for developing successful conservation strategies. In this study, we evaluated the fine-scale spatial genetic structure (SGS) of Dalbergia nigra from a regenerating secondary forest fragment and compared it with previous data from a primary forest of a large reserve. A total of 107 adult and 111 saplings were mapped and genotyped for seven microsatellite loci. The genetic diversity was high and similar in adults (H _e?=?0.682) and saplings (H _e?=?0.680). The spatial extent of SGS was higher in adults than in saplings. Overlapping generations in the potentially reproductive individuals is the likely explanation for the higher SGS in adults (Sp?=?0.016) in relation to the saplings (Sp?=?0.010). The SGS in the adults from the secondary forest fragment was similar to that found in the primary forest. Considering the SGS found in adults, from both the secondary and primary forests, seeds for ex situ conservation should be collected from trees at least 80 m apart to reduce the genetic similarity between samples. These results highlight the importance of preserving small forest fragments to allow successful regeneration and maintenance of the genetic diversity in D. nigra.     

Solution NMR analysis of the interaction between the actinoporin Sticholysin I and DHPC micelles—Correlation with backbone dynamics

Sticholysin I (StI), an actinoporin expressed as a water‐soluble protein by the sea anemone Stichodactyla helianthus, binds to natural and model membranes, forming oligomeric pores. It is proposed that the first event of a multistep pore formation mechanism consists of the monomeric protein attachment to the lipid bilayer. To date there is no high‐resolution structure of the actinoporin pore or other membrane‐bound form available. Here we evaluated StI:micelle complexes of variable lipid composition to look for a suitable model for NMR studies. Micelles of pure or mixed lysophospholipids and of dihexanoyl phosphatidylcholine (DHPC) were examined. The StI:DHPC micelle was found to be the best system, yielding a stable sample and good quality spectra. A comprehensive chemical shift perturbation analysis was performed to map the StI membrane recognition site in the presence of DHPC micelles. The region mapped (residues F⁵¹, R⁵², S⁵³ in loop 3; F¹⁰⁷, D¹⁰⁸, Y¹⁰⁹, W¹¹¹, Y¹¹², W¹¹⁵ in loop 7; Q¹²⁹, Y¹³², D¹³⁴, M¹³⁵, Y¹³⁶, Y¹³⁷, G¹³⁸ in helix‐α2) is in agreement with previously reported data, but additional residues were found to interact, especially residues V⁸¹, A⁸², T⁸³, G⁸⁴ in loop 5, and A⁸⁵, A⁸⁷ in strand‐β5. Backbone dynamics measurements of StI free in solution and bound to micelles highlighted the relevance of protein flexibility for membrane binding and suggested that a conformer selection process may take place during protein–membrane interaction. We conclude that the StI:DHPC micelles system is a suitable model for further characterization of an actinoporin membrane‐bound form by solution NMR. Proteins 2014; 82:1022–1034. © 2013 Wiley Periodicals, Inc.