Genome-wide association mapping of sexual incompatibility genes in cacao (<Emphasis Type="Italic">Theobroma cacao</Emphasis> L.)

Sexual compatibility limits the production of cacao plantations, being an important selection criterion in breeding programs. However, the current method for characterizing compatibility, based on the frequency of flower setting after controlled pollination, is time consuming, requiring a long time to identify self-compatible individuals. The identification of molecular markers in genomic regions can be an alternative to allow early selection of self-compatible plants. The present study aimed to identify SNP markers associated with sexual compatibility in cacao, by utilizing genome-wide association (GWAS) mapping. A population of 295 individuals mostly from third-generation breeding populations, but also founder clones, was used. This population was phenotypically characterized by hand pollinating 8199 flowers and evaluating the flower retention 15 days after pollination. In addition, leaf samples of each individual were collected and DNA extracted for genotyping by sequencing, generating 5301 SNP markers after cleaning. Genome-wide association mapping analysis was performed using Synbreed, GCTA, and TASSEL softwares. Significant markers associated to incompatibility, likely in strong linkage disequilibrium, were found within a region of 196 kb, in the proximal end of chromosome 4, suggesting the existence of a major gene in that region. However, this result should be validated in a larger population, considering that only 295 trees were used here. When the SNP effects were treated as random in the estimation process, many other regions in the genome appears to be involved with sexual incompatibility in cacao. Candidate genes were found not only in the proximal end of chromosome 4 but also spread in several other regions of the genome.     

Microbial Diversity in Cerrado Biome (Neotropical Savanna) Soils

The Cerrado, the largest savanna region in South America, is located in central Brazil. Cerrado physiognomies, which range from savanna grasslands to forest formations, combined with the highly weathered, acidic clay Cerrado soils form a unique ecoregion. In this study, high-throughput sequencing of ribosomal RNA genes was combined with shotgun metagenomic analysis to explore the taxonomic composition and potential functions of soil microbial communities in four different vegetation physiognomies during both dry and rainy seasons. Our results showed that changes in bacterial, archaeal, and fungal community structures in cerrado denso, cerrado sensu stricto, campo sujo, and gallery forest soils strongly correlated with seasonal patterns of soil water uptake. The relative abundance of AD3, WPS-2, Planctomycetes, Thermoprotei, and Glomeromycota typically decreased in the rainy season, whereas the relative abundance of Proteobacteria and Ascomycota increased. In addition, analysis of shotgun metagenomic data revealed a significant increase in the relative abundance of genes associated with iron acquisition and metabolism, dormancy, and sporulation during the dry season, and an increase in the relative abundance of genes related to respiration and DNA and protein metabolism during the rainy season. These gene functional categories are associated with adaptation to water stress. Our results further the understanding of how tropical savanna soil microbial communities may be influenced by vegetation covering and temporal variations in soil moisture.     

Barefoot Plantar Pressure Indicates Progressive Neurological Damage in Patients with Human T-Cell Lymphotropic Virus Type 1 Infection

Background

The human T-Cell Lymphotropic Virus Type 1 (HTLV-1) is a retrovirus associated with neurological alterations; individuals with HTLV-1 infection may develop HTLV-1 associated myelopathy / tropical spastic paraparesis (HAM/TSP). Frequent neurological complaints include foot numbness and leg weakness. In this study, we compared the distribution of the body weight on different areas of the foot in HTLV-1 patients with HAM/TSP, asymptomatic HTLV-1 patients, and healthy individuals.

Methodology

We studied 36 HTLV-1 infected patients, who were divided in two groups of 18 patients each based on whether or not they had been diagnosed with HAM/TSP, and 17 control subjects. The evaluation included an interview on the patient’s clinical history and examinations of the patient’s reflexes, foot skin tactile sensitivity, and risk of falling. The pressure distribution on different areas of the foot was measured with baropodometry, using a pressure platform, while the patients had their eyes open or closed.

Main Findings

The prevalence of neurological disturbances—altered reflexes and skin tactile sensitivity and increased risk of falling—was higher in HTLV-1 HAM/TSP patients than in HTLV-1 asymptomatic patients. The medium and maximum pressure values were higher in the forefoot than in the midfoot and hindfoot in both HTLV-1 groups. In addition, the pressure on the hindfoot was lower in HAM/TSP patients compared to control subjects.

Conclusions

The neurological disturbances associated with HTLV-1 infection gradually worsened from HTLV-1 asymptomatic patients to HAM/TSP patients. Baropodometry is a valuable tool to establish the extent of neurological damage in patients suffering from HTLV-1 infection.     

Comparative proteomic analysis of growth hormone secretagogue A233 treatment of murine macrophage cells J774A.2 indicates it has a role in antiviral innate response

BackgroundGrowth hormone secretagogues (GHS), among other factors, regulate the release of GH. The biological activity of the secretagogue peptide A233 as a promoter of growth and innate immunity in teleost fish has previously been demonstrated, but its role in the immune system of mammals is not well understood.MethodsThe effect of the peptide was investigated in J774A.2 macrophage cells using a comparative proteomics approach after 6 and 12 h of peptide stimulation.ResultsThe functional analysis of differentially modulated proteins showed that A233 peptide treatment appears to promote activation and ROS-dependent cytotoxic functions in macrophages and enhanced expression of antiviral protein complexes such as MAVS. In accordance with this hypothesis, we found that A233 treatment enhanced superoxide anion production and the IFN-γ level in J774A.2 cells and mouse splenocytes, respectively, and reduced viral load in a dengue virus mouse model of infection.ConclusionsThe growth hormone secretagogue A233 peptide promotes activation of ROS-dependent cytotoxic functions and exerts immunomodulatory effects that enable an antiviral state in a dengue virus mouse model.General SignificanceThe increase of IFN-γ level and the differential modulation of antiviral proteins by the A233 peptide suggest that the molecule could activate an innate immune response with a possible further impact in the treatment of acute and chronic diseases.     

Modeling bond correlations in denatured proteins and polypeptides

Bond‐orientational correlations for finite‐length homopolypeptides and a selected group of denatured proteins are obtained by numerical simulations using a polypeptide model with a potential of mean force. These correlations characterize the stiffness of the polypeptide backbone and are generally described by either an exponential or a power‐law decay in the asymptotic limit. However, for finite length polypeptides and unfolded proteins the correlations significantly deviate from either single exponential or power‐law behavior. A heuristic model is developed to analyze the correlations of homopolypeptides, which depends on the chain length and the side‐chain properties. The model contains power‐law and multi‐exponential terms, the latter which could be interpreted as local persistence lengths. In the asymptotic limit, the model reduces to the expected power‐law behavior. Simulations of denatured proteins show that the power‐law behavior of the correlations is significantly suppressed and only the multi‐exponential term is needed to model the correlations. In addition, average persistence lengths (ranging from 2.0 to 2.5 nm) are obtained from the correlations by fitting single exponentials and shown to be in general agreement with experiments, which also assume single exponential decay. © 2016 Wiley Periodicals, Inc. Biopolymers 105: 312–323, 2016.     

Salt-induced NO<Subscript>3</Subscript><Superscript>-</Superscript> uptake inhibition in cowpea roots is dependent on the ionic composition of the salt and its osmotic effect

Salinity remarkably inhibits NO₃ ^- uptake but the mechanisms are not well understood. This study was addressed to elucidate the role of ionic and osmotic components of salinity on NO₃ ^- influx and efflux employing classic kinetics involving a low affinity transport system (LATS) and a high affinity transport system (HATS). In the presence of KCl, NaCl, and Na₂SO₄ at 100 mM concentrations, in both LATS and HATS, Michaelis constant (K_m) was similar for the three salts and maximum rate (V_max) decreased as follows: KCl > NaCl > Na₂SO₄, compared to control indicating a non-competitive interaction with NO₃ ^-. Unexpectedly, iso-osmotic solutions (osmotic potential Ψ_π = -0.450) of polyethylene glycol (PEG, 17.84 %, v/v) and mannitol (100 mM) remarkably increased K_m in both the LATS and the HATS, but V_max did not change indicating a competitive inhibition. Under the PEG and mannitol treatments, K_m and V_max were higher than under the salt treatments. The salts increased slightly NO₃ ^- efflux in the following order KCl > NaCl > Na₂SO₄. In contrast, mannitol strongly stimulated and the PEG inhibited NO₃ ^- efflux. The obtained data reveal that salinity effects were not dependent on the anion type (Cl^- versus SO₄ ^2-) indicating a non-competitive inhibition mechanism between Cl^- and NO₃ ^-. In contrast, the cation types (K⁺ versus Na⁺) had a pronounced effect. The osmotic component is important to net NO₃ ^- uptake affecting remarkably the influx in both LATS and HATS components of cowpea roots.     

Diet–demography relationships in a long‐lived predator: from territories to populations

Understanding the mechanisms that shape animal population dynamics is of fundamental interest in ecology, evolution and conservation biology. Food supply is an important limiting factor in most animal populations and may have demographic consequences. Optimal foraging theory predicts greater consumption of preferred prey and less diet diversity when food is abundant, which may benefit key fitness parameters such as productivity and survival. Nevertheless, the correspondence between individual resource use and demographic processes in populations of avian predators inhabiting large geographic areas remains largely unexplored, particularly in complex ecosystems such as those of the Mediterranean basin. Based on a long‐term monitoring program of the diet and demography of Bonelli's eagle Aquila fasciata in western Europe, here we test the hypothesis that a predator's diet is correlated to its breeding productivity and survival at both the territorial and population levels, and ultimately to its population growth rate. At the territorial level, we found that productivity increased with greater consumption of European rabbits Oryctolagus cuniculus, the Bonelli's eagle's preferred prey, and pigeons, an important alternative prey for this predator. The survival of territorial pairs was negatively affected by higher diet diversity, which probably reflected the inability to find sufficient high quality prey. Diet effects at the population level were similar but more noticeable than at the territorial level, i.e. a greater consumption of rabbits, together with lesser consumption of small‐to‐medium avian species (‘other birds’; non‐preferred prey), increased productivity, while greater diet diversity and lower consumption of rabbits was associated with reduced survival and population growth rate. Overall, our study illustrates how the diet of a predator species can be closely related to key individual vital rates, which, in turn, leave a measurable fingerprint on population dynamics within and among populations across large spatial scales.     

How do primates affect seed germination? A meta‐analysis of gut passage effects on neotropical plants

Biotic seed dispersal is a key process maintaining biodiversity in tropical forests where most trees produce vertebrate‐dispersed seeds. Existing meta‐analyses suggest an overall positive effect of vertebrate gut passage on seed germination, but no significant effects for non‐flying mammals. However, previous meta‐analyses combined rodents (seed predators) and primates (seed dispersers) into the non‐flying mammals category, which may confound specific effects of each group on seed germination. However positive effects of monkeys on germination had previously been found in some studies. Here we disentangle the role of Neotropical primates as contributors to seed dispersal in tropical forests by running a meta‐analysis to determine the overall magnitude of gut passage effects on seed germination percentage and mean time to germination. We also compare effect sizes as a function of different feeding guilds, gut complexities, and seed size. Our results show a strong, positive effect of primates on seed germination percentage and on the number of days to first germination. Strictly frugivorous monkeys, the group most threatened by extinction, showed the highest dispersal quality, increasing germination percentage by 75%. Primates that include insects in their diets had no average effect on germination percentage or time. Gut passage had different outcomes on seeds with different sizes; both large and small seeds showed similar increases in germination percentages after gut passage, but only large seeds germinated faster than control seeds after gut passage. Our results show a relevant role for primates in providing high seed dispersal quality and as drivers of forest regeneration. The combined effects of defaunation and forest fragmentation may result in decreased regeneration of trees, which has the potential to affect negatively both forest structure and ecosystem processes. Finally, we provide general guidelines for standardizing research on seed dispersal by primates. Synthesis Consuming fleshy fruits and dispersing seeds is the main ecological service provided by vertebrates to plants. Vertebrate increases seed germination due to treatment given during digestive system passage. Previous meta‐analyses suggest an overall positive effect of vertebrate gut passage on germination, but no insights are available on its variation among different functional groups of mammals. Our analyses indicated that gut passage by Neotropical primates increased seed germination. Strict frugivores, the ones most threatened by extinction, were the most efficient. Our results show a relevant role for primates in providing high seed dispersal quality and as drivers of forest regeneration, which can be meaningful for conservation in a community scale.