The role of very small fragments in conserving genetic diversity of a common tree in a hyper fragmented Brazilian Atlantic forest landscape

In hyper fragmented biomes, conservation of extant biota relies on preservation and proper management of remnants. The maintenance of genetic diversity and functional connectivity in a landscape context is probably key to long-term conservation of remnant populations. We measured the genetic diversity in seedlings and adults of tree Copaifera langsdorffii and evaluated whether edge and density-dependent effects drive natural regeneration in a set of very small and degraded Brazilian Atlantic forest fragments. We evaluated the role of small remnants in the conservation of genetic diversity in a hyper fragmented landscape and discuss the challenge of long-term population sustainability of such altered habitats. High genetic diversity in adults indicated these fragments are valuable targets for C. langsdorffii in situ conservation, but both genetic diversity and divergence among patches decreased in seedlings. In our landscape, regeneration increased as it neared edges and adults; suggesting this population is resilient to fragmentation. However, at a broader scale, current levels of gene flow have not been sufficient to prevent the loss of genetic diversity across generations. Restoration plans, even at a small scale, are necessary to promote fragment connectivity and spatially expand opportunities for the fairly restricted gene flow observed in this severely fragmented Brazilian Atlantic forest region.     

In vivo assessment of subcutaneous fat in dogs by real-time ultrasonography and image analysis

Background

Systems for estimating body condition score (BCS) are currently used in canine practice to monitor fatness levels. These tools are cheap and easy to use but lack the necessary precision to monitor small changes in body fat, particularly during weight control treatments or in research. The present work aims to study the application of real-time ultrasonography (RTU) together with image analysis in the assessment of subcutaneous fat depots in dogs. Ultrasound images were collected from five anatomical locations (chest, flank, abdomen, thigh and lumbar) from 28 healthy dogs of different breeds and with a body weight (BW) ranging from 5.2 to 33.0 kg. BCS was collected by visual appraisal using a 5-point scale. Subcutaneous fat thickness (SFT) was estimated from RTU images, using the average of three measurements taken in fat deposits located above the muscles represented in each image. Correlations were established between SFT and BW or BCS as well as a classification of BCS-based fatness [overweight (BCS = 4), ideal (BCS = 3) and lean (BCS = 2)].

Results

SFT was found to differ between the five regions considered (P < 0.001). Abdomen and thigh were the areas displaying the widest variation for the different dogs included in the study and also those correlating most with BW, in contrast to the chest, which showed the least variation. Overall, a strong correlation was found between BCS and SFT. The highest correlations were established for the flank, abdomen and lumbar areas. In every anatomical area, a decrease in SFT was observed across all three BCS classes, ranging from 48 to 65 % among overweight and ideal dogs, and from 46 to 83 % among ideal and lean dogs.

Conclusions

Preliminary data showed that within this population there was a strong correlation between BCS and SFT estimated from RTU images. It was also observed that RTU measurements for fat thickness differed among the anatomical points surveyed suggesting differences in their sensitivity to a change in BCS. The images displaying the best prediction value for fatness variations were those collected at the lumbar and abdomen areas.

     

Evolution of Socioeconomic Conditions and Its Relation to Spatial–Temporal Changes of Giardiasis and Helminthiasis in Amazonian Children

EcoHealth - This study analyzed the evolution of socioeconomic, sanitary, and personal factors as well as spatiotemporal changes in the prevalence of helminthiasis and giardiasis in urban Amazonian...     

Importance of N2-Fixation on the Productivity at the North-Western Azores Current/Front System,and the Abundance of Diazotrophic Unicellular Cyanobacteria

To understand the impact of the northwestern Azores Current Front (NW-AzC/AzF) system on HCO₃⁻-and N₂-fixation activities and unicellular diazotrophic cyanobacteria (UCYN) distribution, we combined geochemical and biological approaches from the oligotrophic surface to upper mesopelagic waters. N₂-fixation was observed to sustain 45–85% of the HCO₃⁻-fixation in the picoplanktonic fraction performing 47% of the total C-fixation at the deep chlorophyll maximum north and south of the AzF. N₂-fixation rates as high as 10.9 μmol N m^-3 d^-1 and surface nitrate δ¹⁵N as low as 2.7‰ were found in the warm (18–24°C), most saline (36.5–37.0) and least productive waters south of the AzF, where UCYN were the least abundant. However, picoplanktonic UCYN abundances up to 55 cells mL^-1 were found at 45–200m depths in the coolest nutrient-rich waters north of the AzF. In this area, N₂-fixation rates up to 4.5 μmol N m^-3 d^-1 were detected, associated with depth-integrated H¹³CO₃⁻-fixation rates at least 50% higher than observed south of the AzF. The numerous eddies generated at the NW-AzC/AzF seem to enhance exchanges of plankton between water masses, as well as vertical and horizontal diapycnal diffusion of nutrients, whose increase probably enhances the growth of diazotrophs and the productivity of C-fixers.     

Exonic Splicing Mutations Are More Prevalent than Currently Estimated and Can Be Predicted by Using In Silico Tools

The identification of a causal mutation is essential for molecular diagnosis and clinical management of many genetic disorders. However, even if next-generation exome sequencing has greatly improved the detection of nucleotide changes, the biological interpretation of most exonic variants remains challenging. Moreover, particular attention is typically given to protein-coding changes often neglecting the potential impact of exonic variants on RNA splicing. Here, we used the exon 10 of MLH1, a gene implicated in hereditary cancer, as a model system to assess the prevalence of RNA splicing mutations among all single-nucleotide variants identified in a given exon. We performed comprehensive minigene assays and analyzed patient’s RNA when available. Our study revealed a staggering number of splicing mutations in MLH1 exon 10 (77% of the 22 analyzed variants), including mutations directly affecting splice sites and, particularly, mutations altering potential splicing regulatory elements (ESRs). We then used this thoroughly characterized dataset, together with experimental data derived from previous studies on BRCA1, BRCA2, CFTR and NF1, to evaluate the predictive power of 3 in silico approaches recently described as promising tools for pinpointing ESR-mutations. Our results indicate that ΔtESRseq and ΔHZ_EI-based approaches not only discriminate which variants affect splicing, but also predict the direction and severity of the induced splicing defects. In contrast, the ΔΨ-based approach did not show a compelling predictive power. Our data indicates that exonic splicing mutations are more prevalent than currently appreciated and that they can now be predicted by using bioinformatics methods. These findings have implications for all genetically-caused diseases.     

Robust Inference of Cell-to-Cell Expression Variations from Single- and K-Cell Profiling

Quantifying heterogeneity in gene expression among single cells can reveal information inaccessible to cell-population averaged measurements. However, the expression level of many genes in single cells fall below the detection limit of even the most sensitive technologies currently available. One proposed approach to overcome this challenge is to measure random pools of k cells (e.g., 10) to increase sensitivity, followed by computational “deconvolution” of cellular heterogeneity parameters (CHPs), such as the biological variance of single-cell expression levels. Existing approaches infer CHPs using either single-cell or k-cell data alone, and typically within a single population of cells. However, integrating both single- and k-cell data may reap additional benefits, and quantifying differences in CHPs across cell populations or conditions could reveal novel biological information. Here we present a Bayesian approach that can utilize single-cell, k-cell, or both simultaneously to infer CHPs within a single condition or their differences across two conditions. Using simulated as well as experimentally generated single- and k-cell data, we found situations where each data type would offer advantages, but using both together can improve precision and better reconcile CHP information contained in single- and k-cell data. We illustrate the utility of our approach by applying it to jointly generated single- and k-cell data to reveal CHP differences in several key inflammatory genes between resting and inflammatory cytokine-activated human macrophages, delineating differences in the distribution of ‘ON’ versus ‘OFF’ cells and in continuous variation of expression level among cells. Our approach thus offers a practical and robust framework to assess and compare cellular heterogeneity within and across biological conditions using modern multiplexed technologies.     

Determinant Factors of Untreated Dental Caries and Lesion Activity in Preschool Children Using ICDAS

The aim of the present study was to investigate determinant factors associated with the presence of dental caries and lesion activity in preschool children. A population-based, cross-sectional study was carried out with 843 children of aged three to five years enrolled at public and private preschools in the city of Campina Grande, Brazil. A questionnaire addressing socio-demographic data and oral health care was self-administered by parents/caregivers. Three dentists previously calibrated examined the children for the diagnosis of dental caries and lesion activity using the International Caries Detection and Assessment System (ICDAS). Nutritional status was evaluated based on the body mass index. Logistic regression analysis for complex samples was performed (α = 5%). The prevalence of dental caries was 66.3%. Among the children with caries, 88.0% had active lesions. Dental caries was more prevalent in girls (OR = 1.53, 95%CI: 1.05–2.23), in children from families with a monthly household income ≤US$312.50 (OR = 2.38, 95%CI: 1.65–3.43) and those whose mothers had up to eight years of schooling (OR = 1.55, 95%CI: 1.07–2.23). Lesion activity was significantly associated with mother’s schooling ≤ 8 years (OR = 2.15, 95%CI: 1.15–4.00). The prevalence rates of dental caries and lesion activity were high and mainly associated with a lower socioeconomic status and mother’s schooling.     

Functional Dentition in Brazilian Adults: An Investigation of Social Determinants of Health (SDH) Using a Multilevel Approach

Objectives

Estimate the prevalence of functional dentition among Brazilian adults using four different definitions and identify associated factors.

Methods

A cross-sectional study was conducted involving 9564 Brazilian adults aged 35–44 years who participated in the 2010 National Oral Health Survey. Data collection involved oral examinations and the administration of questionnaires. The following definitions were used: 1—WHO Functional Dentition (FDWHO: ≥ 20 teeth present); 2—well-distributed teeth (WDT: ≥ 10 teeth in each arch); 3 –Functional dentition classified by esthetics and occlusion (FD_Class5: dentitions that sequentially exhibit at least one tooth in each arch, at least 10 teeth in each arch, all maxillary and mandibular anterior teeth, three or four premolar posterior occluding pairs [POPs], and at least one molar POP bilaterally); 4—Functional dentition classified by esthetics, occlusion and periodontal status (FD_Class6: corresponds to FD_Class5 with the addition of periodontal status of all sextants in the oral cavity with, at most, shallow pockets and/or clinical attachment level of 5 mm (CPI ≤ 3 and/or CAL ≤ 1). The independent variables were individual factors (gender, self-declared skin color, schooling, monthly household income, age group, self-rated treatment need, dental pain, dental appointment in the previous 12 months and dental services) and contextual factors (Municipal Human Development Index [MHDI]), Gini coefficient, fluoridated water supply and oral health coverage). Multilevel mixed-effect Poisson regression analyses were performed.

Results

The prevalence of functional dentition based on the FDWHO, WDT, FD_Class5 and FD_Class6 definitions was 77.9%, 72.9%, 42.6% and 40.3%, respectively. Adults with ≥12 years of schooling and monthly household income from US$ 853 to 2557 had higher prevalence rates of FDWHO (PR: 1.41 and 1.10, respectively), WDT (PR: 1.58 and 1.14, respectively), FD_Class5 (PR: 2.03 and 1.27, respectively) and FD_Class6 (PR: 2.15 and 1.35, respectively). These values in the final models were adjusted for gender, self-declared skin color (FD_Class5), age group, self-rated treatment need (FDWHO, FD_Class5 and FD_Class6), dental appointment in the previous 12 months (FDWHO and WDT), dental services (FDWHO and WDT) and contextual factors. A very high MHDI and presence of fluoridated water supply were associated with higher prevalence rates of the four outcomes.

Conclusions

The incorporation of the criteria of new definitions of functional dentition led to a lower prevalence rate among Brazilian adults. Striking individual and contextual inequalities were identified with regard to the four definitions analyzed, which need to be addressed through inter-sector efforts.     

In silico Identification and Validation of a Linear and Naturally Immunogenic B-Cell Epitope of the Plasmodium vivax Malaria Vaccine Candidate Merozoite Surface Protein-9

Synthetic peptide vaccines provide the advantages of safety, stability and low cost. The success of this approach is highly dependent on efficient epitope identification and synthetic strategies for efficacious delivery. In malaria, the Merozoite Surface Protein-9 of Plasmodium vivax (PvMSP9) has been considered a vaccine candidate based on the evidence that specific antibodies were able to inhibit merozoite invasion and recombinant proteins were highly immunogenic in mice and humans. However the identities of linear B-cell epitopes within PvMSP9 as targets of functional antibodies remain undefined. We used several publicly-available algorithms for in silico analyses and prediction of relevant B cell epitopes within PMSP9. We show that the tandem repeat sequence EAAPENAEPVHENA (PvMSP9_E795-A808) present at the C-terminal region is a promising target for antibodies, given its high combined score to be a linear epitope and located in a putative intrinsically unstructured region of the native protein. To confirm the predictive value of the computational approach, plasma samples from 545 naturally exposed individuals were screened for IgG reactivity against the recombinant PvMSP9-RIRII_729-972 and a synthetic peptide representing the predicted B cell epitope PvMSP9_E795-A808. 316 individuals (58%) were responders to the full repetitive region PvMSP9-RIRII, of which 177 (56%) also presented total IgG reactivity against the synthetic peptide, confirming it validity as a B cell epitope. The reactivity indexes of anti-PvMSP9-RIRII and anti-PvMSP9_E795-A808 antibodies were correlated. Interestingly, a potential role in the acquisition of protective immunity was associated with the linear epitope, since the IgG1 subclass against PvMSP9_E795-A808 was the prevalent subclass and this directly correlated with time elapsed since the last malaria episode; however this was not observed in the antibody responses against the full PvMSP9-RIRII. In conclusion, our findings identified and experimentally confirmed the potential of PvMSP9_E795-A808 as an immunogenic linear B cell epitope within the P. vivax malaria vaccine candidate PvMSP9 and support its inclusion in future subunit vaccines.