Response of polychaetes to oil spills in natural and defaunated subtropical mangrove sediments from Paranaguá bay (SE Brazil)

A short-term short-scale field manipulation experiment was designed to assess the effects of total or partial defaunation, by sediment drying or diesel oil respectively, on polychaete recolonization rates in mangrove sediments of Paranaguá Bay, SE Brazil. After replacement of defaunated cores in the field, disturbed and adjacent undisturbed control sites were subsequently sampled together with adjacent undisturbed control sites on different dates over a 64-day period. Analyses of variance were carried out to test for differences in polychaete populational densities among experimental treatments and sampling dates. Examination of cores impacted by oil showed that most polychaete species kept rather active, quickly reacting to mechanical or light stimuli or moving rapidly. Polychaete recolonization of local mangroves after small-scale disturbance by oil was a fast process, in contrast to that following total defaunation by sediment drying. Rapid recolonization was largely dependent upon the differing mobility of adults of individual species from unaffected areas nearby, epifaunal crawlers or infaunal predators exhibiting the most rapid recovery rates. Conversely, the slow-paced recolonization of completely defaunated areas was due to the modification of sediment properties by drying and to the absence of larvae or juveniles of local species during the experiment.     

Evaluation of Cell Type Annotation R Packages on Single-cell RNA-seq Data

Annotating cell types is a critical step in single-cell RNA sequencing(scRNA-seq) data analysis. Some supervised or semi-supervised classification methods have recently emerged to enable automated cell type identification. However, comprehensive evaluations of these methods are lacking. Moreover, it is not clear whether some classification methods originally designed for analyzing other bulk omics data are adaptable to scRNA-seq analysis. In this study, we evaluated ten cell type annotation methods publicly available as R packages. Eight of them are popular methods developed specifically for single-cell research, including Seurat, scmap, SingleR, CHETAH, SingleCellNet, scID, Garnett, and SCINA. The other two methods were repurposed from deconvoluting DNA methylation data, i.e., linear constrained projection(CP) and robust partial correlations(RPC). We conducted systematic comparisons on a wide variety of public scRNA-seq datasets as well as simulation data. We assessed the accuracy through intra-dataset and inter-dataset predictions; the robustness over practical challenges such as gene filtering, high similarity among cell types, and increased cell type classes; as well as the detection of rare and unknown cell types. Overall, methods such as Seurat, SingleR, CP, RPC, and SingleCellNet performed well, with Seurat being the best at annotating major cell types. Additionally, Seurat, SingleR, CP, and RPC were more robust against downsampling. However, Seurat did have a major drawback at predicting rare cell populations, and it was suboptimal at differentiating cell types highly similar to each other,compared to SingleR and RPC. All the code and data are available from https://github.com/qianhuiSenn/scRNA_cell_deconv_benchmark.     

Distribution patterns of the crab Ucides cordatus (Brachyura, Ucididae) at different spatial scales in subtropical mangroves of Paranaguá Bay (southern Brazil)

Heterogeneity in the distribution of organisms occurs at a range of spatial scales, which may vary from few centimeters to hundreds of kilometers. The exclusion of small-scale variability from routine sampling designs may confound comparisons at larger scales and lead to inconsistent interpretation of data. Despite its ecological and social-economic importance, little is known about the spatial structure of the mangrove crab Ucides cordatus in the southwest Atlantic. Previous studies have commonly compared densities at relatively broad scales, relying on alleged distribution patterns (e.g., mangroves of distinct composition and structure). We have assessed variability patterns of U. cordatus in mangroves of Paranaguá Bay at four levels of spatial hierarchy (10?s?km, km, 10?s?m and m) using a nested ANOVA and variance components measures. The potential role of sediment parameters, pneumatophore density, and organic matter content in regulating observed patterns was assessed by multiple regression models. Densities of total and non-commercial size crabs varied mostly at 10?s?m to km scales. Densities of commercial size crabs differed at the scales of 10?s?m and 10?s?km. Variance components indicated that small-scale variation was the most important, contributing up to 70% of the crab density variability. Multiple regression models could not explain the observed variations. Processes driving differences in crab abundance were not related to the measured variables. Small-scale patchy distribution has direct implications to current management practices of U. cordatus. Future studies should consider processes operating at smaller scales, which are responsible for a complex mosaic of patches within previously described patterns.     

The polymorphism − 1131T > C in apolipoprotein A5 gene is associated with dyslipidemia in Brazilian subjects

Background

Polymorphisms in apolipoprotein A5 gene (APOA5) have been associated with higher triglyceride levels in many populations. The aim of the study was to determine the allelic and genotypic distribution of the APOA5 − 1131T > C polymorphism and to identify the association of the genetic variant and the risk for dyslipidemia.

Methods

We genotyped 109 dyslipidemic subjects and 107 controls. The total cholesterol, triglycerides and HDL-c were determined enzymatically. Comparison of means among groups was calculated by ANOVA. Significant differences among groups were evaluated by Student–Newman–Keuls test.

Results

The minor allele C was more frequent in dyslipidemic subjects than controls (p = 0.019) and confers an increased individual risk for dyslipidemia (OR = 1.726, CI 95% = 1.095–2.721). The genotype analysis by gender showed that this allele was more frequent in dyslipidemic males (p = 0.037; OR = 2.050, CI 95% = 1.042–4.023). When participants were analyzed according to genotypes TT and TC/CC, C-carriers presented higher cholesterol and triglycerides levels than TT homozygous (p = 0.046 and 0.049, respectively).

Conclusions

The allele C confers higher total cholesterol and triglycerides levels in dyslipidemic adults. The APOA5 − 1131T > C polymorphism is associated with dyslipidemia in male subjects.     

Comorbidity between major depressive disorder and physical diseases: a comprehensive review of epidemiology,mechanisms and management

Populations with common physical diseases – such as cardiovascular diseases, cancer and neurodegenerative disorders – experience substantially higher rates of major depressive disorder (MDD) than the general population. On the other hand, people living with MDD have a greater risk for many physical diseases. This high level of comorbidity is associated with worse outcomes, reduced adherence to treatment, increased mortality, and greater health care utilization and costs. Comorbidity can also result in a range of clinical challenges, such as a more complicated therapeutic alliance, issues pertaining to adaptive health behaviors, drug-drug interactions and adverse events induced by medications used for physical and mental disorders. Potential explanations for the high prevalence of the above comorbidity involve shared genetic and biological pathways. These latter include inflammation, the gut microbiome, mitochondrial function and energy metabolism, hypothalamic-pituitary-adrenal axis dysregulation, and brain structure and function. Furthermore, MDD and physical diseases have in common several antecedents related to social factors (e.g., socioeconomic status), lifestyle variables (e.g., physical activity, diet, sleep), and stressful live events (e.g., childhood trauma). Pharmacotherapies and psychotherapies are effective treatments for comorbid MDD, and the introduction of lifestyle interventions as well as collaborative care models and digital technologies provide promising strategies for improving management. This paper aims to provide a detailed overview of the epidemiology of the comorbidity of MDD and specific physical diseases, including prevalence and bidirectional risk; of shared biological pathways potentially implicated in the pathogenesis of MDD and common physical diseases; of socio-environmental factors that serve as both shared risk and protective factors; and of management of MDD and physical diseases, including prevention and treatment. We conclude with future directions and emerging research related to optimal care of people with comorbid MDD and physical diseases.     

Use of potassium depletion to assess adaptation of ruminal bacteria to ionophores.

When mixed ruminal bacteria from cattle fed timothy hay were suspended in a medium containing a low concentration of potassium, monensin and lasalocid catalyzed a rapid depletion of potassium from cells. The ionophore-mediated potassium depletion was concentration dependent, and it was possible to describe the relationship with saturation constants. Mixed ruminal bacteria never lost more than 50% of their potassium (Kmax = 46%), and the concentrations of monensin and lasalocid needed to cause half-maximal potassium depletion (Kd) were 178 and 141 nM, respectively. When cattle were fed 350 mg of monensin per day, the ratio of ruminal acetate to propionate decreased from 4.2 to 2.9, and the Kd of monensin was eightfold greater than the value for mixed ruminal bacteria from control animals. Monensin supplementation also caused a twofold increase in the Kd of lasalocid. Lasalocid supplementation (350 mg per day) had no effect on the ruminal acetate-to-propionate ratio, but it caused a twofold increase in the Kd values of monensin and lasalocid. Increases in Kd occurred almost immediately after ionophore was added to the ration, and the Kd values returned to their prefeeding values within 14 days of withdrawal. Ionophore supplementation had no effect on the Kmax values, and approximately 50% of the population was always highly ionophore resistant. Because the Kd values of even adapted ruminal bacteria were low (< 1.5 microM), it appears that a large proportion of the ruminal ionophore is bound nonselectively to feed particles or ionophore-resistant bacteria.     

Intracellular coagulation inhibits the extraction of proteins from Prochloron

Protein extraction from the prokaryotic alga Prochloron LP (isolated from the ascidian host Lissoclinum patella) was complicated by an irrevers