Allergen-Specific Immunotherapy Alters the Frequency,as well as the FcR and CLR Expression Profiles of Human Dendritic Cell Subsets

Allergen-specific immunotherapy (AIT) induces tolerance and shifts the Th2 response towards a regulatory T-cell profile. The underlying mechanisms are not fully understood, but dendritic cells (DC) play a vital role as key regulators of T-cell responses. DCs interact with allergens via Fc receptors (FcRs) and via certain C-type lectin receptors (CLRs), including CD209/DC-SIGN, CD206/MR and Dectin-2/CLEC6A. In this study, the effect of AIT on the frequencies as well as the FcR and CLR expression profiles of human DC subsets was assessed. PBMC was isolated from peripheral blood from seven allergic donors before and after 8 weeks and 1 year of subcutaneous AIT, as well as from six non-allergic individuals. Cells were stained with antibodies against DC subset-specific markers and a panel of FcRs and CLRs and analyzed by flow cytometry. After 1 year of AIT, the frequency of CD123⁺ DCs was increased and a larger proportion expressed FcεRI. Furthermore, the expression of CD206 and Dectin-2 was reduced on CD141⁺ DCs after 1 year of treatment and CD206 as well as Dectin-1 was additionally down regulated in CD1c⁺ DCs. Interestingly, levels of DNGR1/CLEC9A on CD141⁺ DCs were increased by AIT, reaching levels similar to cells isolated from non-allergic controls. The modifications in phenotype and occurrence of specific DC subsets observed during AIT suggest an altered capacity of DC subsets to interact with allergens, which can be part of the mechanisms by which AIT induces allergen tolerance.     

Rearing performances and environmental assessment of sea cage farming in Tunisia using life cycle assessment (LCA) combined with PCA and HCPC

Purpose

The present study aims to understand the influence of rearing practices and the contributions of production phases of fish farming to their environmental impacts and determine which practices and technical characteristics can best improve the farms’ environmental performance. Another objective is to identify the influence of variability in farming practices on the environmental performances of sea cage aquaculture farms of sea bass and sea bream in Tunisia by using principal component analysis (PCA) and hierarchical clustering on principal components (HCPC) methods and then combining the classification with life cycle assessment (LCA).

Methods

The approach consisted of three major steps: (i) of the 24 aquaculture farms in Tunisia, 18 were selected which follow intensive rearing practices in sea cages of European sea bass (Dicentrarchus labrax) and gilthead sea bream (Sparus aurata) and then a typology was developed to classify the studied farms into rearing practice groups using HCPC; (ii) LCA was performed on each aquaculture farm and (iii) mean impacts and contributions of production phases were calculated for each group of farms. Impact categories included acidification, eutrophication, global warming, land occupation, total cumulative energy demand and net primary production use.

Results and discussion

Results revealed high correlation between rearing practices and impacts. The feed-conversion ratio (FCR), water column depth under the cages and cage size had the greatest influence on impact intensity. Rearing practices and fish feed were the greatest contributors to the impacts studied due to the production of fish meal and oil and the low efficiency of feed use, which generated large amounts of nitrogen and phosphorus emissions. It is necessary to optimise the diet formulation and to follow better feeding strategies to lower the FCR and improve farm performance. Water column depth greatly influenced the farms’ environmental performance due to the increase in waste dispersion at deeper depths, while shallow depths resulted in accumulation of organic matter and degradation of water quality. Cage size influences environmental performances of aquaculture farms. Thus, from an environmental viewpoint, decision makers should grant licences for farms in deeper water with larger cages and encourage them to improve their FCRs.

Conclusions

This study is the first attempt to combine the HCPC method and the LCA framework to study the environmental performance of aquacultural activity. The typology developed captures the variability among farms because it considers several farm characteristics in the classification. The LCA demonstrated that technical parameters in need of improvement are related to the technical expertise of farm managers and workers and to the location of the farm.

     

Selective MicroRNA-Offset RNA Expression in Human Embryonic Stem Cells

Small RNA molecules, including microRNAs (miRNAs), play critical roles in regulating pluripotency, proliferation and differentiation of embryonic stem cells. miRNA-offset RNAs (moRNAs) are similar in length to miRNAs, align to miRNA precursor (pre-miRNA) loci and are therefore believed to derive from processing of the pre-miRNA hairpin sequence. Recent next generation sequencing (NGS) studies have reported the presence of moRNAs in human neurons and cancer cells and in several tissues in mouse, including pluripotent stem cells. In order to gain additional knowledge about human moRNAs and their putative development-related expression, we applied NGS of small RNAs in human embryonic stem cells (hESCs) and fibroblasts. We found that certain moRNA isoforms are notably expressed in hESCs from loci coding for stem cell-selective or cancer-related miRNA clusters. In contrast, we observed only sparse moRNAs in fibroblasts. Consistent with earlier findings, most of the observed moRNAs derived from conserved loci and their expression did not appear to correlate with the expression of the adjacent miRNAs. We provide here the first report of moRNAs in hESCs, and their expression profile in comparison to fibroblasts. Moreover, we expand the repertoire of hESC miRNAs. These findings provide an expansion on the known repertoire of small non-coding RNA contents in hESCs.     

Osmotic pressure: resisting or promoting DNA ejection from phage?

Recent in vitro experiments have shown that DNA ejection from bacteriophage can be partially stopped by surrounding osmotic pressure when ejected DNA is digested by DNase I in the course of ejection. In this work, we argue by a combination of experimental techniques (osmotic suppression without DNase I monitored by UV absorbance, pulse-field electrophoresis, and cryo-transmission electron microscopy visualization) and simple scaling modeling that intact genome (i.e., undigested) ejection in a crowded environment is, on the contrary, enhanced or eventually complete with the help of a pulling force resulting from DNA condensation induced by the osmotic stress itself. This demonstrates that in vivo, the osmotically stressed cell cytoplasm will promote phage DNA ejection rather than resist it. The further addition of DNA-binding proteins under crowding conditions is shown to enhance the extent of ejection. We also found some optimal crowding conditions for which DNA content remaining in the capsid upon ejection is maximum, which correlates well with the optimal conditions of maximum DNA packaging efficiency into viral capsids observed almost 20 years ago. Biological consequences of this finding are discussed.     

Multiple properties of the splicing repressor SRp38 distinguish it from typical SR proteins

The SR protein SRp38 is a general splicing repressor that is activated by dephosphorylation during mitosis and in response to heat shock. Here we describe experiments that provide insights into the mechanism by which SRp38 functions in splicing repression. We first show that SRp38 redistributes and colocalizes with snRNPs, but not with a typical SR protein, SC35, during mitosis and following heat shock. Supporting the functional significance of this association, a micrococcal nuclease-sensitive component, i.e., an snRNP(s), completely rescued heat shock-induced splicing repression in vitro, and purified U1 snRNP did so partially. SRp38 contains an N-terminal RNA binding domain (RBD) and a C-terminal RS domain composed of two subdomains (RS1 and RS2 domains). Unexpectedly, an RS1 deletion mutant derivative specifically inhibited the second step of splicing, while an RS2 deletion mutant retained significant dephosphorylation-dependent repression activity. Using chimeric SRp38/SC35 proteins, we show that SC35-RBD/SRp38-RS can function as a general splicing activator and that the dephosphorylated version can act as a strong splicing repressor. SRp38-RBD/SC35-RS, however, was essentially inactive in these assays. Together, our results help to define the unusual features of SRp38 that distinguish it from other SR proteins.     

Ontogeny, understorey light interception and simulated carbon gain of juvenile rainforest evergreens differing in shade tolerance

Background and Aims

A long-running debate centres on whether shade tolerance of tree seedlings is mainly a function of traits maximizing net carbon gain in low light, or of traits minimizing carbon loss. To test these alternatives, leaf display, light-interception efficiency, and simulated net daily carbon gain of juvenile temperate evergreens of differing shade tolerance were measured, and how these variables are influenced by ontogeny was queried.

Methods

The biomass distribution of juveniles (17–740 mm tall) of seven temperate rainforest evergreens growing in low (approx. 4 %) light in the understorey of a second-growth stand was quantified. Daytime and night-time gas exchange rates of leaves were also determined, and crown architecture was recorded digitally. YPLANT was used to model light interception and carbon gain.

Results

An index of species shade tolerance correlated closely with photosynthetic capacities and respiration rates per unit mass of leaves, but only weakly with respiration per unit area. Accumulation of many leaf cohorts by shade-tolerant species meant that their ratios of foliage area to biomass (LAR) decreased more gradually with ontogeny than those of light-demanders, but also increased self-shading; this depressed the foliage silhouette-to-area ratio (STAR), which was used as an index of light-interception efficiency. As a result, displayed leaf area ratio (LAR_d = LAR × STAR) of large seedlings was not related to species shade tolerance. Self-shading also caused simulated net daily carbon assimilation rates of shade-tolerant species to decrease with ontogeny, leading to a negative correlation of shade tolerance with net daily carbon gain of large (500 mm tall) seedlings in the understorey.

Conclusions

The results suggest that efficiency of energy capture is not an important correlate of shade tolerance in temperate rainforest evergreens. Ontogenetic increases in self-shading largely nullify the potential carbon gain advantages expected to result from low respiration rates and long leaf lifespans in shade-tolerant evergreens. The main advantage of their long-lived leaves is probably in reducing the costs of crown maintenance.     

Epicardial Fat from Echocardiography: A New Method for Visceral Adipose Tissue Prediction

Objective: To validate transthoracic echocardiography as an easy and reliable imaging method for visceral adipose tissue (VAT) prediction. VAT is recognized as an important indicator of high cardiovascular and metabolic risk. Several methods are applied to estimate VAT, with different results. Research Methods and Procedures: We selected 60 healthy subjects (29 women, 31 men, 49.5 ± 16.2 years) with a wide range of body mass indexes. Each subject underwent transthoracic echocardiogram and magnetic resonance imaging (MRI) to measure epicardial fat thickness on the right ventricle. Measurements of epicardial adipose tissue thickness were obtained from the same echocardiographic and MRI views and points. MRI was also used to measure VAT cross‐sectional areas at the level of L4 to L5. Anthropometric indexes were also measured. Results: Subjects with predominant visceral fat accumulation showed higher epicardial adipose tissue thickness than subjects with predominant peripheral fat distribution: 9.97 ± 2.88 vs. 4.34 ± 1.98 (p = 0.005) and 7.19 ± 2.74 vs. 3.43 ± 1.64 (p = 0.004) in men and women, respectively. Simple linear regression analysis showed an excellent correlation between epicardial adipose tissue and waist circumference (r = 0.895, p = 0.01) and MRI abdominal VAT (r = 0.864, p = 0.01). Multiple regression analysis showed that epicardial adipose tissue thickness (r² = 0.442, p = 0.02) was the strongest independent variable correlated to MRI VAT. Bland test confirmed the good agreement between the two methods. Discussion: Epicardial adipose tissue showed a strong correlation with anthropometric and imaging measurements of VAT. Hence, transthoracic echocardiography could be an easy and reliable imaging method for VAT prediction.     

Multi-Organ Contribution to the Metabolic Plasma Profile Using Hierarchical Modelling

Hierarchical modelling was applied in order to identify the organs that contribute to the levels of metabolites in plasma. Plasma and organ samples from gut, kidney, liver, muscle and pancreas were obtained from mice. The samples were analysed using gas chromatography time-of-flight mass spectrometry (GC TOF-MS) at the Swedish Metabolomics centre, Umeå University, Sweden. The multivariate analysis was performed by means of principal component analysis (PCA) and orthogonal projections to latent structures (OPLS). The main goal of this study was to investigate how each organ contributes to the metabolic plasma profile. This was performed using hierarchical modelling. Each organ was found to have a unique metabolic profile. The hierarchical modelling showed that the gut, kidney and liver demonstrated the greatest contribution to the metabolic pattern of plasma. For example, we found that metabolites were absorbed in the gut and transported to the plasma. The kidneys excrete branched chain amino acids (BCAAs) and fatty acids are transported in the plasma to the muscles and liver. Lactic acid was also found to be transported from the pancreas to plasma. The results indicated that hierarchical modelling can be utilized to identify the organ contribution of unknown metabolites to the metabolic profile of plasma.     

Prediction of reversible IgG1 aggregation occurring in a size exclusion chromatography column is enabled through a model based approach

One important aspect of antibody separation being studied today is aggregation, as this not only leads to a loss in yield, but aggregates can also be hazardous if injected into the body. The aim of this study was to determine whether the methodology applied in the previous study could be used to predict the aggregation of a different batch of IgG1, and to model the aggregation occurring in a SEC column. Aggregation was found to be reversible. The equilibrium parameter was found to be 272 M^‐1 and the reaction kinetic parameter 1.33 × 10^‐5 s^‐1, both within the 95% confidence interval of the results obtained in the previous work. The effective diffusivities were estimated to be 1.45 × 10^‐13 and 1.90 10^‐14 m²/s for the monomers and dimers, respectively. Good agreement was found between the new model and the chromatograms obtained in the SEC experiments. The model was also able to predict the decrease of dimers due to the dilution and separation in the SEC column during long retention times.