Potential effects of ethnicity in genetic and environmental sources of variability in the stature, mass, and body mass index of children

We examined sources of variability in stature, body mass, and body mass index (BMI) in families of black and white elementary schoolchildren from Philadelphia, Pennsylvania. The sample consisted of 445 black and 379 white children, 7-13 years old, and their parents (total n = 2016). The sample was distributed among 596 nuclear families, each representing an independent pedigree. Maximum-likelihood-based variance decomposition methods were used to simultaneously estimate ethnic group-specific effects of genes, sex, age by sex, and unmeasured environmental factors on stature, body mass, and BMI. Likelihood ratio tests were performed to assess the significance of h2 estimates and differences in sigma g and sigma e between black and white families. Genes account for moderate proportions of the phenotypic variance (h2) of these traits in black and white children. In black and white children, respectively, h2 estimates were 0.37 and 0.53 for stature, 0.37 and 0.31 for body mass, and 0.38 and 0.24 for BMI (p < 0.0005). Although the differences in h2 between ethnic groups were not significant (stature, p = 0.23; body mass, p = 0.49; BMI, p = 0.14), black children exhibited a significantly greater total residual phenotypic standard deviation (sigma e and sigma g) in body mass and BMI and a significantly greater sigma e for stature compared with white children. The larger residual phenotypic variance in the black sample is likely due to exposure to unmeasured environmental factors that are not accounted for in this model. Given that sigma g for stature is not significantly different between ethnic groups, the slightly lower estimates in black children are due to the increased contribution of the environment to the phenotypic variance in this trait.     

Plasticity in flower size as an adaptation to variation in pollinator specificity

1. Mutualisms, including plant-pollinator interactions, are an important component of ecosystems. 2. Plants can avoid the costs of variation in pollinator benefit by maintaining specificity. 3. We hypothesise a novel mechanism to ensure specificity, which takes advantage of the cognitive abilities of specific pollinators to exclude non-specific flower visitors. 4. Inflorescences of the tropical vine genus Psiguria produce flowers at regular intervals, with subsequent flowers smaller than predecessors. 5. The principle pollinators, Heliconius spp., possess an excellent spatial memory. 6. Therefore, decreasing flower size may ensure specific pollination: once Heliconius individuals have learnt the location of an inflorescence they will return, but inconspicuous flowers should reduce visits by non-specific pollinators with poorer spatial memories. 7. We tested the predictions of this hypothesis with field experiments in Panama. We confirmed that flowers on inflorescences are smaller than their predecessors. 8. Paired experiments showed that larger flowers attracted more pollinators and that the presence of an initial large flower increased subsequent visitation by Heliconius spp. to small flowers, indicating learning behaviour. 9. These results suggest that learning behaviour and decreasing flower size maintain visits from specific pollinators while reducing those from non-specific pollinators. We propose this as a novel mechanism for promoting pollinator specificity and discuss its ecological significance.     

A power-law rheology-based finite element model for single cell deformation

Physical forces can elicit complex time- and space-dependent deformations in living cells. These deformations at the subcellular level are difficult to measure but can be estimated using computational approaches such as finite element (FE) simulation. Existing FE models predominantly treat cells as spring-dashpot viscoelastic materials, while broad experimental data are now lending support to the power-law rheology (PLR) model. Here, we developed a large deformation FE model that incorporated PLR and experimentally verified this model by performing micropipette aspiration on fibroblasts under various mechanical loadings. With a single set of rheological properties, this model recapitulated the diverse micropipette aspiration data obtained using three protocols and with a range of micropipette sizes. More intriguingly, our analysis revealed that decreased pipette size leads to increased pressure gradient, potentially explaining our previous counterintuitive finding that decreased pipette size leads to increased incidence of cell blebbing and injury. Taken together, our work leads to more accurate rheological interpretation of micropipette aspiration experiments than previous models and suggests pressure gradient as a potential determinant of cell injury.     

Metabolic Profiling and Flux Analysis of MEL-2 Human Embryonic Stem Cells during Exponential Growth at Physiological and Atmospheric Oxygen Concentrations

As human embryonic stem cells (hESCs) steadily progress towards regenerative medicine applications there is an increasing emphasis on the development of bioreactor platforms that enable expansion of these cells to clinically relevant numbers. Surprisingly little is known about the metabolic requirements of hESCs, precluding the rational design and optimisation of such platforms. In this study, we undertook an in-depth characterisation of MEL-2 hESC metabolic behaviour during the exponential growth phase, combining metabolic profiling and flux analysis tools at physiological (hypoxic) and atmospheric (normoxic) oxygen concentrations. To overcome variability in growth profiles and the problem of closing mass balances in a complex environment, we developed protocols to accurately measure uptake and production rates of metabolites, cell density, growth rate and biomass composition, and designed a metabolic flux analysis model for estimating internal rates. hESCs are commonly considered to be highly glycolytic with inactive or immature mitochondria, however, whilst the results of this study confirmed that glycolysis is indeed highly active, we show that at least in MEL-2 hESC, it is supported by the use of oxidative phosphorylation within the mitochondria utilising carbon sources, such as glutamine to maximise ATP production. Under both conditions, glycolysis was disconnected from the mitochondria with all of the glucose being converted to lactate. No difference in the growth rates of cells cultured under physiological or atmospheric oxygen concentrations was observed nor did this cause differences in fluxes through the majority of the internal metabolic pathways associated with biogenesis. These results suggest that hESCs display the conventional Warburg effect, with high aerobic activity despite high lactate production, challenging the idea of an anaerobic metabolism with low mitochondrial activity. The results of this study provide new insight that can be used in rational bioreactor design and in the development of novel culture media for hESC maintenance and expansion.     

FunRich: An open access standalone functional enrichment and interaction network analysis tool

As high‐throughput techniques including proteomics become more accessible to individual laboratories, there is an urgent need for a user‐friendly bioinformatics analysis system. Here, we describe FunRich, an open access, standalone functional enrichment and network analysis tool. FunRich is designed to be used by biologists with minimal or no support from computational and database experts. Using FunRich, users can perform functional enrichment analysis on background databases that are integrated from heterogeneous genomic and proteomic resources (>1.5 million annotations). Besides default human specific FunRich database, users can download data from the UniProt database, which currently supports 20 different taxonomies against which enrichment analysis can be performed. Moreover, the users can build their own custom databases and perform the enrichment analysis irrespective of organism. In addition to proteomics datasets, the custom database allows for the tool to be used for genomics, lipidomics and metabolomics datasets. Thus, FunRich allows for complete database customization and thereby permits for the tool to be exploited as a skeleton for enrichment analysis irrespective of the data type or organism used. FunRich ( http://www.funrich.org ) is user‐friendly and provides graphical representation (Venn, pie charts, bar graphs, column, heatmap and doughnuts) of the data with customizable font, scale and color (publication quality).     

Increased levels of (class switched) memory B cells in peripheral blood of current smokers

There is increasing evidence that a specific immune response contributes to the pathogenesis of COPD. B-cell follicles are present in lung tissue and increased anti-elastin titers have been found in plasma of COPD patients. Additionally, regulatory T cells (Tregs) have been implicated in its pathogenesis as they control immunological reactions. We hypothesize that the specific immune response in COPD is smoke induced, either by a direct effect of smoking or as a result of smoke-induced lung tissue destruction (i.e. formation of neo-epitopes or auto antigens). Furthermore, we propose that Tregs are involved in the suppression of this smoke-induced specific immune response.The presence of B cells, memory B cells and Tregs was assessed by flow cytometry in peripheral blood of 20 COPD patients and 29 healthy individuals and related to their current smoking status.COPD patients had lower (memory) B-cell percentages and higher Treg percentages in peripheral blood than healthy individuals, with a significant negative correlation between these cells. Interestingly, current smokers had higher percentages of (class-switched) memory B cells than ex-smokers and never smokers, irrespective of COPD.This increase in (class-switched) memory B cells in current smokers is intriguing and suggests that smoke-induced neo-antigens may be constantly induced in the lung. The negative correlation between B cells and Tregs in blood is in line with previously published observations that Tregs can suppress B cells. Future studies focusing on the presence of these (class switched) memory B cells in the lung, their antigen specificity and their interaction with Tregs are necessary to further elucidate the specific B-cell response in COPD.     

<Emphasis Type="Italic">In vitro</Emphasis> and <Emphasis Type="Italic">ex vivo</Emphasis> effect of hyaluronic acid on erythrocyte flow properties

Background  

Hyaluronic acid (HA) is present in many tissues; its presence in serum may be related to certain inflammatory conditions, tissue damage, sepsis, liver malfunction and some malignancies. In the present work, our goal was to investigate the significance of hyaluronic acid effect on erythrocyte flow properties. Therefore we performed in vitro experiments incubating red blood cells (RBCs) with several HA concentrations. Afterwards, in order to corroborate the pathophysiological significance of the results obtained, we replicated the in vitro experiment with ex vivo RBCs from diagnosed rheumatoid arthritis (RA) patients, a serum HA-increasing pathology.     

Assessment of the relative contribution of asexual propagation in a population of the coral-excavating sponge Cliona delitrix from the Bahamas

Cliona delitrix is a very destructive coral-excavating sponge in Caribbean coral reef systems, particularly for Montastraea species. Little is known about how these excavating sponges propagate across coral reefs. In this study a hypothesis was tested that coral breakage caused by the bioeroding activity facilitates the asexual propagation of this sponge and in turn favors the spread of the most aggressive sponge genotypes. An allozyme analysis, involving 12 loci systems of 52 sponge individuals from a total of 13 Montastraea heads, found that no two sponges possessed identical multi-locus genotypes. Contrary to the pattern expected for fragmenting species, the incidence of clonality and asexual propagation at the population level was minimal. The lack of correlation between genetic and physical distances for the studied sponges also suggests that population maintenance appears to derive from larval dispersal, with a spatial range of dispersal larger than the average distance between the coral heads (10–10² m).     

Neural network modelling of the influence of channelopathies on reflex visual attention

This paper introduces a model of Emergent Visual Attention in presence of calcium channelopathy (EVAC). By modelling channelopathy, EVAC constitutes an effort towards identifying the possible causes of autism. The network structure embodies the dual pathways model of cortical processing of visual input, with reflex attention as an emergent property of neural interactions. EVAC extends existing work by introducing attention shift in a larger-scale network and applying a phenomenological model of channelopathy. In presence of a distractor, the channelopathic network’s rate of failure to shift attention is lower than the control network’s, but overall, the control network exhibits a lower classification error rate. The simulation results also show differences in task-relative reaction times between control and channelopathic networks. The attention shift timings inferred from the model are consistent with studies of attention shift in autistic children.