Pan-genome sequence analysis using Panseq: an online tool for the rapid analysis of core and accessory genomic regions

Background  

The pan-genome of a bacterial species consists of a core and an accessory gene pool. The accessory genome is thought to be an important source of genetic variability in bacterial populations and is gained through lateral gene transfer, allowing subpopulations of bacteria to better adapt to specific niches. Low-cost and high-throughput sequencing platforms have created an exponential increase in genome sequence data and an opportunity to study the pan-genomes of many bacterial species. In this study, we describe a new online pan-genome sequence analysis program, Panseq.     

Dispersion modelling and measurement of emissions from the co-combustion of meat and bone meal with peat in a fluidised bed

Due to the ban on meat and bone meal (MBM) as an animal feed, combustion with energy recovery has been considered a viable alternative usage for the mounting stocks of MBM. The effects of the co-combustion of MBM and peat on flue gas emissions and fluidisation were studied using a bubbling fluidised bed (BFB) test facility (20 kW). The dispersion of emissions such as nitrogen dioxide (NO2), sulphur dioxide (SO2), carbon monoxide (CO), hydrogen chloride (HCl) and particulates was investigated for a proposed site and compared to the relevant national and international regulations. Concentrations of NO2, CO and HCl were less than 10% of legislative and guideline thresholds while ground level concentrations of SO2 were also below relevant EU and world guidelines. The results indicate the potential for using MBM as a co-fuel with peat in a BFB while maintaining high air quality standards.     

Pathological effects of the microsporidium Nosema ceranae on honey bee queen physiology (Apis mellifera)

Nosema ceranae, a microsporidian parasite originally described in the Asian honey bee Apis cerana, has recently been found to be cross-infective and to also parasitize the European honey bee Apis mellifera. Since this discovery, many studies have attempted to characterize the impact of this parasite in A. mellifera honey bees. Nosema species can infect all colony members, workers, drones and queens, but the pathological effects of this microsporidium has been mainly investigated in workers, despite the prime importance of the queen, who monopolizes the reproduction and regulates the cohesion of the society via pheromones. We therefore analyzed the impact of N. ceranae on queen physiology. We found that infection by N. ceranae did not affect the fat body content (an indicator of energy stores) but did alter the vitellogenin titer (an indicator of fertility and longevity), the total antioxidant capacity and the queen mandibular pheromones, which surprisingly were all significantly increased in Nosema-infected queens. Thus, such physiological changes may impact queen health, leading to changes in pheromone production, that could explain Nosema-induced supersedure (queen replacement).     

The design and synthesis of guanosine compounds with in vitro activity against the colon cancer cell line SW480: non-taxane derived mimics of taxol?

In the course of our investigation into the use of taxol as a lead compound to design new molecules with anti-cancer activity, we have synthesized four compounds based on protected guanosine coupled to taxol isoserine side-chain analogues. These analogues show in vitro anti-cancer activity against the colon cancer cell line SW480 that their constituent parts do not.     

The jensen symposium; a tribute to a pioneer in the field of nuclear receptor biology

The Jensen Symposium was held at the University of Cincinnati in December 2003 to honor the pioneering contributions of Dr. Elwood Jensen to the field of nuclear hormone action. Those in attendance were treated to an outstanding scientific program that served as an update of recent progress and illustrated the breadth of activity in the nuclear receptor field. Here we highlight recent findings presented at the Symposium that provide new insights into the mechanisms of nuclear receptor action and the diverse roles of members of the nuclear receptor superfamily in development and homeostasis.     

Xenotransplantation Models to Study the Effects of Toxicants on Human Fetal Tissues

Many diseases that manifest throughout the lifetime are influenced by factors affecting fetal development. Fetal exposure to xenobiotics, in particular, may influence the development of adult diseases. Established animal models provide systems for characterizing both developmental biology and developmental toxicology. However, animal model systems do not allow researchers to assess the mechanistic effects of toxicants on developing human tissue. Human fetal tissue xenotransplantation models have recently been implemented to provide human‐relevant mechanistic data on the many tissue‐level functions that may be affected by fetal exposure to toxicants. This review describes the development of human fetal tissue xenotransplant models for testis, prostate, lung, liver, and adipose tissue, aimed at studying the effects of xenobiotics on tissue development, including implications for testicular dysgenesis, prostate disease, lung disease, and metabolic syndrome. The mechanistic data obtained from these models can complement data from epidemiology, traditional animal models, and in vitro studies to quantify the risks of toxicant exposures during human development     

Assessment of therapeutic responses to gametocytocidal drugs in Plasmodium falciparum malaria

Background

Effective mating between laboratory-reared males and wild females is paramount to the success of vector control strategies aiming to decrease disease transmission via the release of sterile or genetically modified male mosquitoes. However mosquito colonization and laboratory maintenance have the potential to negatively affect male genotypic and phenotypic quality through inbreeding and selection, which in turn can decrease male mating competitiveness in the field. To date, very little is known about the impact of those evolutionary forces on the reproductive biology of mosquito colonies and how they ultimately affect male reproductive fitness.

Methods

Here several male reproductive physiological traits likely to be affected by inbreeding and selection following colonization and laboratory rearing were examined. Sperm length, and accessory gland and testes size were compared in male progeny from field-collected females and laboratory strains of Anopheles gambiae sensu stricto colonized from one to over 25 years ago. These traits were also compared in the parental and sequentially derived, genetically modified strains produced using a two-phase genetic transformation system. Finally, genetic crosses were performed between strains in order to distinguish the effects of inbreeding and selection on reproductive traits.

Results

Sperm length was found to steadily decrease with the age of mosquito colonies but was recovered in refreshed strains and crosses between inbred strains therefore incriminating inbreeding costs. In contrast, testes size progressively increased with colony age, whilst accessory gland size quickly decreased in males from colonies of all ages. The lack of heterosis in response to crossing and strain refreshing in the latter two reproductive traits suggests selection for insectary conditions.

Conclusions

These results show that inbreeding and selection differentially affect reproductive traits in laboratory strains overtime and that heterotic ‘supermales’ could be used to rescue some male reproductive characteristics. Further experiments are needed to establish the exact relationship between sperm length, accessory gland and testes size, and male reproductive success in the laboratory and field settings.     

Energy requirements and environmental impacts associated with the production of short rotation willow (Salix sp.) chip in Ireland

Willow Salix sp. is currently cultivated as a short rotation forestry crop in Ireland as a source of biomass to contribute to renewable energy goals. The aim of this study is to evaluate the energy requirements and environmental impacts associated with willow (Salix sp.) cultivation, harvest, and transport using life cycle assessment (LCA). In this study, only emissions from the production of the willow chip are included, end‐use emissions from combustion are not considered. In this LCA study, three impact categories are considered; acidification potential, eutrophication potential and global warming potential. In addition, the cumulative energy demand and energy ratio of the system are evaluated. The results identify three key processes in the production chain which contribute most to all impact categories considered; maintenance, harvest and transportation of the crop. Sensitivity analysis on the type of fertilizers used, harvesting technologies and transport distances highlights the effects of these management techniques on overall system performance. Replacement of synthetic fertilizer with biosolids results in a reduction in overall energy demand, but raises acidification potential, eutrophication potential and global warming potential. Rod harvesting compares unfavourably in comparison with direct chip harvesting in each of the impact categories considered due to the additional chipping step required. The results show that dedicated truck transport is preferable to tractor‐trailer transport in terms of energy demand and environmental impacts. Finally, willow chip production compares favourably with coal provision in terms of energy ratio and global warming potential, while achieving a higher energy ratio than peat provision but also a higher global warming potential.     

Using genetic variation to disentangle the complex relationship between food intake and health outcomes

Diet is considered as one of the most important modifiable factors influencing human health, but efforts to identify foods or dietary patterns associated with health outcomes often suffer from biases, confounding, and reverse causation. Applying Mendelian randomization in this context may provide evidence to strengthen causality in nutrition research. To this end, we first identified 283 genetic markers associated with dietary intake in 445,779 UK Biobank participants. We then converted these associations into direct genetic effects on food exposures by adjusting them for effects mediated via other traits. The SNPs which did not show evidence of mediation were then used for MR, assessing the association between genetically predicted food choices and other risk factors, health outcomes. We show that using all associated SNPs without omitting those which show evidence of mediation, leads to biases in downstream analyses (genetic correlations, causal inference), similar to those present in observational studies. However, MR analyses using SNPs which have only a direct effect on the exposure on food exposures provided unequivocal evidence of causal associations between specific eating patterns and obesity, blood lipid status, and several other risk factors and health outcomes.     

Ion channel noise can explain firing correlation in auditory nerves

Sensory neurons code information about stimuli in their sequence of action potentials (spikes). Intuitively, the spikes should represent stimuli with high fidelity. However, generating and propagating spikes is a metabolically expensive process. It is therefore likely that neural codes have been selected to balance energy expenditure against encoding error. Our recently proposed optimal, energy-constrained neural coder (Jones et al. Frontiers in Computational Neuroscience, 9, 61 2015) postulates that neurons time spikes to minimize the trade-off between stimulus reconstruction error and expended energy by adjusting the spike threshold using a simple dynamic threshold. Here, we show that this proposed coding scheme is related to existing coding schemes, such as rate and temporal codes. We derive an instantaneous rate coder and show that the spike-rate depends on the signal and its derivative. In the limit of high spike rates the spike train maximizes fidelity given an energy constraint (average spike-rate), and the predicted interspike intervals are identical to those generated by our existing optimal coding neuron. The instantaneous rate coder is shown to closely match the spike-rates recorded from P-type primary afferents in weakly electric fish. In particular, the coder is a predictor of the peristimulus time histogram (PSTH). When tested against in vitro cortical pyramidal neuron recordings, the instantaneous spike-rate approximates DC step inputs, matching both the average spike-rate and the time-to-first-spike (a simple temporal code). Overall, the instantaneous rate coder relates optimal, energy-constrained encoding to the concepts of rate-coding and temporal-coding, suggesting a possible unifying principle of neural encoding of sensory signals.