Setting the Tempo in Development: An Investigation of the Zebrafish Somite Clock Mechanism

The somites of the vertebrate embryo are clocked out sequentially from the presomitic mesoderm (PSM) at the tail end of the embryo. Formation of each somite corresponds to one cycle of oscillation of the somite segmentation clock—a system of genes whose expression switches on and off periodically in the cells of the PSM. We have previously proposed a simple mathematical model explaining how the oscillations, in zebrafish at least, may be generated by a delayed negative feedback loop in which the products of two Notch target genes, her1 and her7, directly inhibit their own transcription, as well as that of the gene for the Notch ligand DeltaC; Notch signalling via DeltaC keeps the oscillations of neighbouring cells in synchrony. Here we subject the model to quantitative tests. We show how to read temporal information from the spatial pattern of stripes of gene expression in the anterior PSM and in this way obtain values for the biosynthetic delays and molecular lifetimes on which the model critically depends. Using transgenic lines of zebrafish expressing her1 or her7 under heat-shock control, we confirm the regulatory relationships postulated by the model. From the timing of somite segmentation disturbances following a pulse of her7 misexpression, we deduce that although her7 continues to oscillate in the anterior half of the PSM, it governs the future somite segmentation behaviour of the cells only while they are in the posterior half. In general, the findings strongly support the mathematical model of how the somite clock works, but they do not exclude the possibility that other oscillator mechanisms may operate upstream from the her7/her1 oscillator or in parallel with it

Proposed revision of the higher tier testing requirements for EPPO Standard PP1/170: Test methods for evaluating the side-effects of plant protection products on honeybees

contribution to session I  Regulatory issues Background: Regulatory evaluations for the effects of pesticides on honeybees in the EU are based on the honeybee test guidelines and risk assessment scheme of the European Plant Protection Organisation (EPPO). While this is considered to be robust and effective, it is also recognised that a continuous process of review and appropriate development is necessary. A working group of the International Commission for Plant-Bee Relationships (ICPBR) had been set up to review the current guidance set out in the EPPO PP1/170 standard for higher tier testing i.e. semi-field (cage) test and full field studies. The aim of this group was to utilise the considerable experience obtained with honey bee testing. This paper presents the working group’s proposed revision to the EPPO standard PP1/170, taking into account feedback received from the 10th ICPBR Symposium in Bucharest.Results: The primary aim of the group has been to produce guidance that is sufficiently detailed yet suitably flexible so that it enables tests to be conducted and evaluated without being too prescriptive. In particular, it recognises that higher tier testing may arise as a result of various initial concerns e.g. adult toxicity, brood effects and systemic toxicity. The guidance is designed to provide the different emphasis that is required to meet the specific requirements of individual studies. Conclusion: The revision of higher tier testing for honeybees presented in this paper is proposed as an update to the current EPPO PP1/170 standard.Keywords: honey bees, test guidelines, higher tier, semi-field (cage) tests, field tests

The timing of tuberculosis after isoniazid preventive therapy among gold miners in South Africa: a prospective cohort study

BackgroundThe durability of isoniazid preventive therapy (IPT) in preventing tuberculosis (TB) is limited in high-prevalence settings. The underlying mechanism (reactivation of persistent latent TB or reinfection) is not known. We aimed to investigate the timing of TB incidence during and after IPT and associated risk factors in a very high TB and HIV-prevalence setting, and to compare the observed rate with a modelled estimate of TB incidence rate after IPT due to reinfection.MethodsIn a post-hoc analysis of a cluster-randomized trial of community-wide IPT among South African gold miners, all intervention arm participants that were dispensed IPT for at least one of the intended 9months were included. An incident TB case was defined as any participant with a positive sputum smear or culture, or with a clinical TB diagnosis assigned by a senior study clinician. Crude TB incidence rates were calculated during and after IPT, overall and by follow-up time. HIV status was not available. Multivariable Cox regression was used to analyse risk factors by follow-up time after IPT. Estimates from a published mathematical model of trial data were used to calculate the average reinfection TB incidence in the first year after IPT.ResultsAmong 18,520 participants (96% male, mean age 41years, median follow-up 2.1years), 708 developed TB. The TB incidence rate during the intended IPT period was 1.3/100 person-years (pyrs; 95% confidence interval (CI), 1.0–1.6) and afterwards 2.3/100 pyrs (95% CI, 1.9–2.7). TB incidence increased within 6months followed by a stable rate over time. There was no evidence for changing risk factors for TB disease over time after miners stopped IPT. The average TB incidence rate attributable to reinfection in the first year was estimated at 1.3/100 pyrs, compared to an observed rate of 2.2/100 pyrs (95% CI, 1.8–2.7).ConclusionsThe durability of protection by IPT was lost within 6–12 months in this setting with a high HIV prevalence and a high annual risk of M. tuberculosis infection. The observed rate was higher than the modelled rate, suggesting that reactivation of persistent latent infection played a role in the rapid return to baseline TB incidence.Electronic supplementary materialThe online version of this article (doi:10.1186/s12916-016-0589-3) contains supplementary material, which is available to authorized users

Two closely related ureotelic fish species of the genus Alcolapia express different levels of ammonium transporters in gills

Most fish excrete their nitrogenous waste across the gills as ammonia through the activity of the Rhesus glycoprotein ammonium transporters. In contrast, fish of the subgenus Alcolapia (Oreochromis) are the only vertebrates that survive the extreme conditions of the soda lakes of Natron and Magadi in East Africa and have evolved adaptations to the highly alkaline waters including the ability to excrete their nitrogenous waste as urea. Nevertheless, Alcolapia retain the Rhesus glycoprotein genes in their genomes and using two heterologous expression systems, we demonstrate that Alcolapia Rhbg is capable of moving ammonia. Comparing ammonia and urea excretion from two closely related Alcolapia species from the same aquarium, we found that while Alcolapia grahami remains fully ureotelic after many generations in lab conditions, Alcolapia alcalica excretes some of its nitrogenous waste as ammonia. Using in situ hybridisation, we demonstrate robust, localised gene expression of Rhbg, rhcg1 and rhcg2 in the gill tissue in both A. alcalica embryos and adults, similar to that in other ammoniotelic fish. In contrast, the expression of these genes in A. grahami gills is much lower than in A. alcalica, suggesting the rapid evolution of a molecular mechanism underlying the complete ureotelism of A. grahami

Guidance for the assessment of risks to bees from the use of plant protection products applied as seed coating and soil applications – conclusions of the ICPBR dedicated working group

contribution to session IRegulatory issuesBackground: Soil or seed applied plant protection products (PPPs) aim at bringing the amount of active substance involved to the only parts of the plant that have to be protected. Despite a reduced exposure of non target organisms by this way, an exposure of honey bees through residues in pollen and/or nectar may not be excluded for substances that migrate towards the upper plant parts. Directive 91/414/EEC, related guidance documents and literature data were reviewed and discussed by a working group of the ICPBR (International Commission for Plant-Bee Relationships) with the aim to provide adequate guidance to proceed in a risk assessment in such cases.Results: The review and expert knowledge collected within ecotoxicology, entomology and plant residue area allowed to identify the key parameters that trigger a risk assessment as well as basic hypotheses to consider in deciding for the experimentations required (laboratory, semi-field and field tests). A stepwise, tiered approach is proposed, which has been checked for its ability to discriminate substances that may pose a risk to bees from substances of low concern. Conclusion: The present scheme is proposed to update the current EPPO risk assessment scheme with a special issue on systemic PPPs.Keywords: risk assessment, honey bees, soil or seed treatments, systemic

Environmental risk assessment scheme for plant protection products - Chapter 10: Honeybees – Proposed scheme

contribution to session I Regulatory issue

Reconstruction of the Primordial Power Spectrum by Direct Inversion

We introduce a new method for reconstructing the primordial power spectrum, $P(k)$, directly from observations of the Cosmic Microwave Background (CMB). We employ Singular Value Decomposition (SVD) to invert the radiation perturbation transfer function. The degeneracy of the multipole $\ell$ to wavenumber $k$ linear mapping is thus reduced. This enables the inversion to be carried out at each point along a Monte Carlo Markov Chain (MCMC) exploration of the combined $P(k)$ and cosmological parameter space. We present best--fit $P(k)$ obtained with this method along with other cosmological parameters.Comment: 23 pages, 9 figure