The origin of the Hox/ParaHox genes, the Ghost Locus hypothesis and the complexity of the first animal

A key aim in evolutionary biology is to deduce ancestral states in order to better understand the evolutionary origins of clades of interest and the diversification process(es) that have elaborated them. These ancestral deductions can hit difficulties when undetected loss events are misinterpreted as ancestral absences. With the ever-increasing amounts of animal genomic sequence data we are gaining a much clearer view of the preponderance of differential gene losses across animal lineages. This has become particularly clear with recent progress in our understanding of the origins of the Hox/ParaHox developmental control genes relative to the earliest branching lineages of the animal kingdom: the sponges (Porifera), comb jellies (Ctenophora) and placozoans (Placozoa). These reassessments of the diversity and complexity of developmental control genes in the earliest animal ancestors need to go hand-in-hand with complementary advances in comparative morphology, phylogenetics and palaeontology in order to clarify our understanding of the complexity of the last common ancestor of all animals. The field is currently undergoing a shift from the traditional consensus of a sponge-like animal ancestor from which morphological and molecular elaboration subsequently evolved, to a scenario of a more complex animal ancestor, with subsequent losses and simplifications in various lineages.Peer reviewe

Connection between slow and fast dynamics of molecular liquids around the glass transition

The mean-square displacement (MSD) was measured by neutron scattering at various temperatures and pressures for a number of molecular glass-forming liquids. The MSD is invariant along the glass-transition line at the pressure studied, thus establishing an ``intrinsic'' Lindemann criterion for any given liquid. A one-to-one connection between the MSD's temperature dependence and the liquid's fragility is found when the MSD is evaluated on a time scale of approximately 4 nanoseconds, but does not hold when the MSD is evaluated at shorter times. The findings are discussed in terms of the elastic model and the role of relaxations, and the correlations between slow and fast dynamics are addressed.Comment: accepted by Phys Rev E (2010

Amphioxus SYCP1 : a case of retrogene replacement and co-option of regulatory elements adjacent to the ParaHox cluster

MGG was supported by the University of St Andrews School of Biology Biotechnology and Biological Sciences Research Council DTG and the Wellcome Trust ISSF. Work in the authors’ laboratory is also supported by the Leverhulme Trust.Retrogenes are formed when an mRNA is reverse transcribed and re-inserted into the genome in a location unrelated to the original locus. If this retrocopy inserts into a transcriptionally favourable locus and is able to carry out its original function, it can, in rare cases, lead to retrogene replacement. This involves the original, often multi-exonic, parental copy being lost whilst the newer single-exon retrogene copy ‘replaces’ the role of the ancestral parent gene. One example of this is amphioxus SYCP1, a gene that encodes a protein used in synaptonemal complex formation during meiosis, and which offers the opportunity to examine how a retrogene evolves after the retrogene replacement event. SYCP1 genes exist as large multi-exonic genes in most animals. AmphiSYCP1, however, contains a single coding exon of ~3200bp and has inserted next to the ParaHox cluster of amphioxus, whilst the multi-exonic ancestral parental copy has been lost. Here, we show that AmphiSYCP1 has not only replaced its parental copy, but has evolved additional regulatory function by co- opting a bidirectional promoter from the nearby AmphiCHIC gene. AmphiSYCP1 has also evolved a de novo, multi-exonic 5’untranslated region that displays distinct regulatory states, in the form of two different isoforms, and has evolved novel expression patterns during amphioxus embryogenesis in addition to its ancestral role in meiosis. Absence of ParaHox-like expression of AmphiSYCP1, despite its proximity to the ParaHox cluster, also suggests this gene is not influenced by any potential pan-cluster regulatory mechanisms, which are seemingly restricted to only the ParaHox genes themselves.Publisher PDFPeer reviewe

Microwave response of an NS ring coupled to a superconducting resonator

A long phase coherent normal (N) wire between superconductors (S) is characterized by a dense phase dependent Andreev spectrum . We probe this spectrum in a high frequency phase biased configuration, by coupling an NS ring to a multimode superconducting resonator. We detect a dc flux and frequency dependent response whose dissipative and non dissipative components are related by a simple Debye relaxation law with a characteristic time of the order of the diffusion time through the N part of the ring. The flux dependence exhibits $h/2e$ periodic oscillations with a large harmonics content at temperatures where the Josephson current is purely sinusoidal. This is explained considering that the populations of the Andreev levels are frozen on the time-scale of the experiments.Comment: 5 pages,4 figure

Foundation degrees in biomedical science: the student experience

The first cohort of students on a University of Westminster foundation degree completed the course recently. Here, Chrystalla Ferrier, Kelly Brookwell and Paul Quinn employ some reflective practice

Optical Line Width Broadening Mechanisms at the 10 kHz Level in Eu3+:Y2O3 Nanoparticles

We identify the physical mechanisms responsible for the optical homogeneous broadening in Eu3+:Y2O3 nanoparticles to determine whether rare-earth crystals can be miniaturized to volumes less than λ3 whilst preserving their appeal for quantum technology hardware. By studying how the homogeneous line width depends on temperature, applied magnetic field, and measurement time scale the dominant broadening interactions for various temperature ranges above 3 K were characterized. Below 3 K the homogeneous line width is dominated by an interaction not observed in bulk crystal studies. These measurements demonstrate that broadening due to size-dependent phonon interactions is not a significant contributor to the homogeneous line width, which contrasts previous studies in rare-earth ion nanocrystals. Importantly, the results provide strong evidence that for the 400 nm diameter nanoparticles under study the minimum line width achieved (45±1 kHz at 1.3 K) is not fundamentally limited. In addition, we highlight that the expected broadening caused by electric field fluctuations arising from surface charges is comparable to the observed broadening. Under the assumption that such Stark broadening is a significant contribution to the homogeneous line width, several strategies for reducing this line width to below 10 kHz are discussed. Furthermore, it is demonstrated that the Eu3+ hyperfine state lifetime is sufficiently long to preserve spectral features for timescales up to 1 s. These results allow integrated rare-earth ion quantum optics to be pursued at a sub-micron scale and hence, open up directions for greater scaling of rare-earth quantum technology

Incorporating expert opinion and fine-scale vegetation mapping into statistical models of faunal distribution

1. Abiotic environmental predictors and broad-scale vegetation have been used widely to model the regional distributions of faunal species within forested regions of Australia. These models have been developed using stepwise statistical procedures but incorporate only limited expert involvement of the type sometimes advocated in distribution modelling. The objectives of this study were twofold. First, to evaluate techniques for incorporating fine-scaled vegetation and growth-stage mapping into models of species distribution. Secondly, to compare methods that incorporate expert opinion directly into statistical models derived using stepwise statistical procedures. 2. Using faunal data from north-east New South Wales, Australia, logistic regression models using fine-scale vegetation and expert opinion were compared with models employing only abiotic and broad vegetation variables. 3. Vegetation and growth-stage information was incorporated into models of species distribution in two ways, both of which used expert opinion to derive new explanatory variables. The first approach amalgamated fine-scaled vegetation classes into broader classes of ecological relevance to fauna. In the second approach, ordinal habitat indices were derived from vegetation and growth-stage mapping using rules specified by an expert panel. These indices described habitat features thought to be relevant to the faunal groups studied (e.g. tree hollow availability, fleshy fruit production). Landscape composition was calculated using these new variables within a 500-m and 2-km radius of each site. Each habitat index generated a spatially neutral variable and two spatial context variables. 4. Expert opinion was incorporated during the pre-modelling, model-fitting and post -modelling stages. At the pre-modelling stage experts developed new explanatory variables based on mapped fine-scale vegetation and growth-stage information. At the model-fitting stage an expert panel selected a subset of potential explanatory variables from the available set. At the post-modelling stage expert opinion modified or refined maps of predicted species distribution generated by statistical models. For comparative purposes expert opinion was also used to develop maps of species distribution by defining rules within a geographical information system, without the aid of statistical modelling. 5. Predictive accuracy was not improved significantly by incorporating habitat indices derived by applying expert opinion to fine-scaled vegetation and growth-stage mapping. Use of expert input at the pre-modelling stage to derive and select potential explanatory variables therefore does not provide more information than that provided by remotely mapped vegetation. 6. The incorporation of expert opinion at the model-fitting or post-modelling stages resulted in small but insignificant gains in predictive accuracy. The predictive accuracy of purely expert models was less than that achieved by approaches based on statistical modelling. 7. The study, one of few available evaluations of expert opinion in models of species distribution, suggests that expert modification of fitted statistical models should be confined to species for which models are grossly in error, or for which insufficient data exist to construct solely statistical models

Horizons in evolutionary genomics : an interview with David Ferrier

Research in the author’s laboratory is funded by the Leverhulme Trust, BBSRC, EU Horizon2020 CORBEL and ASSEMBLE+, and the University of St Andrews, School of Biology.David Ferrier is a Reader at the University of St Andrews and Deputy Director of the Scottish Oceans Institute, where his lab studies how the diversity of form in the animal kingdom evolved, with an emphasis on using comparative genomics. In this interview, David shares his thoughts on how to escape the ‘straitjacket’ of traditional model systems, transparency in peer review, and the past and future of genome sequencing.Publisher PDFNon peer reviewe