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

Comparative Durability Analysis of CFRP Strengthened RC Highway Bridges

The paper presents parametric analysis of durability factors of RC highway bridges strengthened with CFRP laminates during their service life. Durability factors considered are concrete cover and CFRP laminate thickness. Three deterioration factors were considered. First, growth of live load with time. Second, resistance reduction due to chloride-attack corrosion which causes reduction in steel properties. Corrosion losses are evaluated through a time–temperature dependent corrosion current. Two types of corrosion are considered; uniform and pitting corrosion. Third, deterioration due to aging of CFRP. The reliability analysis is controlled by three failure modes; concrete crushing, CFRP mid span debonding and CFRP rupture. Monte-Carlo simulation is used to develop time dependent statistical models for rebar steel area and live load extreme effect. Reliability is estimated in term of reliability index using FORM algorithm. For illustrative purpose, a RC bridge is assumed as an example. The reliability of interior beam of the bridge is evaluated under various traffic volumes and different corrosion environments. The bridge design options follow AASHTO-LRFD specifications. The present work also extends to calibrate CFRP resistance safety factor corresponds to three target reliability levels, β = 3.5, 3.85, and 4.2. The results of the analysis have shown that corrosion has the most significant effect on bridge life time followed by live load growth. Pitting corrosion type is more hazardous than uniform. Also, initial safety index is proved to be traffic dependent. AASHTO design equation (that corresponds βtarget = 3.5) seems to be overestimated for strengthening purpose. Strengthening with (βtarget = 4.2) provide better reliability than βtarget proposed by AASHTO provision with no significant differences in CFRP amounts required

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

Improving Performance of M-to-N Processing and Data Redistribution in In Transit Analysis and Visualization

In an in transit setting, a parallel data producer, such as a numerical simulation, runs on one set of ranks M, while a data consumer, such as a parallel visualization application, runs on a different set of ranks N. One of the central challenges in this in transit setting is to determine the mapping of data from the set of M producer ranks to the set of N consumer ranks. This is a challenging problem for several reasons, such as the producer and consumer codes potentially having different scaling characteristics and different data models. The resulting mapping from M to N ranks can have a significant impact on aggregate application performance. In this work, we present an approach for performing this M-to-N mapping in a way that has broad applicability across a diversity of data producer and consumer applications. We evaluate its design and performance with a study that runs at high concurrency on a modern HPC platform. By leveraging design characteristics, which facilitate an “intelligent” mapping from M-to-N, we observe significant performance gains are possible in terms of several different metrics, including time-to-solution and amount of data moved

Geometrical dependence of decoherence by electronic interactions in a GaAs/GaAlAs square network

We investigate weak localization in metallic networks etched in a two dimensional electron gas between $25\:$mK and $750\:$mK when electron-electron (e-e) interaction is the dominant phase breaking mechanism. We show that, at the highest temperatures, the contributions arising from trajectories that wind around the rings and trajectories that do not are governed by two different length scales. This is achieved by analyzing separately the envelope and the oscillating part of the magnetoconductance. For $T\gtrsim0.3\:$K we find \Lphi^\mathrm{env}\propto{T}^{-1/3} for the envelope, and \Lphi^\mathrm{osc}\propto{T}^{-1/2} for the oscillations, in agreement with the prediction for a single ring \cite{LudMir04,TexMon05}. This is the first experimental confirmation of the geometry dependence of decoherence due to e-e interaction.Comment: LaTeX, 5 pages, 4 eps figure

Benevolence and gift giving in backyard blitz

The prevalence of gift-giving in Australian home makeover programs, and the way that it functions in their narrative, driving the makeover and grounding it in a meaningful social and national context is discussed. Australian Nine Network's Backyard Blitz is taken as a case study to explore its narrative and symbolic function of gift-giving and the mythologizing of benevolence as a desirable nation trait

Least Squares Adjustment of Satellite Observations for Simultaneous Directions or Ranges. Part 3 - Subroutines

Subroutines used in computer programs for least squares adjustment of satellite observations for simultaneous directions or range

The food contaminant deoxynivalenol, decreases intestinal barrier permeability and reduces claudin expression

The gastrointestinal tract represents the first barrier against food contaminants as well as the first target for these toxicants. Deoxynivalenol (DON) is a mycotoxin that commonly contaminates cereals and causes various toxicological effects. Through consumption of contaminated cereals and cereal products, human and pigs are exposed to this mycotoxin. Using in vitro, ex vivo, and in vivo approaches, we investigated the effects of DON on the intestinal epithelium. We demonstrated that, in intestinal epithelial cell lines from porcine (IPEC-1) or human (Caco-2) origin, DON decreases trans-epithelial electric resistance (TEER) and increases in a time and dose-dependent manner the paracellular permeability to 4 kDa dextran and to pathogenic Escherichia Coli across intestinal cell monolayers. In pig explants treated with DON, we also observed an increased permeability of intestinal tissue. These alterations of barrier function were associated with a specific reduction in the expression of claudins, which was also seen in vivo in the jejunum of piglets exposed to DON-contaminated feed. In conclusion, DON alters claudin expression and decreases the barrier function of the intestinal epithelium. Considering that high levels of DON may be present in food or feed, consumption of DON-contaminated food/feed may induce intestinal damage and has consequences for human and animal health