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

Searching for the Kardar-Parisi-Zhang phase in microcavity polaritons

Recent approximate analytical work has suggested that, at certain values of the external pump, the optical parametric oscillator (OPO) regime of microcavity polaritons may provide a long sought realisation of Kardar-Parisi-Zhang (KPZ) physics in 2D. Here, by solving the full microscopic model numerically using the truncated Wigner method, we prove that this predicted KPZ phase for OPO is robust against the appearance of vortices or other effects. For those pump strengths, spatial correlations in the direction perpendicular to the pump, and the distribution of phase fluctuations, match closely to the forms characteristic of the KPZ universality. This strongly indicates the viability of observing KPZ behaviour in future polariton OPO experiments

Potential of Retrofitting Sustainable Urban Drainage Systems Using an Integrated Geographical Information System Remote Sensing Based Approach

Flooding is a major problem in urban areas worldwide. Methodologies that can rapidly assess the scale and identify the reasons causing these flooding events at minimal cost are urgently required. This study has used the City of Kingston-upon-Hull to evaluate the capability of an integrated remote sensing and geographical information system based approach to provide the critical information on the spatial extent of flooding and flood water volumes and overcome the limitations in current monitoring based on ground-based visual mapping and household flooding surveys. Airborne and Terrestrial LiDAR datasets were combined with digital aerial photography, flood assessment surveys, and maps of housing, infrastructure and the sewer network. The integration of these datasets provided an enhanced understanding of the sources and pathways of the flood water runoff, accurate quantification of the water volumes associated with each flooding event and the identification of the optimum locations and size of potential retrofit Sustainable Urban Drainage systems.n/

Evaluation Context Impacts Neuropsychological Performance of OEF/OIF Veterans with Reported Combat-Related Concussion

Although soldiers of Operations Iraqi Freedom (OIF) and Enduring Freedom (OEF) encounter combat-related concussion at an unprecedented rate, relatively few studies have examined how evaluation context, insufficient effort, and concussion history impact neuropsychological performances in the years following injury. The current study explores these issues in a sample of 119 U.S. veterans (OEF/OIF forensic concussion, n = 24; non-OEF/OIF forensic concussion, n = 20; OEF/OIF research concussion, n = 38; OEF/OIF research without concussion, n = 37). The OEF/OIF forensic concussion group exhibited significantly higher rates of insufficient effort relative to the OEF/OIF research concussion group, but a comparable rate of insufficient effort relative to the non-OEF/OIF forensic concussion group. After controlling for effort, the research concussion and the research non-concussion groups demonstrated comparable neuropsychological performance. Results highlight the importance of effort assessment among OEF/OIF and other veterans with concussion history, particularly in forensic contexts

Neuropsychological evaluation of blast-related concussion: Illustrating the challenges and complexities through OEF/OIF case studies

Background/objective: Soldiers of Operations Enduring Freedom (OEF) and Iraqi Freedom (OIF) sustain blast-related mild traumatic brain injury (concussion) with alarming regularity. This study discusses factors in addition to concussion, such as co-morbid psychological difficulty (e.g. post-traumatic stress) and symptom validity concerns that may complicate neuropsychological evaluation in the late stage of concussive injury. Case report: The study presents the complexities that accompany neuropsychological evaluation of blast concussion through discussion of three case reports of OEF/OIF personnel. Discussion: The authors emphasize uniform assessment of blast concussion, the importance of determining concussion severity according to acute-injury characteristics and elaborate upon non-concussion-related factors that may impact course of cognitive limitation. The authors conclude with a discussion of the need for future research examining the impact of blast concussion (particularly recurrent concussion) and neuropsychological performance

Searching for the Kardar-Parisi-Zhang phase in microcavity polaritons

Recent analytical work has shown that, at certain values of the external pump, the optical parametric oscillator (OPO) regime of microcavity polaritons may provide a realisation of Kardar-Parisi-Zhang (KPZ) physics in 2D. Here, we verify this by solving the full microscopic model numerically using the truncated Wigner method, and studying the first order spatial correlations. For the predicted pump strengths, these correlations decay much faster and, perpendicular to the pump, fit closely to the stretched exponential form predicted by the KPZ equation, in contrast to the usual algebraic decay. This strongly indicates the viability of observing KPZ behaviour in future polariton OPO experiments.Comment: Main text (6 pages, 5 figures) plus supplementary material (3 pages, 5 figures

An Investigation of the Maximum Specimen Thickness for Differential Phase Contrast Lorentz Microscopy

Examination of magnetic domain structure in the transmission electron microscope is generally confined to very thin foils, where the specimen approximates to a pure phase object, and is achieved by the long established methods of Fresnel or Foucault contrast Lorentz microscopy, or by differential phase contrast (DPC) imaging in a scanning transmission electron microscope (STEM). If no quantitative interpretation of the image is required then magnetic contrast can be observed from thicker foils, and in this paper we describe an attempt to determine experimentally the range of foil thickness over which this is possible. To this end we have examined electropolished foils of single crystal Incalloy using an extended VG HB501 STEM to produce both DPC and Fresnel contrast images of the same area. The foil thickness at points along the domain walls was measured from the change in the Lorentz deflection angle as the STEM probe was moved across the domain wall, and this led to an estimate of ~ 700nm for the limiting thickness at which domain contrast was still visible in the DPC images. This value is obviously influenced by a number of factors, including the degree of inelastic scattering and the saturation magnetisation of the material, but it is sufficiently high that there might exist a range of thickness over which both transmission and scanning electron microscopes could be used to study the domain structure in the same areas of specimen

Fully Quantum Scalable Description of Driven-Dissipative Lattice Models

Methods for modeling large driven-dissipative quantum systems are becoming increasingly urgent due to recent experimental progress in a number of photonic platforms. We demonstrate the positive-P method to be ideal for this purpose across a wide range of parameters, focusing on the archetypal driven-dissipative Bose-Hubbard model. Notably, these parameters include intermediate regimes where interactions and dissipation are comparable, and especially cases with low occupations for which common semiclassical approximations can break down. The presence of dissipation can alleviate instabilities in the method that are known to occur for closed systems, allowing the simulation of dynamics up to and including the steady state. Throughout the parameter space of the model, we determine the magnitude of dissipation that is sufficient to make the method useful and stable, finding its region of applicability to be complementary to that of the truncated Wigner method. We then demonstrate its use in a number of examples with nontrivial quantum correlations, including a demonstration of solving the urgent open problem of large and highly nonuniform systems with tens of thousands of sites

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