Identification of highly conserved putative developmental enhancers bound by SOX3 in neural progenitors using ChIP-Seq

The transcription factor SOX3 is expressed within most neural progenitor (NP) cells of the vertebrate central nervous system (CNS) and is essential for normal brain development in mice and humans. However, despite the widespread expression of Sox3, CNS defects in null mice are relatively mild due to functional redundancy with the other SOXB1 sub-group members Sox1 and Sox2. To further understand the molecular function of SOX3, we investigated the genome-wide binding profile of endogenous SOX3 in NP cells using ChIP-seq. SOX3 binding was identified at over 8,000 sites, most of which were intronic or intergeneic and were significantly associated with neurodevelopmental genes. The majority of binding sites were moderately or highly conserved (phastCons scores .0.1 and 0.5, respectively) and included the previously characterised, SOXB1-binding Nestin NP cell enhancer. Comparison of SOX3 and published ChIP-Seq data for the co-activator P300 in embryonic brain identified hundreds of highly conserved putative enhancer elements. In addition, we identified a subset of highly conserved putative enhancers for CNS development genes common to SOXB1 members in NP cells, all of which contained the SOX consensus motif (ACAAWR). Together these data implicate SOX3 in the direct regulation of hundreds of NP genes and provide molecular insight into the overlapping roles of SOXB1 proteins in CNS development.Dale McAninch, Paul Thoma

Validation of Ray Tracing Code Refraction Effects

NASA's current predictive capabilities using the ray tracing program (RTP) are validated using helicopter noise data taken at Eglin Air Force Base in 2007. By including refractive propagation effects due to wind and temperature, the ray tracing code is able to explain large variations in the data observed during the flight test

Dbx1 is a direct target of SOX3 in the spinal cord

SoxB1 sub-family of transcriptional regulators are expressed in progenitor (NP) cells throughout the neuroaxis and are generally downregulated during neuronal differentiation. Gain- and loss-of-function studies indicate that Sox1, Sox2 and Sox3 are key regulators of NP differentiation and that their roles in CNS development are largely redundant. Nevertheless, mutation of each SoxB1 individually results in a different array of CNS defects, raising the possibility that SoxB1 proteins have subtly different functions in NP cells. To explore the mechanism of SOXB1 functional redundancy, and to identify genes that are most sensitive to loss of the Sox3 gene, we performed genome wide expression profiling of Sox3 null NP cells. Nineteen genes with abnormal expression were identified, including the homeobox gene Dbx1. Analysis of Sox3 null embryos revealed that Dbx1 was significantly reduced in the neural tube and developing brain and that SOX3 bound directly to conserved elements associated with this gene in cultured NP cells and in vivo. These data define Dbx1 as a direct SOX3 target gene whose expression, intriguingly, is not fully rescued by other SOXB1 transcription factors, suggesting that there are inherent differences in SOXB1 protein activity.Nicholas Rogers, Dale McAninch, Paul Thoma

Protocadherin 19 (PCDH19) interacts with paraspeckle protein NONO to co-regulate gene expression with estrogen receptor alpha (ERalpha)

De novo and inherited mutations of X-chromosome cell adhesion molecule protocadherin 19 (PCDH19) cause frequent, highly variable epilepsy, autism, cognitive decline and behavioural problems syndrome. Intriguingly, hemizygous null males are not affected while heterozygous females are, contradicting established X-chromosome inheritance. The disease mechanism is not known. Cellular mosaicism is the likely driver. We have identified p54nrb/NONO, a multifunctional nuclear paraspeckle protein with known roles in nuclear hormone receptor gene regulation, as a PCDH19 protein interacting partner. Using breast cancer cells we show that PCDH19-NONO complex is a positive co-regulator of ERα-mediated gene expression. Expression of mutant PCDH19 affects at least a subset of known ERα-regulated genes. These data are consistent with our findings that genes regulated by nuclear hormone receptors and those involved in the metabolism of neurosteroids in particular are dysregulated in PCDH19-epilepsy girls and affected mosaic males. Overall we define and characterize a novel mechanism of gene regulation driven by PCDH19, which is mediated by paraspeckle constituent NONO and is ERα-dependent. This PCDH19-NONO-ERα axis is of relevance not only to PCDH19-epilepsy and its comorbidities but likely also to ERα and generally nuclear hormone receptor-associated cancers.Duyen H. Pham, Chuan C. Tan, Claire C. Homan, Kristy L. Kolc, Mark A. Corbett, Dale McAninch, Archa H. Fox, Paul Q. Thomas, Raman Kumar Jozef Gec

Bulge formed cooling channels with a variable lead helix on a hollow body of revolution

A method of constructing a nozzle having cooling channels comprises a shell and a liner which are formed into a body of revolution having an axis of revolution. Helical welds are formed to hold the liner and shell to each other with a channel position being defined between each pair of helical welds. Pressurized fluid which may be a gas or a liquid, is introduced between the weld pairs to outwardly bulge the material of at least one of the liner and shell to define the channels

Closure development for high-level nuclear waste containers for the tuff repository; Phase 1, Final report

This report summarizes Phase 1 activities for closure development of the high-level nuclear waste package task for the tuff repository. Work was conducted under U.S. Department of Energy (DOE) Contract 9172105, administered through the Lawrence Livermore National Laboratory (LLNL), as part of the Yucca Mountain Project (YMP), funded through the DOE Office of Civilian Radioactive Waste Management (OCRWM). The goal of this phase was to select five closure processes for further evaluation in later phases of the program. A decision tree methodology was utilized to perform an objective evaluation of 15 potential closure processes. Information was gathered via a literature survey, industrial contacts, and discussions with project team members, other experts in the field, and the LLNL waste package task staff. The five processes selected were friction welding, electron beam welding, laser beam welding, gas tungsten arc welding, and plasma arc welding. These are felt to represent the best combination of weldment material properties and process performance in a remote, radioactive environment. Conceptual designs have been generated for these processes to illustrate how they would be implemented in practice. Homopolar resistance welding was included in the Phase 1 analysis, and developments in this process will be monitored via literature in Phases 2 and 3. Work was conducted in accordance with the YMP Quality Assurance Program. 223 refs., 20 figs., 9 tabs

Knockout of the epilepsy gene Depdc5 in mice causes severe embryonic dysmorphology with hyperactivity of mTORC1 signalling

Published online: 03 October 2017DEPDC5 mutations have recently been shown to cause epilepsy in humans. Evidence from in vitro studies has implicated DEPDC5 as a negative regulator of mTORC1 during amino acid insufficiency as part of the GATOR1 complex. To investigate the role of DEPDC5 in vivo we generated a null mouse model using targeted CRISPR mutagenesis. Depdc5 homozygotes display severe phenotypic defects between 12.5-15.5 dpc, including hypotrophy, anaemia, oedema, and cranial dysmorphology as well as blood and lymphatic vascular defects. mTORC1 hyperactivity was observed in the brain of knockout embryos and in fibroblasts and neurospheres isolated from knockout embryos and cultured in nutrient deprived conditions. Heterozygous mice appeared to be normal and we found no evidence of increased susceptibility to seizures or tumorigenesis. Together, these data support mTORC1 hyperactivation as the likely pathogenic mechanism that underpins DEPDC5 loss of function in humans and highlights the potential utility of mTORC1 inhibitors in the treatment of DEPDC5-associated epilepsy.James Hughes, Ruby Dawson, Melinda Tea, Dale McAninch, Sandra Piltz, Dominique Jackson, Laura Stewart, Michael G. Ricos, Leanne M. Dibbens, Natasha L. Harvey and Paul Thoma

Can the magnetic moment contribution explain the A_y puzzle?

We evaluate the full one-photon-exchange Born amplitude for $Nd$ scattering. We include the contributions due to the magnetic moment of the proton or neutron, and the magnetic moment and quadrupole moment of the deuteron. It is found that the inclusion of the magnetic-moment interaction in the theoretical description of the $Nd$ scattering observables cannot resolve the long-standing $A_y$ puzzle.Comment: 7 pages, 2 Postscript figures; to appear in Phys.Rev.

Analyzing power in nucleon-deuteron scattering and three-nucleon forces

Three-nucleon forces have been considered to be one possibility to resolve the well known discrepancy between experimental values and theoretical calculations of the nucleon analyzing power in low energy nucleon-deuteron scattering. In this paper, we investigate possible effects of two-pion exchange three-nucleon forces on the analyzing power and the differential cross section. We found that the reason for different effects on the analyzing power by different three-nucleon forces found in previous calculations is related to the existence of the contact term. Effects of some variations of two-pion exchange three-nucleon forces are investigated. Also, an expression for the measure of the nucleon analyzing power with quartet P-wave phase shifts is presented.Comment: 11 pages including 2 eps figures, use epsfig.sty, to appear in Phys. Rev.

The AyA_y Puzzle and the Nuclear Force

The nucleon-deuteron analyzing power $A_y$ in elastic nucleon-deuteron scattering poses a longstanding puzzle. At energies $E_{lab}$ below approximately 30 MeV $A_y$ cannot be described by any realistic NN force. The inclusion of existing three-nucleon forces does not improve the situation. Because of recent questions about the $^3P_J$ NN phases, we examine whether reasonable changes in the NN force can resolve the puzzle. In order to do this we investigate the effect on the $^3P_J$ waves produced by changes in different parts of the potential (viz., the central force, tensor force, etc.), as well as on the 2-body observables and on $A_y$. We find that it is not possible with reasonable changes in the NN potential to increase the 3-body $A_y$ and at the same time to keep the 2-body observables unchanged. We therefore conclude that the $A_y$ puzzle is likely to be solved by new three-nucleon forces, such as those of spin-orbit type, which have not yet been taken into account.Comment: 35 pages in REVTeX, 1 figure in postscript and 3 figures in PiCTe