Using mouse transgenic and human stem cell technologies to model genetic mutations associated with schizophrenia and autism

Funding M.J. is funded by a Wellcome Trust Clinical Postdoctoral Research Fellowship, the Sackler Foundation and the RS Macdonald Trust. Acknowledgements We are grateful to the Royal Society for their support of the costs of attending the meeting ‘Of mice and mental health: facilitating dialogue between basic and clinical neuroscientists' convened by Amy Milton and Emily A. Holmes.Peer reviewedPublisher PD

Evaluating Launch Vehicle / Reentry Vehicle (LV/RV) Separation Concepts

Launch Vehicle/Reentry Vehicle (LV/RV) operations are expected to increase across the National Airspace System (NAS) as their reliability and availability improve. LV/RV designs and the industry landscape have vastly changed since the 1960’s, and the Federal Aviation Administration’s (FAA) methods for handling these operations need to evolve to support the expected growth. Currently, large amounts of airspace are segregated for every LV/RV operation. This increases costs for NAS users and may limit LV/RV opportunities. The FAA’s NextGen office recently proposed two more efficient separation concepts for LV/RV operations called Space Transition Corridors, and Four-Dimensional Trajectory Deconfliction. Prior safety research for LV/RV separation concepts has been limited to the interactions between falling debris and aircraft during in-flight breakup. However, there have been limited studies on the interactions between aircraft and LV/RV, aircraft and aircraft, and impacts on controller workload for LV/RV separation concepts and standards. Understanding these interactions is critical to implementing more efficient separation concepts and standards. The MITRE Corporation (MITRE) is building a flexible, fast-time modeling and simulation capability that fills this gap and provides operational measures of safety for each type of LV/RV operation using different separation concepts and associated standards, which helps support the FAA’s Safety Management System process. This capability will allow the FAA to determine which separation concepts meet a target level of safety for each type of LV/RV operation and will provide insight into the required surveillance performance, air traffic control and pilot response times, and traffic limits to enable the concepts. This paper describes the research, modeling, and current progress of MITRE’s analytic capability

Manifold Elastic Net: A Unified Framework for Sparse Dimension Reduction

It is difficult to find the optimal sparse solution of a manifold learning based dimensionality reduction algorithm. The lasso or the elastic net penalized manifold learning based dimensionality reduction is not directly a lasso penalized least square problem and thus the least angle regression (LARS) (Efron et al. \cite{LARS}), one of the most popular algorithms in sparse learning, cannot be applied. Therefore, most current approaches take indirect ways or have strict settings, which can be inconvenient for applications. In this paper, we proposed the manifold elastic net or MEN for short. MEN incorporates the merits of both the manifold learning based dimensionality reduction and the sparse learning based dimensionality reduction. By using a series of equivalent transformations, we show MEN is equivalent to the lasso penalized least square problem and thus LARS is adopted to obtain the optimal sparse solution of MEN. In particular, MEN has the following advantages for subsequent classification: 1) the local geometry of samples is well preserved for low dimensional data representation, 2) both the margin maximization and the classification error minimization are considered for sparse projection calculation, 3) the projection matrix of MEN improves the parsimony in computation, 4) the elastic net penalty reduces the over-fitting problem, and 5) the projection matrix of MEN can be interpreted psychologically and physiologically. Experimental evidence on face recognition over various popular datasets suggests that MEN is superior to top level dimensionality reduction algorithms.Comment: 33 pages, 12 figure

Preparation and C-13 NMR study on 1-aryl-3,3-difluoro-2-(phenylethynyl)cyclopropenes: long distance Hammett substituent effect

[[abstract]]Coupling of 1-aryl-3,3-difluoro-2-chlorocyclopropenes and phenylacetylene using Sonogashira reaction with Pd(OAc)(2) and CuI as the catalyst with K2CO3 as a base yields phenylethynylcyclopropenes in high selectivity and good yields. The C-13 chemical shifts of C epsilon of similar to 105 ppm on acetylene group significantly different from phenylacetylene (84 ppm) suggest that the acetylene group possesses less sp hybrid character due to an unusual long distance Hammett substituent effect. It is also confirmed by the substituent parameter analysis, while the C beta and C epsilon display the strong resonance effect (their values are 6.89 and 3.37, respectively). (c) 2008 Elsevier Ltd. All rights reserved

Methylation profiling of Epstein-Barr virus immediate-early gene promoters, BZLF1 and BRLF1 in tumors of epithelial, NK- and B-cell origins

<p>Abstract</p> <p>Background</p> <p>Epstein-Barr virus (EBV) establishes its latency in EBV-associated malignancies, accompanied by occasionally reactivated lytic cycle. Promoter CpG methylation of EBV genome plays an essential role in maintaining viral latency. Two immediate-early (IE) genes, BZLF1 and BRLF1, induce the switch from latent to lytic infection. Studies of methylation-dependent binding of BZLF1 and BRLF1 to EBV promoters have been well reported, but little is known about the methylation status of <it>BZLF1 </it>and <it>BRLF1 </it>promoters (Zp and Rp) in tumor samples.</p> <p>Methods</p> <p>We evaluated the methylation profiles of Zp and Rp by methylation-specific PCR (MSP) and bisulfite genomic sequencing (BGS), as well as <it>BZLF1 </it>and <it>BRLF1 </it>expression by semiquantitative reverse transcription (RT)-PCR in tumors of epithelial, NK- and B-cell origins.</p> <p>Results</p> <p>We found that both Zp and Rp were hypermethylated in all studied EBV-positive cell lines and tumors of lymphoid (B- or NK cell) or epithelial origin, while unmethylated Zp and Rp alleles were detected in cell lines expressing <it>BZLF1 </it>and <it>BRLF1</it>. Following azacytidine treatment or combined with trichostatin A (TSA), the expression of <it>BZLF1 </it>and <it>BRLF1 </it>was restored along with concomitant promoter demethylation, which subsequently induced the reactivation of early lytic gene <it>BHRF1 </it>and late lytic gene <it>BLLF1</it>.</p> <p>Conclusions</p> <p>Hypermethylation of Zp and Rp mediates the frequent silencing of <it>BZLF1 </it>and <it>BRLF1 </it>in EBV-associated tumors, which could be reactivated by demethylation agent and ultimately initiated the EBV lytic cascade.</p

Massive stereo-based DTM production for Mars on cloud computers

Digital Terrain Model (DTM) creation is essential to improving our understanding of the formation processes of the Martian surface. Although there have been previous demonstrations of open-source or commercial planetary 3D reconstruction software, planetary scientists are still struggling with creating good quality DTMs that meet their science needs, especially when there is a requirement to produce a large number of high quality DTMs using "free" software. In this paper, we describe a new open source system to overcome many of these obstacles by demonstrating results in the context of issues found from experience with several planetary DTM pipelines. We introduce a new fully automated multi-resolution DTM processing chain for NASA Mars Reconnaissance Orbiter (MRO) Context Camera (CTX) and High Resolution Imaging Science Experiment (HiRISE) stereo processing, called the Co-registration Ames Stereo Pipeline (ASP) Gotcha Optimised (CASP-GO), based on the open source NASA ASP. CASP-GO employs tie-point based multi-resolution image co-registration, and Gotcha sub-pixel refinement and densification. CASP-GO pipeline is used to produce planet-wide CTX and HiRISE DTMs that guarantee global geo-referencing compliance with respect to High Resolution Stereo Colour imaging (HRSC), and thence to the Mars Orbiter Laser Altimeter (MOLA); providing refined stereo matching completeness and accuracy. All software and good quality products introduced in this paper are being made open-source to the planetary science community through collaboration with NASA Ames, United States Geological Survey (USGS) and the Jet Propulsion Laboratory (JPL), Advanced Multi-Mission Operations System (AMMOS) Planetary Data System (PDS) Pipeline Service (APPS-PDS4), as well as browseable and visualisable through the iMars web based Geographic Information System (webGIS) system

Population screening for colorectal cancer means getting FIT:the past, present, and future of colorectal cancer screening using the fecal immunochemical test for hemoglobin (FIT)

Fecal immunochemical tests for hemoglobin (FIT) are changing the manner in which colorectal cancer (CRC) is screened. Although these tests are being performed worldwide, why is this test different from its predecessors? What evidence supports its adoption? How can this evidence best be used? This review addresses these questions and provides an understanding of FIT theory and practices to expedite international efforts to implement the use of FIT in CRC screening

The Spinal Cord Expression of Neuronal and Inducible Nitric Oxide Synthases and Their Contribution in the Maintenance of Neuropathic Pain in Mice

Background: Nitric oxide generated by neuronal (NOS1), inducible (NOS2) or endothelial (NOS3) nitric oxide synthases contributes to pain processing, but the exact role of NOS1 and NOS2 in the maintenance of chronic peripheral neuropathic pain as well as the possible compensatory changes in their expression in the spinal cord of wild type (WT) and NOS knockout (KO) mice at 21 days after total sciatic nerve ligation remains unknown. Methodology/Principal Findings: The mechanical and thermal allodynia as well as thermal hyperalgesia induced by sciatic nerve injury was evaluated in WT, NOS1-KO and NOS2-KO mice from 1 to 21 days after surgery. The mRNA and protein levels of NOS1, NOS2 and NOS3 in the spinal cord of WT and KO mice, at 21 days after surgery, were also assessed. Sciatic nerve injury led to a neuropathic syndrome in WT mice, in contrast to the abolished mechanical allodynia and thermal hyperalgesia as well as the decreased or suppressed thermal allodynia observed in NOS1-KO and NOS2-KO animals, respectively. Sciatic nerve injury also increases the spinal cord expression of NOS1 and NOS2 isoforms, but not of NOS3, in WT and NOS1-KO mice respectively. Moreover, the presence of NOS2 is required to increase the spinal cord expression of NOS1 whereas an increased NOS1 expression might avoid the up-regulation of NOS2 in the spinal cord of nerve injured WT mice. Conclusions/Significance: These data suggest that the increased spinal cord expression of NOS1, regulated by NOS2, might be responsible for the maintenance of chronic peripheral neuropathic pain in mice and propose these enzymes as interesting therapeutic targets for their treatment

RASSF1A–LATS1 signalling stabilizes replication forks by restricting CDK2-mediated phosphorylation of BRCA2

Genomic instability is a key hallmark of cancer leading to tumour heterogeneity and therapeutic resistance. ​BRCA2 has a fundamental role in error-free DNA repair but also sustains genome integrity by promoting ​RAD51 nucleofilament formation at stalled replication forks. ​CDK2 phosphorylates ​BRCA2 (pS3291-​BRCA2) to limit stabilizing contacts with polymerized ​RAD51; however, how replication stress modulates ​CDK2 activity and whether loss of pS3291-​BRCA2 regulation results in genomic instability of tumours are not known. Here we demonstrate that the Hippo pathway kinase ​LATS1 interacts with ​CDK2 in response to genotoxic stress to constrain pS3291-​BRCA2 and support ​RAD51 nucleofilaments, thereby maintaining genomic fidelity during replication stalling. We also show that ​LATS1 forms part of an ​ATR-mediated response to replication stress that requires the tumour suppressor ​RASSF1A. Importantly, perturbation of the ​ATR–​RASSF1A–​LATS1 signalling axis leads to genomic defects associated with loss of ​BRCA2 function and contributes to genomic instability and ‘BRCA-ness’ in lung cancers

Apolipoprotein M Gene (APOM) Polymorphism Modifies Metabolic and Disease Traits in Type 2 Diabetes

This study aimed at substantiating the associations of the apolipoproein M gene (APOM) with type 2 diabetes (T2D) as well as with metabolic traits in Hong Kong Chinese. In addition, APOM gene function was further characterized to elucidate its activity in cholesterol metabolism. Seventeen APOM SNPs documented in the NCBI database were genotyped. Five SNPs were confirmed in our study cohort of 1234 T2D and 606 control participants. Three of the five SNPs rs707921(C+1871A), rs707922(G+1837T) and rs805264(G+203A) were in linkage disequilibrium (LD). We chose rs707922 to tag this LD region for down stream association analyses and characterized the function of this SNP at molecular level. No association between APOM and T2D susceptibility was detected in our Hong Kong Chinese cohort. Interestingly, the C allele of rs805297 was significantly associated with T2D duration of longer than 10 years (OR = 1.245, p = 0.015). The rs707922 TT genotype was significantly associated with elevated plasma total- and LDL- cholesterol levels (p = 0.006 and p = 0.009, respectively) in T2D patients. Molecular analyses of rs707922 lead to the discoveries of a novel transcript APOM5 as well as the cryptic nature of exon 5 of the gene. Ectopic expression of APOM5 transcript confirmed rs707922 allele-dependent activity of the transcript in modifying cholesterol homeostasis in vitro. In conclusion, the results here did not support APOM as a T2D susceptibility gene in Hong Kong Chinese. However, in T2D patients, a subset of APOM SNPs was associated with disease duration and metabolic traits. Further molecular analysis proved the functional activity of rs707922 in APOM expression and in regulation of cellular cholesterol content