The Effect of the LISA Response Function on Observations of Monochromatic Sources

The Laser Interferometer Space Antenna (LISA) is expected to provide the largest observational sample of binary systems of faint sub-solar mass compact objects, in particular white-dwarfs, whose radiation is monochromatic over most of the LISA observational window. Current astrophysical estimates suggest that the instrument will be able to resolve about 10000 such systems, with a large fraction of them at frequencies above 3 mHz, where the wavelength of gravitational waves becomes comparable to or shorter than the LISA arm-length. This affects the structure of the so-called LISA transfer function which cannot be treated as constant in this frequency range: it introduces characteristic phase and amplitude modulations that depend on the source location in the sky and the emission frequency. Here we investigate the effect of the LISA transfer function on detection and parameter estimation for monochromatic sources. For signal detection we show that filters constructed by approximating the transfer function as a constant (long wavelength approximation) introduce a negligible loss of signal-to-noise ratio -- the fitting factor always exceeds 0.97 -- for f below 10mHz, therefore in a frequency range where one would actually expect the approximation to fail. For parameter estimation, we conclude that in the range 3mHz to 30mHz the errors associated with parameter measurements differ from about 5% up to a factor of 10 (depending on the actual source parameters and emission frequency) with respect to those computed using the long wavelength approximation.Comment: replacement version with typos correcte

LISA Response Function and Parameter Estimation

We investigate the response function of LISA and consider the adequacy of its commonly used approximation in the high-frequency range of the observational band. We concentrate on monochromatic binary systems, such as white dwarf binaries. We find that above a few mHz the approxmation starts becoming increasingly inaccurate. The transfer function introduces additional amplitude and phase modulations in the measured signal that influence parameter estmation and, if not properly accounted for, lead to losses of signal-to-noise ratio.Comment: 4 pages, 2 figures, amaldi 5 conference proceeding

High throughput mutagenesis for identification of residues regulating human prostacyclin (hIP) receptor

The human prostacyclin receptor (hIP receptor) is a seven-transmembrane G protein-coupled receptor (GPCR) that plays a critical role in vascular smooth muscle relaxation and platelet aggregation. hIP receptor dysfunction has been implicated in numerous cardiovascular abnormalities, including myocardial infarction, hypertension, thrombosis and atherosclerosis. Genomic sequencing has discovered several genetic variations in the PTGIR gene coding for hIP receptor, however, its structure-function relationship has not been sufficiently explored. Here we set out to investigate the applicability of high throughput random mutagenesis to study the structure-function relationship of hIP receptor. While chemical mutagenesis was not suitable to generate a mutagenesis library with sufficient coverage, our data demonstrate error-prone PCR (epPCR) mediated mutagenesis as a valuable method for the unbiased screening of residues regulating hIP receptor function and expression. Here we describe the generation and functional characterization of an epPCR derived mutagenesis library compromising >4000 mutants of the hIP receptor. We introduce next generation sequencing as a useful tool to validate the quality of mutagenesis libraries by providing information about the coverage, mutation rate and mutational bias. We identified 18 mutants of the hIP receptor that were expressed at the cell surface, but demonstrated impaired receptor function. A total of 38 non-synonymous mutations were identified within the coding region of the hIP receptor, mapping to 36 distinct residues, including several mutations previously reported to affect the signaling of the hIP receptor. Thus, our data demonstrates epPCR mediated random mutagenesis as a valuable and practical method to study the structurefunction relationship of GPCRs. © 2014 Bill et al

Impact of gene variants on sex-specific regulation of human Scavenger receptor class B type 1 (SR-BI) expression in liver and association with lipid levels in a population-based study

<p>Abstract</p> <p>Background</p> <p>Several studies have noted that genetic variants of <it>SCARB1</it>, a lipoprotein receptor involved in reverse cholesterol transport, are associated with serum lipid levels in a sex-dependent fashion. However, the mechanism underlying this gene by sex interaction has not been explored.</p> <p>Methods</p> <p>We utilized both epidemiological and molecular methods to study how estrogen and gene variants interact to influence <it>SCARB1 </it>expression and lipid levels. Interaction between 35 <it>SCARB1 </it>haplotype-tagged polymorphisms and endogenous estradiol levels was assessed in 498 postmenopausal Caucasian women from the population-based Rancho Bernardo Study. We further examined associated variants with overall and <it>SCARB1 </it>splice variant (SR-BI and SR-BII) expression in 91 human liver tissues using quantitative real-time PCR.</p> <p>Results</p> <p>Several variants on a haplotype block spanning intron 11 to intron 12 of <it>SCARB1 </it>showed significant gene by estradiol interaction affecting serum lipid levels, the strongest for rs838895 with HDL-cholesterol (p = 9.2 × 10^-4) and triglycerides (p = 1.3 × 10^-3) and the triglyceride:HDL cholesterol ratio (p = 2.7 × 10^-4). These same variants were associated with expression of the SR-BI isoform in a sex-specific fashion, with the strongest association found among liver tissue from 52 young women <45 years old (p = 0.002).</p> <p>Conclusions</p> <p>Estrogen and <it>SCARB1 </it>genotype may act synergistically to regulate expression of <it>SCARB1 </it>isoforms and impact serum levels of HDL cholesterol and triglycerides. This work highlights the importance of considering sex-dependent effects of gene variants on serum lipid levels.</p

The Type III Effectors NleE and NleB from Enteropathogenic E. coli and OspZ from Shigella Block Nuclear Translocation of NF-κB p65

Many bacterial pathogens utilize a type III secretion system to deliver multiple effector proteins into host cells. Here we found that the type III effectors, NleE from enteropathogenic E. coli (EPEC) and OspZ from Shigella, blocked translocation of the p65 subunit of the transcription factor, NF-κB, to the host cell nucleus. NF-κB inhibition by NleE was associated with decreased IL-8 expression in EPEC-infected intestinal epithelial cells. Ectopically expressed NleE also blocked nuclear translocation of p65 and c-Rel, but not p50 or STAT1/2. NleE homologues from other attaching and effacing pathogens as well OspZ from Shigella flexneri 6 and Shigella boydii, also inhibited NF-κB activation and p65 nuclear import; however, a truncated form of OspZ from S. flexneri 2a that carries a 36 amino acid deletion at the C-terminus had no inhibitory activity. We determined that the C-termini of NleE and full length OspZ were functionally interchangeable and identified a six amino acid motif, IDSY(M/I)K, that was important for both NleE- and OspZ-mediated inhibition of NF-κB activity. We also established that NleB, encoded directly upstream from NleE, suppressed NF-κB activation. Whereas NleE inhibited both TNFα and IL-1β stimulated p65 nuclear translocation and IκB degradation, NleB inhibited the TNFα pathway only. Neither NleE nor NleB inhibited AP-1 activation, suggesting that the modulatory activity of the effectors was specific for NF-κB signaling. Overall our data show that EPEC and Shigella have evolved similar T3SS-dependent means to manipulate host inflammatory pathways by interfering with the activation of selected host transcriptional regulators

Helios is a key transcriptional regulator of outer hair cell maturation

The sensory cells that are responsible for hearing include the cochlear inner hair cells (IHCs) and outer hair cells (OHCs), with the OHCs being necessary for sound sensitivity and tuning1. Both cell types are thought to arise from common progenitors; however, our understanding of the factors that control the fate of IHCs and OHCs remains limited. Here we identify Ikzf2 (which encodes Helios) as an essential transcription factor in mice that is required for OHC functional maturation and hearing. Helios is expressed in postnatal mouse OHCs, and in the cello mouse model a point mutation in Ikzf2 causes early-onset sensorineural hearing loss. Ikzf2cello/cello OHCs have greatly reduced prestin-dependent electromotile activity, a hallmark of OHC functional maturation, and show reduced levels of crucial OHC-expressed genes such as Slc26a5 (which encodes prestin) and Ocm. Moreover, we show that ectopic expression of Ikzf2 in IHCs: induces the expression of OHC-specific genes; reduces the expression of canonical IHC genes; and confers electromotility to IHCs, demonstrating that Ikzf2 can partially shift the IHC transcriptome towards an OHC-like identity

Long-read sequencing reveals the complex splicing profile of the psychiatric risk gene CACNA1C in human brain

RNA splicing is a key mechanism linking genetic variation with psychiatric disorders. Splicing profiles are particularly diverse in brain and difficult to accurately identify and quantify. We developed a new approach to address this challenge, combining long-range PCR and nanopore sequencing with a novel bioinformatics pipeline. We identify the full-length coding transcripts of CACNA1C in human brain. CACNA1C is a psychiatric risk gene that encodes the voltage-gated calcium channel CaV1.2. We show that CACNA1C’s transcript profile is substantially more complex than appreciated, identifying 38 novel exons and 241 novel transcripts. Importantly, many of the novel variants are abundant, and predicted to encode channels with altered function. The splicing profile varies between brain regions, especially in cerebellum. We demonstrate that human transcript diversity (and thereby protein isoform diversity) remains under-characterised, and provide a feasible and cost-effective methodology to address this. A detailed understanding of isoform diversity will be essential for the translation of psychiatric genomic findings into pathophysiological insights and novel psychopharmacological targets

Within-river nutrient processing in Chalk streams: The Pang and Lambourn, UK

This work examines baseflow nutrient concentrations and loads along two rural Chalk streams, the Pang and Lambourn. Soluble reactive phosphorus (SRP) and boron (B) concentrations in these streams were heavily influenced by point-source inputs and the effects of downstream flow accretion and dilution. Unlike B (which is chemically conservative), SRP loads were also strongly influenced by in-stream processing resulting in uptake of SRP, particularly immediately downstream of sewage effluent discharges, where rates of SRP uptake were highest. For the upper River Pang, up to 80% of SRP loads were lost within 4 km downstream of Compton sewage treatment works (STW) and on the River Lambourn up to 55% of SRP loads were lost within 1.6 km downstream of East Shefford STW. In contrast, nitrate (NO3) concentrations at sites along the Pang and Lambourn were largely controlled by groundwater inputs and plant uptake during periods of high photosynthetic activity in spring and summer and silicon (Si) by diatom uptake in April/May. There were net gains in NO3 loads along the river reaches, as a result of volumetric increases in groundwater discharge, and, compared with SRP, the role of in-stream processing of NO3 appeared low. Examination of SRP exchange by bed sediment and uptake of SRP into algal biofilms indicated that biofilms accounted for only a very small percentage of in-stream P-uptake, but that bed sediment SRP-exchanges had a more important control on baseflow SRP concentrations and loads. Point source P remediation at East Shefford STW, by removal of P from final effluent (P-stripping), resulted in 70–90% reductions in river-water SRP loads. After introduction of P-stripping at East Shefford STW, bed sediments immediately downstream of the STW switched from being net sinks to net sources of SRP. Our results show that, in the immediate aftermath of P-stripping, bed sediment SRP-release was responsible for a 30 μg-P l−1 rise in river-water SRP along this reach. While this increase in SRP concentration, as a result of bed sediment SRP release, is potentially ecologically significant, it is small in relation to the increase in SRP concentrations from effluent prior to P-stripping, which resulted in increases in SRP concentration of up to 500 μg-P l−1. There was a six-month lag between the introduction of P-stripping at East Shefford STW and bed sediment EPC0 recovering to equilibrium levels with the overlying river water (and thus negligible SRP release). Recovery of bed sediments to equilibrium levels is likely to have occurred as a result of winnowing and removal of high-EPC0 sediment and delivery of lower EPC0 sediment from upstream. Under higher/more variable flow conditions and greater rates of in-channel sediment erosion/delivery, more rapid recovery of bed sediment EPC0 levels following P-stripping might be expected