Determination of suitable housekeeping genes for normalisation of quantitative real time PCR analysis of cells infected with human immunodeficiency virus and herpes viruses

The choice of an appropriate housekeeping gene for normalisation purposes has now become an essential requirement when designing QPCR experiments. This is of particular importance when using QPCR to measure viral and cellular gene transcription levels in the context of viral infections as viruses can significantly interfere with host cell pathways, the components of which traditional housekeeping genes often encode. In this study we have determined the reliability of 10 housekeeping genes in context of four heavily studied viral infections; human immunodeficiency virus type 1, herpes simplex virus type 1, cytomegalovirus and varicella zoster virus infections using a variety of cell types and virus strains. This provides researchers of these viruses with a shortlist of potential housekeeping genes to use as normalisers for QPCR experiments

Frictional quantum decoherence

The dynamics associated with a measurement-based master equation for quantum Brownian motion are investigated. A scheme for obtaining time evolution from general initial conditions is derived. This is applied to analyze dissipation and decoherence in the evolution of both a Gaussian and a Schr\"{o}dinger cat initial state. Dependence on the diffusive terms present in the master equation is discussed with reference to both the coordinate and momentum representations.Comment: 18 pages, 7 figure

Associations between gestational anthropometry, maternal HIV, and fetal and early infancy growth in a prospective rural/semi-rural Tanzanian cohort, 2012-13.

BACKGROUND: Healthcare access and resources differ considerably between urban and rural settings making cross-setting generalizations difficult. In resource-restricted rural/semi-rural environments, identification of feasible screening tools is a priority. The objective of this study was to evaluate gestational anthropometry in relation to birth and infant growth in a rural/semi-rural Tanzanian prospective cohort of mothers and their infants. METHODS: Mothers (n = 114: 44 HIV-positive) attending antenatal clinic visits were recruited in their second or third trimester between March and November, 2012, and followed with their infants through 6-months post-partum. Demographic, clinical, and infant feeding data were obtained using questionnaires administered by a Swahili-speaking research nurse on demographic, socioeconomic, clinical, and infant feeding practices. Second or third trimester anthropometry (mid-upper arm circumference [MUAC], triceps skinfold thickness, weight, height), pregnancy outcomes, birth (weight, length, head circumference) and infant anthropometry (weight-for-age z-score [WAZ], length-for-age z-score [LAZ]) were obtained. Linear regression and mixed effect modeling were used to evaluate gestational factors in relation to pregnancy and infant outcomes. RESULTS AND DISCUSSION: Gestational MUAC and maternal HIV status (HIV-positive mothers = 39%) were associated with infant WAZ and LAZ from birth to 6-months in multivariate models, even after adjustment for infant feeding practices. The lowest gestational MUAC tertile was associated with lower WAZ throughout early infancy, as well as lower LAZ at 3 and 6-months. In linear mixed effects models through 6-months, each 1 cm increase in gestational MUAC was associated with a 0.11 increase in both WAZ (P < 0.001) and LAZ (P = 0.001). Infant HIV-exposure was negatively associated with WAZ (β = -0.65, P < 0.001) and LAZ (β = -0.49, P < 0.012) from birth to 6-months. CONCLUSIONS: Lower gestational MUAC, evaluated using only a tape measure and minimal training that is feasible in non-urban clinic and community settings, was associated with lower infant anthropometric measurements. In this rural and semi-rural setting, HIV-exposure was associated with poorer anthropometry through 6-months despite maternal antiretroviral access. Routine assessment of MUAC has the potential to identify at-risk women in need of additional health interventions designed to optimize pregnancy outcomes and infant growth. Further research is needed to establish gestational MUAC reference ranges and to define interventions that successfully improve MUAC during pregnancy

Benznidazole-resistance in Trypanosoma cruzi: evidence that distinct mechanisms can act in concert.

Benznidazole is the main drug used to treat Trypanosoma cruzi infections. However, frequent instances of treatment failure have been reported. To better understand potential resistance mechanisms, we analysed three clones isolated from a single parasite population that had undergone benznidazole-selection. These clones exhibited differing levels of benznidazole-resistance (varying between 9 and 26-fold), and displayed cross-resistance to nifurtimox (2 to 4-fold). Each clone had acquired a stop-codon-generating mutation in the gene which encodes the nitroreductase (TcNTR) that is responsible for activating nitroheterocyclic pro-drugs. In addition, one clone had lost a copy of the chromosome containing TcNTR. However, these processes alone are insufficient to account for the extent and diversity of benznidazole-resistance. It is implicit from our results that additional mechanisms must also operate and that T. cruzi has an intrinsic ability to develop drug-resistance by independent sequential steps, even within a single population. This has important implications for drug development strategies

Optical Structure and Proper-Motion Age of the Oxygen-rich Supernova Remnant 1E 0102-7219 in the Small Magellanic Cloud

We present new optical emission-line images of the young SNR 1E 0102-7219 (E0102) in the SMC obtained with the HST Advanced Camera for Surveys (ACS). E0102 is a member of the oxygen-rich class of SNRs showing strong oxygen, neon , and other metal-line emissions in its optical and X-ray spectra, and an absence of H and He. The progenitor of E0102 may have been a Wolf-Rayet star that underwent considerable mass loss prior to exploding as a Type Ib/c or IIL/b SN. The ejecta in this SNR are fast-moving (V > 1000 km/s) and emit as they are compressed and heated in the reverse shock. In 2003, we obtained optical [O III], H-alpha, and continuum images with the ACS Wide Field Camera. The [O III] image captures the full velocity range of the ejecta, and shows considerable high-velocity emission projected in the middle of the SNR that was Doppler-shifted out of the narrow F502N bandpass of a previous Wide Field and Planetary Camera 2 image from 1995. Using these two epochs separated by ~8.5 years, we measure the transverse expansion of the ejecta around the outer rim in this SNR for the first time at visible wavelengths. From proper-motion measurements of 12 ejecta filaments, we estimate a mean expansion velocity for the bright ejecta of ~2000 km/s and an inferred kinematic age for the SNR of \~2050 +/- 600 years. The age we derive from HST data is about twice that inferred by Hughes et al.(2000) from X-ray data, though our 1-sigma error bars overlap. Our proper-motion age is consistent with an independent optical kinematic age derived by Eriksen et al.(2003) using spatially resolved [O III] radial-velocity data. We derive an expansion center that lies very close to X-ray and radio hotspots, which could indicate the presence of a compact remnant (neutron star or black hole).Comment: 28 pages, 8 figures. Accepted to the Astrophysical Journal, to appear in 20 April 2006 issue. Full resolution figures are posted at: http://stevenf.asu.edu/figure

A novel method to characterise levels of pharmaceutical pollution in large-scale aquatic monitoring campaigns

Much of the current understanding of pharmaceutical pollution in the aquatic environment is based on research conducted in Europe, North America and other select high-income nations. One reason for this geographic disparity of data globally is the high cost and analytical intensity of the research, limiting accessibility to necessary equipment. To reduce the impact of such disparities, we present a novel method to support large-scale monitoring campaigns of pharmaceuticals at different geographical scales. The approach employs the use of a miniaturised sampling and shipping approach with a high throughput and fully validated direct-injection High-Performance Liquid Chromatography-Tandem Mass Spectrometry method for the quantification of 61 active pharmaceutical ingredients (APIs) and their metabolites in tap, surface, wastewater treatment plant (WWTP) influent and WWTP effluent water collected globally. A 7-day simulated shipping and sample stability assessment was undertaken demonstrating no significant degradation over the 1-3 days which is typical for global express shipping. Linearity (r 2 ) was consistently ≥0.93 (median = 0.99 ± 0.02), relative standard deviation of intra- and inter-day repeatability and precision was < 20% for 75% and 68% of the determinations made at three concentrations, respectively, and recovery from Liquid Chromatography Mass Spectrometry grade water, tap water, surface water and WWTP effluent were within an acceptable range of 60-130% for 87%, 76%, 77% and 63% of determination made at three concentrations respectively. Limits of detection and quantification were determined in all validated matrices and were consistently in the ng/L level needed for environmentally relevant API research. Independent validation of method results was obtained via an interlaboratory comparison of three surface-water samples and one WWTP effluent sample collected in North Liberty, Iowa (USA). Samples used for the interlaboratory validation were analysed at the University of York Centre of Excellence in Mass Spectrometry (York, UK) and the U.S. Geological Survey NationalWater Quality Laboratory in Denver (Colorado, USA). These results document the robustness of using this method on a global scale. Such application of this method would essentially eliminate the interlaboratory analytical variability typical of such large-scale datasets where multiple methods were used

Carbapenemase-producing Enterobacteriaceae in hospital wastewater:a reservoir that may be unrelated to clinical isolates [star]

Summary Background: Carbapenemase-producing Enterobacteriaceae (CPE) are an emerging infection control problem in hospitals worldwide. Identifying carriers can help reduce potential spread and infections. Aim: To assess whether testing hospital wastewater for CPE can supplement patient based screening for infection prevention purposes in a hospital without a recognised endemic CPE problem. Methods: Wastewater collected from hospital pipework on 16 occasions during February-March 2014 was screened for CPE using chromID®CARBA agar and chromID®CPS agar with a 10 μg ertapenem disc and combination disc testing. MICs were determined using British Society for Antimicrobial Chemotherapy methodology and carbapenemase genes detected by PCR or wholegenome sequencing. Selected isolates were typed by PFGE. Findings: Suspected CPE were recovered from all 16 wastewater samples. Of 17 isolates sent to Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, six (four Citrobacter freundii and two Enterobacter cloacae complex) were New Delhi metallo–beta-lactamase (NDM) producers and the remaining 11 (six Klebsiella oxytoca and five Enterobacter cloacae complex), Guiana-Extended-Spectrum-5 (GES-5) producers, the first to be described in Enterobacteriaceae in the UK. The four NDM-producing C. freundii, two NDM-producing E. cloacae complex and 4/5 GES-5-producing E. cloacae complex were each indistinguishable isolates of the same three strains, whereas the six GES-5-producing K. oxytoca overall shared 79% similarity. Conclusion: CPE are readily isolated from hospital wastewater using simple culture methods. There are either undetected carriers of CPE excreting into the wastewater, or these CPE represent colonisation of the pipework. Surveillance of hospital wastewater for CPE does not appear helpful for infection control purposes

Intrinsic aerobic capacity sets a divide for aging and longevity

&lt;p&gt;&lt;b&gt;Rationale:&lt;/b&gt; Low aerobic exercise capacity is a powerful predictor of premature morbidity and mortality for healthy adults as well as those with cardiovascular disease. For aged populations, poor performance on treadmill or extended walking tests indicates closer proximity to future health declines. Together, these findings suggest a fundamental connection between aerobic capacity and longevity.&lt;/p&gt; &lt;p&gt;&lt;b&gt;Objectives:&lt;/b&gt; Through artificial selective breeding, we developed an animal model system to prospectively test the association between aerobic exercise capacity and survivability (aerobic hypothesis).&lt;/p&gt; &lt;p&gt;&lt;b&gt;Methods and Results:&lt;/b&gt; Laboratory rats of widely diverse genetic backgrounds (N:NIH stock) were selectively bred for low or high intrinsic (inborn) treadmill running capacity. Cohorts of male and female rats from generations 14, 15, and 17 of selection were followed for survivability and assessed for age-related declines in cardiovascular fitness including maximal oxygen uptake (VO&lt;sub&gt;2max&lt;/sub&gt;), myocardial function, endurance performance, and change in body mass. Median lifespan for low exercise capacity rats was 28% to 45% shorter than high capacity rats (hazard ratio, 0.06; P&#60;0.001). VO&lt;sub&gt;2max&lt;/sub&gt;, measured across adulthood was a reliable predictor of lifespan (P&#60;0.001). During progression from adult to old age, left ventricular myocardial and cardiomyocyte morphology, contractility, and intracellular Ca&lt;sup&gt;2+&lt;/sup&gt; handling in both systole and diastole, as well as mean blood pressure, were more compromised in rats bred for low aerobic capacity. Physical activity levels, energy expenditure (Vo&lt;sub&gt;2&lt;/sub&gt;), and lean body mass were all better sustained with age in rats bred for high aerobic capacity.&lt;/p&gt; &lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; These data obtained from a contrasting heterogeneous model system provide strong evidence that genetic segregation for aerobic exercise capacity can be linked with longevity and are useful for deeper mechanistic exploration of aging.&lt;/p&gt

Towards an Understanding of Changing-Look Quasars: An Archival Spectroscopic Search in SDSS

The uncertain origin of the recently-discovered `changing-looking' quasar phenomenon -- in which a luminous quasar dims significantly to a quiescent state in repeat spectroscopy over ~10 year timescales -- may present unexpected challenges to our understanding of quasar accretion. To better understand this phenomenon, we take a first step to building a sample of changing-look quasars with a systematic but simple archival search for these objects in the Sloan Digital Sky Survey Data Release 12. By leveraging the >10 year baselines for objects with repeat spectroscopy, we uncover two new changing-look quasars, and a third discovered previously. Decomposition of the multi-epoch spectra and analysis of the broad emission lines suggest that the quasar accretion disk emission dims due to rapidly decreasing accretion rates (by factors of >2.5), while disfavoring changes in intrinsic dust extinction for the two objects where these analyses are possible. Broad emission line energetics also support intrinsic dimming of quasar emission as the origin for this phenomenon rather than transient tidal disruption events or supernovae. Although our search criteria included quasars at all redshifts and transitions from either quasar-like to galaxy-like states or the reverse, all of the clear cases of changing-look quasars discovered were at relatively low-redshift (z ~ 0.2 - 0.3) and only exhibit quasar-like to galaxy-like transitions.Comment: 15 pages, 8 figures. Updated to accepted versio