INVESTIGATING THE ESCAPE MECHANISM OF SRE BEARING MRNA TRANSCRIPTS DURING VIRAL HOST SHUTOFF

During viral infection, the virus and host clash for control over gene expression in an evolutionarily arms race that has raged for thousands of years. During lytic replication, Kaposi’s sarcoma associated herpesvirus (KSHV) triggers a massive RNA decay event known as host shut off. This causes over 70% of all RNA to be degraded suppressing the host antiviral response while freeing resources for viral replication. Our lab focuses on a subset of transcripts that escape from this viral degradation event using a cis acting 3’ UTR element known as a “SOX resistant element” or SRE. Although we have identified a couple of these transcripts and some of the proteins involved in their protection, the complete mechanism of protection from host shutoff has yet to be elucidated. In the first chapter, we used m6A-eCLIP to identify m6A modifications on SRE transcripts. We also characterized that this modification is necessary for SRE escape. In the second chapter we further characterized NCL/SRE densities during host shutoff through subcellular localization and mass spec and RNA sequencing. Finally in the third chapter we explored a method of SRE transcripts escaping from host shutoff induced nuclear retention of new transcripts through their interaction with a CRM-1 export pathway

An Adaptable Interleaved DC-DC Boost Converter

A.H. Weinberg presented his classic boost topology in his 1974 publication intended for use in satellites. It comprises minimal external components and uses multiple coupled coil systems to provide a boost of up to 2x. Its simplicity makes it inherently robust and reliable as minimal components means lower chance of failure. While its simplicity makes it attractive it has limited boost capability which makes it unsuitable for many modern day applications. No significant investigation has been carried out on adapting the Weinberg topology for high boost operation so far as can be ascertained. An investigation into adapting the Weinberg converter for high boost operation is presented in this thesis. A novel topology is developed which preserves the simplicity, reliability and efficiency of the Weinberg design while achieving boost ratios >2x. An analysis of the proposed topology is provided and mathematical expressions are derived to quantify the voltages and currents in relevant component for a given set of operating conditions. All coupled windings share a single core and are arranged so the magnetic flux does not reverse direction which further reduces loss in the magnetic core material. The coupled coils clamp the MOSFET drain voltage to an amount much lower than the output voltage which allows lower breakdown versions with lower intrinsic ON-resistance to be used leading to reduced conduction losses. Modelling of circuit losses and their sources allows optimal selection and positioning of components and finds wound component and MOSFET conduction losses contribute around 70% of the total circuit loss. Modelling and trialling of wound component geometries is carried out to optimise magnetic coupling and reduce leakage inductance. Working prototypes are developed and used to verify the mathematical claims through experimentation. Overall system efficiency of 94.1% is achieved at a boost ratio of 8.8x and an output power of 257W. Overall system losses are reduced from 11% to 6% by simply optimising the magnetic assembly. However optimisation of the magnetic assembly is more involved and may be less tolerant to variation which may hinder repeatability but the results are very positive despite crude, hand-wound magnetic coils and standard quality silicon components being used; which is a promising sign

Stealing the Show: KSHV Hijacks Host RNA Regulatory Pathways to Promote Infection

Kaposi’s sarcoma-associated herpesvirus (KSHV) induces life-long infections and has evolved many ways to exert extensive control over its host’s transcriptional and post-transcriptional machinery to gain better access to resources and dampened immune sensing. The hallmark of this takeover is how KSHV reshapes RNA fate both to control expression of its own gene but also that of its host. From the nucleus to the cytoplasm, control of RNA expression, localization, and decay is a process that is carefully tuned by a multitude of factors and that can adapt or react to rapid changes in the environment. Intriguingly, it appears that KSHV has found ways to co-opt each of these pathways for its own benefit. Here we provide a comprehensive review of recent work in this area and in particular recent advances on the post-transcriptional modifications front. Overall, this review highlights the myriad of ways KSHV uses to control RNA fate and gathers novel insights gained from the past decade of research at the interface of RNA biology and the field of KSHV research

Circulating microRNAs in sera correlate with soluble biomarkers of immune activation but do not predict mortality in ART treated individuals with HIV-1 infection: A case control study

Introduction: The use of anti-retroviral therapy (ART) has dramatically reduced HIV-1 associated morbidity and mortality. However, HIV-1 infected individuals have increased rates of morbidity and mortality compared to the non-HIV-1 infected population and this appears to be related to end-organ diseases collectively referred to as Serious Non-AIDS Events (SNAEs). Circulating miRNAs are reported as promising biomarkers for a number of human disease conditions including those that constitute SNAEs. Our study sought to investigate the potential of selected miRNAs in predicting mortality in HIV-1 infected ART treated individuals. Materials and Methods: A set of miRNAs was chosen based on published associations with human disease conditions that constitute SNAEs. This case: control study compared 126 cases (individuals who died whilst on therapy), and 247 matched controls (individuals who remained alive). Cases and controls were ART treated participants of two pivotal HIV-1 trials. The relative abundance of each miRNA in serum was measured, by RTqPCR. Associations with mortality (all-cause, cardiovascular and malignancy) were assessed by logistic regression analysis. Correlations between miRNAs and CD4+ T cell count, hs-CRP, IL-6 and D-dimer were also assessed. Results: None of the selected miRNAs was associated with all-cause, cardiovascular or malignancy mortality. The levels of three miRNAs (miRs -21, -122 and -200a) correlated with IL-6 while miR-21 also correlated with D-dimer. Additionally, the abundance of miRs -31, -150 and -223, correlated with baseline CD4+ T cell count while the same three miRNAs plus miR- 145 correlated with nadir CD4+ T cell count. Discussion: No associations with mortality were found with any circulating miRNA studied. These results cast doubt onto the effectiveness of circulating miRNA as early predictors of mortality or the major underlying diseases that contribute to mortality in participants treated for HIV-1 infection

Development and Validation of a Risk Score for Chronic Kidney Disease in HIV Infection Using Prospective Cohort Data from the D:A:D Study

Ristola M. on työryhmien DAD Study Grp ; Royal Free Hosp Clin Cohort ; INSIGHT Study Grp ; SMART Study Grp ; ESPRIT Study Grp jäsen.Background Chronic kidney disease (CKD) is a major health issue for HIV-positive individuals, associated with increased morbidity and mortality. Development and implementation of a risk score model for CKD would allow comparison of the risks and benefits of adding potentially nephrotoxic antiretrovirals to a treatment regimen and would identify those at greatest risk of CKD. The aims of this study were to develop a simple, externally validated, and widely applicable long-term risk score model for CKD in HIV-positive individuals that can guide decision making in clinical practice. Methods and Findings A total of 17,954 HIV-positive individuals from the Data Collection on Adverse Events of Anti-HIV Drugs (D:A:D) study with >= 3 estimated glomerular filtration rate (eGFR) values after 1 January 2004 were included. Baseline was defined as the first eGFR > 60 ml/min/1.73 m2 after 1 January 2004; individuals with exposure to tenofovir, atazanavir, atazanavir/ritonavir, lopinavir/ritonavir, other boosted protease inhibitors before baseline were excluded. CKD was defined as confirmed (>3 mo apart) eGFR In the D:A:D study, 641 individuals developed CKD during 103,185 person-years of follow-up (PYFU; incidence 6.2/1,000 PYFU, 95% CI 5.7-6.7; median follow-up 6.1 y, range 0.3-9.1 y). Older age, intravenous drug use, hepatitis C coinfection, lower baseline eGFR, female gender, lower CD4 count nadir, hypertension, diabetes, and cardiovascular disease (CVD) predicted CKD. The adjusted incidence rate ratios of these nine categorical variables were scaled and summed to create the risk score. The median risk score at baseline was -2 (interquartile range -4 to 2). There was a 1: 393 chance of developing CKD in the next 5 y in the low risk group (risk score = 5, 505 events), respectively. Number needed to harm (NNTH) at 5 y when starting unboosted atazanavir or lopinavir/ritonavir among those with a low risk score was 1,702 (95% CI 1,166-3,367); NNTH was 202 (95% CI 159-278) and 21 (95% CI 19-23), respectively, for those with a medium and high risk score. NNTH was 739 (95% CI 506-1462), 88 (95% CI 69-121), and 9 (95% CI 8-10) for those with a low, medium, and high risk score, respectively, starting tenofovir, atazanavir/ritonavir, or another boosted protease inhibitor. The Royal Free Hospital Clinic Cohort included 2,548 individuals, of whom 94 individuals developed CKD (3.7%) during 18,376 PYFU (median follow-up 7.4 y, range 0.3-12.7 y). Of 2,013 individuals included from the SMART/ESPRIT control arms, 32 individuals developed CKD (1.6%) during 8,452 PYFU (median follow-up 4.1 y, range 0.6-8.1 y). External validation showed that the risk score predicted well in these cohorts. Limitations of this study included limited data on race and no information on proteinuria. Conclusions Both traditional and HIV-related risk factors were predictive of CKD. These factors were used to develop a risk score for CKD in HIV infection, externally validated, that has direct clinical relevance for patients and clinicians to weigh the benefits of certain antiretrovirals against the risk of CKD and to identify those at greatest risk of CKD.Peer reviewe

Investigations into visual hyperacuity

SIGLEAvailable from British Library Document Supply Centre- DSC:DX96539 / BLDSC - British Library Document Supply CentreGBUnited Kingdo

Emulation Of Uniform Cracking

H. Steinhaus noted that the pattern of cracks in dried up homogeneous mud or tiles of earthenware as a rule has two characteristics: 1) The cracks intersect at right angles. 2) The cracks are such as to minimize their lengths. First we prove that for a closed convex graph of line segments and circular arcs, such an arc exists from every point whose tangent exists. And any closed figure smooth except for a finite number of corners facing inward has such an arc through any point. Emulating the natural process, an arbitrary tile is chosen, and a sequence of points on the tile is selected. For each point in the sequence, the shortest arc is drawn through the point that intersects the innermost tile perpendicular to its ends. This is done repeatedly, using the various subtiles that result from the previous crackings. The average properties reported are: the ratio of the area to that of a circle of the same perimeter, the ratio of the area of the new tiles to the area of the parent tile. Key..

Investigations into visual hyperacuity

Visual hyperacuities.are a group of thresholds whose values surpass that expected by the anatomical and optical constraints of the eye. There are many variables which affect hyperacuities of which this thesis considers the following .. 1. The effect of contrast on displacement detection and bisection acuity. It is proposed that spatial summation may account for the different response of these two hyperacuities compared with the contrast response of vernier acuity. 2. The effect of references on displacement detection. These were shown to greatly enhance performance when present. Their effect was, however, dependent upon the temporal characteristics of the displacement. 3. The effect of spatial frequency on vernier acuity. Evidence from this experiment suggests that vernier performance can be explained on the basis of the output of orientationally selective spatial frequency filters. 4. Evidence for a weighting function for visual location using random dot clusters. The weighting attached to different parts of the retinal light distribution was found to alter non-linearly with increasing offset from the geometric center of the cluster. A relationship between dot density and peak amplitude of the weighting function was found. 5. Spatial scaling of vernier acuity in the peripheral field. With careful choice of a technique which did not allow separation and eccentricity to co-vary it was found possible to scale vernier acuity both for two lines and two separated dots. 6. The effect of increasing age on hyperacuity. No change in vernier acuity with age was found which contrasted with displacement detection and bisection acuity both of which showed a significant decline with increasing age

Decorated Dissection Trees

In this paper I look at a method of building a binary search tree for storing a two-dimensional figure with all its subfigures. The problem is to store lines and curves such that searching and retrieval will be fast. When we do a partitioning, we must insert the partitioning arc and the subfigures such that a further data point will find the correct subfigure. What is distinctive about this insertion is the way we insert figures into the tree before any of the points within them. This paper continues a work written up in a previous conference by MacVeigh (1995), in which a method of partitioning figures in the plane by arcs of circles and straight line segments was described. Each time we wish to partition the figure (for example ABCD in figure 1), we first generate a random point (for example '1' in figure 1) within the figure. We then search the tree to find the innermost figure within which the point falls. At each interior node that contains a line segment, if the point is to the l..