Impact of future HERA data on the determination of proton parton distribution functions using the ZEUS QCD fit

The high precision and large kinematic coverage of the data from the HERA-I running period (1994-2000) have already allowed precise extractions of proton parton distribution functions (PDFs). The HERA-II running program is now underway and is expected to provide a substantial increase in the luminosity collected at HERA. In this paper, a study is presented which investigates the potential impact of future data from HERA on the proton PDF uncertainties, within the currently planned running scenario. In addition, the effect of a possible future measurement of the longitudinal structure function, FL, on the gluon distribution is investigated.Comment: 5 pages, 2 figures, in proceedings of the XIII International Workshop on Deep Inelastic Scattering - DIS 2005, Madison, Wisconsin, 200

Characterisation of the HSV-1 DNA Packaging Protein Encoded by the UL25 Gene

Herpes simplex virus type 1 (HSV-1) DNA replication results in the formation of head- to-tail concatemers which are cleaved into genome size units and packaged into the procapsid in the nuclei of virus-infected cells. The procapsid is a spherical structure with icosahedral symmetry and contains an internal protein scaffold which is removed at the same time viral DNA is encapsidated. During the DNA packaging process the procapsid angularises and the DNA-containing capsid can subsequently mature into an infectious virion. The product of the HSV-1 UL25 gene is a minor component of the viral capsid and has been implicated in the HSV-1 DNA packaging process. The overall goal of this thesis was to investigate the role of the UL25 protein in the HSV-1 lytic cycle. Before a detailed study of this protein could be undertaken, a number of reagents had to be prepared, including potent UL25-specitlc antibodies. Therefore, an initial aim of the project was to express the UL25 protein in a variety of in vivo recombinant protein expression systems and to purify the soluble recombinant UL25 protein for use as an antigen in the production of UL25-specific monoclonal antibodies. Maltose binding protein (MBP)-tagged UL25 and polyhistidine (His)-tagged UL25 were expressed in Escherichia coli and recombinant baculovirus-infected Sf21 cells respectively. BALB/c mice were immunised with purified soluble MBP-UL25 fusion protein and given a final boost with purified soluble His-tagged UL25 protein. Twelve hybridoma cell lines secreting UL25-specific monoclonal antibodies were isolated. The monoclonal antibodies were characterised using Western blot, immunoprecipitation and immunofluorescence assays. From this analysis a monoclonal antibody that reacted strongly with the UL25 protein in each of the immunoassays was purified for use in subsequent experiments. In the absence of other HSV-1 proteins, UL25 localised predominantly to the cytoplasm of cells transiently expressing the protein. In cells infected with HSV-I, however, UL25 protein was concentrated in the nuclei at late times. To investigate whether the HSV-1 capsid shell proteins, VP5, VP23 and VP19C, were required for the nuclear localisation of UL25 in HSV-I-infected cells, the distribution of UL25 protein was examined in cells infected with HSV-1 mutants which fail to express these proteins. In non-complementing cells infected with VP23 or VPS null mutants, the distribution of UL25 protein was similar to the pattern in wild-type (wt) virus-infected cells indicating that neither VP23 nor VP5 were necessary for the nuclear localisation of the UL25 protein during HSV-1 infection. Since capsid assembly did not occur under these conditions (Desai et al., 1993), nuclear localisation of UL25 was independent of capsid assembly. The intracellular distribution of UL25 was also examined in non-complementing cells infected with a VP19C null mutant of HSV-1. However, this virus appeared to have an additional mutation, one which affected late viral protein production, and no conclusive results were obtained through the use of this virus. The localisation of the UL25 protein was therefore investigated in cells infected with ts2, a mutant of HSV-1 that contains a temperature sensitive (ts) lesion in the VP19C protein. In cells infected with ts2 at the non-permissive temperature (NPT), UL25 co-localised with the capsid shell proteins at the perinuclear region of cells with little, if any, UL25 protein observed in the nuclei. These findings suggested that the VP19C protein was necessary for the nuclear distribution of UL25 during wt HSV-1 infection. However, in cells infected with a ts2 marker rescuant at the NPT, UL25 remained localised to the perinuclear region while the capsid shell proteins were found in the nuclei. This result indicated that the altered intracellular distribution of UL25 in cells infected with ts2 at the NPT was not a consequence of the ts lesion in the VP19C protein. Furthermore, UL25 also localised to the perinuclear region of cells infected with HSV-1 A44, the parental syncytial strain of ts2, at the NPT. This virus formed syncytia to a greater extent in cells infected at the NPT compared to the permissive temperature and it is possible that the altered intracellular distribution of UL25 protein in cells infected with HSV-1 A44 at the NPT may have resulted from the formation of syncytia or from an aberrant interaction with a component of the HSV-1 tegument. The association of UL25 protein with the capsid was initially examined using the recombinant baculovirus expression system to obtain information about the copy number and the location of the UL25 protein in the capsid as well as its interaction with capsid shell proteins. The UL25 protein was incorporated into capsids generated in insect cells multiply infected with recombinant baculoviruses expressing the HSV-1 capsid shell, scaffolding and the UL25 proteins, suggesting that the UL25 protein can interact with capsids in the absence of other viral proteins. This finding is in agreement with earlier results of McNab et al. (1998). (Abstract shortened by ProQuest.)

Lipid Metabolism and HCV Infection

Chronic infection by hepatitis C virus (HCV) can lead to severe liver disease and is a global healthcare problem. The liver is highly metabolically active and one of its key functions is to control the balance of lipid throughout the body. A number of pathologies have been linked to the impact of HCV infection on liver metabolism. However, there is also growing evidence that hepatic metabolic processes contribute to the HCV life cycle. This review summarizes the relationship between lipid metabolism and key stages in the production of infectious HCV

Bidirectional lipid droplet velocities are controlled by differential binding strengths of HCV Core DII protein

Host cell lipid droplets (LD) are essential in the hepatitis C virus (HCV) life cycle and are targeted by the viral capsid core protein. Core-coated LDs accumulate in the perinuclear region and facilitate viral particle assembly, but it is unclear how mobility of these LDs is directed by core. Herein we used two-photon fluorescence, differential interference contrast imaging, and coherent anti-Stokes Raman scattering microscopies, to reveal novel core-mediated changes to LD dynamics. Expression of core protein’s lipid binding domain II (DII-core) induced slower LD speeds, but did not affect directionality of movement on microtubules. Modulating the LD binding strength of DII-core further impacted LD mobility, revealing the temporal effects of LD-bound DII-core. These results for DII-core coated LDs support a model for core-mediated LD localization that involves core slowing down the rate of movement of LDs until localization at the perinuclear region is accomplished where LD movement ceases. The guided localization of LDs by HCV core protein not only is essential to the viral life cycle but also poses an interesting target for the development of antiviral strategies against HCV

Genome-to-genome analysis highlights the effect of the human innate and adaptive immune systems on the hepatitis C virus

Outcomes of hepatitis C virus (HCV) infection and treatment depend on viral and host genetic factors. Here we use human genome-wide genotyping arrays and new whole-genome HCV viral sequencing technologies to perform a systematic genome-to-genome study of 542 individuals who were chronically infected with HCV, predominantly genotype 3. We show that both alleles of genes encoding human leukocyte antigen molecules and genes encoding components of the interferon lambda innate immune system drive viral polymorphism. Additionally, we show that IFNL4 genotypes determine HCV viral load through a mechanism dependent on a specific amino acid residue in the HCV NS5A protein. These findings highlight the interplay between the innate immune system and the viral genome in HCV control

Combined transcriptomic-(1)H NMR metabonomic study reveals yhat monoethylhexyl phthalate stimulates adipogenesis and glyceroneogenesis in human adipocytes

Adipose tissue is a major storage site for lipophilic environmental contaminants. The environmental metabolic disruptor hypothesis postulates that some pollutants can promote obesity or metabolic disorders by activating nuclear receptors involved in the control of energetic homeostasis. In this context, monoethylhexyl phthalate (MEHP) is of particular concern since it was shown to activate the peroxisome proliferator-activated receptor γ (PPARγ) in 3T3-L1 murine preadipocytes. In the present work, we used an untargeted, combined transcriptomic-(1)H NMR-based metabonomic approach to describe the overall effect of MEHP on primary cultures of human subcutaneous adipocytes differentiated in vitro. MEHP stimulated rapidly and selectively the expression of genes involved in glyceroneogenesis, enhanced the expression of the cytosolic phosphoenolpyruvate carboxykinase, and reduced fatty acid release. These results demonstrate that MEHP increased glyceroneogenesis and fatty acid reesterification in human adipocytes. A longer treatment with MEHP induced the expression of genes involved in triglycerides uptake, synthesis, and storage; decreased intracellular lactate, glutamine, and other amino acids; increased aspartate and NAD, and resulted in a global increase in triglycerides. Altogether, these results indicate that MEHP promoted the differentiation of human preadipocytes to adipocytes. These mechanisms might contribute to the suspected obesogenic effect of MEHP

Does the new rugby union scrum sequence positively influence the hooker's in situ spinal kinematics?

Background: Scrummaging is unique to rugby union and involves 2 ‘packs’ of 8 players competing to regain ball possession. Intending to serve as a quick and safe method to restart the game, injury prevalence during scrummaging necessitates further evaluation of this environment. Aims: The aim of this study was to determine the effect of scrummage engagement sequences on spinal kinematics of the hooker. The conditions investigated were: (1) live competitive scrummaging using the new ‘crouch, bind, set’ sequence; (2) live competitive scrummaging using the old ‘crouch touch pause engage’ sequence and (3) training scrummaging using a scrum machine. Methods: Inertial sensors provided three-dimensional kinematic data across 5 spinal regions. Participants (n=29) were adult, male community club and university-level hookers. Results: Engagement sequence had no effect on resultant kinematics of any spinal region. Machine scrummaging resulted in lesser magnitudes of motion in the upper spinal regions. Around two-thirds of the total available cervical motion was utilised during live scrummaging. Conclusions: This study indicates that the most recent laws do not influence the spinal kinematics of the hooker during live scrummaging; however, there may be other benefits from these law changes that fall outside the scope of this investigation

Alternative Antigen Processing for MHC Class I: Multiple Roads Lead to Rome

The well described conventional antigen processing pathway is accountable for most peptides that end up in MHC class I molecules at the cell surface. These peptides experienced liberation by the proteasome and transport by the peptide transporter TAP. However, there are multiple roads that lead to Rome, illustrated by the increasing number of alternative processing pathways that have been reported during last years. Interestingly, TAP-deficient individuals do not succumb to viral infections, suggesting that CD8 T cell immunity is sufficiently supported by alternative TAP-independent processing pathways. To date, a diversity of viral and endogenous TAP-independent peptides have been identified in the grooves of different MCH class I alleles. Some of these peptides are not displayed by normal TAP-positive cells and we therefore called them TEIPP, for ‘T-cell epitopes associated with impaired peptide processing’. TEIPPs are hidden self-antigens, are derived from normal housekeeping proteins and are processed via unconventional processing pathways. Per definition, TEIPPs are presented via TAP-independent pathways, but recent data suggest that part of this repertoire still depend on proteasome and metalloprotease activity. An exception is the C-terminal peptide of the ER-membrane spanning ceramide synthase Trh4 that is surprisingly liberated by the signal peptide peptidase (SPP), the proteolytic enzyme involved in cleaving leader sequences. The intramembrane cleaving SPP is thereby an important contributor of TAP-independent peptides. Its family members, like the Alzheimer’s related presenilins, might as well, according to our preliminary data. Finally, alternative peptide routing is an emerging field and includes processes like the unfolded protein response, the ER-associated degradation and autophagy-associated vesicular pathways. These data convince us that there is a world to be discovered in the field of unconventional antigen processing

Search for lepton-flavor violation at HERA

A search for lepton-flavor-violating interactions $e p \to \mu X$ and $e p\to \tau X$ has been performed with the ZEUS detector using the entire HERA I data sample, corresponding to an integrated luminosity of 130 pb^{-1}. The data were taken at center-of-mass energies, $\sqrt{s}$, of 300 and 318 GeV. No evidence of lepton-flavor violation was found, and constraints were derived on leptoquarks (LQs) that could mediate such interactions. For LQ masses below $\sqrt{s}$, limits were set on $\lambda_{eq_1} \sqrt{\beta_{\ell q}}$, where $\lambda_{eq_1}$ is the coupling of the LQ to an electron and a first-generation quark $q_1$, and $\beta_{\ell q}$ is the branching ratio of the LQ to the final-state lepton $\ell$ ($\mu$ or $\tau$) and a quark $q$. For LQ masses much larger than $\sqrt{s}$, limits were set on the four-fermion interaction term $\lambda_{e q_\alpha} \lambda_{\ell q_\beta} / M_{\mathrm{LQ}}^2$ for LQs that couple to an electron and a quark $q_\alpha$ and to a lepton $\ell$ and a quark $q_\beta$, where $\alpha$ and $\beta$ are quark generation indices. Some of the limits are also applicable to lepton-flavor-violating processes mediated by squarks in $R$-Parity-violating supersymmetric models. In some cases, especially when a higher-generation quark is involved and for the process $e p\to \tau X$, the ZEUS limits are the most stringent to date.Comment: 37 pages, 10 figures, Accepted by EPJC. References and 1 figure (Fig. 6) adde