bluuebunny/crossref_metadata_2025 huggingface dataset:
Mesoscale Gradients of Herb Richness and Abundance in Central Amazonia1
Authors: Costa Flávia R. C.
Published: August 2006

There are few hypotheses to explain local understory diversity patterns. There is a consensus that climate and soil fertility affect understory density and diversity at large scales, but few studies addressed the mechanisms controlling density and diversity locally. Here, I examine patterns of abundance and diversity of three understory herb groups along gradients of soil nutrients and topography at the mesoscale (64 km2) in a wet tropical forest, and possible factors causing them. Herb richness, diversity, density, and cover were measured in fifty‐nine 250 × 2 m plots systematically distributed over Reserva Ducke, Manaus. Herb groups responded differently to environmental gradients. Whereas density and cover of pteridophytes increased with altitude and slope, Marantaceae density and cover decreased. Density of sedges increased with altitude, but did not vary with slope. Density and cover of Marantaceae and sedges but not pteridophytes increased with the soil cation content. Pteridophyte richness increased with slope whereas Marantaceae richness decreased, richness of both groups increased with cation content. Diversity increased with altitude for Marantaceae and decreased for pteridophytes. Some of these patterns agree with what is expected from herbs, such as the greater abundance of Marantaceae and sedges in flat and low altitude plots, where water availability is higher and probably also light, and the greater richness of Marantaceae and pteridophytes in higher nutrient plots. The unexpected results of higher abundance and richness of pteridophytes in slopes, instead of in bottomlands, suggest that biotic or litter‐mediated controls may be important to set these patterns.
Human prion diseases: biology and transmission by blood
Authors: Ironside J. W.
Published: August 2006

Human prion diseases are a group of rare fatal transmissible neurodegenerative disorders that occur in sporadic, acquired and familial forms. In 1996, a new type of human prion disease, variant Creutzfeldt‐Jakob disease (vCJD), was first identified and has subsequently been identified in 10 additional countries. vCJD results from human exposure to the bovine spongiform encephalopathy (BSE) agent, most likely through the consumption of BSE‐contaminated meat products. Unlike other human prion diseases, both infectivity and the disease‐associated form of the prion protein are readily detected in lymphoid tissues in vCJD, suggesting that infectivity may also be present in blood. Three recent cases of apparent iatrogenic vCJD infection by blood transfusion have occurred in the UK, following red blood cell transfusions from asymptomatic donors who subsequently died from vCJD. The first and third cases resulted in a clinical illness identical to vCJD, while the second case was an asymptomatic infection only detected at autopsy. There are no current means of detecting vCJD infection in asymptomatic donors, so continuing surveillance is required in the UK and other countries to monitor the incidence of vCJD and further cases of secondary transmission by blood transfusion.
Complications of massive transfusion in trauma patients
Authors: Hardcastle T. C.
Published: August 2006

Massive transfusion is a common consequence of major haemorrhage in the trauma patient. It affects the entire process of care, both for the clinicians involved in the patient's care and for the blood bank, given the consequences and complications of transfusions. This article will highlight the pathophysiology leading to the need for massive transfusion and provide some modern surgical approaches to decrease the transfusion requirement and lessen its effect on the individual patient. Practical suggestions for a massive transfusion protocol, based on our experience and the available literature will be provided. Finally the article will examine the complications of a massive transfusion and outline the steps in the prevention and management of these complications.
What quality of red blood cells shall we offer the transfused patient?
Authors: Högman C. F.
Published: August 2006

Individual units of red blood cells (RBCs) can vary widely in their benefit to recipients depending on how the unit is prepared and the duration and quality of pretransfusion storage. The haemoglobin (Hb) concentration of the donor blood, the volume of the collection, leucocyte depletion procedures and the composition of the additive solution are all factors that will influence the final product. It may not be generally appreciated that, as red cell preparation is currently practiced, the haemoglobin content of viable RBCs in an individual blood unit collected within current standards may range from as little as 30 g to as much as 90 g, a variation of which the transfusing physician is generally unaware and which should no longer be considered acceptable. The transfusion community is currently in the untenable position of attempting to balance the quality of transfused blood against perceived cost, a balance that needs to be re‐examined in the light of recent developments. A number of measures are currently available that can readily eliminate many of these shortcomings.

There are four obvious ways by which the quality and uniformity of RBC units can be improved: (1) The volume of blood collected from the donor should be adjusted depending on the donor's haemoglobin concentration. (2) Red cell losses during preparation should be minimized and accounted for in the collection (3) The subsequent preservation procedure should both maintain RBC viability during storage and minimize the loss of 2,3‐DPG and of membrane flexibility. (4) The haemoglobin content of a unit of red cells should be standardized. We recommend 50 g ± 5 g of haemoglobin as the amount of blood that should be collected from a donor.

For all of these measures the technology is currently available and may be readily introduced, especially through the use of automated collection systems. It is the responsibility of the transfusion organisations to redefine their goals and, in collaboration with industry, develop routine procedures that do not unnecessarily sacrifice to economics the best interests of blood recipients and their prescribing physicians.
Testing for rare blood donors by DNA analysis
Authors: Lomas‐Francis C.
Published: August 2006

Alloantibodies to blood group antigens are produced because there are differences between the blood group antigens on recipient and donor red blood cells. Historically, and currently, blood group antibodies and antigens are detected by haemagglutination, which requires appropriate reagents and considerable skill. Over the past two decades there has been an astounding pace of growth in the field of molecular biology techniques and even more recently in the understanding of the basis of many blood group antigens and phenotypes. Thus, we are now able to determine blood group polymorphisms and predict blood group antigen expression using molecular approaches. This article reviews molecular approaches to identify donors with rare blood types, either due to the absence of a high prevalence antigen or an absence of a combination of antigens.
Enhanced Yield of Hydrogen From Wastes Using High Temperature Steam Gasification
Authors: Jangsawang W. , Klimanek A. , Gupta Ashwani K.
Published: August 2006

Equilibrium calculations using the element potential method have been used to determine optimum conditions for the gasification of wood pellets and to understand the limitations and influence of preheated gasifying agent on the product gas composition. The calculations were carried out under isobaric (1 atm) and isothermal conditions using cellulose as the waste fuel. For each isothermal case results were obtained for the effect of feed gas composition. Various mixtures of steam/cellulose [mol/mol] and oxygen/steam [mol/mol] were examined to determine conditions for high yields of H2 and CO at a given temperature. The yield of hydrogen and carbon monoxide with different input feed composition and temperature of the process are therefore considered. The results showed strong effect of temperature on hydrogen and carbon monoxide yield in the gasified product stream. High temperatures resulted in high yields of hydrogen. Pure steam resulted in higher yields of hydrogen than steam-air gasifying agent. The experimental results using a fixed bed reactor showed good trends with the calculated data. These results assist in the design and development of enhanced hydrogen production from steam gasification of wastes.
The Regenerative Criteria of an Irreversible Brayton Heat Engine and its General Optimum Performance Characteristics
Authors: Zhang Yue , Ou Congjie , Lin Bihong , Chen Jincan
Published: August 2006

An irreversible cycle model of the Brayton heat engine is established, in which the irreversibilities resulting from the internal dissipation of the working substance in the adiabatic compression and expansion processes and the finite-rate heat transfer in the regenerative and constant-pressure processes are taken into account. The power output and efficiency of the cycle are expressed as functions of temperatures of the working substance and the heat sources, heat transfer coefficients, pressure ratio, regenerator effectiveness, and total heat transfer area including the heat transfer areas of the regenerator and other heat exchangers. The regenerative criteria are given. The power output is optimized for a given efficiency. The general optimal performance characteristics of the cycle are revealed. The optimal performance of the Brayton heat engines with and without regeneration is compared quantitatively. The advantages of using the regenerator are expounded. Some important parameters of an irreversible regenerative Brayton heat engine, such as the temperatures of the working substance at different states, pressure ratio, maximum value of the pressure ratio, regenerator effectiveness and ratios of the various heat transfer areas to the total heat transfer area of the cycle, are further optimized. The optimal relations between these parameters and the efficiency of the cycle are presented by a set of characteristic curves for some assumed compression and expansion efficiencies. The results obtained may be helpful to the comprehensive understanding of the optimal performance of the Brayton heat engines with and without regeneration and play a theoretical instructive role for the optimal design of a regenerative Brayton heat engine.
Exergy Costs and Inefficiency Diagnosis of a Dual-Purpose Power and Desalination Plant
Authors: Uche J. , Serra L. , Valero A.
Published: August 2006

Two applications of the thermoeconomic analysis technique have been performed to an interesting and complex system, which is an integrated dual plant composed of a steam power plant and a multi-stage desalination plant. A complete exergy and thermoeconomic costs analysis of different plant performances and the diagnosis of inefficiencies in a plant component are discussed in this paper. The results show that the knowledge of the physical cost of the two products of the plant and also the intermediate costs of every plant flowstream are essential to manage the plant in the best feasible condition. The inefficiency diagnosis computes the penalties of those inefficiencies, translates them into economical charges, and allows unexpected relationships between different plant components to be discovered.
Rapid Adaptation of a Recombinant Vesicular Stomatitis Virus to a Targeted Cell Line
Authors: Gao Yanhua , Whitaker-Dowling Patricia , Watkins Simon C. , Griffin Judith A. , Bergman Ira
Published: August 2006

Vesicular stomatitis virus (VSV) is being developed for cancer therapy. We created a recombinant replicating VSV (rrVSV) that preferentially infected Her2/neu-expressing breast cancer cells. This rrVSV did not express the native VSV-G glycoprotein (gp). Instead, it expressed a chimeric Sindbis gp which included a single-chain antibody (SCA) directed to the human Her2/neu receptor. The virus infected mouse mammary carcinoma cells (D2F2/E2) expressing Her2/neu 23-fold better than the parent cells (D2F2). However, viral growth in cultured D2F2/E2 cells was curtailed after several cycles, and viral yield was very poor at 2 × 10
4
infectious doses (ID)/ml. We performed in vitro serial passage in D2F2/E2 cells to evolve a virus with improved growth that could be used for preclinical therapy trials in mice. Fifteen passes generated an adapted virus that progressed through multiple cycles in cultured D2F2/E2 cells until all cells were infected and had a viral yield of 1 × 10
8
ID/ml. Sequencing of the entire viral genomes found only 2 mutations in the adapted virus. Both mutations occurred in the gp gene segment coding for the SCA. An additional N-glycosylation site was created by one of the mutations. The adapted virus showed higher density of gp on the viral envelope, improved infectivity, much greater stability, higher burst size, and decreased induction of cellular interferon. The specificity for cells expressing the Her2/neu receptor was unchanged. These studies demonstrate that serial passage can be used to rapidly evolve a VSV genome encoding an improved chimeric glycoprotein.
Gammaherpesvirus Persistence Alters Key CD8 T-Cell Memory Characteristics and Enhances Antiviral Protection
Authors: Obar Joshua J. , Fuse Shinichiro , Leung Erica K. , Bellfy Sarah C. , Usherwood Edward J.
Published: August 2006

In herpesvirus infections, the virus persists for life but is contained through T-cell-mediated immune surveillance. How this immune surveillance operates is poorly understood. Recent studies of other persistent infections have indicated that virus persistence is associated with functional deficits in the CD8+T-cell response. To test whether this is the case in a herpesvirus infection, we used a mutant murine gammaherpesvirus that is defective in its ability to persist in the host. By comparing the immune response to this virus with a revertant virus that can persist, we were able to dissect the changes in the antiviral CD8+T-cell response that are induced by virus persistence. Surprisingly, persistently infected mice controlled a secondary challenge infection more rapidly than nonpersistently infected mice, indicating enhanced rather than diminished effector functions. Consistent with this, virus-specific CD8 T cells from these mice exhibited faster upregulation of the cytotoxic mediator granzyme B. Another unexpected finding was that CD8+T cells from neither infection responded efficiently to homeostatic cytokines. The unresponsiveness of the memory cells from the nonpersistently infected mice appears to be linked to the prolonged replication of virus within the lungs. Other changes seen in different chronic infection models were also observed, such as changes in Bcl-2 levels, interleukin-2 production, and the immunodominance hierarchy. These data show persistence of gammaherpesvirus type 68 alters the properties of CD8+T cells and illustrates that immune surveillance does not require CD8 T cells with the same attributes as “classical” memory CD8+T cells.
Identification of Conserved Residues in the E2 Envelope Glycoprotein of the Hepatitis C Virus That Are Critical for CD81 Binding
Authors: Owsianka Ania M. , Timms Judith M. , Tarr Alexander W. , Brown Richard J. P. , Hickling Timothy P. , Szwejk Aleksandra , Bienkowska-Szewczyk Krystyna , Thomson Brian J. , Patel Arvind H. , Ball Jonathan K.
Published: August 2006

Hepatitis C virus (HCV) cell entry involves interaction between the viral envelope glycoprotein E2 and the cell surface receptor CD81. Knowledge of conserved E2 determinants important for successful binding will facilitate development of entry inhibitors designed to block this interaction. Previous studies have assigned the CD81 binding function to a number of discontinuous regions of E2. To better define specific residues involved in receptor binding, a panel of mutants of HCV envelope proteins was generated, where conserved residues within putative CD81 binding regions were sequentially mutated to alanine. Mutant proteins were tested for binding to a panel of monoclonal antibodies and CD81 and for their ability to form noncovalent heterodimers and confer infectivity in the retroviral pseudoparticle (HCVpp) assay. Detection by conformation-sensitive monoclonal antibodies indicated that the mutant proteins were correctly folded. Mutant proteins fell into three groups: those that bound CD81 and conferred HCVpp infectivity, those that abrogated both CD81 binding and HCVpp infectivity, and a final group containing mutants that were able to bind CD81 but were noninfectious in the HCVpp assay. Specific amino acids conserved across all genotypes that were critical for CD81 binding were W420, Y527, W529, G530, and D535. These data significantly increase our understanding of the CD81 receptor-E2 binding process.
The Charge Structure of Helix 1 in the Prion Protein Regulates Conversion to Pathogenic PrPSc
Authors: Norstrom Eric M. , Mastrianni James A.
Published: August 2006

The prion diseases are transmissible neurodegenerative disorders linked to a pathogenic conformer (PrPSc) of the normal prion protein (PrPC). Accumulation of PrPScoccurs via a poorly defined process in which PrPSccomplexes with and converts endogenous PrPCto nascent PrPSc. Recent experiments have focused on the highly charged first alpha helix (H1) of PrP. It has been proposed that two putative asparagine-to-arginine intrahelical salt bridges stabilize H1 in PrPCyet form intermolecular ionic bonds with adjacent PrP molecules during conversion of PrPCto PrPSc(M. P. Morrissey and E. I. Shakhnovich, Proc. Natl. Acad. Sci. USA 96:11293-11298, 1999). Subsequent work (J. O. Speare et al., J. Biol. Chem. 278:12522-12529, 2003 using a cell-free assay of PrPScconversion suggested that rather than promoting conversion, the salt bridges stabilize PrPCagainst it. However, the role of individual H1 charges in PrPScgeneration has not yet been investigated. To approach this question, we systematically reversed or neutralized each charged residue in H1 and tested the effect on conversion to PrPScin scrapie-infected murine neuroblastoma (ScN2a) cells. We find that replacements of charged H1 residues with like charges permit conversion, while charge reversals hinder it. Neutralization of charges in the N-terminal (amino acids 143 to 146) but not the C-terminal (amino acids 147 to 151) half of H1 permits conversion, while complete reversal of charge orientation of the putative salt bridges produces a nonconvertible PrP. Circular dichroism spectroscopy studies and confocal microscopy immunofluorescence localization studies indicated that charge substitutions did not alter the secondary structure or cell surface expression of PrPC. These data support the necessity of specific charge orientations in H1 for a productive PrPSc-PrPCcomplex.
Human T-Cell Leukemia Virus Type 1 (HTLV-1) and HTLV-2 Use Different Receptor Complexes To Enter T Cells
Authors: Jones Kathryn S. , Fugo Kazunori , Petrow-Sadowski Cari , Huang Ying , Bertolette Daniel C. , Lisinski Ivonne , Cushman Samuel W. , Jacobson Steven , Ruscetti Francis W.
Published: August 2006

Studies using adherent cell lines have shown that glucose transporter-1 (GLUT-1) can function as a receptor for human T-cell leukemia virus type 1 (HTLV). In primary CD4
+
T cells, heparan sulfate proteoglycans (HSPGs) are required for efficient entry of HTLV-1. Here, the roles of HSPGs and GLUT-1 in HTLV-1 and HTLV-2 Env-mediated binding and entry into primary T cells were studied. Examination of the cell surface of activated primary T cells revealed that CD4
+
T cells, the primary target of HTLV-1, expressed significantly higher levels of HSPGs than CD8
+
T cells. Conversely, CD8
+
T cells, the primary target of HTLV-2, expressed GLUT-1 at dramatically higher levels than CD4
+
T cells. Under these conditions, the HTLV-2 surface glycoprotein (SU) binding and viral entry were markedly higher on CD8
+
T cells while HTLV-1 SU binding and viral entry were higher on CD4
+
T cells. Binding studies with HTLV-1/HTLV-2 SU recombinants showed that preferential binding to CD4
+
T cells expressing high levels of HSPGs mapped to the C-terminal portion of SU. Transfection studies revealed that overexpression of GLUT-1 in CD4
+
T cells increased HTLV-2 entry, while expression of HSPGs on CD8
+
T cells increased entry of HTLV-1. These studies demonstrate that HTLV-1 and HTLV-2 differ in their T-cell entry requirements and suggest that the differences in the in vitro cellular tropism for transformation and in vivo pathobiology of these viruses reflect different interactions between their Env proteins and molecules on CD4
+
and CD8
+
T cells involved in entry.
Human Cytomegalovirus pUS24 Is a Virion Protein That Functions Very Early in the Replication Cycle
Authors: Feng Xuyan , Schröer Jörg , Yu Dong , Shenk Thomas
Published: August 2006

We have characterized the function of the human cytomegalovirus US24 gene, a US22 gene family member. Two US24-deficient mutants (BAD
in
US24 and BAD
sub
US24) exhibited a 20- to 30-fold growth defect, compared to their wild-type parent (BAD
wt
), after infection at a relatively low (0.01 PFU/cell) or high (1 PFU/cell) input multiplicity. Representative virus-encoded proteins and viral DNA accumulated with normal kinetics to wild-type levels after infection with mutant virus when cells received equal numbers of mutant and wild-type infectious units. Further, the proteins were properly localized and no ultrastructural differences were found by electron microscopy in mutant-virus-infected cells compared to wild-type-virus-infected cells. However, virions produced by US24-deficient mutants had a 10-fold-higher genome-to-PFU ratio than wild-type virus. When infections were performed using equal numbers of input virus particles, the expression of immediate-early, early, and late viral proteins was substantially delayed and decreased in the absence of US24 protein. This delay is not due to inefficient virus entry, since two tegument proteins and viral DNA moved to the nucleus equally well in mutant- and wild-type-virus-infected cells. In summary, US24 is a virion protein and virions produced by US24-deficient viruses exhibit a block to the human cytomegalovirus replication cycle after viral DNA reaches the nucleus and before immediate-early mRNAs are transcribed.
Importance of Neuraminidase Active-Site Residues to the Neuraminidase Inhibitor Resistance of Influenza Viruses
Authors: Yen Hui-Ling , Hoffmann Erich , Taylor Garry , Scholtissek Christoph , Monto Arnold S. , Webster Robert G. , Govorkova Elena A.
Published: August 2006

Neuraminidase inhibitors (NAIs) are antivirals designed to target conserved residues at the neuraminidase (NA) enzyme active site in influenza A and B viruses. The conserved residues that interact with NAIs are under selective pressure, but only a few have been linked to resistance. In the A/Wuhan/359/95 (H3N2) recombinant virus background, we characterized seven charged, conserved NA residues (R118, R371, E227, R152, R224, E276, and D151) that directly interact with the NAIs but have not been reported to confer resistance to NAIs. These NA residues were replaced with amino acids that possess side chains having similar properties to maintain their original charge. The NA mutations we introduced significantly decreased NA activity compared to that of the A/Wuhan/359/95 recombinant wild-type and R292K (an NA mutation frequently reported to confer resistance) viruses, which were analyzed for comparison. However, the recombinant viruses differed in replication efficiency when we serially passaged them in vitro; the growth of the R118K and E227D viruses was most impaired. The R224K, E276D, and R371K mutations conferred resistance to both zanamivir and oseltamivir, while the D151E mutation reduced susceptibility to oseltamivir only (∼10-fold) and the R152K mutation did not alter susceptibility to either drug. Because the R224K mutation was genetically unstable and the emergence of the R371K mutation in the N2 subtype is statistically unlikely, our results suggest that only the E276D mutation is likely to emerge under selective pressure. The results of our study may help to optimize the design of NAIs.
Potential Role for p53 in the Permissive Life Cycle of Human Cytomegalovirus
Authors: Casavant N. C. , Luo M. H. , Rosenke K. , Winegardner T. , Zurawska A. , Fortunato E. A.
Published: August 2006

Infection of primary fibroblasts with human cytomegalovirus (HCMV) causes a rapid stabilization of the cellular protein p53. p53 is a major effector of the cellular damage response, and activation of this transcription factor can lead either to cell cycle arrest or to apoptosis. Viruses employ many tactics to avoid p53-mediated effects. One method HCMV uses to counteract p53 is sequestration into its viral replication centers. In order to determine whether or not HCMV benefits from this sequestration, we infected a p53
−/−
fibroblast line. We find that although these cells are permissive for viral infection, several parameters are substantially altered compared to wild-type (wt) fibroblasts. p53
−/−
cells show delayed and decreased accumulation of infectious viral particles compared to control fibroblasts, with the largest difference of 100-fold at 72 h post infection (p.i.) and peak titers decreased by approximately 10- to 20-fold at 144 h p.i. Viral DNA accumulation is also delayed and somewhat decreased in p53
−/−
cells; however, on average, levels of DNA are not more than fivefold lower than wt at any time p.i. and thus cannot account entirely for the observed differences in titers. In addition, there are delays in the expression of several key viral proteins, including the early replication protein UL44 and some of the late structural proteins, pp28 (UL99) and MCP (UL86). UL44 localization also indicates delayed formation and maturation of the replication centers throughout the course of infection. Localization of the major tegument protein pp65 (UL83) is also altered in these p53
−/−
cells. Partial reconstitution of the p53
−/−
cells with a wt copy of p53 returns all parameters toward wt, while reconstitution with mutant p53 does not. Taken together, our data suggest that wt p53 enhances the ability of HCMV to replicate and produce high concentrations of infectious virions in permissive cells.
Highly Conserved Regions within the Spike Proteins of Human Coronaviruses 229E and NL63 Determine Recognition of Their Respective Cellular Receptors
Authors: Hofmann Heike , Simmons Graham , Rennekamp Andrew J. , Chaipan Chawaree , Gramberg Thomas , Heck Elke , Geier Martina , Wegele Anja , Marzi Andrea , Bates Paul , Pöhlmann Stefan
Published: August 2006

We have recently demonstrated that the severe acute respiratory syndrome coronavirus (SARS-CoV) receptor angiotensin converting enzyme 2 (ACE2) also mediates cellular entry of the newly discovered human coronavirus (hCoV) NL63. Here, we show that expression of DC-SIGN augments NL63 spike (S)-protein-driven infection of susceptible cells, while only expression of ACE2 but not DC-SIGN is sufficient for entry into nonpermissive cells, indicating that ACE2 fulfills the criteria of a bona fide hCoV-NL63 receptor. As for SARS-CoV, murine ACE2 is used less efficiently by NL63-S for entry than human ACE2. In contrast, several amino acid exchanges in human ACE2 which diminish SARS-S-driven entry do not interfere with NL63-S-mediated infection, suggesting that SARS-S and NL63-S might engage human ACE2 differentially. Moreover, we observed that NL63-S-driven entry was less dependent on a low-pH environment and activity of endosomal proteases compared to infection mediated by SARS-S, further suggesting differences in hCoV-NL63 and SARS-CoV cellular entry. NL63-S does not exhibit significant homology to SARS-S but is highly related to the S-protein of hCoV-229E, which enters target cells by engaging CD13. Employing mutagenic analyses, we found that the N-terminal unique domain in NL63-S, which is absent in 229E-S, does not confer binding to ACE2. In contrast, the highly homologous C-terminal parts of the NL63-S1 and 229E-S1 subunits in conjunction with distinct amino acids in the central regions of these proteins confer recognition of ACE2 and CD13, respectively. Therefore, despite the high homology of these sequences, they likely form sufficiently distinct surfaces, thus determining receptor specificity.
Structural and Functional Basis for ADP-Ribose and Poly(ADP-Ribose) Binding by Viral Macro Domains
Authors: Egloff Marie-Pierre , Malet Hélène , Putics Ákos , Heinonen Maarit , Dutartre Hélène , Frangeul Antoine , Gruez Arnaud , Campanacci Valérie , Cambillau Christian , Ziebuhr John , Ahola Tero , Canard Bruno
Published: August 2006

Macro domains constitute a protein module family found associated with specific histones and proteins involved in chromatin metabolism. In addition, a small number of animal RNA viruses, such as corona- and toroviruses, alphaviruses, and hepatitis E virus, encode macro domains for which, however, structural and functional information is extremely limited. Here, we characterized the macro domains from hepatitis E virus, Semliki Forest virus, and severe acute respiratory syndrome coronavirus (SARS-CoV). The crystal structure of the SARS-CoV macro domain was determined at 1.8-Å resolution in complex with ADP-ribose. Information derived from structural, mutational, and sequence analyses suggests a close phylogenetic and, most probably, functional relationship between viral and cellular macro domain homologs. The data revealed that viral macro domains have relatively poor ADP-ribose 1"-phosphohydrolase activities (which were previously proposed to be their biologically relevant function) but bind efficiently free and poly(ADP-ribose) polymerase 1-bound poly(ADP-ribose) in vitro. Collectively, these results suggest to further evaluate the role of viral macro domains in host response to viral infection.
Integration Site Choice of a Feline Immunodeficiency Virus Vector
Authors: Kang Yubin , Moressi Christopher J. , Scheetz Todd E. , Xie Litao , Tran Diane Thi , Casavant Thomas L. , Ak Prashanth , Benham Craig J. , Davidson Beverly L. , McCray Paul B.
Published: August 2006

We mapped 226 unique integration sites in human hepatoma cells following gene transfer with a feline immunodeficiency virus (FIV)-based lentivirus vector. FIV integrated across the entire length of the transcriptional units. Microarray data indicated that FIV integration favored actively transcribed genes. Approximately 21% of FIV integrations within transcriptional units occurred in genes regulated by the LEDGF/p75 transcriptional coactivator. DNA in regions of FIV insertion sites exhibited a “bendable” structure and a pattern of duplex destabilization favoring strand separation. FIV integration preferences are more similar to those of primate lentiviruses and distinct from those of Moloney murine leukemia virus, avian sarcoma leukosis virus, and foamy virus.
Inhibition by Woodchuck Hepatitis Virus of Class I Major Histocompatibility Complex Presentation on Hepatocytes Is Mediated by Virus Envelope Pre-S2 Protein and Can Be Reversed by Treatment with Gamma Interferon
Authors: Wang Jinguo , Michalak Tomasz I.
Published: August 2006

Presentation of class I major histocompatibility complex (MHC) is severely down-regulated on hepatocytes in chronic hepatitis caused by woodchuck hepatitis virus (WHV). To determine which of the viral proteins mediates class I MHC antigen suppression, cultured normal woodchuck hepatocytes were transfected with the complete WHV genome, sequences encoding individual virus proteins, or whole virus genomes in which transcription of selected proteins was disabled by site-specific mutagenesis. It was found that hepatocyte presentation of class I MHC antigen was significantly inhibited following transfection with complete WHV genome or with viral subgenomic fragments encoding envelope pre-S2 protein or pre-S1 protein, which naturally encompasses pre-S2 amino acid sequence. In contrast, hepatocytes transfected with WHV X gene alone demonstrated a profound enhancement in the class I antigen display, whereas those expressing virus major S protein or nucleocapsid (core) protein were not different from control hepatocytes. Analysis of the mutated WHV sequences confirmed that the envelope pre-S2 protein was responsible for inhibition of the class I MHC antigen display. Interestingly, treatment with recombinant woodchuck gamma interferon (rwIFN-γ) restored the inhibited presentation of the class I antigen. Moreover, the class I antigen suppression was not associated with down-regulation of hepatocyte genes for class I MHC heavy chain, β
2
-microglobulin, transporters associated with antigen processing, and proteasome subunits. These findings indicate that the defective presentation of class I MHC antigen on hepatocytes transcribing WHV is a consequence of posttranscriptional suppression exerted by virus pre-S2 protein and that this hindrance can be fully reversed by IFN-γ.
Functional Entry of Baculovirus into Insect and Mammalian Cells Is Dependent on Clathrin-Mediated Endocytosis
Authors: Long Gang , Pan Xiaoyu , Kormelink Richard , Vlak Just M.
Published: August 2006

Entry of the budded virus form of baculoviruses into insect and mammalian cells is generally thought to occur through a low-pH-dependent endocytosis pathway, possibly through clathrin-coated pits. This insight is primarily based on (immuno)electron microscopy studies but requires biochemical support to exclude the use of other pathways. Here, we demonstrate using various inhibitors that functional entry of baculoviruses into insect and mammalian cells is primarily dependent on clathrin-mediated endocytosis. Our results further suggest that caveolae are somehow involved in baculovirus entry in mammalian cells. A caveolar endocytosis inhibitor, genistein, enhances baculovirus transduction in these cells considerably.
Identification of Protective Lassa Virus Epitopes That Are Restricted by HLA-A2
Authors: Botten Jason , Alexander Jeff , Pasquetto Valerie , Sidney John , Barrowman Polly , Ting Joey , Peters Bjoern , Southwood Scott , Stewart Barbara , Rodriguez-Carreno Maria P. , Mothe Bianca , Whitton J. Lindsay , Sette Alessandro , Buchmeier Michael J.
Published: August 2006

Recovery from Lassa virus (LASV) infection usually precedes the appearance of neutralizing antibodies, indicating that cellular immunity plays a primary role in viral clearance. To date, the role of LASV-specific CD8+T cells has not been evaluated in humans. To facilitate such studies, we utilized a predictive algorithm to identify candidate HLA-A2 supertype epitopes from the LASV nucleoprotein and glycoprotein precursor (GPC) genes. We identified three peptides (GPC42-50, GLVGLVTFL; GPC60-68, SLYKGVYEL; and GPC441-449, YLISIFLHL) that displayed high-affinity binding (≤98 nM) to HLA-A*0201, induced CD8+T-cell responses of high functional avidity in HLA-A*0201 transgenic mice, and were naturally processed from native LASV GPC in human HLA-A*0201-positive target cells. HLA-A*0201 mice immunized with either GPC42-50or GPC60-68were protected against challenge with a recombinant vaccinia virus that expressed LASV GPC. The epitopes identified in this study represent potential diagnostic reagents and candidates for inclusion in epitope-based vaccine constructs. Our approach is applicable to any pathogen with existing sequence data, does not require manipulation of the actual pathogen or access to immune human donors, and should therefore be generally applicable to category A through C agents and other emerging pathogens.
Reovirus Outer Capsid Protein μ1 Induces Apoptosis and Associates with Lipid Droplets, Endoplasmic Reticulum, and Mitochondria
Authors: Coffey Caroline M. , Sheh Alexander , Kim Irene S. , Chandran Kartik , Nibert Max L. , Parker John S. L.
Published: August 2006

The mechanisms by which reoviruses induce apoptosis have not been fully elucidated. Earlier studies identified the mammalian reovirus S1 and M2 genes as determinants of apoptosis induction. However, no published results have demonstrated the capacities of the proteins encoded by these genes to induce apoptosis, either independently or in combination, in the absence of reovirus infection. Here we report that the mammalian reovirus μ1 protein, encoded by the M2 gene, was sufficient to induce apoptosis in transfected cells. We also found that μ1 localized to lipid droplets, endoplasmic reticulum, and mitochondria in both transfected cells and infected cells. Two small
regions encompassing amphipathic α-helices within a carboxyl-terminal portion of μ1 were necessary for efficient
induction of apoptosis and association with lipid droplets, endoplasmic reticulum, and mitochondria in transfected cells. Induction of
apoptosis by μ1 and its association with lipid droplets and intracellular membranes in transfected cells were abrogated whenμ
1 was coexpressed with σ3, with which it is known to coassemble. We propose that μ1 plays a direct role in the
induction of apoptosis in infected cells and that this property may relate to the capacity of μ1 to associate with intracellular
membranes. Moreover, during reovirus infection, association with σ3 may regulate apoptosis induction byμ
1.
Differences and Similarities in Viral Life Cycle Progression and Host Cell Physiology after Infection of Human Dendritic Cells with Modified Vaccinia Virus Ankara and Vaccinia Virus
Authors: Chahroudi Ann , Garber David A. , Reeves Patrick , Liu Luzheng , Kalman Daniel , Feinberg Mark B.
Published: August 2006

Modified vaccinia virus Ankara (MVA) is an attenuated strain of vaccinia virus (VV) that has attracted significant attention as a candidate viral vector vaccine for immunization against infectious diseases and treatment of malignancies. Although MVA is unable to replicate in most nonavian cells, vaccination with MVA elicits immune responses that approximate those seen after the administration of replication-competent strains of VV. However, the mechanisms by which these viruses elicit immune responses and the determinants of their relative immunogenicity are incompletely understood. Studying the interactions of VV and MVA with cells of the human immune system may elucidate these mechanisms, as well as provide a rational basis for the further enhancement of the immunogenicity of recombinant MVA vectors. Toward this end, we investigated the consequences of MVA or VV infection of human dendritic cells (DCs), key professional antigen-presenting cells essential for the generation of immune responses. We determined that a block to the formation of intracellular viral replication centers results in abortive infection of DCs with both VV and MVA. MVA inhibited cellular protein synthesis more rapidly than VV and displayed a distinct pattern of viral protein expression in infected DCs. MVA also induced apoptosis in DCs more rapidly than VV, and DC apoptosis after MVA infection was associated with an accelerated decline in the levels of intracellular Bcl-2 and Bcl-XL. These findings suggest that antigen presentation pathways may contribute differentially to the immunogenicity of VV and MVA and that targeted modifications of virus-induced DC apoptosis may further increase the immunogenicity of MVA-vectored vaccines.
THE BLACK SCHOLES BARENBLATT EQUATION FOR OPTIONS WITH UNCERTAIN VOLATILITY AND ITS APPLICATION TO STATIC HEDGING
Authors: MEYER GUNTER H.
Published: August 2006

The Black Scholes Barenblatt (BSB) equation for the envelope of option prices with uncertain volatility and interest rate is derived from the Black Scholes equation with the maximum principle for diffusion equations and shown to be equivalent to a readily solvable standard Black Scholes equation with a nonlinear source term. Analogous arguments yield the envelope for the delta of option prices. We then interpret the concept of static hedging for narrowing the envelope in terms of partial differential equations and define the optimal static hedge and computable approximations to it. We apply the BSB equation to find numerically some optimally hedged portfolios of representative European and American options.
LONG MEMORY AND SAMPLING FREQUENCIES: EVIDENCE IN STOCK INDEX FUTURES MARKETS
Authors: SHIEH SHWU-JANE
Published: August 2006

The long-term dependent behavior in the close prices of the S&P 500, Nikkei 225, and Dow Jones index futures contracts are investigated by using the ARFIMA (p, d, q) model to estimate the order of the fractional integration parameters for a large range of sampling frequencies: from one-minute to monthly frequencies. The empirical evidence shows that the close prices exhibit anti-persistence properties for most of the sampling frequencies. This suggests that the contrarian's trading strategies in relation to stock index futures markets have a positive value. Moreover, the empirical evidence indicates that the higher frequency of the data, the stronger degree of contrarian behaviors, particularly for S&P 500 and Dow Jones stock index futures contracts.
HOT CARRIER EFFECTS ON JITTER PERFORMANCE IN CMOS VOLTAGE-CONTROLLED OSCILLATORS
Authors: ZHANG CHI , SRIVASTAVA ASHOK
Published: August 2006

The effects of hot carrier stress on CMOS voltage-controlled oscillators (VCO) are investigated. A model of the threshold voltage degradation in MOSFETs due to hot carrier stress has been used to model jitter in voltage-controlled oscillators. The relation between the stress time which induces the hot carrier effects due to generation of interface traps near the drain of the n-MOSFETs, and the degradation of the VCO performance is presented. The VCO performance degradation takes into consideration decrease in operation frequency and increase in jitter. The experimental circuits have been designed in 0.5 μm n-well CMOS technology for operation at 3 V. Experimental results show that after four hours hot-carrier stress the jitter is increased by 40 ps for single-ended current starved VCOs.
INVESTIGATING THE TEMPORAL FLUCTUATIONS IN SATELLITE ADVANCED VERY HIGH RESOLUTION RADIOMETER THERMAL SIGNALS MEASURED IN THE VOLCANIC AREA OF ETNA (ITALY)
Authors: MARCHESE FRANCESCO , PERGOLA NICOLA , TELESCA LUCIANO
Published: August 2006

The time dynamics of long-term time series of satellite thermal signal, measured at Mount Etna, has been investigated. The signal has been analyzed by means of a recently proposed multi-temporal and robust technique (RST), which has already shown to be better capable to detect and monitor volcanic hotspots, compared to traditional satellite approaches. The temporal fluctuations of the thermal signal detected by RST over a long series (1995-2005) of Advanced Very High Resolution Radiometer (AVHRR) satellite data, have been characterized by means of the correlation function and the power spectrum analysis, which have shown the presence of correlation structures in the thermal time series recorded in the crater area.
THE EXISTENCE OF CERTAIN (CO-)LIMITS IN THE CATEGORY OF CHAIN FUNCTORS
Authors: BAUER FRIEDRICH W. , DATUASHVILI TAMAR
Published: August 2006

Chain functors A*, B* have been introduced for calculating generalized homology theories by using chains and cycles, as one is doing for ordinary homology theories by means of chain complexes. Like chain complexes these chain functors form a category ℭh displaying interesting properties by themselves. The present paper emphasizes more the algebraic aspescts of this category ℭh. Although not every morphism f ∈ ℭh(A*, B*) in the category of chain functors admits a kernel or a cokernel, it turns out that: (1) all cofibrations have a cokernel, (2) all regular fibrations have a kernel, (3) the pushout of a cofibration along a cofibration exists in ℭh, respectively the dual statement for fibrations, (4) there are interesting results about exact sequences involving (co-)fibrations.
FUNCTIONAL DECOMPOSITION — THE VALUE AND IMPLICATION FOR BOTH NEURAL NETWORKS AND DIGITAL DESIGNING
Authors: SELVARAJ HENRY , SAPIECHA PIOTR , RAWSKI MARIUSZ , ŁUBA TADEUSZ
Published: August 2006

General functional decomposition is mainly perceived as a logic synthesis method for implementing Boolean functions into FPGA-based architectures. However it also has important applications in many other fields of modern engineering and science.

In this paper, advantages of functional decomposition are demonstrated on "real life" examples. Application of decomposition-based methods in other fields of modern engineering is presented. In the case of decision tables, application of decomposition methods leads to significant benefits in the analysis process of data dependencies, especially in cases when the input decision tables are unmanageably large. Experimental results demonstrate that it can help implementing sequential machines using flip-flops or ROM memory. It also can be efficiently used as multilevel logic synthesis method for VLSI technology.
Redefining classroom instruction
Authors: Goldberg Harry R. , Haase Eileen , Shoukas Artin , Schramm Lawrence
Published: August 2006

In this study, the role of the classroom instructor was redefined from a “lecturer” responsible for delivering the core curriculum to a “facilitator” at the center of an active learning environment. Web-based lectures were used to provide foundation content to students outside of the classroom, which made it possible to improve the quality of student-faculty contact time in the classroom. Students reported that this hybrid format of instruction afforded them a better understanding of the content, a higher probability of retaining the content, and the opportunity to spend more time thinking about the application of the content compared with more traditional lecture-based methods of instruction.
Passing on the legacy: teaching capillary filtration and developing presentation skills using classic papers
Authors: McGeown J. Graham
Published: August 2006

Capillary filtration is a key area in the understanding of cardiovascular function and has both physiological and pathophysiological relevance in nearly every organ system. This article describes how classic papers in the Legacy collection of American Physiological Society publications can be used in a teaching symposium exploring the evidence supporting current concepts of capillary fluid exchange. Individual students are given papers to read, edit, and present to the class. The appropriate selection and sequencing of these papers allows the development of important physiological concepts to be tracked. A series of papers concerned with capillary filtration is suggested, and the contribution of each to the developing story is outlined. This approach allows students to develop critical and presentation skills and provides them with a case study of the scientific method as it is applied to physiology as well as establishing an appropriate knowledge base concerning the role of hydrostatic and oncotic forces in capillary fluid exchange. Relevant teaching points are explored further using questions based on a figure from one of the three classic papers used: “Microinjection studies of capillary permeability: II. The relationship between capillary pressure and the rate at which fluid passes through the walls of single capillaries,” by E. M. Landis ( Am J Physiol 82: 217–238, 1927).