bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mesoscale Gradients of Herb Richness and Abundance in Central Amazonia1
Authors: Costa Flávia R. C. 
Published: August 2006

ABSTRACTThere 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.
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.
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

ABSTRACT

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

ABSTRACTIn 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

ABSTRACT
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

ABSTRACTThe 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

ABSTRACT

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

ABSTRACT

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

ABSTRACTNeuraminidase 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

ABSTRACT

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

ABSTRACT
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

ABSTRACT
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

ABSTRACT
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.