bluuebunny/crossref_metadata_2025 huggingface dataset:
A Naturally Occurring Deletion in Its NS Gene Contributes to the Attenuation of an H5N1 Swine Influenza Virus in Chickens
Authors: Zhu Qiyun , Yang Huanliang , Chen Weiye , Cao Wenyan , Zhong Gongxun , Jiao Peirong , Deng Guohua , Yu Kangzhen , Yang Chinglai , Bu Zhigao , Kawaoka Yoshihiro , Chen Hualan
Published: October 2007

In 2001 and 2003, we isolated two H5N1 viruses, A/swine/Fujian/1/01 (SW/FJ/01) and A/swine/Fujian/1/03 (SW/FJ/03), from pigs in Fujian Province, southern China. Genetically, these two viruses are similar, although the NS gene of the SW/FJ/03 virus has a 15-nucleotide deletion at coding positions 612 to 626. The SW/FJ/01 virus is highly lethal for chickens, whereas the SW/FJ/03 virus is nonpathogenic for chickens when administrated intravenously or intranasally. To understand the molecular basis for the difference in virulence, we used reverse genetics to create a series of single-gene recombinants of both viruses. We found that a recombinant virus containing the mutated NS gene from the SW/FJ/03 virus in the SW/FJ/01 virus background was completely attenuated in chickens. We also found that viruses expressing the mutant NS1 protein of SW/FJ/03 did not antagonize the induction of interferon (IFN) protein. Conversely, only the recombinant virus containing the wild-type SW/FJ/01 NS gene in the SW/FJ/03 background was lethal in chickens and antagonized IFN protein levels. Further, we proved that the NS1 genes of the two viruses differ in their stabilities in the host cells and in their abilities to interact with the chicken cleavage and polyadenylation specificity factor. These results indicate that the deletion of amino acids 191 to 195 of the NS1 protein is critical for the attenuation of the SW/FJ/03 virus in chickens and that this deletion affects the ability of the virus to antagonize IFN induction in host cells.
Antigen-Specific B-Cell Responses to Porcine Reproductive and Respiratory Syndrome Virus Infection
Authors: Mulupuri Prasad , Zimmerman Jeffrey J. , Hermann Joseph , Johnson Craig R. , Cano Jean Paul , Yu Wanqin , Dee Scott A. , Murtaugh Michael P.
Published: October 2007

Porcine reproductive and respiratory syndrome virus (PRRSV) causes an acute, viremic infection of 4 to 6 weeks, followed by a persistent infection lasting for several months. We characterized antibody and B-cell responses to viral proteins in acute and persistent infection to better understand the immunological basis of the prolonged infection. The humoral immune response to PRRSV was robust overall and varied among individual viral proteins, with the important exception of a delayed and relatively weak response to envelope glycoprotein 5 (GP5). Memory B cells were in secondary lymphoid organs, not in bone marrow or Peyer's patches, in contrast to the case for many mammalian species. Potent anti-PRRSV memory responses were elicited to recall antigen in vitro, even though a second infection did not increase the B-cell response in vivo, suggesting that productive reinfection does not occur in vivo. Antibody titers to several viral proteins decline over time, even though abundant antigen is known to be present in lymphoid tissues, possibly indicating ineffective antigen presentation. The appearance of antibodies to GP5 is delayed relative to the resolution of viremia, suggesting that anti-GP5 antibodies are not crucial for resolving viremia. Lastly, viral infection had no immunosuppressive effect on the humoral response to a second, unrelated antigen. Taking these data together, the active effector and memory B-cell responses to PRRSV are robust, and over time the humoral immune response to PRRSV is effective. However, the delayed response against GP5 early in infection may contribute to the prolonged acute infection and the establishment of persistence.
Basal Expression Levels of IFNAR and Jak-STAT Components Are Determinants of Cell-Type-Specific Differences in Cardiac Antiviral Responses
Authors: Zurney Jennifer , Howard Kristina E. , Sherry Barbara
Published: October 2007

Viral myocarditis is an important human disease, and reovirus-induced murine myocarditis provides an excellent model system for study. Cardiac myocytes, like neurons in the central nervous system, are not replenished, yet there is no cardiac protective equivalent to the blood-brain barrier. Thus, cardiac myocytes may have evolved a unique antiviral response relative to readily replenished cell types, such as cardiac fibroblasts. Our previous comparisons of these two cell types revealed a conundrum: reovirus T3D induces more beta-interferon (IFN-β) mRNA in cardiac myocytes, yet there is a greater induction of IFN-stimulated genes (ISGs) in cardiac fibroblasts. Here, we investigated possible underlying molecular determinants. We found that greater basal expression of IFN-β in cardiac myocytes results in greater basal activated nuclear STAT1 and STAT2 and greater basal ISG mRNA expression and provides greater basal antiviral protection relative to cardiac fibroblasts. Conversely, cardiac fibroblasts express greater basal IFN-α/β receptor 1 (IFNAR1) and greater basal cytoplasmic Jak1, Tyk2, STAT2, and IRF9, leading to a greater increase in reovirus T3D- or IFN-induced nuclear activated STAT1 and STAT2 and greater induction of ISGs for a greater IFN-induced antiviral protection relative to cardiac myocytes. Our results suggest that high basal IFN-β expression in cardiac myocytes prearms this vulnerable, nonreplenishable cell type, while high basal expression of IFNAR1 and latent Jak-STAT components in adjacent cardiac fibroblasts renders these cells more responsive to IFN and prevents them from inadvertently serving as a reservoir for viral replication and spread to cardiac myocytes. These studies provide the first indication of an integrated network of cell-type-specific innate immune components for organ protection.
Direct Interaction between the N- and C-Terminal Portions of the Herpes Simplex Virus Type 1 Origin Binding Protein UL9 Implies the Formation of a Head-to-Tail Dimer
Authors: Chattopadhyay Soma , Weller Sandra K.
Published: October 2007

UL9, a superfamily II helicase, is a multifunctional protein required for herpes simplex virus type 1 replication in vivo. Although the C-terminal 317-amino-acid DNA binding domain of UL9 exists as a monomer, the full-length protein behaves as a dimer in solution. Thus, it has been assumed that the N-terminal 534 residues contain a region necessary for efficient dimerization and that UL9 dimers are in a head-to-head configuration. We recently showed, however, that residues in the N terminus could modulate the inhibitory properties of UL9 by decreasing the DNA binding ability of the C terminus (S. Chattopadhyay and S. K. Weller, J. Virol. 80:4491-4500, 2006). We suggested that a direct interaction between the N- and C-terminal portions of UL9 might exist and serve to modulate the DNA binding activities of the C terminus. In this study, we used a coimmunoprecipitation assay to show that the N-terminal portion of UL9 can indeed directly interact with the C terminus. A series of truncation mutant proteins were used to show that a region in the N terminus between residues 293 and 321 is necessary for efficient interaction. Similarly, a region in the C terminus between residues 600 and 800 is required for this interaction. The simplest model to explain these data is that UL9 dimers are oriented in a head-to-tail arrangement in which the N terminus is in contact with the C terminus.
A Highly Divergent Picornavirus in a Marine Mammal
Authors: Kapoor A. , Victoria J. , Simmonds P. , Wang C. , Shafer R. W. , Nims R. , Nielsen O. , Delwart E.
Published: October 2007

Nucleic acids from an unidentified virus from ringed seals (
Phoca hispida
) were amplified using sequence-independent PCR, subcloned, and then sequenced. The full genome of a novel RNA virus was derived, identifying the first sequence-confirmed picornavirus in a marine mammal. The phylogenetic position of the tentatively named seal picornavirus 1 (SePV-1) as an outlier to the grouping of parechoviruses was found consistently in alignable regions of the genome. A mean protein sequence identity of only 19.3 to 30.0% was found between the 3D polymerase gene sequence of SePV-1 and those of other picornaviruses. The predicted secondary structure of the short 506-base 5′-untranslated region showed some attributes of a type IVB internal ribosome entry site, and the polyprotein lacked an apparent L peptide, both properties associated with the
Parechovirus
genus. The presence of two SePV-1 2A genes and of the canonical sequence required for cotranslational cleavage resembled the genetic organization of Ljungan virus. Minor genetic variants were detected in culture supernatants derived from 8 of 108 (7.4%) seals collected in 2000 to 2002, indicating a high prevalence of SePV-1 in this hunted seal population. The high level of genetic divergence of SePV-1 compared to other picornaviruses and its mix of characteristics relative to its closest relatives support the provisional classification of SePV-1 as the prototype for a new genus in the family
Picornaviridae
.
Inhibition of Methyltransferases Results in Induction of G
2
/M Checkpoint and Programmed Cell Death in Human T-Lymphotropic Virus Type 1-Transformed Cells
Authors: Dasgupta Arindam , Jung Kyung-Jin , Jeong Soo-Jin , Brady John N.
Published: October 2007

Human T-lymphotropic virus type 1 (HTLV-1) is the etiologic agent for adult T-cell leukemia. The HTLV-1-encoded protein Tax transactivates the viral long terminal repeat and plays a critical role in virus replication and transformation. Previous work from our laboratory demonstrated that coactivator-associated arginine methytransferase 1, a protein arginine methytransferase, was important for Tax-mediated transactivation. To further investigate the role of methyltransferases in viral transcription, we utilized adenosine-2,3-dialdehyde (AdOx), an adenosine analog and
S
-adenosylmethionine-dependent methyltransferase inhibitor. The addition of AdOx decreased Tax transactivation in C81, Hut102, and MT-2 cells. Unexpectedly, we found that AdOx potently inhibited the growth of HTLV-1-transformed cells. Further investigation revealed that AdOx inhibited the Tax-activated NF-κB pathway, resulting in reactivation of p53 and induction of p53 target genes. Analysis of the NF-κB pathway demonstrated that AdOx treatment resulted in degradation of the IκB kinase complex and inhibition of NF-κB through stabilization of the NF-κB inhibitor IκBα. Our data further demonstrated that AdOx induced G
2
/M cell cycle arrest and cell death in HTLV-1-transformed but not control lymphocytes. These studies demonstrate that protein methylation plays an important role in NF-κB activation and survival of HTLV-1-transformed cells.
Attenuation of Recombinant Vesicular Stomatitis Virus-Human Immunodeficiency Virus Type 1 Vaccine Vectors by Gene Translocations and G Gene Truncation Reduces Neurovirulence and Enhances Immunogenicity in Mice
Authors: Cooper David , Wright Kevin J. , Calderon Priscilla C. , Guo Min , Nasar Farooq , Johnson J. Erik , Coleman John W. , Lee Margaret , Kotash Cheryl , Yurgelonis Irene , Natuk Robert J. , Hendry R. Michael , Udem Stephen A. , Clarke David K.
Published: October 2007

Recombinant vesicular stomatitis virus (rVSV) has shown great potential as a new viral vector for vaccination. However, the prototypic rVSV vector described previously was found to be insufficiently attenuated for clinical evaluation when assessed for neurovirulence in nonhuman primates. Here, we describe the attenuation, neurovirulence, and immunogenicity of rVSV vectors expressing human immunodeficiency virus type 1 Gag. These rVSV vectors were attenuated by combinations of the following manipulations: N gene translocations (N4), G gene truncations (CT1 or CT9), noncytopathic M gene mutations (Mncp), and positioning of the
gag
gene into the first position of the viral genome (gag1). The resulting N4CT1-gag1, N4CT9-gag1, and MncpCT1-gag1 vectors demonstrated dramatically reduced neurovirulence in mice following direct intracranial inoculation. Surprisingly, in spite of a very high level of attenuation, the N4CT1-gag1 and N4CT9-gag1 vectors generated robust Gag-specific immune responses following intramuscular immunization that were equivalent to or greater than immune responses generated by the more virulent prototypic vectors. MncpCT1-gag1 also induced Gag-specific immune responses following intramuscular immunization that were equivalent to immune responses generated by the prototypic rVSV vector. Placement of the
gag
gene in the first position of the VSV genome was associated with increased in vitro expression of Gag protein, in vivo expression of Gag mRNA, and enhanced immunogenicity of the vector. These findings demonstrate that through directed manipulation of the rVSV genome, vectors that have reduced neurovirulence and enhanced immunogenicity can be made.
Kaposi's Sarcoma-Associated Herpesvirus K-Cyclin Interacts with Cdk9 and Stimulates Cdk9-Mediated Phosphorylation of p53 Tumor Suppressor
Authors: Chang Pei-Ching , Li Mengtao
Published: October 2007

K-cyclin, encoded by Kaposi's sarcoma-associated herpesvirus, has previously been demonstrated to activate cyclin-dependent kinase 6 (Cdk6) to induce the phosphorylation of various cell cycle regulators. In this study, we identified Cdk9 as a new K-cyclin-associated Cdk and showed that K-cyclin interacted with Cdk9 through its basic domain. We hypothesized that K-cyclin served as a regulatory subunit for the activity of Cdk9. Recent reports show that Cdk9 phosphorylates tumor suppressor p53, and we found that the K-cyclin/Cdk9 interaction greatly enhanced the kinase activity of Cdk9 toward p53. The phosphorylation site(s) of K-cyclin/Cdk9 kinase complexes was mapped in the transactivation domain of p53. We showed that the ectopic expression of K-cyclin led to a sustained increase of p53 phosphorylation on Ser
33
in vivo, and the phosphorylation could be inhibited by a dominant negative Cdk9 mutant, dn-Cdk9. Using p53-positive U2OS and p53-null SaOS2 cells, we demonstrated that K-cyclin-induced growth arrest was associated with the presence of p53. In addition, K-cyclin-induced p53-dependent growth arrest was rescued by the dn-Cdk9- or Cdk9-specific short hairpin RNA in SaOS2 cells. Together, our findings for the first time demonstrated the interaction of K-cyclin and Cdk9 and revealed a new molecular link between K-cyclin and p53.
Inhibition of the Cyclin-Dependent Kinases at the Beginning of Human Cytomegalovirus Infection Specifically Alters the Levels and Localization of the RNA Polymerase II Carboxyl-Terminal Domain Kinases cdk9 and cdk7 at the Viral Transcriptosome
Authors: Kapasi Anokhi J. , Spector Deborah H.
Published: October 2007

We previously reported that defined components of the host transcription machinery are recruited to human cytomegalovirus immediate-early (IE) transcription sites, including cdk9 and cdk7 (S. Tamrakar, A. J. Kapasi, and D. H. Spector, J. Virol. 79:15477-15493, 2005). In this report, we further document the complexity of this site, referred to as the transcriptosome, through identification of additional resident proteins, including viral UL69 and cellular cyclin T1, Brd4, histone deacetylase 1 (HDAC1), and HDAC2. To examine the role of cyclin-dependent kinases (cdks) in the establishment of this site, we used roscovitine, a specific inhibitor of cdk1, cdk2, cdk7, and cdk9, that alters processing of viral IE transcripts and inhibits expression of viral early genes. In the presence of roscovitine, IE2, cyclin T1, Brd4, HDAC1, and HDAC2 accumulate at the transcriptosome. However, accumulation of cdk9 and cdk7 was specifically inhibited. Roscovitine treatment also resulted in decreased levels of cdk9 and cdk7 RNA. There was a corresponding reduction in cdk9 protein but only a modest decrease in cdk7 protein. However, overexpression of cdk9 does not compensate for the effects of roscovitine on cdk9 localization or viral gene expression. Delaying the addition of roscovitine until 8 h postinfection prevented all of the observed effects of the cdk inhibitor. These data suggest that IE2 and multiple cellular factors needed for viral RNA synthesis accumulate within the first 8 h at the viral transcriptosome and that functional cdk activity is required for the specific recruitment of cdk7 and cdk9 during this time interval.
Nuclear Domain 10 Components Promyelocytic Leukemia Protein and hDaxx Independently Contribute to an Intrinsic Antiviral Defense against Human Cytomegalovirus Infection
Authors: Tavalai Nina , Papior Peer , Rechter Sabine , Stamminger Thomas
Published: October 2007

Infection with DNA viruses commonly results in the association of viral genomes with a cellular subnuclear structure known as nuclear domain 10 (ND10). Recent studies demonstrated that individual ND10 components, like hDaxx or promyelocytic leukemia protein (PML), mediate an intrinsic immune response against human cytomegalovirus (HCMV) infection, strengthening the assumption that ND10 components are part of a cellular antiviral defense mechanism. In order to further define the role of hDaxx and PML for HCMV replication, we generated either primary human fibroblasts with a stable, individual knockdown of PML or hDaxx (PML-kd and hDaxx-kd, respectively) or cells exhibiting a double knockdown. Comparative analysis of HCMV replication in PML-kd or hDaxx-kd cells revealed that immediate-early (IE) gene expression increased to a similar extent, regardless of which ND10 constituent was depleted. Since a loss of PML, the defining component of ND10, results in a dispersal of the entire nuclear substructure, the increased replication efficacy of HCMV in PML-kd cells could be a consequence of the dissociation of the repressor protein hDaxx from its optimal subnuclear localization. However, experiments using three different recombinant HCMVs revealed a differential growth complementation in PML-kd versus hDaxx-kd cells, strongly arguing for an independent involvement in suppressing HCMV replication. Furthermore, infection experiments using double-knockdown cells devoid of both PML and hDaxx illustrated an additional enhancement in the replication efficacy of HCMV compared to the single-knockdown cells. Taken together, our data indicate that both proteins, PML and hDaxx, mediate an intrinsic immune response against HCMV infection by contributing independently to the silencing of HCMV IE gene expression.
Accelerated Evolution of Maribavir Resistance in a Cytomegalovirus Exonuclease Domain II Mutant
Authors: Chou Sunwen , Marousek Gail I.
Published: October 2007

A human cytomegalovirus (CMV) UL54
pol
exonuclease domain II mutation, D413A, found in a clinical specimen, conferred ganciclovir (GCV) and cidofovir resistance but not foscarnet resistance when incorporated into laboratory strain T2294. After several passages without drug, mutation was observed in five of eight plaques of T2294, and its plating efficiency under foscarnet was increased ∼30-fold over that of a control strain. When T2294 was serially passed under maribavir (MBV), phenotypic changes and viral UL97 mutations were detected by passage 5, much earlier than previously reported for other CMV strains. By passage 15, mutations included two cases of H411Y, one each of H411L and H411N, three of T409M, five of V353A, and one of L397R. Five instances of codon 409 or 411 mutations evolved into double mutations including V353A. Marker transfer experiments showed H411N/Y/L to confer 9- to 70-fold-increased MBV resistance and combinations of H411L/Y and V353A to confer >150-fold-increased MBV resistance, but no GCV resistance. These findings are consistent with defective exonuclease activity of the
pol
D413A mutant T2294, leading to the accelerated evolution of UL97 mutations under MBV. This recapitulated the known resistance mutations V353A, L397R, and T409M; suggested their relative frequency; and identified new ones at codon 411. These UL97 mutations predict an MBV binding region overlapping the kinase ATP binding site and located upstream of known GCV resistance mutations. The existence of viable
pol
D413A mutants may facilitate the selection of additional drug resistance mutations in vivo and the study of these mutations in vitro.
3′ RNA Elements in Hepatitis C Virus Replication: Kissing Partners and Long Poly(U)
Authors: You Shihyun , Rice Charles M.
Published: October 2007

The hepatitis C virus (HCV) genomic RNA possesses conserved structural elements that are essential for its replication. The 3′ nontranslated region (NTR) contains several of these elements: a variable region, the poly(U/UC) tract, and a highly conserved 3′ X tail, consisting of stem-loop 1 (SL1), SL2, and SL3. Studies of drug-selected, cell culture-adapted subgenomic replicons have indicated that an RNA element within the NS5B coding region, 5BSL3.2, forms a functional kissing-loop tertiary structure with part of the 3′ NTR, 3′ SL2. Recent advances now allow the efficient propagation of unadapted HCV genomes in the context of a complete infectious life cycle (HCV cell culture [HCVcc]). Using this system, we determine that the kissing-loop interaction between 5BSL3.2 and 3′ SL2 is required for replication in the genotype 2a HCVcc context. Remarkably, the overall integrity of the 5BSL3 cruciform is not an absolute requirement for the kissing-loop interaction, suggesting a model in which
trans
-acting factor(s) that stabilize this interaction may interact initially with the 3′ X tail rather than 5BSL3. The length and composition of the poly(U/UC) tract were also critical determinants of HCVcc replication, with a length of 33 consecutive U residues required for maximal RNA amplification. Interrupting the U homopolymer with C residues was deleterious, implicating a
trans
-acting factor with a preference for U over mixed pyrimidine nucleotides. Finally, we show that both the poly(U) and kissing-loop RNA elements can function outside of their normal genome contexts. This suggests that the poly(U/UC) tract does not function simply as an unstructured spacer to position the kissing-loop elements.
Human Cytomegalovirus Specifically Controls the Levels of the Endoplasmic Reticulum Chaperone BiP/GRP78, Which Is Required for Virion Assembly
Authors: Buchkovich Nicholas J. , Maguire Tobi G. , Yu Yongjun , Paton Adrienne W. , Paton James C. , Alwine James C.
Published: October 2007

The endoplasmic reticulum (ER) chaperone BiP/GRP78 regulates ER function and the unfolded protein response (UPR). Human cytomegalovirus infection of human fibroblasts induces the UPR but modifies it to benefit viral replication. BiP/GRP78 protein levels are tightly regulated during infection, rising after 36 h postinfection (hpi), peaking at 60 hpi, and decreasing thereafter. To determine the effects of this regulation on viral replication, BiP/GRP78 was depleted using the SubAB subtilase cytotoxin, which rapidly and specifically cleaves BiP/GRP78. Toxin treatment of infected cells for 12-h periods beginning at 36, 48, 60, and 84 hpi caused complete loss of BiP but had little effect on viral protein synthesis. However, progeny virion formation was significantly inhibited, suggesting that BiP/GRP78 is important for virion formation. Electron microscopic analysis showed that infected cells were resistant to the toxin and showed none of the cytotoxic effects seen in uninfected cells. However, all viral activity in the cytoplasm ceased, with nucleocapsids remaining in the nucleus or concentrated in the cytoplasmic space just outside of the outer nuclear membrane. These data suggest that one effect of the controlled expression of BiP/GRP78 in infected cells is to aid in cytoplasmic virion assembly and egress.
Rotavirus Replication in Intestinal Cells Differentially Regulates Integrin Expression by a Phosphatidylinositol 3-Kinase-Dependent Pathway, Resulting in Increased Cell Adhesion and Virus Yield
Authors: Halasz Peter , Holloway Gavan , Turner Stephen J. , Coulson Barbara S.
Published: October 2007

Changes in the interactions between intestinal cells and their surrounding environment during virus infection have not been well documented. The growth and survival of intestinal epithelial cells, the main targets of rotavirus infection, are largely dependent on the interaction of cell surface integrins with the extracellular matrix. In this study, we detected alterations in cellular integrin expression following rotavirus infection, identified the signaling components required, and analyzed the subsequent effects on cell binding to the matrix component collagen. After rotavirus infection of intestinal cells, expression of α2β1 and β2 integrins was up-regulated, whereas that of αVβ3, αVβ5, and α5β1 integrins, if present, was down-regulated. This differential regulation of integrins was reflected at the transcriptional level. It was unrelated to the use of integrins as rotavirus receptors, as both integrin-using and integrin-independent viruses induced integrin regulation. Using pharmacological agents that inhibit kinase activity, integrin regulation was shown to be dependent on phosphatidylinositol 3-kinase (PI3K) but independent of the activities of the mitogen-activated protein kinases p38 and ERK1/2, and cyclooxygenase-2. Replication-dependent activation of the PI3K/Akt pathway was observed following infection of intestinal and nonintestinal cell lines. Rotavirus activation of PI3K was important for regulation of α2β1 expression. Blockade of integrin regulation by PI3K inhibition led to decreased adherence of infected intestinal cells to collagen and a concomitant decrease in virus titer. These findings indicate that rotavirus-induced PI3K activation causes regulation of integrin expression in intestinal cells, leading to prolonged adherence of infected cells to collagen and increased virus production.
Accumulation of Substrates of the Anaphase-Promoting Complex (APC) during Human Cytomegalovirus Infection Is Associated with the Phosphorylation of Cdh1 and the Dissociation and Relocalization of APC Subunits
Authors: Tran Karen , Mahr Jeffrey A. , Choi Jiwon , Teodoro Jose G. , Green Michael R. , Spector Deborah H.
Published: October 2007

Cell cycle dysregulation upon human cytomegalovirus (HCMV) infection of human fibroblasts is associated with the inactivation of the anaphase-promoting complex (APC), a multisubunit E3 ubiquitin ligase, and accumulation of its substrates. Here, we have further elucidated the mechanism(s) by which HCMV-induced inactivation of the APC occurs. Our results show that Cdh1 accumulates in a phosphorylated form that may prevent its association with and activation of the APC. The accumulation of Cdh1, but not its phosphorylation, appears to be cyclin-dependent kinase dependent. The lack of an association of exogenously added Cdh1 with the APC from infected cells indicates that the core APC also may be impaired. This is further supported by an examination of the localization and composition of the APC. Coimmunoprecipitation studies show that both Cdh1 and the subunit APC1 become dissociated from the complex. In addition, immunofluorescence analysis demonstrates that as the infection progresses, several subunits redistribute to the cytoplasm, while APC1 remains nuclear. Dissociation of the core complex itself would account for not only the observed inactivity but also its inability to bind to Cdh1. Taken together, these results illustrate that HCMV has adopted multiple mechanisms to inactivate the APC, which underscores its importance for a productive infection.
Friend Virus Utilizes the BMP4-Dependent Stress Erythropoiesis Pathway To Induce Erythroleukemia
Authors: Subramanian Aparna , Hegde Shailaja , Porayette Prashanth , Yon Michele , Hankey Pamela , Paulson Robert F.
Published: October 2007

More than 50 years of genetic analysis has identified a number of host genes that are required for the expansion of infected cells during the progression of Friend-virus-induced erythroleukemia. In this report, we show that Friend virus induces the bone morphogenetic protein 4 (BMP4)-dependent stress erythropoiesis pathway in the spleen, which rapidly amplifies target cells, propagating their infection and resulting in acute splenomegaly. This mechanism mimics the response to acute anemia, in which BMP4 expressed in the spleen drives the expansion of a specialized population of stress erythroid progenitors. Previously we demonstrated that these progenitors, termed stress BFU-E, are targets for Friend virus in the spleen (A. Subramanian, H. E. Teal, P. H. Correll, and R. F. Paulson, J. Virol.
79:
14586-14594, 2005). Here, we extend those findings by showing that Friend virus infects two distinct populations of bone marrow cells. One population, when infected, differentiates into mature erythrocytes in an Epo-independent manner, while a second population migrates to the spleen after infection, where it induces BMP4 expression and acts as a reservoir of virus. The activation of the stress erythropoiesis pathway in the spleen by Friend virus results in the rapid expansion of stress BFU-E, providing abundant target cells for viral infection. These observations suggest a novel mechanism by which a virus induces a stress response pathway that amplifies target cells for the virus, leading to acute expansion of infected cells.
METAPLECTIC REPRESENTATION, CONLEY–ZEHNDER INDEX, AND WEYL CALCULUS ON PHASE SPACE
Authors: DE GOSSON MAURICE
Published: October 2007

We define and study a metaplectically covariant class of pseudo-differential operators acting on functions on symplectic space and generalizing a modified form of the usual Weyl calculus. This construction requires a precise calculation of the twisted Weyl symbol of a class of generators of the metaplectic group and the use of a Conley–Zehnder type index for symplectic paths, defined without restrictions on the endpoint. Our calculus is related to the usual Weyl calculus using a family of isometries of L2(ℝn) on closed subspaces of L2(ℝ2n) and to an irreducible representation of the Heisenberg algebra distinct from the usual Schrödinger representation.
SYMMETRIES AND CONSERVATION LAWS IN THE GÜNTHER k-SYMPLECTIC FORMALISM OF FIELD THEORY
Authors: ROMÁN-ROY NARCISO , SALGADO MODESTO , VILARIÑO SILVIA
Published: October 2007

This paper is devoted to studying symmetries of k-symplectic Hamiltonian and Lagrangian first-order classical field theories. In particular, we define symmetries and Cartan symmetries and study the problem of associating conservation laws to these symmetries, stating and proving Noether's theorem in different situations for the Hamiltonian and Lagrangian cases. We also characterize equivalent Lagrangians, which lead to an introduction of Lagrangian gauge symmetries, as well as analyzing their relation with Cartan symmetries.
MORE ABOUT SUPERPARTICLE SUM RULES IN GRAND UNIFIED THEORIES
Authors: KAWAMURA YOSHIHARU , KINAMI TEPPEI
Published: October 2007

Sum rules among superparticle masses are derived under the assumption that models beyond the MSSM are four-dimensional supersymmetric grand unified theories or five-dimensional supersymmetric orbifold grand unified theories. Sfermion sum rules are classified into four types and those sum rules can be useful probes of the MSSM and beyond.
MITIGATION OF RF GUN BREAKDOWN BY REMOVAL OF TUNING RODS IN HIGH FIELD REGIONS
Authors: COOK A. M. , ROSENZWEIG J. B. , DUNNING M. , FRIGOLA P. , SERRATTO K.
Published: October 2007

The π-mode resonant frequency of the 1.6 cell SLAC/BNL/UCLA style RF photoinjector electron gun is conventionally tuned using cylindrical copper tuning pieces that extend into the full-cell cavity through holes in the side of the gun. This design begins to fail in many versions of this popular gun design at higher voltage levels, when the cavity undergoes electric breakdown in the vicinity of the tuners. In order to remove the tuners from the region of high electric field, mitigating this problem, one must change the full cell geometry significantly. We have investigated a method for accomplishing this, in which we stretch the gun structure to tune the resonant frequency up by over 2 MHz. We constructed a device to perform this stretching and tested the modified photoinjector in an RF test bed. We succeeded in putting approximately 8.4 MW of RF power into the gun, an improvement over the 4 MW routinely achieved with a similar gun using conventional tuning methods installed at the UCLA Neptune laboratory. Recent results in testing this gun with a magnesium cathode insert are reported as well.
MEASUREMENTS OF QUANTUM EFFICIENCY OF MG FILMS PRODUCED BY PULSED LASER ABLATION DEPOSITION FOR APPLICATION TO BRIGHT ELECTRON SOURCES
Authors: Gatti G. , Cultrera L. , Tazzioli F. , Vicario C. , Fiori A. , Perrone A. , Ristoscu C.
Published: October 2007

We report the results of preliminary tests on Mg film photocathodes deposited by pulsed laser ablation deposition on various substrates. A comparison with other deposition techniques is presented. We illustrate briefly the technique of deposition of thick films (up to several microns). Scanning electron microscope analysis of the films before and after laser cleaning has been performed to characterize the changes occurred on the surface. Measurements of the distribution and integrated value of quantum efficiency over the illuminated surface are reported. Plans for the deposition on the back flange of an RF gun are illustrated.
THE S-BAND 1.6 CELL RF GUN CORRELATED ENERGY SPREAD DEPENDENCE ON π AND 0 MODE RELATIVE AMPLITUDE
Authors: SCHMERGE J. F. , CASTRO J. , CLENDENIN J. E. , DOWELL D. H. , GIERMAN S. M. , LOOS H.
Published: October 2007

The π mode or accelerating mode in a 1.6 cell rf gun is normally the only mode considered in rf gun simulations. However, due to the finite Q there is a small but measurable 0 mode present even at steady state. The π mode by definition has a 180° phase shift between cells but this phase shift for the total field is several degrees different. This results in a correlated energy spread exiting the gun. A comparison of simulation and experiment will be shown.
SUMMARY OF WORKING GROUP 2: DIAGNOSTICS AND BEAM MANIPULATION
Authors: TRAVISH G.
Published: October 2007

The efforts of the working group on diagnostics and beam manipulation held at the ICFA sponsored workshop, "The Physics and Applications of High Brightness Beams" are presented.
EXPERIMENTAL TESTING OF DYNAMICALLY OPTIMIZED PHOTOELECTRON BEAMS
Authors: ROSENZWEIG J. B. , COOK A. M. , DUNNING M. , ENGLAND R. J. , MUSUMECI P. , BELLAVEGLIA M. , BOSCOLO M. , CATANI L. , CIANCHI A. , DI PIRRO G. , FERRARIO M. , FILLIPETTO D. , GATTI G. , PALUMBO L. , SERAFINI L. , VICARIO C.
Published: October 2007

We discuss the design of and initial results from an experiment in space-charge dominated beam dynamics which explores a new regime of high-brightness electron beam generation at the SPARC (located at INFN-LNF, Frascati) photoinjector. The scheme under study employs the natural tendency in intense electron beams to configure themselves to produce a uniform density, giving a nearly ideal beam from the viewpoint of space charge-induced emittance. The experiments are aimed at testing the marriage of this idea with a related concept, emittance compensation, We show that the existing infrastructure at SPARC is nearly ideal for the proposed tests, and that this new regime of operating photoinjector may be the preferred method of obtaining highest brightness beams with lower energy spread. We discuss the design of the experiment, including developing of a novel time-dependent, aerogel-based imaging system. This system has been installed at SPARC, and first evidence for nearly uniformly filled ellipsoidal charge distributions recorded.
METHOD OF BUNCH RADIATION PHOTOCHRONOGRAPHY WITH 10 FEMTOSECOND AND LESS RESOLUTION
Authors: TRON ALEXANDER , MERINOV IGOR
Published: October 2007

The success in creation of the proposed facilities, where the required electron bunch duration can be of about 100 fs and less, will be depend directly on the ability to measure the bunch longitudinal profile with resolution of the order of 10 fs and less. The only method for the bunch monitoring with the mentioned temporal resolution is the method of photochronography of the bunch incoherent radiation, for example, in the frequency range of visible light and at realizing streak camera with new principles of its operation. Results of novel type streak camera design and its investigation with photoelectron dynamics simulation taking into account space-charge effect are presented.
EMITTANCE DEGRADATION DUE TO WAKE FIELDS IN A HIGH BRIGHTNESS PHOTOINJECTOR
Authors: FERRARIO M. , FUSCO V. , MIGLIORATI M. , PALUMBO L.
Published: October 2007

Wake fields effects in addition to space charge forces may have an important impact during the emittance compensation process in a high brightness photo-injector. To study this effect we developed an upgraded version of the Homdyn code including off axis beam dynamics and wake fields.

Homdyn describes a bunch as a uniformly charged cylinder, divided in cylindrical slices; in the upgraded version each slice's centroid can be transversally displaced from the nominal axis thus inducing wake fields. When the bunch is short as compared to the beam pipe radius, wake fields for a single cavity are calculated using methods of diffraction theory; instead we use, for a periodic collection of cavities, an asymptotic wake field obtained numerically at SLAC and then fitted to a simple function.

As a first application we studied and verified a correction scheme for the SPARC photo-injector to control the bunch trajectory and angle at the entrance of the undulator. The correction scheme consists of a number of steering magnets and beam position monitors placed along the photo-injector. Two different steering approaches are analyzed and the emittance degradation is studied. The code demonstrates the steering positions and number do correct the bunch's orbit and angle and gives good results concerning the emittance degradation.

The emittance and energy spread degradation due to wake fields in the emittance meter experiment is also discussed.
SUMMARY OF WORKING GROUP 4: APPLICATIONS OF HIGH BRIGHTNESS BEAMS TO ADVANCED ACCELERATORS AND LIGHTS SOURCES
Authors: UESAKA MITSURU , ROSSI ANDREA
Published: October 2007

We categorized 16 contributions into the three sub-fields. Those are 1. Compton scattering X-ray sources, 2. FEL and RF photoinjectors and 3. Plasma wakefield acceleration/innovative acceleration schemes. We performed a half day working group for each sub-field. The titles and summaries of the contributions appear in the article.
CHANNELING PROJECTS AT LNF: FROM CRYSTAL UNDULATORS TO CAPILLARY WAVEGUIDES
Authors: DABAGOV S. B. , FERRARIO M. , PALUMBO L. , SERAFINI L.
Published: October 2007

Frascati's National Laboratories (LNF INFN) are well known in the world for pioneering research in the particle interaction and synchrotron radiation physics fields. Good experience in designing accelerators, storage rings and beamlines for synchrotron radiation allows presently LNF to be in the frontier for the construction of new X-ray generation sources. This report is an introduction to new research activity "Coherent Scattering Phenomena for Radiations in Solids" started in Frascati within the approved projects SPARC, SPARX and PLASMON-X. The main purpose of the project is to develop research area for studying the channeling phenomena of charged and neutral particles in periodic solid structures.
A HIGH-DENSITY ELECTRON BEAM AND QUAD-SCAN MEASUREMENTS AT PLEIADES THOMSON X-RAY SOURCE
Authors: LIM J. K. , ROSENZWEIG J. B. , ANDERSON S. G. , TREMAINE A. M.
Published: October 2007

A recent development of the photo-cathode injector technology has greatly enhanced the beam quality necessary for the creation of high density/high brightness electron beam sources. In the Thomson backscattering x-ray experiment, there is an immense need for under 20 micron electron beam spot at the interaction point with a high-intensity laser in order to produce a large x-ray flux. This has been demonstrated successfully at PLEIADES in Lawrence Livermore National Laboratory. For this Thomson backscattering experiment, we employed an asymmetric triplet, high remanence permanent-magnet quads to produce smaller electron beams. Utilizing highly efficient optical transition radiation (OTR) beam spot imaging technique and varying electron focal spot sizes enabled a quadrupole scan at the interaction zone. Comparisons between Twiss parameters obtained upstream to those parameter values deduced from PMQ scan will be presented in this report.
LASER PULSE CIRCULATION SYSTEM FOR COMPACT MONOCHROMATIC TUNABLE HARD X-RAY SOURCE
Authors: OGINO HARUYUKI , DE MENG , YAMAMOTO TOMOHIKO , SAKAMOTO FUMITO , DOBASHI KATSUHIRO , UESAKA MITSURU
Published: October 2007

We are construcing a laser electron Compton scattering monochromatic tunable hard X-ray source. It consists of the X-band (11.424 GHz) electron linear accelerator and Q-switch Nd : YAG laser. This work is a part of the JST (Japan Science and Technology Agency) project. The whole system is a part of the national project on the advanced compact medical accelerator development, hosted by NIRS (National Institute for Radiological Science). The University of Tokyo and KEK are working for the X-ray source. Main advantage of this X-ray source is monochromatic tunable hard X-rays (10-50keV) with the intensities of 108-109 photons/s. The table-top size X-ray source can generate dual energy monochromatic hard X-ray by turns and it takes about 40ms to chage the X-ray energy. It is calculated that the X-ray intensity is 107 photons/RF-pulse (108 photons/s in 10 pps) by the 35MeV electron and YAG laser (2J/pulse). The X-band beam line for the demonstration is under construction. We designed a laser pulse circulation system to increase the X-ray yield 10 times higer (up to 108 photons/RF-pulse, 109 photons/s). It can be proved that the laser total energy increases 10 times higher by the principle experiment with the lower energy laser (25mJ/pulse).
LIMITS ON PRODUCTION OF NARROW BAND PHOTONS FROM INVERSE COMPTON SCATTERING
Authors: ROSENZWEIG J. , WILLIAMS O.
Published: October 2007

In using the inverse Compton scattering (ICS) interaction as a high brilliance, short wavelength radiation source, one collides two beams, one an intense laser, and the other a high charge, short pulse electron beam. In order to maximize the flux of photons from ICS, one must focus both beams strongly, which implies both use of short beams and the existence of large angles in the interaction. One aspect of brilliance is the narrowness of the wavelength band emitted by the source. This paper explores the limits of ICS-based source brilliance based on inherent wavelength broadening effects that arise due to focal angles, laser energy density, and finite laser pulse length effects. It is shown that for a nominal 1% desired bandwidth, that one obtains approximately one scattered photon per electron in a head-on collision geometry.
STATUS OF THE POLARIZED NONLINEAR INVERSE COMPTON SCATTERING EXPERIMENT AT UCLA
Authors: WILLIAMS O. , DOYURAN A. , ENGLAND R. J. , LIM J. , ROSENZWEIG J. B. , TRAVISH G. , JOSHI C. , TOCHITSKY S.
Published: October 2007

An Inverse Compton Scattering (ICS) experiment investigating the polarized harmonic production in the nonlinear regime has begun which will utilize the existing terawatt CO 2 laser system and 15 MeV photoinjector in the Neptune Laboratory at UCLA. A major motivation for a source of high brightness polarized x-rays is the production of polarized positrons for use in future linear collider experiments. Analytical calculations have been performed to predict the angular and frequency spectrums for various polarizations and different scattering angles. We report on the experimental set-up and status.
COUPLING LASER POWER INTO A SLAB-SYMMETRIC ACCELERATOR STRUCTURE
Authors: YODER R. B. , ROSENZWEIG J. B.
Published: October 2007

We present a detailed analysis of the coupling of external laser fields into a resonant acceleration structure. The structure is slab-symmetric and consists of metal boundaries lined with dielectric; coupling is accomplished via an array of narrow, equally-spaced slots in the upper structure boundary. Effects of the couplers on the structure fields are investigated using both theory and 2-dimensional time-dependent simulation. Details of the resonance are found to be highly sensitive to the coupling slot geometry: the presence of the couplers can lead to frequency detuning, changes in the field breakdown limits and overall Q-factor, and distortions of the field pattern. Beam wakefields are enhanced by the presence of the slots, but found to have no significant effect on the beam transport. The resonant accelerating fields in this case are nearly constant along the short transverse direction and are found to have between 10 and 15 times the amplitude of the driving radiation.
THE EFFECTS OF CLOSURE MODEL OF FIBER ORIENTATION TENSOR ON THE INSTABILITY OF FIBER SUSPENSIONS IN THE TAYLOR–COUETTE FLOW
Authors: WAN Z. H. , LIN J. Z. , YOU Z. J.
Published: October 2007

An analysis for the linear stability of fiber suspensions in the Taylor–Couette flow is conducted. The orientation state of fibers is determined using the linear, quadratic and composite HL-I closure model and the model of the fiber contribution to the total stress is established based on the slender-body theory. The linear stability equation is derived and solved with the Chebyshev spectral method. The results show that the suppression effect is most predominant for the composite HL-I model, while least predominant for the linear closure model. The longer fibers and suspensions with high volume fraction have a more predominant influence on suppressing the instability. The contribution of the suspending fluid to the change rate of the disturbance energy dominates the energy dissipation. While the contribution of the fiber shear stress increases monotonously with increasing fiber aspect ratio for the three closure models, the contribution based on the composite HL-I closure model is the largest, and that based on the linear closure model is the smallest. The effect of fiber aspect ratio on the change rate of the disturbance energy caused by the fiber shear stress is more predominant than that of the fiber volume fraction. The positive energy caused by the fiber shear stress consumes the gross energy of the fluid system and leads to a suppression of the flow instability.
Coal and coal-bearing strata: recent advances and future prospects
Authors: Scott Andrew C.
Published: October 2007

Recent advances in coal geology are highlighted. The increase in our knowledge of peat formation is emphasized and the application of hydrological models of mire systems to coal-bearing strata is advocated. The importance of coalification studies to the geological community as a whole should not be underestimated. Consideration of the original peat-forming vegetation by coal geologists is advocated. Both conceptual and technical advances in coal geology are reviewed. Integration of different disciplines is likely to yield further insights into the study of coal and coal-bearing strata.
Sulphur in peat and coal
Authors: Casagrande D. J.
Published: October 2007

Coal sulphur content is a major consideration in coal marketing. To predict sulphur content and distribution in a coal basin, a sulphur geochemical model needs to be developed. A series of questions are posed regarding coal sulphur distribution, forms and origins. Salient aspects of literature on coal sulphur content and distribution are reviewed to establish a framework for developing a sulphur geochemical model.

Some coal sulphur originates from peat-forming processes. Sulphate, ferrous iron, and microorganisms are key ingredients for the origins of coal pyrite and organic sulphur. Hydrogen sulphide is an important intermediate for pyrite and organic sulphur formation in peats. Sulphur isotope values for peat sulphate, plant sulphur, peat pyrite and peat organic sulphur corroborate the hypothesis that microorganisms reduce sulphate to hydrogen sulphide, which in turn reacts with available ferrous iron or organic matter to produce pyrite and organic sulphur respectively.