bluuebunny/crossref_metadata_2025 huggingface dataset:
Consumption and its discontents: addiction, identity and the problems of freedom
Authors: Reith Gerda
Published: June 2004

The focus of this paper is on the notion of ‘addictive consumption’, conceived as a set of discourses that are embedded within wider socio‐historical processes of governance and control. It examines the discursive convergences and conflicts between practices of consumption and notions of addiction, which it notes are consistently represented in terms of the oppositional categories of self‐control vs. compulsion and freedom vs. determinism. These interrelations are explored with reference to the development of notions of addiction, and their relation to shifting configurations of identity, subjectivity and governance.

Finally, it suggests that the notion of ‘addiction’ has particular valence in advanced liberal societies, where an unprecedented emphasis on the values of freedom, autonomy and choice not only encourage the conditions for its proliferation into ever wider areas of social life, but also reveal deep tensions within the ideology of consumerism itself.
High‐ratio differentiation of embryonic stem cells into hepatocytes in vitro
Authors: Hu An‐Bin , Cai Ji‐Ye , Zheng Qi‐Chang , He Xiao‐Qing , Shan Yu , Pan Yun‐Long , Zeng Gu‐Cheng , Hong An , Dai Yun , Li Ling‐Song
Published: June 2004

Abstract: Background/Purpose: To date, in differentiating system of embryonic stem (ES) cells into hepatocytes, hepatic differentiation ratio was still not shown. Here, after investigating hepatic differentiation from ES cells, we determined the differentiation ratios of hepatocytes and studied how to improve the ratios in ES cell differentiating system.

Methods: Embryonic bodies (EBs) formed from ES cells for 5 days were plated onto culture dishes and some growth factors were added into medium for hepatic differentiation. Expressions of hepatic genes and proteins were analysed using reverse transcriptase‐polymerase chain reaction, immunocytochemistry (ICC) and radioimmunoassay. The relative counts of hepatocyte‐like cells among all EBs cells were analysed by flow cytometry by which hepatic differentiation ratios were determined. Then, we observed the spatial distribution of ICC‐positive cells in EB cells cluster and isolated the cells of positive areas in other EBs clusters without ICC examined. At last, isolated cells were re‐cultured with previous condition and hepatic differentiation ratios were also determined.

Results: The hepatic genes and proteins were, respectively, expressed in cytoplasm. Hepatic differentiation ratio was first determined at day 11 to be 12.1% and the level reached maximum to be 33.4% at day 21. In isolated cells culture system, hepatic genes and proteins expressed stronger than that expressed in EBs cluster and hepatic differentiation ratio was got to 72.6% at day 21.

Conclusions: Isolating hepatocyte‐like cells from EBs cell cluster and re‐culturing them could produce hepatocytes with high differentiation ratio. This culture system may produce a new source of cell types for hepatocytes replacement therapies in hepatic failure.
Critical soft tissue parameters of the zygomatic implant
Authors: Al‐Nawas B. , Wegener J. , Bender C. , Wagner W.
Published: June 2004

Aim: Zygomatic implants have been introduced for the rehabilitation of patients with severe bone defects of the maxilla. The soft tissue aspects of the palatal emergence situation have not been described yet. The aim of this study was to evaluate the incidence and clinical impact of possible periimplant alterations of zygomatic implants.

Materials and methods: From 1998 to 2001 all patients with zygomatic implants were included into this study (24 patients, 37 zygomatic implants). One implant was lost in the loading phase giving a survival rate of 97%. Fourteen patients with 20 zygomatic implants fulfilled the inclusion criteria and were all available for the recall examination. Thirteen zygomatic implants were inserted in cases of severe maxillary atrophy, seven in cases of tumour‐resection of the maxilla. Clinical examination and microbial analysis using a DNA probe was performed. The implants had a mean time in situ of 598 days (min: 326, max: 914).

Results: Colonisation with periodontal pathogens was found at four of the 20 implants. A positive microbiologic result of the periimplant pocket and the maximum pocket probing depth were not statistically related. Nine of the 20 implants showed bleeding on probing, four of these had positive microbiologic results. At sites without bleeding on probing only negative microbiologic samples were found (p=0.026). The mean palatal and mesial probing depth was 1 mm deeper than at the vestibular and distal aspect. Thus at nine out of the 20 implants both, bleeding on probing and pocket probing depth 5 mm indicated soft tissue problems resulting in a success rate of only 55%. The patient's history (tumor versus atrophy) or smoking habits seemed not to have influence the situation.

Conclusion: These soft tissue problems should be taken into account if zygomatic implants are considered as an alternative therapy option in the maxilla.
Plasminogen activators and plasminogen activator inhibitors in gingival crevicular fluid of cyclosporin A‐treated patients
Authors: Buduneli Nurcan , Buduneli Eralp , Çιnar Sema , Atilla Gül , Lappin David , Kinane Denis
Published: June 2004

Background: The plasminogen activator (PA) system plays many roles in the inflammatory process and tissue remodelling and repair and is considered to play a significant role in periodontal tissue destruction and healing. The aim of this study was to evaluate the role of the PA system in cyclosporin A (CsA)‐induced gingival overgrowth in renal transplant patients.

Methods: Eighteen renal transplant patients exhibiting moderate to severe CsA‐induced gingival overgrowth, 10 other renal transplant patients receiving CsA therapy but showing no sign of CsA‐induced gingival overgrowth (CsA‐H), 16 chronic gingivitis patients (CG) and 16 systemically and periodontally healthy control subjects (H) were included in the study. Gingival crevicular fluid (GCF) samples were obtained from four randomly selected sites in each subject with the exception of the CsA‐induced gingival overgrowth group, where four GCF samples were harvested from sites with severe overgrowth (CsA GO+) and from four sites without any gingival overgrowth (CsA GO−). The GCF levels of albumin, tissue‐type plasminogen activator (t‐PA), urokinase‐type plasminogen activator (u‐PA), plasminogen activator inhibitor 1 (PAI‐1) and plasminogen activator inhibitor 2 (PAI‐2) were analysed by enzyme‐linked immunosorbent assay. The results were tested for statistical differences.

Results: In CsA GO+ sites t‐PA levels were significantly elevated in comparison with gingivitis and healthy sites, while PAI‐2 levels in these sites showed statistically significant differences only with CsA‐H and gingivitis sites (p<0.05). The levels of t‐PA and PAI‐2 were significantly higher in CsA GO− sites compared with those of CsA‐H, gingivitis and healthy sites (p<0.05). The levels of u‐PA and PAI‐1 failed to show significant differences between the study groups.

Conclusions: The findings of the present study indicate alterations in GCF t‐PA and PAI‐2 levels in CsA‐induced gingival overgrowth and might suggest involvement of the plasminogen activating system in the pathogenesis of this side‐effect of CsA therapy. However, to what extent these molecules contribute to the pathogenesis of CsA‐induced gingival overgrowth remains to be determined.
Alterations in expression of retinoid receptor β and p53 in oral submucous fibrosis
Authors: Kaur J , Chakravarti N , Mathur M , Srivastava A , Ralhan R
Published: June 2004

Objective:  Knowledge of the molecular pathogenesis of oral submucous fibrosis (OSF), a potentially malignant condition with high risk of transition to oral cancer, is meagre. Alterations in the expression of retinoic acid receptor β (RARβ) and tumor suppressor gene, p53 are early events in oral tumorigenesis. The aim of this study was to investigate the alterations in the expression of RARβ and p53 in OSF lesions and determine their association with disease pathogenesis.

Methods:  The expression of RARβ and p53 proteins was analyzed by immunohistochemistry in 50 cases of OSF and 30 histologically normal oral tissues.

Results:  No detectable RARβ expression was observed in 35 of 50 (70%) OSF cases. p53 protein accumulation was observed in 24 of 50 (48%) OSF cases analyzed. Thirty‐six percent OSF lesions showed loss of RARβ and p53 overexpression. Interestingly, 41 of 50 (82%) of OSF lesions showed altered expression of at least one of these two proteins.

Conclusion:  Altered expression of either RARβ or p53 in majority of OSF lesions suggests their association with disease pathogenesis and warrants follow‐up to determine whether OSF lesions harboring concomitant alterations in RARβ and p53 are at a high risk of transition to malignancy.
Update on diabetes mellitus and related oral diseases
Authors: Manfredi M , McCullough MJ , Vescovi P , Al‐Kaarawi ZM , Porter SR
Published: June 2004

Diabetes mellitus (DM) is a group of complex multisystem metabolic disorders characterized by a relative or absolute insufficiency of insulin secretion and/or concomitant resistance to the metabolic action of insulin on target tissues. The chronic hyperglycaemia of diabetes is associated with long‐term systemic dysfunction. The present article summarizes current knowledge of DM and details the oral and dental implications of this common endocrine disorder.
Homing Endonucleases Encoded by Germ Line-Limited Genes in
Tetrahymena thermophila
Have APETELA2 DNA Binding Domains
Authors: Wuitschick Jeffrey D. , Lindstrom Paul R. , Meyer Alison E. , Karrer Kathleen M.
Published: June 2004

Three insertion elements were previously found in a family of germ line-limited mobile elements, the Tlr elements, in the ciliate
Tetrahymena
. Each of the insertions contains an open reading frame (ORF). Sequence analysis of the deduced proteins encoded by the elements suggests that they are homing endonucleases. The genes are designated
TIE1-1
,
TIE2-1
, and
TIE3-1
for
Tetrahymena
insertion-homing endonuclease. The endonuclease motif occupies the amino terminal half of each TIE protein. The C-terminal regions of the proteins are similar to the APETELA2 DNA binding domain of plant transcription factors. The TIE1 and TIE3 elements belong to families of repeated sequences in the germ line micronuclear genome. Comparison of the genes and the deduced proteins they encode suggests that there are at least two distinct families of homing endonuclease genes, each of which appears to be preferentially associated with a specific region of the Tlr elements. The TIE1 and TIE3 elements and their cognates undergo programmed elimination from the developing somatic macronucleus of
Tetrahymena
. The possible role of homing endonuclease-like genes in the DNA breakage step in developmentally programmed DNA elimination in
Tetrahymena
is discussed.
Inducible Defense Mechanism against Nitric Oxide inCandida albicans
Authors: Ullmann Breanna D. , Myers Hadley , Chiranand Wiriya , Lazzell Anna L. , Zhao Qiang , Vega Luis A. , Lopez-Ribot Jose L. , Gardner Paul R. , Gustin Michael C.
Published: June 2004

The yeastCandida albicansis an opportunistic pathogen that threatens patients with compromised immune systems. Immune cell defenses againstC. albicansare complex but typically involve the production of reactive oxygen species and nitrogen radicals such as nitric oxide (NO) that damage the yeast or inhibit its growth. WhetherCandidadefends itself against NO and the molecules responsible for this defense have yet to be determined. The defense against NO in various bacteria and the yeastSaccharomyces cerevisiaeinvolves an NO-scavenging flavohemoglobin. TheC. albicansgenome contains three genes encoding flavohemoglobin-related proteins,CaYHB1,CaYHB4, andCaYHB5. To assess their roles in NO metabolism, we constructed strains lacking each of these genes and demonstrated that just one,CaYHB1, is responsible for NO consumption and detoxification. InC. albicans, NO metabolic activity andCaYHB1mRNA levels are rapidly induced by NO and NO-generating agents. Loss ofCaYHB1increases the sensitivity ofC. albicansto NO-mediated growth inhibition. In mice, infections withCandidastrains lackingCaYHB1still resulted in lethality, but virulence was decreased compared to that in wild-type strains. Thus,C. albicanspossesses a rapid, specific, and highly inducible NO defense mechanism involving one of three putative flavohemoglobin genes.
Cdc42p GTPase Regulates the Budded-to-Hyphal-Form Transition and Expression of Hypha-Specific Transcripts in
Candida albicans
Authors: vandenBerg Alysia L. , Ibrahim Ashraf S. , Edwards John E. , Toenjes Kurt A. , Johnson Douglas I.
Published: June 2004

The yeast
Candida albicans
is a major opportunistic pathogen of immunocompromised individuals. It can grow in several distinct morphological states, including budded and hyphal forms, and the ability to make the dynamic transition between these forms is strongly correlated with virulence. Recent studies implicating the Cdc42p GTPase in hypha formation relied on
cdc42
mutations that affected the mitotic functions of the protein, thereby precluding any substantive conclusions about the specific role of Cdc42p in the budded-to-hypha-form transition and virulence. Therefore, we took advantage of several
Saccharomyces cerevisiae cdc42
mutants that separated Cdc42p's mitotic functions away from its role in filamentous growth. The homologous
cdc42-S26I
,
cdc42-E100G
, and
cdc42-S158T
mutations in
C. albicans
Cdc42p caused a dramatic defect in the budded-to-hypha-form transition in response to various hypha-inducing signals without affecting normal budded growth, strongly supporting the conclusion that Cdc42p has an integral function in orchestrating the morphological transition in
C. albicans
. In addition, the
cdc42-S26I
and
cdc42-E100G
mutants demonstrated a reduced ability to damage endothelial cells, a process that is strongly correlated to virulence. The three mutants also had reduced expression of several hypha-specific genes, including those under the regulation of the Efg1p transcription factor. These data indicate that Cdc42p-dependent signaling pathways regulate the budded-to-hypha-form transition and the expression of hypha-specific genes.
The Gβ-Subunit-Encoding Gene
bpp1
Controls Cyclic-AMP Signaling in
Ustilago maydis
Authors: Müller Philip , Leibbrandt Andreas , Teunissen Hedwich , Cubasch Stephanie , Aichinger Christian , Kahmann Regine
Published: June 2004

In the phytopathogenic fungus
Ustilago maydis
, fusion of haploid cells is a prerequisite for infection. This process is controlled by a pheromone-receptor system. The receptors belong to the seven-transmembrane class that are coupled to heterotrimeric G proteins. Of four Gα subunits in
U. maydis
, only
gpa3
has a function during mating and cyclic AMP (cAMP) signaling. Activation of the cAMP cascade induces pheromone gene expression; however, it does not lead to the induction of conjugation tubes seen after pheromone stimulation. To investigate the possibility that a Gβ subunit participates in pheromone signaling, we isolated the single β subunit gene,
bpp1
, from
U. maydis. bpp1
deletion mutants grew filamentously and showed attenuated pheromone gene expression, phenotypes associated with
Δgpa3
strains. In addition, a constitutively active allele of
gpa3
suppressed the phenotype of the
bpp1
deletion strains. We suggest that Bpp1 and Gpa3 are components of the same heterotrimeric G protein acting on adenylyl cyclase. Interestingly, while
Δgpa3
strains are impaired in pathogenicity, Δ
bpp1
mutants are able to induce plant tumors. This could indicate that Gpa3 operates independently of Bpp1 during pathogenic development.
Functional Interaction between Class II Histone Deacetylases and ICP0 of Herpes Simplex Virus Type 1
Authors: Lomonte Patrick , Thomas Joëlle , Texier Pascale , Caron Cécile , Khochbin Saadi , Epstein Alberto L.
Published: June 2004

This study describes the physical and functional interactions between ICP0 of herpes simplex virus type 1 and class II histone deacetylases (HDACs) 4, 5, and 7. Class II HDACs are mainly known for their participation in the control of cell differentiation through the regulation of the activity of the transcription factor MEF2 (myocyte enhancer factor 2), implicated in muscle development and neuronal survival. Immunofluorescence experiments performed on transfected cells showed that ICP0 colocalizes with and reorganizes the nuclear distribution of ectopically expressed class I and II HDACs. In addition, endogenous HDAC4 and at least one of its binding partners, the corepressor protein SMRT (for silencing mediator of retinoid and thyroid receptor), undergo changes in their nuclear distribution in ICP0-transfected cells. As a result, during infection endogenous HDAC4 colocalizes with ICP0. Coimmunoprecipitation and glutathione
S
-transferase pull-down assays confirmed that class II but not class I HDACs specifically interacted with ICP0 through their amino-terminal regions. This region, which is not conserved in class I HDACs but homologous to the MITR (MEF2-interacting transcription repressor) protein, is responsible for the repression, in a deacetylase-independent manner, of MEF2 by sequestering it under an inactive form in the nucleus. Consequently, we show that ICP0 is able to overcome the HDAC5 amino-terminal- and MITR-induced MEF2A repression in gene reporter assays. This is the first report of a viral protein interacting with and controlling the repressor activity of class II HDACs. We discuss the putative consequences of such an interaction for the biology of the virus both during lytic infection and reactivation from latency.
Identification of the Human Rhinovirus Serotype 1A Binding Site on the Murine Low-Density Lipoprotein Receptor by Using Human-Mouse Receptor Chimeras
Authors: Herdy Barbara , Snyers Luc , Reithmayer Manuela , Hinterdorfer Peter , Blaas Dieter
Published: June 2004

Human rhinovirus serotype 1A (HRV1A) binds more strongly to the mouse low-density lipoprotein receptor (LDLR) than to the human homologue (M. Reithmayer, A. Reischl, L. Snyers, and D. Blaas, J. Virol.
76:
6957-6965, 2002). Here, we used this fact to determine the binding site of HRV1A by replacing selected ligand binding modules of the human receptor with the corresponding ligand binding modules of the mouse receptor. The chimeric proteins were expressed in mouse fibroblasts deficient in endogenous LDLR and LDLR-related protein, both used by minor group HRVs for cell entry. Binding was assessed by virus overlay blots, by immunofluorescence microscopy, and by measuring cell attachment of radiolabeled virus. Replacement of ligand binding repeat 5 of the human LDLR with the corresponding mouse sequence resulted in a substantial increase in HRV1A binding, whereas substitution of repeats 3 and 4 was without effect. Replacement of human receptor repeats 1 and 2 with the murine homologues also increased virus binding. Finally, murine receptor modules 1, 2, and 5 simultaneously introduced into the human receptor resulted in HRV1A binding indistinguishable from mouse wild-type receptor. Thus, repeats 1 and/or 2 and repeat 5 are involved in HRV1A attachment. Changing CDG

GP

D in the acidic cluster of module 5 in the human receptor to CDG

EA

D present in the mouse receptor led to substantially increased binding of HRV1A, indicating an important role of the glutamate residue in HRV1A recognition.
Complete DNA Sequence Analyses of the First Two Varicella-Zoster Virus Glycoprotein E (D150N) Mutant Viruses Found in North America: Evolution of Genotypes with an Accelerated Cell Spread Phenotype
Authors: Grose Charles , Tyler Shaun , Peters Geoff , Hiebert Joanne , Stephens Gwen M. , Ruyechan William T. , Jackson Wallen , Storlie Johnathan , Tipples Graham A.
Published: June 2004

Varicella-zoster virus (VZV) is considered to be one of the most genetically stable of all the herpesviruses. Yet two VZV strains with a D150N missense mutation within the gE glycoprotein were isolated in North America in 1998 and 2002. The mutant strains have an accelerated cell spread phenotype, which distinguishes them from all wild-type and laboratory viruses. Since the VZV genome contains 70 additional open reading frames (ORFs), the possibility existed that the phenotypic change was actually due to an as-yet-undiscovered mutation or deletion elsewhere in the genome. To exclude this hypothesis, the entire genomes of the two mutant viruses were sequenced and found to contain 124,883 (VZV-MSP) and 125,459 (VZV-BC) nucleotides. Coding single-nucleotide polymorphisms (SNPs) were identified in 14 ORFs. One missense mutation was discovered in gH, but none was found in gB, gI, gL, or gK. There were no coding SNPs in the major regulatory protein ORF 62. One polymorphism was discovered which could never have been anticipated based on current knowledge of herpesvirus genomics, namely, the origins of replication differed from those in the prototype strain but not in a manner expected to affect cell spread. When the two complete mutant VZV sequences were surveyed in their entirety, the most reasonable conclusion was that the increased cell spread phenotype was dependent substantially or solely on the single D150N polymorphism in glycoprotein gE. The genomic results also expanded the evolutionary database by identifying which VZV ORFs were more likely to mutate over time.
Critical Role of CD4 T Cells in an Antibody-Independent Mechanism of Vaccination against Gammaherpesvirus Latency
Authors: McClellan James Scott , Tibbetts Scott A. , Gangappa Shivaprakash , Brett Kelly A. , Virgin Herbert W.
Published: June 2004

We have previously demonstrated that it is possible to effectively vaccinate against long-term murine gammaherpesvirus 68 (γHV68) latency by using a reactivation-deficient virus as a vaccine (S. A. Tibbetts, J. S. McClellan, S. Gangappa, S. H. Speck, and H. W. Virgin IV, J. Virol. 77:2522-2529, 2003). Immune antibody was capable of recapitulating aspects of this vaccination. This led us to determine whether antibody is required for vaccination against latency. Using mice lacking antigen-specific antibody responses, we demonstrate here that antibody and B cells are not required for vaccination against latency. We also show that surveillance of latent infection in normal animals depends on CD4 and CD8 T cells, suggesting that T cells might be capable of preventing the establishment of latency. In the absence of an antibody response, CD4 T cells but not CD8 T cells are required for effective vaccination against latency in peritoneal cells, while either CD4 or CD8 T cells can prevent the establishment of splenic latency. Therefore, CD4 T cells play a critical role in immune surveillance of gammaherpesvirus latency and can mediate vaccination against latency in the absence of antibody responses.
Postinternalization Inhibition of Adenovirus Gene Expression and Infectious Virus Production in Human T-Cell Lines
Authors: McNees Adrienne L. , Mahr Jeff A. , Ornelles David , Gooding Linda R.
Published: June 2004

Detection of adenovirus DNA in human tonsillar T cells in the absence of active virus replication suggests that T cells may be a site of latency or of attenuated virus replication in persistently infected individuals. The lytic replication cycle of Ad5 in permissive epithelial cells (A549) was compared to the behavior of Ad5 in four human T-cell lines, Jurkat, HuT78, CEM, and KE37. All four T-cell lines expressed the integrin coreceptors for Ad2 and Ad5, but only Jurkat and HuT78 express detectable surface levels of the coxsackie adenovirus receptor (CAR). Jurkat and HuT78 cells supported full lytic replication of Ad5, albeit at a level ∼10% of that of A549, while CAR-transduced CEM and KE37 cells (CEM-CARhi and KE37-CARhi, respectively) produced no detectable virus following infection. All four T-cell lines bind and internalize fluorescently labeled virus. In A549, Jurkat, and HuT78 cells, viral proteins were detected in 95% of cells. In contrast, only a small subpopulation of CEM-CARhi and KE37-CARhi cells contained detectable viral proteins. Interestingly, Jurkat and HuT78 cells synthesize four to six times more copies of viral DNA per cell than did A549 cells, indicating that these cells produce infectious virions with much lower efficiency than A549. Similarly, CEM-CARhi and KE37-CARhi cells, which produce no detectable infectious virus, synthesize three times more viral genomes per cell than A549. The observed blocks to adenovirus gene expression and replication in all four human T-cell lines may contribute to the maintenance of naturally occurring persistent adenovirus infections in human T cells.
Integrin α
v
β
6
Is an RGD-Dependent Receptor for Coxsackievirus A9
Authors: Williams Çiğdem H. , Kajander Tommi , Hyypiä Timo , Jackson Terry , Sheppard Dean , Stanway Glyn
Published: June 2004

Coxsackievirus A9 (CAV9), a member of the
Enterovirus
genus of
Picornaviridae
, is a common human pathogen and is one of a significant number of viruses containing a functional arginine-glycine-aspartic acid (RGD) motif in one of their capsid proteins. Previous studies identified the RGD-recognizing integrin α
v
β
3
as its cellular receptor. However, integrin α
v
β
6
has been shown to be an efficient receptor for another RGD-containing picornavirus, foot-and-mouth disease virus (FMDV). In view of the similarity in sequence context of the RGD motifs in CAV9 and FMDV, we investigated whether α
v
β
6
can also serve as a receptor for CAV9. We found that CAV9 can bind to purified α
v
β
6
and also to SW480 cells transfected with β
6
cDNA, allowing expression of α
v
β
6
on their surface, but it cannot bind to mock-transfected cells. In addition, a higher yield of CAV9 was obtained in β
6
-expressing cells than in mock-transfected cells. There was no similar enhancement in infection with an RGD-less CAV9 mutant. We also found β
6
on the surface of GMK cells, a cell line which CAV9 infects efficiently by an RGD-dependent mechanism. Significantly, this infection is blocked by an antibody to α
v
β
6
, while this antibody did not block the low level of infection by the RGD-less mutant. Thus, integrin α
v
β
6
is an RGD-dependent receptor for CAV9 and may be important in natural CAV9 infections.
The VP7 Outer Capsid Protein of Rotavirus Induces Polyclonal B-Cell Activation
Authors: Blutt Sarah E. , Crawford Sue E. , Warfield Kelly L. , Lewis Dorothy E. , Estes Mary K. , Conner Margaret E.
Published: June 2004

The early response to a homologous rotavirus infection in mice includes a T-cell-independent increase in the number of activated B lymphocytes in the Peyer's patches. The mechanism of this activation has not been previously determined. Since rotavirus has a repetitively arranged triple-layered capsid and repetitively arranged antigens can induce activation of B cells, one or more of the capsid proteins could be responsible for the initial activation of B cells during infection. To address this question, we assessed the ability of rotavirus and virus-like particles to induce B-cell activation in vivo and in vitro. Using infectious rotavirus, inactivated rotavirus, noninfectious but replication-competent virus, and virus-like particles, we determined that neither infectivity nor RNA was necessary for B-cell activation but the presence of the rotavirus outer capsid protein, VP7, was sufficient for murine B-cell activation. Preincubation of the virus with neutralizing VP7 antibodies inhibited B-cell activation. Polymyxin B treatment and boiling of the virus preparation were performed, which ruled out possible lipopolysaccharide contamination as the source of activation and confirmed that the structural conformation of VP7 is important for B-cell activation. These findings indicate that the structure and conformation of the outer capsid protein, VP7, initiate intestinal B-cell activation during rotavirus infection.
Complete Genome Sequence of Lymphocystis Disease Virus Isolated from China
Authors: Zhang Qi-Ya , Xiao Feng , Xie Jian , Li Zheng-Qiu , Gui Jian-Fang
Published: June 2004

Lymphocystis diseases in fish throughout the world have been extensively described. Here we report the complete genome sequence of lymphocystis disease virus isolated in China (LCDV-C), an LCDV isolated from cultured flounder (
Paralichthys olivaceus
) with lymphocystis disease in China. The LCDV-C genome is 186,250 bp, with a base composition of 27.25% G+C. Computer-assisted analysis revealed 240 potential open reading frames (ORFs) and 176 nonoverlapping putative viral genes, which encode polypeptides ranging from 40 to 1,193 amino acids. The percent coding density is 67%, and the average length of each ORF is 702 bp. A search of the GenBank database using the 176 individual putative genes revealed 103 homologues to the corresponding ORFs of LCDV-1 and 73 potential genes that were not found in LCDV-1 and other iridoviruses. Among the 73 genes, there are 8 genes that contain conserved domains of cellular genes and 65 novel genes that do not show any significant homology with the sequences in public databases. Although a certain extent of similarity between putative gene products of LCDV-C and corresponding proteins of LCDV-1 was revealed, no colinearity was detected when their ORF arrangements and coding strategies were compared to each other, suggesting that a high degree of genetic rearrangements between them has occurred. And a large number of tandem and overlapping repeated sequences were observed in the LCDV-C genome. The deduced amino acid sequence of the major capsid protein (MCP) presents the highest identity to those of LCDV-1 and other iridoviruses among the LCDV-C gene products. Furthermore, a phylogenetic tree was constructed based on the multiple alignments of nine MCP amino acid sequences. Interestingly, LCDV-C and LCDV-1 were clustered together, but their amino acid identity is much less than that in other clusters. The unexpected levels of divergence between their genomes in size, gene organization, and gene product identity suggest that LCDV-C and LCDV-1 shouldn't belong to a same species and that LCDV-C should be considered a species different from LCDV-1.
Potent Neutralizing Serum Immunoglobulin A (IgA) in Human Immunodeficiency Virus Type 2-Exposed IgG-Seronegative Individuals
Authors: Lizeng Qin , Nilsson Charlotta , Sourial Samer , Andersson Sören , Larsen Olav , Aaby Peter , Ehnlund Mariethe , Björling Ewa
Published: June 2004

The mechanisms behind the resistance to human immunodeficiency virus type 2 (HIV-2) infection are still not fully understood. In the present study, we explored the HIV-2-specific humoral serum immunoglobulin A (IgA) immune response in HIV-2-exposed IgG-seronegative (EGSN) individuals. Serum samples from heterosexual EGSN individuals and their known HIV-2-infected partners, as well as controls originating from Guinea-Bissau in Africa, were studied. Antibody reactivity to native and recombinant envelope glycoproteins was investigated, and the capacity of purified serum IgA to neutralize HIV-2SBL6669was tested. Our results showed that 16 of 25 EGSN samples exhibited reactivity against whole HIV-2 antigen, 6 of 25 samples reacted with recombinant gp36 (rgp36), and 3 of 25 samples were positive against HIV-2 rgp105; no reactivity to native HIV-2 gp125 was detected. Purified serum IgA antibodies from both EGSN and HIV-2-positive individuals, but not that from the negative controls, exhibited neutralization of HIV-2SBL6669. The most potent neutralization activity was exhibited by IgA purified from EGSN compared to infected individuals' IgA. The antigenic pattern of the HIV-2-positive partners showed that all serum IgA samples were reactive to whole HIV-2 antigen, and 14 of 15 reacted with rgp36. For rgp105 and gp125, 5 of 15 and 4 of 15 samples exhibited binding, respectively. The serum of the EGSN group had a higher mean IgA concentration than that of the negative controls (P< 0.05). Thus, we describe HIV-2-specific serum IgA antigen reactivity and show a more potent serum IgA-mediated HIV-2-neutralizing activity in EGSN individuals than in HIV-2-infected patients.
Antisense-Mediated Inhibition of Human Immunodeficiency Virus (HIV) Replication by Use of an HIV Type 1-Based Vector Results in Severely Attenuated Mutants Incapable of Developing Resistance
Authors: Lu Xiaobin , Yu Qiao , Binder Gwendolyn K. , Chen Ziping , Slepushkina Tatiana , Rossi John , Dropulic Boro
Published: June 2004

We have constructed a human immunodeficiency virus type 1 (HIV-1)-based lentiviral vector expressing a 937-base antisense sequence against the HIV-1 envelope gene. Transduction of CD4
+
T lymphocytes with this vector results in expression of the therapeutic antisense sequence and subsequent inhibition of productive HIV-1 replication. In this report, we examined the effect of antisense-mediated suppression on the potential development of virus escape mutants using a permissive T-cell line cultured under conditions that over serial passages specifically allowed for generation and amplification of mutants selected for by antisense pressure. In the resulting virus clones, we found a significant increase in the number of deletions at the envelope target region (91% compared to 27.5% in wild-type HIV). Deletions were most often greater than 1 kb in length. These data demonstrate for the first time that during antisense-mediated suppression of HIV, mutants develop as a direct result of selective pressure on the HIV genomic RNA. Interestingly, in clones where deletions were not observed, there was a high rate of A-G transitions in mutants at the antisense target region but not outside this region, which is consistent with those mutations that are predicted as a result of antisense-mediated modification of double-stranded RNA by the enzyme double-stranded RNA-specific adenosine deaminase. These clones were not found to be escape mutants, as their replicative ability was severely attenuated, and they did not replicate in the presence of vector.
Sequencing-Based Detection of Low-Frequency Human Immunodeficiency Virus Type 1 Drug-Resistant Mutants by an RNA/DNA Heteroduplex Generator-Tracking Assay
Authors: Kapoor Amit , Jones Morris , Shafer R. W. , Rhee Soo-Yon , Kazanjian Powel , Delwart Eric L.
Published: June 2004

Drug-resistant viruses may be present as minority variants during early treatment failures or following discontinuation of failed antiretroviral regimens. A limitation of the traditional direct PCR population sequencing method is its inability to detect human immunodeficiency virus type 1 (HIV-1) variants present at frequencies lower than 20%. A drug resistance genotyping assay based on the isolation and DNA sequencing of minority HIV protease variants is presented here. A multiple-codon-specific heteroduplex generator probe was constructed to improve the separation of HIV protease genes varying in sequence at 12 codons associated with resistance to protease inhibitors. Using an RNA molecule as probe allowed the simple sequencing of protease variants isolated as RNA/DNA heteroduplexes with different electrophoretic mobilities. The protease gene RNA heteroduplex generator-tracking assay (RNA-HTA) was tested on plasma quasispecies from 21 HIV-1-infected persons in whom one or more protease resistance mutations emerged during therapy or following initiation of salvage regimens. In 11 of 21 cases, RNA-HTA testing of virus from the first episode of virologic failure identified protease resistance mutations not seen by population-based PCR sequencing. In 8 of these 11 cases, all of the low-frequency drug resistance mutations detected exclusively by RNA-HTA during the first episode became detectable by population-based PCR sequencing at the later time point. Distinct sets of protease mutations could be linked on different genomes in patients with high-frequency protease gene lineages. The enhanced detection of minority drug resistance variants using a sequencing-based assay may improve the efficacy of genotype-assisted salvage therapies.
Modulation of p53 Cellular Function and Cell Death by African Swine Fever Virus
Authors: Granja Aitor G. , Nogal María L. , Hurtado Carolina , Salas José , Salas María L. , Carrascosa Angel L. , Revilla Yolanda
Published: June 2004

Modulation of the activity of tumor suppressor p53 is a key event in the replication of many viruses. We have studied the function of p53 in African swine fever virus (ASFV) infection by determining the expression and activity of this transcription factor in infected cells. p53 levels are increased at early times of infection and are maintained throughout the infectious cycle. The protein is transcriptionally active, stabilized by phosphorylation, and localized in the nucleus. p53 induces the expression of p21 and Mdm2. Strikingly, these two proteins are located at the cytoplasmic virus factories. The retention of Mdm2 at the factory may represent a viral mechanism to prevent p53 inactivation by the protein. The expression of apoptotic proteins, such as Bax or active caspase-3, is also increased following ASFV infection, although the increase in caspase-3 does not appear to be, at least exclusively, p53 dependent. Bax probably plays a role in the induction of apoptosis in the infected cells, as suggested by the release of cytochrome
c
from the mitochondria. The significance of p21 induction and localization is discussed in relation to the shutoff of cellular DNA synthesis that is observed in ASFV-infected cells.
An Exposed Domain in the Severe Acute Respiratory Syndrome Coronavirus Spike Protein Induces Neutralizing Antibodies
Authors: Zhou Tong , Wang Hong , Luo Danlin , Rowe Thomas , Wang Zheng , Hogan Robert J. , Qiu Shihong , Bunzel Robert J. , Huang Guoqiang , Mishra Vinod , Voss Thomas G. , Kimberly Robert , Luo Ming
Published: June 2004

Exposed epitopes of the spike protein may be recognized by neutralizing antibodies against severe acute respiratory syndrome (SARS) coronavirus (CoV). A protein fragment (S-II) containing predicted epitopes of the spike protein was expressed in
Escherichia coli
. The properly refolded protein fragment specifically bound to the surface of Vero cells. Monoclonal antibodies raised against this fragment recognized the native spike protein of SARS CoV in both monomeric and trimeric forms. These monoclonal antibodies were capable of blocking S-II attachment to Vero cells and exhibited in vitro antiviral activity. These neutralizing antibodies mapped to epitopes in two peptides, each comprising 20 amino acids. Thus, this region of the spike protein might be a target for generation of therapeutic neutralizing antibodies against SARS CoV and for vaccine development to elicit protective humoral immunity.
Mitotic Chromosome-Binding Activity of Latency-Associated Nuclear Antigen 1 Is Required for DNA Replication from Terminal Repeat Sequence of Kaposi's Sarcoma-Associated Herpesvirus
Authors: Lim Chunghun , Choi Changtaek , Choe Joonho
Published: June 2004

Latency-associated
nuclear antigen 1 (LANA1) of Kaposi's sarcoma-associated
herpesvirus (KSHV) is implicated in the persistence of the viral genome
during latent infection. It has been suggested that LANA1 tethers the
viral genome to the host chromosome and also participates actively in
DNA replication from the terminal repeat of KSHV. Here we show by
mutational analysis that the mitotic chromosome-binding activity of
LANA1 is tightly coupled to its replication activity. Thus, KSHV
appears to have evolved a unique tactic for its stable
maintenance.
Inhibition of Virus Production in JC Virus-Infected Cells by Postinfection RNA Interference
Authors: Orba Yasuko , Sawa Hirofumi , Iwata Hiroshi , Tanaka Shinya , Nagashima Kazuo
Published: June 2004

RNA interference has been applied for the prevention of virus infections in mammalian cells but has not succeeded in eliminating infections from already infected cells. We now show that the transfection of JC virus-infected SVG-A human glial cells with small interfering RNAs that target late viral proteins, including agnoprotein and VP1, results in a marked inhibition both of viral protein expression and of virus production. RNA interference directed against JC virus genes may thus provide a basis for the development of new strategies to control infections with this polyomavirus.
The utility of the nontranscribed spacer of 5S rDNA units grouped into unit classes assigned to haplomes – a test on cultivated wheat and wheat progenitors
Authors: Baum Bernard R , Bailey L Grant , Belyayev Alexander , Raskina Olga , Nevo Eviatar
Published: June 2004

Data is presented on the evolutionary dynamics of non-transcribed spacers (NTSs) of 5S rRNA genes in some diploid and polyploid Triticum and Aegilops species. FISH experiments with probes representing different unit classes revealed presence and (or) absence of these sequences in genomes or separate chromosomes of the species. Among the three diploid species only Aegilops speltoides has all of the different unit classes in ribosomal clusters as detected by the probes. Triticum urartu does not have the long D1 signals and Aegilops tauschii does not have the long A1 signals. Both polyploids possess all types of sequences, but because of genome rearrangements after polyploidization there is significant repatterning of single different rDNA unit classes in chromosomal positions when compared with those in diploid progenitors. Additional refined work is needed to ascertain if the sequences in the polyploids are mixed or are located in mini clusters in close proximity to each other. Mantel tests for association between the presence of the FISH signals of the A, B, and D genomes together and separately with the unit class data of the material, i.e., the probes used in FISH, indicated that all signals were associated with their respective probe material, but that there was no association of the unit classes found and the signals to each haplome. All combinations of the partial Mantel tests, e.g., between the A and B haplomes while controlling the effect of the all probes signals, with correlations ranging from 0.48 to 0.79 were all significant. Principal coordinate analysis showed that the signals of most unit class specific probes were more or less equally distant except for the long {S1 and short G1 signals, which were not different, and that the short A1 signals were closely related to the former two, whereas the signals of the long G1 were even less related.Key words: in situ hybridization, non-transcribed spacers, 5S rRNA genes, Triticeae.
Molecular architecture and rates of DNA substitutions of the mitochondrial control region of cracid birds
Authors: Pereira Sergio L , Grau Erwin T , Wajntal Anita
Published: June 2004

The control region (CR) plays an important role in replication and transcription in the mitochondrial genome. Its supposedly high rate of DNA substitution makes it a suitable marker for studies of population and closely related species. Three domains can be identified in CR, each having its own characteristics regarding base composition, pattern of variability and rate of DNA substitution. We sequenced the complete CR for 27 cracids, including all 11 genera to characterize its molecular organization, describe patterns of DNA substitution along the gene, and estimate absolute rates of DNA substitution. Our results show that cracid CR organization and patterns of DNA substitution are typical of other birds. Conserved blocks C and B, fused CSB2/3, and a putative segment for bidirectional replication not usually present in birds were identified in cracids. We also suggest a new delimitation for domains to allow better comparisons among CRs at different taxonomic ranking. Our estimates of absolute rates of DNA substitution show that, in general, CR evolves at a rate slower than that of two protein-coding genes (CR, 0.14%–0.3%; ND2, 0.37%–0.47%; and cytochrome b, 0.29%–0.35% per site per million years within genera). Within CR domains, rates within genera ranged from 0.05% to 0.8% per site per million years.Key words: mitochondrial control region, molecular evolution, Cracidae, Aves.
Comment on "AFLP data and the origins of domesticated crops"
Authors: Salamini F , Heun M , Brandolini A , Özkan H , Wunder J
Published: June 2004

We review some concepts and methods of handling and using DNA fingerprinting in phylogenetic analyses related to crop domestication. Particular reference is made to AFLP markers and mode and place of einkorn, barley, and tetraploid wheat domestication in the Neolithic by human communities in the Fertile Crescent. The reconsideration of AFLP databases of domesticated and wild lines demonstrates that phylogenetic tree topologies, originally described for the three species, match closely the new results obtained by principle coordinate analyse.Key words: AFLPs, discontinuous markers, crop domestication, einkorn wheat, barley, tetraploid wheat.
CELLULAR AUTOMATA MODELS FOR TRAFFIC FLOW WITH "SLOW-TO-START" RULE: EFFECT OF RANDOMIZATION
Authors: MOUSSA NAJEM
Published: June 2004

In this paper, we study the effect of randomization probability p on the fundamental diagrams of the Nagel–Schreckenberg model (NS) with "slow-to-start" rule introduced by Benjamin, Johnson and Hui (BJH). It is shown that this model exhibits metastable states (which leads to the occurrence of hysteresis) only for very low values of the randomization probability (p≤0.08). Here we propose a simple generalization of the BJH model by introducing a distance-dependent randomization. With such simple generalization, the hysteresis effect and phase separation exist for all values of randomization probability. The new fundamental diagrams are analyzed within the framework of the distributions of time and distance headways.
LARGE-SCALE MOLECULAR-DYNAMICS SIMULATION OF 19 BILLION PARTICLES
Authors: KADAU KAI , GERMANN TIMOTHY C. , LOMDAHL PETER S.
Published: June 2004

We have performed parallel large-scale molecular-dynamics simulations on the QSC-machine at Los Alamos. The good scalability of the SPaSM code is demonstrated together with its capability of efficient data analysis for enormous system sizes up to 19 000 416 964 particles. Furthermore, we introduce a newly-developed graphics package that renders in a very efficient parallel way a huge number of spheres necessary for the visualization of atomistic simulations. These abilities pave the way for future atomistic large-scale simulations of physical problems with system sizes on the μ-scale.
VORONOI AND FRACTAL COMPLEX NETWORKS AND THEIR CHARACTERIZATION
Authors: DA FONTOURA COSTA LUCIANO
Published: June 2004

Real world networks are often characterized by spatial constraints such as the relative position and adjacency of nodes. The present work describes how Voronoi tessellations of the space where the network is embedded provide not only a natural means for relating such networks with metric spaces, but also a natural means for obtaining fractal complex networks. A series of comprehensive measurements closely related to spatial aspects of these networks is proposed, which includes the effective length, adjacency, as well as the fractal dimension of the network in terms of the spatial scales defined by successive shortest paths starting from a specific node. The potential of such features is illustrated with respect to the random, small-world, scale-free and fractal network models.
ON THE DIFFERENTIAL EQUATIONS OF THE CHARACTERS FOR THE RENORMALIZATION GROUP
Authors: SAKAKIBARA MASATO
Published: June 2004

Owing to the analogy between the Connes–Kreimer theory of the renormalization and the integrable systems, we derive the differential equations of the unit mass for the renormalized character ϕ+ and the counter term ϕ-. We give another proof of the scattering type formula of ϕ-. The differential equation of ϕ- of the coordinate ε on ℙ1 is also given. The hierarchy of the renormalization groups is defined as the integrable systems.