bluuebunny/crossref_metadata_2025 huggingface dataset:
DNA Microarray Based on Arrayed-Primer Extension Technique for Identification of Pathogenic Fungi Responsible for Invasive and Superficial Mycoses
Authors: Campa Daniele , Tavanti Arianna , Gemignani Federica , Mogavero Crocifissa S. , Bellini Ilaria , Bottari Fabio , Barale Roberto , Landi Stefano , Senesi Sonia
Published: December 2007

An oligonucleotide microarray based on the arrayed-primer extension (APEX) technique has been developed to simultaneously identify pathogenic fungi frequently isolated from invasive and superficial infections. Species-specific oligonucleotide probes complementary to the internal transcribed spacer 1 and 2 (ITS1 and ITS2) region were designed for 24 species belonging to 10 genera, including
Candida
species (
Candida albicans
,
Candida dubliniensis
,
Candida famata
,
Candida glabrata
,
Candida tropicalis
,
Candida kefyr
,
Candida krusei
,
Candida guilliermondii
,
Candida lusitaniae
,
Candida metapsilosis
,
Candida orthopsilosis
,
Candida parapsilosis
, and
Candida pulcherrima
),
Cryptococcus neoformans
,
Aspergillus
species (
Aspergillus fumigatus
and
Aspergillus terreus
),
Trichophyton
species (
Trichophyton rubrum
and
Trichophyton tonsurans
),
Trichosporon cutaneum
,
Epidermophyton floccosum
,
Fusarium solani
,
Microsporum canis
,
Penicillium marneffei
, and
Saccharomyces cerevisiae
. The microarray was tested for its specificity with a panel of reference and blinded clinical isolates. The APEX technique was proven to be highly discriminative, leading to unequivocal identification of each species, including the highly related ones
C. parapsilosis
,
C. orthopsilosis
, and
C. metapsilosis
. Because of the satisfactory basic performance traits obtained, such as reproducibility, specificity, and unambiguous interpretation of the results, this new system represents a reliable method of potential use in clinical laboratories for parallel one-shot detection and identification of the most common pathogenic fungi.
Determination of Accessory Gene Patterns Predicts the Same Relatedness among Strains of
Streptococcus pneumoniae
as Sequencing of Housekeeping Genes Does and Represents a Novel Approach in Molecular Epidemiology
Authors: Dagerhamn Jessica , Blomberg Christel , Browall Sarah , Sjöström Karin , Morfeldt Eva , Henriques-Normark Birgitta
Published: December 2007

Relatedness between isolates of
Streptococcus pneumoniae
can be determined from sequences of multiple genes belonging to the core genome (multilocus sequence typing [MLST]), but these do not provide information on gene content that may affect the potential of isolates to cause invasive pneumococcal disease. Gene content data, obtained using microarrays, were gathered for 40 clinical isolates of 12 serotypes belonging to 30 multilocus sequence types. We found that sequence variations in housekeeping genes assessed by MLST correlated well with whole-genome microarray analyses identifying the presence/absence of accessory genes/regions. However, isolates belonging to the same clonal complex, as determined by MLST, may not have identical gene contents, potentially affecting virulence. We found fewer intraclonal (same MLST sequence type) differences associated with pneumococcal serotypes of high invasive disease potential, i.e., serotypes rarely found among carriers compared to serotypes frequently found in carriage. Molecular typing of pneumococci based on the presence/absence of 25 genes localized to accessory regions shows the same relatedness among pneumococcal strains as MLST does. We conclude that molecular typing of pneumococci based on variation in the nucleotide sequences of parts of housekeeping genes (MLST) correlates with the presence/absence of genes in the accessory part of the genome. This covariation is likely due to the fact that both sequence variations and gene content variations are created primarily by recombination events in pneumococci.
Identification of Clinical Coryneform Bacterial Isolates: Comparison of Biochemical Methods and Sequence Analysis of 16S rRNA and
rpoB
Genes
Authors: Adderson Elisabeth E. , Boudreaux Jan W. , Cummings Jessica R. , Pounds Stanley , Wilson Deborah A. , Procop Gary W. , Hayden Randall T.
Published: December 2007

We compared the relative levels of effectiveness of three commercial identification kits and three nucleic acid amplification tests for the identification of coryneform bacteria by testing 50 diverse isolates, including 12 well-characterized control strains and 38 organisms obtained from pediatric oncology patients at our institution. Between 33.3 and 75.0% of control strains were correctly identified to the species level by phenotypic systems or nucleic acid amplification assays. The most sensitive tests were the API Coryne system and amplification and sequencing of the 16S rRNA gene using primers optimized for coryneform bacteria, which correctly identified 9 of 12 control isolates to the species level, and all strains with a high-confidence call were correctly identified. Organisms not correctly identified were species not included in the test kit databases or not producing a pattern of reactions included in kit databases or which could not be differentiated among several genospecies based on reaction patterns. Nucleic acid amplification assays had limited abilities to identify some bacteria to the species level, and comparison of sequence homologies was complicated by the inclusion of allele sequences obtained from uncultivated and uncharacterized strains in databases. The utility of
rpoB
genotyping was limited by the small number of representative gene sequences that are currently available for comparison. The correlation between identifications produced by different classification systems was poor, particularly for clinical isolates.
Acinetobacter septicus
sp. nov. Association with a Nosocomial Outbreak of Bacteremia in a Neonatal Intensive Care Unit
Authors: Kilic Abdullah , Li Haijing , Mellmann Alexander , Basustaoglu Ahmet C. , Kul Mustafa , Senses Zeynep , Aydogan Hakan , Stratton Charles W. , Harmsen Dag , Tang Yi-Wei
Published: December 2007

Acinetobacter
species other than
Acinetobacter baumannii
have rarely been reported to be associated with nosocomial outbreaks of bloodstream infections. Within a period of 1 week, seven
Acinetobacter
-like isolates were recovered from peripheral blood and catheter specimens of five patients at a neonatal intensive care unit (NICU) in a tertiary hospital in Turkey. All five patients had placement of central venous catheters and had received total parenteral nutrition before the onset of bacteremia. Two of the five patients died. Medical devices, tap water, aerators, water samples, various surfaces, intravenous fluids, and the hands of health care workers in the NICU were sampled and were culture negative for the bacterium. All seven of the isolates had identical biochemical reactions, antimicrobial susceptibility results, and pulsed-field gel electrophoresis patterns, indicating a clonal nosocomial outbreak. A panel of standard biochemical reaction profiles and three phenotypic commercial identification systems failed to identify these isolates. Phenotypically, the isolate differed from
Acinetobacter ursingii
by its hemolysis on sheep blood agar and its negative citrate utilization. Sequences of the full 16S rRNA gene, which contained at least three different gene copies with polymorphic sequences between nucleotide positions 70 and 206, were determined from the first recovered isolate. The complete 1,529- to 1,531-bp 16S rRNA gene sequences and partial 801-bp
rpoB
gene sequences had similarities of 99.5% and 97.2%, respectively, to an
A. ursingii
isolate. The DNA-DNA similarities of the strain against the type strain of
A. ursingii
were 64.7 and 68.7%, which were lower than the recommended threshold value of 70% for the definition of bacterial species. These data indicate that a novel
Acinetobacter
organism caused the nosocomial outbreak of bacteremia in the NICU unit. We propose the designation of
Acinetobacter septicus
sp. nov. for these isolates, with isolate AK001 as the type strain.
Preparation of Armored RNA as a Control for Multiplex Real-Time Reverse Transcription-PCR Detection of Influenza Virus and Severe Acute Respiratory Syndrome Coronavirus
Authors: Yu Xin-Fen , Pan Jing-Cao , Ye Rong , Xiang Hai-Qing , Kou Yu , Huang Zhi-Cheng
Published: December 2007

The common respiratory viruses, including influenza A, influenza B, and newly emerging severe acute respiratory syndrome (SARS) viruses, may cause similar clinical symptoms. Therefore, differential diagnosis of these virus pathogens is frequently required for single clinical samples. In addition, there is an urgent need for noninfectious and stable RNA standards and controls for multivirus detection. In this study, reverse transcription-PCR (RT-PCR) targeting of the RNAs of influenza A and influenza B viruses and SARS coronavirus was performed, and the resulting products were spliced into a fragment which was packaged into armored RNA for use as a noninfectious, quantifiable synthetic substitute. Furthermore, in the present study we developed a multiplex real-time RT-PCR assay in which the armored RNA was used as an external positive control and the three RNA viruses could be detected simultaneously in a single reaction mix. The detection limit of the multiplex real-time PCR was 10 copies/μl of armored RNA.
Rapid Diagnosis of Vivax Malaria by the SD Bioline Malaria Antigen Test When Thrombocytopenia Is Present
Authors: Lee Sei Won , Jeon Kyeongman , Jeon Byung Ryul , Park Inho
Published: December 2007

An easy and reliable diagnostic method for malaria is highly desirable. We examined the recently introduced SD Bioline Malaria Antigen test, which detects
Plasmodium
lactate dehydrogenase, with the additional aid of the presence or absence of thrombocytopenia to diagnose vivax malaria. We enrolled 732 patients with clinically suspected malaria in an area where vivax malaria is endemic. We performed microscopic examination of thin film, applied the SD Bioline Malaria Antigen test, and checked platelet counts. One hundred ninety-five patients were smear positive for vivax malaria. The sensitivity of the SD Bioline Malaria Antigen test was 96.4%, and its specificity was 98.9%. We found that 95.4% of malaria patients had thrombocytopenia, and the proportion with malaria increased as platelet counts decreased. A positive SD Bioline Malaria Antigen test when thrombocytopenia was present showed a 100% positive predictive value for vivax malaria. In conclusion, the SD Bioline Malaria Antigen test is a rapid and accurate diagnostic method for vivax malaria, and a platelet count can facilitate a rapid diagnosis of malaria.
RNA Structure Modulates Splicing Efficiency at the Human Immunodeficiency Virus Type 1 Major Splice Donor
Authors: Abbink Truus E. M. , Berkhout Ben
Published: December 2007

The untranslated leader of the human immunodeficiency virus type 1 (HIV-1) RNA genome encodes essential sequence and structural motifs that control various replication steps. The 5′ splice site or splice donor (SD) is embedded in a semistable hairpin, but the function of this structure is unknown. We stabilized this SD hairpin by creating an additional base pair and demonstrated a severe HIV-1 replication defect. A splicing defect was apparent in RNA analyses of virus-infected cells and cells transfected with appropriate reporter constructs. We selected multiple virus revertants in search for interesting second-site escape pathways. Most revertants acquired an additional mutation that modulated the stability of the mutant SD hairpin. One revertant acquired a single nucleotide change in the upstream DIS hairpin. We demonstrate that a novel SD site is created by this upstream mutation, which obviously reduces the number of leader nucleotides that are included in spliced HIV-1 transcripts. These results suggest a novel role of RNA structure in the regulation of HIV-1 splicing.
Combination of an Antiviral Drug and Immunomodulation against Hepadnaviral Infection in the Woodchuck Model
Authors: Lu Mengji , Yao Xin , Xu Yang , Lorenz Heike , Dahmen Uta , Chi Haidong , Dirsch Olaf , Kemper Thekla , He Lifang , Glebe Dieter , Gerlich Wolfram H. , Wen Yumei , Roggendorf Michael
Published: December 2007

The essential role of multispecific immune responses for the control of hepatitis B virus (HBV) infection implies the need of multimodal therapeutic strategies for chronic HBV infection, including antiviral chemotherapy and immunomodulation. This hypothesis was tested in the woodchuck model by a combination of lamivudine pretreatment and subsequent immunizations of woodchucks chronically infected with woodchuck hepatitis virus. The immunizations were performed with DNA vaccines or antigen-antibody immune complexes (IC)/DNA vaccines. Immunizations with IC/DNA vaccines led to an anti-woodchuck hepatitis virus surface antibody response and significant reductions of viral load and antigenemia, suggesting that such a strategy may be effective against chronic HBV infection.
Alpha/Beta Interferon Inhibits Cap-Dependent Translation of Viral but Not Cellular mRNA by a PKR-Independent Mechanism
Authors: Tesfay Mulu Z. , Yin Jun , Gardner Christina L. , Khoretonenko Mikhail V. , Korneeva Nadejda L. , Rhoads Robert E. , Ryman Kate D. , Klimstra William B.
Published: December 2007

The alpha/beta interferon (IFN-α/β) response is critical for host protection against disseminated replication of many viruses, primarily due to the transcriptional upregulation of genes encoding antiviral proteins. Previously, we determined that infection of mice with Sindbis virus (SB) could be converted from asymptomatic to rapidly fatal by elimination of this response (K. D. Ryman et al., J. Virol. 74:3366-3378, 2000). Probing of the specific antiviral proteins important for IFN-mediated control of virus replication indicated that the double-stranded RNA-dependent protein kinase, PKR, exerted some early antiviral effects prior to IFN-α/β signaling; however, the ability of IFN-α/β to inhibit SB and protect mice from clinical disease was essentially undiminished in the absence of PKR, RNase L, and Mx proteins (K. D. Ryman et al., Viral Immunol. 15:53-76, 2002). One characteristic of the PKR/RNase L/Mx-independent antiviral effect was a blockage of viral protein accumulation early after infection (K. D. Ryman et al., J. Virol. 79:1487-1499, 2005). We show here that IFN-α/β priming induces a PKR-independent activity that inhibits m7G cap-dependent translation at a step after association of cap-binding factors and the small ribosome subunit but before formation of the 80S ribosome. Furthermore, the activity targets mRNAs that enter across the cytoplasmic membrane, but nucleus-transcribed RNAs are relatively unaffected. Therefore, this IFN-α/β-induced antiviral activity represents a mechanism through which IFN-α/β-exposed cells are defended against viruses that enter the cytoplasm, while preserving essential host activities, including the expression of antiviral and stress-responsive genes.
Novel Approach to the Development of Effective H5N1 Influenza A Virus Vaccines: Use of M2 Cytoplasmic Tail Mutants
Authors: Watanabe Tokiko , Watanabe Shinji , Kim Jin Hyun , Hatta Masato , Kawaoka Yoshihiro
Published: December 2007

Outbreaks of highly pathogenic H5N1 influenza viruses in avian species began in Asia and have since spread to other continents. Concern regarding the pandemic potential of these viruses in humans is clearly warranted, and there is an urgent need to develop effective vaccines against them. Previously, we and others demonstrated that deletions of the M2 cytoplasmic tail caused a growth defect in A/WSN/33 (H1N1) influenza A virus in vitro (K. Iwatsuki-Horimoto, T. Horimoto, T. Noda, M. Kiso, J. Maeda, S. Watanabe, Y. Muramoto, K. Fujii, and Y. Kawaoka, J. Virol. 80:5233-5240, 2006; M. F. McCown and A. Pekosz, J. Virol. 79:3595-3605, 2005; M. F. McCown and A. Pekosz, J. Virol. 80:8178-8189, 2006). We therefore tested the feasibility of using M2 tail mutants as live attenuated vaccines against H5N1 virus. First we generated a series of highly pathogenic H5N1 (A/Vietnam/1203/04 [VN1203]) M2 cytoplasmic tail deletion mutants and examined their growth properties in vitro and in vivo. We found that one mutant, which contains an 11-amino-acid deletion from the C terminus (M2del11 virus), grew as well as the wild-type virus but replicated in mice less efficiently. We then generated a recombinant VN1203M2del11 virus whose hemagglutinin (HA) gene was modified by replacing sequences at the cleavage site with those of an avirulent type of HA (M2del11-HAavir virus). This M2del11-HAavir virus protected mice against challenge with lethal doses of homologous (VN1203; clade 1) and antigenically distinct heterologous (A/Indonesia/7/2005; clade 2) H5N1 viruses. Our results suggest that M2 cytoplasmic tail mutants have potential as live attenuated vaccines against H5N1 influenza viruses.
NKG2D Receptor Signaling Enhances Cytolytic Activity by Virus-Specific CD8+T Cells: Evidence for a Protective Role in Virus-Induced Encephalitis
Authors: Walsh Kevin B. , Lanier Lewis L. , Lane Thomas E.
Published: December 2007

Inoculation with the neurotropic JHM strain of mouse hepatitis virus (JHMV) into the central nervous system (CNS) of mice results in an acute encephalitis associated with an immune-mediated demyelinating disease. During acute disease, infiltrating CD8+T cells secrete gamma interferon (IFN-γ) that controls replication in oligodendrocytes, while infected astrocytes and microglia are susceptible to perforin-mediated lysis. The present study was undertaken to reveal the functional contributions of the activating NKG2D receptor in host defense and disease following JHMV infection. NKG2D ligands RAE-1, MULT1, and H60 were expressed within the CNS following JHMV infection. The immunophenotyping of infiltrating cells revealed that NKG2D was expressed on ∼90% of infiltrating CD8+T cells during acute and chronic disease. Blocking NKG2D following JHMV infection resulted in increased mortality that correlated with increased viral titers within the CNS. Anti-NKG2D treatment did not alter T-cell infiltration into the CNS or the generation of virus-specific CD8+T cells, and the expression of IFN-γ was not affected. However, cytotoxic T-lymphocyte (CTL) activity was dependent on NKG2D expression, because anti-NKG2D treatment resulted in a dramatic reduction in lytic activity by virus-specific CD8+T cells. Blocking NKG2D during chronic disease did not affect either T-cell or macrophage infiltration or the severity of demyelination, indicating that NKG2D does not contribute to virus-induced demyelination. These findings demonstrate a functional role for NKG2D in host defense during acute viral encephalitis by selectively enhancing CTL activity by infiltrating virus-specific CD8+T cells.
Functional Analysis of Potential Carboxy-Terminal Cleavage Sites of Tick-Borne Encephalitis Virus Capsid Protein
Authors: Schrauf Sabrina , Schlick Petra , Skern Tim , Mandl Christian W.
Published: December 2007

The mature capsid protein C of flaviviruses is generated through the proteolytic cleavage of the precursor polyprotein by the viral NS2B/3 protease. This cleavage is a prerequisite for the subsequent processing of the viral surface protein prM, and the concerted progression of these events plays a key role in the process of the assembly of infectious virions. Protein C of tick-borne encephalitis virus (TBEV) contains two amino acid sequence motifs within the carboxy-terminal region that match the canonical NS2B/3 recognition site. Site-specific mutagenesis in the context of the full-length TBEV genome was used to investigate the in vivo cleavage specificity of the viral protease in this functionally important domain. The results indicate that the downstream site is necessary and sufficient for efficient cleavage and virion assembly; in contrast, the upstream site is dispensable and placed in a structural context that renders it largely inaccessible to the viral protease. Mutants with impaired C-prM cleavage generally exhibited a significantly increased cytotoxicity. In spite of the clear preference of the protease for only one of the two naturally occurring motifs, the enzyme was unexpectedly tolerant to both the presence of a noncanonical threonine residue at position P2 and the position of cleavage relative to the adjacent internal prM signal sequence. The insertion of three amino acid residues downstream of the cleavage site did not change the viral phenotype. Thus, this study further illuminates the specificity of the TBEV protease and reveals that the carboxy-terminal region of protein C has a remarkable functional flexibility in its role in the assembly of infectious virions.
Nuclear Egress and Envelopment of Herpes Simplex Virus Capsids Analyzed with Dual-Color Fluorescence HSV1(17
+
)
Authors: Nagel Claus-Henning , Döhner Katinka , Fathollahy Mojgan , Strive Tanja , Borst Eva Maria , Messerle Martin , Sodeik Beate
Published: December 2007

To analyze the assembly of herpes simplex virus type 1 (HSV1) by triple-label fluorescence microscopy, we generated a bacterial artificial chromosome (BAC) and inserted eukaryotic Cre recombinase, as well as β-galactosidase expression cassettes. When the BAC pHSV1(17
+
)blueLox was transfected back into eukaryotic cells, the Cre recombinase excised the BAC sequences, which had been flanked with
loxP
sites, from the viral genome, leading to HSV1(17
+
)blueLox. We then tagged the capsid protein VP26 and the envelope protein glycoprotein D (gD) with fluorescent protein domains to obtain HSV1(17
+
)blueLox-GFPVP26-gDRFP and -RFPVP26-gDGFP. All HSV1 BACs had variations in the a-sequences and lost the
oriL
but were fully infectious. The tagged proteins behaved as their corresponding wild type, and were incorporated into virions. Fluorescent gD first accumulated in cytoplasmic membranes but was later also detected in the endoplasmic reticulum and the plasma membrane. Initially, cytoplasmic capsids did not colocalize with viral glycoproteins, indicating that they were naked, cytosolic capsids. As the infection progressed, they were enveloped and colocalized with the viral membrane proteins. We then analyzed the subcellular distribution of capsids, envelope proteins, and nuclear pores during a synchronous infection. Although the nuclear pore network had changed in ca. 20% of the cells, an HSV1-induced reorganization of the nuclear pore architecture was not required for efficient nuclear egress of capsids. Our data are consistent with an HSV1 assembly model involving primary envelopment of nuclear capsids at the inner nuclear membrane and primary fusion to transfer capsids into the cytosol, followed by their secondary envelopment on cytoplasmic membranes.
Human Butyrate-Induced Transcript 1 Interacts with Hepatitis C Virus NS5A and Regulates Viral Replication
Authors: Taguwa Shuhei , Okamoto Toru , Abe Takayuki , Mori Yoshio , Suzuki Tetsuro , Moriishi Kohji , Matsuura Yoshiharu
Published: December 2007

Hepatitis C virus (HCV) nonstructural protein 5A (NS5A) is required for the replication of the viral genome and is involved in several host signaling pathways. To gain further insight into the functional role of NS5A in HCV replication, we screened human cDNA libraries by a yeast two-hybrid system using NS5A as the bait and identified human butyrate-induced transcript 1 (hB-ind1) as a novel NS5A-binding protein. Endogenously and exogenously expressed hB-ind1 was coimmunoprecipitated with NS5A of various genotypes through the coiled-coil domain of hB-ind1. The small interfering RNA (siRNA)-mediated knockdown of hB-ind1 in human hepatoma cell lines suppressed the replication of HCV RNA replicons and the production of infectious particles of HCV genotype 2a strain JFH1. Furthermore, these reductions were canceled by the expression of an siRNA-resistant hB-ind1 mutant. Among the NS5A-binding host proteins involved in HCV replication, hB-ind1 exhibited binding with FKBP8, and hB-ind1 interacted with Hsp90 through the FxxW motif in its N-terminal p23 homology domain. The impairment of the replication of HCV RNA replicons and of the production of infectious particles of JFH1 virus in the hB-ind1 knockdown cell lines was not reversed by the expression of an siRNA-resistant hB-ind1 mutant in which the FxxW motif was replaced by AxxA. These results suggest that hB-ind1 plays a crucial role in HCV RNA replication and the propagation of JFH1 virus through interaction with viral and host proteins.
The PDZ Binding Motif of Human Papillomavirus Type 16 E6 Induces PTPN13 Loss, Which Allows Anchorage-Independent Growth and Synergizes with Ras for Invasive Growth
Authors: Spanos William C. , Hoover Andrew , Harris George F. , Wu Shu , Strand Guinevere L. , Anderson Mary E. , Klingelhutz Aloysius J. , Hendriks Wiljan , Bossler Aaron D. , Lee John H.
Published: December 2007

The human papillomavirus (HPV) oncogene E6 has been shown to perform multiple functions (p53 degradation, telomerase activation, etc.) that play a role in oncogenic transformation. Beyond known E6 functions, an undefined mechanism that allows cellular invasion requires the E6 PDZ binding motif (PDZBM). Here, we show that HPV type 16 (HPV16) E6 interacts with and induces loss of a protein tyrosine phosphatase (PTPN13) in a PDZBM-dependent manner. PTPN13 loss induced either by the presence of E6 or by a short hairpin RNA strategy allows for anchorage-independent growth (AIG) and synergy with a known oncogene, Ras
v12
, resulting in invasive growth in vivo. Restoring PTPN13 expression reverses AIG in cells lacking PTPN13. A genomic analysis of colorectal carcinoma has identified an association between PTPN13 loss-of-function mutations and aberrant Ras signaling. Our findings support this correlation and provide methods for further evaluation of the mechanisms by which PTPN13 loss/Ras expression leads to invasive growth, the results of which will be important for treatment of HPV-related and non-HPV cancer.
Ex Vivo-Generated CD36
+
Erythroid Progenitors Are Highly Permissive to Human Parvovirus B19 Replication
Authors: Wong Susan , Zhi Ning , Filippone Claudia , Keyvanfar Keyvan , Kajigaya Sachiko , Brown Kevin E. , Young Neal S.
Published: December 2007

The pathogenic parvovirus B19 (B19V) has an extreme tropism for human erythroid progenitor cells. In vitro, only a few erythroid leukemic cell lines (JK-1 and KU812Ep6) or megakaryoblastoid cell lines (UT7/Epo and UT7/Epo-S1) with erythroid characteristics support B19V replication, but these cells are only semipermissive. By using recent advances in generating large numbers of human erythroid progenitor cells (EPCs) ex vivo from hematopoietic stem cells (HSCs), we produced a pure population of CD36
+
EPCs expanded and differentiated from CD34
+
HSCs and assessed the CD36
+
EPCs for their permissiveness to B19V infection. Over more than 3 weeks, cells grown in serum-free medium expanded more than 800,000-fold, and 87 to 96% of the CD36
+
EPCs were positive for globoside, the cellular receptor for B19V. Immunofluorescence (IF) staining showed that about 77% of the CD36
+
EPCs were positive for B19V infection, while about 9% of UT7/Epo-S1 cells were B19V positive. Viral DNA detected by real-time PCR increased by more than 3 logs in CD36
+
EPCs; the increase was 1 log in UT7/Epo-S1 cells. Due to the extensive permissivity of CD36
+
EPCs, we significantly improved the sensitivity of detection of infectious B19V by real-time reverse transcription-PCR and IF staining 100- and 1,000-fold, respectively, which is greater than the sensitivity of UT7/Epo-S1 cell-based methods. This is the first description of an ex vivo method to produce large numbers of EPCs that are highly permissive to B19V infection and replication, offering a cellular system that mimics in vivo infection with this pathogenic human virus.
cis
- and
trans
-Acting Functions of Brome Mosaic Virus Protein 1a in Genomic RNA1 Replication
Authors: Yi Guanghui , Kao Cheng
Published: December 2007

RNA viruses employ a combination of mechanisms to regulate their gene expression and replication.
Brome mosaic virus
(BMV) is a tripartite positive-strand RNA virus used to study the requirements for virus infection. BMV genomic RNA1 encodes protein 1a, which contains a methyltransferase (MT) domain and a helicase domain that are required for replication. 1a forms a complex with the 2a RNA-dependent RNA polymerase for the replication and transcription of all BMV RNAs. RNA1 expressed with 2a from
Agrobacterium
-based vectors can result in RNA1 replication in
Nicotiana benthamiana.
A mutation in the 1a translation initiation codon significantly decreased RNA1 accumulation even when wild-type (WT) 1a and 2a were provided in
trans
. Therefore, efficient RNA1 replication requires 1a translation from RNA1 in
cis
, indicating a linkage between replication and translation. Mutation analyses showed that the full-length 1a protein was required for efficient RNA1 replication, not just the process of translation. Three RNA1s with mutations in the 1a MT domain could be partially rescued by WT 1a expressed in
trans
, indicating that the
cis
-acting function of 1a was retained. Furthermore, an RNA motif in the 5′-untranslated region of RNA1, named the B box, was required for 1a to function in
cis
and in
trans
for BMV RNA accumulation. The B box is required for the formation of the replication factory (M. Schwartz, J. Chen, M. Janda, M. Sullivan, J. den Boon, and P. Ahlquist, Mol. Cell 9:505-514, 2002). Results in this work demonstrate a linkage between BMV RNA1 translation and replication.
BK Virus as a Cofactor in the Etiology of Prostate Cancer in Its Early Stages
Authors: Das Dweepanita , Wojno Kirk , Imperiale Michael J.
Published: December 2007

Prostate cancer has been projected to cause almost 10% of all male cancer deaths in the United States in 2007. The incidence of mutations in the tumor suppressor genes
Rb1
and
p53
, especially in the early stages of the disease, is low compared to those for other cancers. This has led to the hypothesis that a human virus such as BK virus (BKV), which establishes a persistent subclinical infection in the urinary tract and encodes oncoproteins that interfere with these tumor suppressor pathways, is involved. Previously, we detected BKV DNA in the epithelial cells of benign and proliferative inflammatory atrophy ducts of cancerous prostate specimens. In the present report, we demonstrate that BKV is present at a much lower frequency in noncancerous prostates. Additionally, in normal prostates, T-antigen (TAg) expression is observed only in specimens harboring proliferative inflammatory atrophy and prostatic intraepithelial neoplasia. We further demonstrate that the
p53
gene from atrophic cells expressing TAg is wild type, whereas tumor cells expressing detectable nuclear p53 contain a mix of wild-type and mutant
p53
genes, suggesting that TAg may inactivate p53 in the atrophic cells. Our results point toward a role for BKV in early prostate cancer progression.
High Level of PD-1 Expression on Hepatitis C Virus (HCV)-Specific CD8
+
and CD4
+
T Cells during Acute HCV Infection, Irrespective of Clinical Outcome
Authors: Kasprowicz Victoria , Schulze zur Wiesch Julian , Kuntzen Thomas , Nolan Brian E. , Longworth Steven , Berical Andrew , Blum Jenna , McMahon Cory , Reyor Laura L. , Elias Nahel , Kwok William W. , McGovern Barbara G. , Freeman Gordon , Chung Raymond T. , Klenerman Paul , Lewis-Ximenez Lia , Walker Bruce D. , Allen Todd M. , Kim Arthur Y. , Lauer Georg M.
Published: December 2007

We monitored expression of PD-1 (a mediator of T-cell exhaustion and viral persistence) on hepatitis C virus (HCV)-specific CD8
+
and CD4
+
T cells from blood and liver during acute and chronic infections and after the resolved infection stage. PD-1 expression on HCV-specific T cells was high early in acute infection irrespective of clinical outcome, and most cells continued to express PD-1 in resolved and chronic stages of infection; intrahepatic expression levels were especially high. Our results suggest that an analysis of PD-1 expression alone is not sufficient to predict infection outcome or to determine T-cell functionality in HCV infection.
A COMPARATIVE STUDY OF STRESS RELAXATION RATE IN UNIRRADIATED AND IRRADIATED PURE TITANIUM AT LOW TEMPERATURES
Authors: GHAURI I. M. , HAIDER KARRAR , AFZAL NAVEED , SIDDIQUE S. A.
Published: December 2007

Stress relaxation rate in unirradiated and electron-beam-irradiated polycrystalline titanium (99.994%) was studied in the temperature range 300–100 K. Titanium specimens were irradiated with 12 MeV electrons to a dose of 0.01 dpa for 12 min. at 300 K. Tensile tests of the specimens were performed using a Universal Testing Machine in the given temperature range. To measure the relaxation of stress with time, the crosshead of the machine was arrested at different fixed loads. Stress relaxation rate s for a given stress level σ0 was found to be temperature dependent, i.e., it decreased with decreasing temperature both in unirradiated and irradiated specimens. However, the decrease was more pronounced in irradiated specimens than that of unirradiated ones. The observed decrease in s values with decrease in temperature is ascribed to the retarding effect of unrelaxed dislocations pinned at defects, especially at the twin boundaries in the course of deformation, which became more conspicuous in irradiated specimens due to the interaction of glide dislocations with radiation-induced defects, in addition to mechanical twins. The activation energy for the movement of dislocations, calculated using the single-barrier model of stress relaxation, was found to be higher in irradiated specimens than that of unirradiated ones at all test temperatures.
THE GROUND-STATE PHASE DIAGRAMS OF THE SPIN-2 ISING MODEL
Authors: ERDİNÇ AHMET
Published: December 2007

The ground-state phase diagrams are obtained for the spin-2 Ising model Hamiltonian with bilinear and biquadratic exchange interactions and a single-ion crystal field. The interactions are assumed to be only between nearest-neighbors. Obtained phase diagrams are presented in the (Δ,J), (K,J), (Δ/J,K/J), (Δ/|J|,K/|J|), (Δ/|K|,J/|K|), (H/J,Δ/J), (H/|J|,Δ/|J|), (H/J,K/J), and (H/|J|,K/|J|) planes where J, K, Δ, and H are the bilinear, biquadratic exchange interactions, the single-ion crystal field, and the external magnetic field, respectively. The influence of the external magnetic field on the spin configurations is investigated.
WEAKLY ALMOST PERIODICITY AND DISTRIBUTIONAL CHAOS IN A SEQUENCE
Authors: WANG LIDONG , HUANG GUIFENG , WANG NA
Published: December 2007

Let (∑, ρ) be a one-sided symbolic space (with two symbols) and σ be the shift on ∑. Denote the set of almost periodic points by A(·) and the set of weakly almost periodic points by W(·). In this paper, we prove that there exists an uncountable set J such that σ|J is distributively chaotic in a sequence, and J⊂W(σ)-A(σ).
EVOLUTION OF QUANTUM FLUCTUATIONS OF A OVER-DAMPED MESOSCOPIC CIRCUIT AT FINITE TEMPERATURE
Authors: HU JU-JU , KE QIANG , JI YING-HUA
Published: December 2007

Time evolution of quantum fluctuations is investigated for an over-damped mesoscopic circuit with the help of the quantum characteristic function. It is found that, for an initial squeezed state, the quantum fluctuations of charge and current evolve with time by hyperbolic functions, and relate not only with the circuit parameters, but also the squeezing parameter. It is also found that with other conditions invariant to reducing the quantum fluctuations of charge and current, we should reduce the squeezing amplitude parameter. The research will be helpful in miniaturizing integrated circuits and electric components. It will also be significant for the further study of quantum information.
TRANSMISSION PROPERTIES OF QUASI-PERIODIC FIBONACCI ONE-DIMENSIONAL PHOTONIC CRYSTAL CONTAINING NEGATIVE PERMITTIVITY/PERMEABILITY MATERIAL
Authors: TAO BO , LI FU-LI , YU FENG
Published: December 2007

The transmission properties of one-dimensional quasi-periodic Fibonacci photonic crystal containing negative permittivity/permeability material are investigated by use of the transfer matrix method. We find that perfect transmission peaks exist at a series of dimensionless wavelength points in the transmission spectra, and the discrete localized modes appear inside the photonic band gap in the case of normal incidence. In the case of oblique incidence, the detailed numerical calculations show that the transmission peaks and angles strongly depend on the polarization of incident waves and the periodicity of the photonic crystals. In addition, we notice that the one-dimensional quasi-periodic photonic crystal can exhibit omni-directional reflection in a certain frequency region for all incident angles and polarizations. We also investigate the possibility of realizing the omni-directional reflection by means of the simple one-dimensional quasi-periodic Fibonacci photonic crystal.
ANOMALOUS INTEGER QUANTUM HALL EFFECT NEAR 1/2 FLUX QUANTA PER PLAQUETTE
Authors: SCHWEITZER LUDWIG
Published: December 2007

We consider non-interacting electrons moving on a two-dimensional square lattice in the presence of quenched correlated disorder potentials and a perpendicular magnetic field with flux density close to 1/2h/e per plaquette. In this situation, the individual sub-bands of the pure system carry σxy=-2e2/h per spin, similar to what has been recently observed in graphene. We find some unusual localization properties in the presence of disorder.
KUNITA-TYPE STOCHASTIC FLOWS OF HOMEOMORPHISMS IN EUCLIDEAN SPACE
Authors: LIANG ZONGXIA
Published: December 2007

In this paper we prove Kunita-type stochastic differential equation (SDE) [Formula: see text], t > s, driven by a spatial continuous semimartingale F (x, t) =(F1 (x, t), …, Fm (x, t)), x ∈ ℜm, with local characteristic (a, b), in the sense of Kunita (Chap. 3 of Ref. 10), can produce a stochastic flow of homeomorphisms of ℜm into itself almost surely under the (a, b) satisfies non-Lipschitz conditions. This result bases on recent works12 by the author.
ON CONVERGENCE TO EQUILIBRIUM IN STRONGLY COUPLED BOGOLIUBOV'S OSCILLATOR MODEL
Authors: STROKOV V.
Published: December 2007

We examine classical Bogoliubov's model of a particle coupled to a heat bath which consists of infinitely many stochastic oscillators. Bogoliubov's result1 suggests that, in the stochastic limit, the model exhibits convergence to thermodynamical equilibrium. It has recently been shown that the system does attain the equilibrium if the coupling constant is small enough.12 We show that in the case of the large coupling constant, the distribution function ρS (q, p, t) → 0 pointwise as t → ∞. This implies that if there is convergence to equilibrium, then the limit measure has no finite momenta. Besides, the probability to find the particle in any finite domain of phase space tends to zero. This is also true for domains in the coordinate space and in the momentum space.
DIRECT AND REVERSE LOG-SOBOLEV INEQUALITIES IN μ-DEFORMED SEGAL–BARGMANN ANALYSIS
Authors: ANGULO AGUILA CARLOS ERNESTO , SONTZ STEPHEN BRUCE
Published: December 2007

Both direct and reverse log-Sobolev inequalities, relating the Shannon entropy with a μ-deformed energy, are shown to hold in a family of μ-deformed Segal–Bargmann spaces. This shows that the μ-deformed energy of a state is finite if and only if its Shannon entropy is finite. The direct inequality is a new result, while the reverse inequality has already been shown by the authors but using different methods. Next the μ-deformed energy of a state is shown to be finite if and only if its Dirichlet form energy is finite. This leads to both direct and reverse log-Sobolev inequalities that relate the Shannon entropy with the Dirichlet energy. We obtain that the Dirichlet energy of a state is finite if and only if its Shannon entropy is finite. The main method used here is based on a study of the reproducing kernel function of these spaces and the associated integral kernel transform.
DRIFT TRANSFORMATIONS OF SYMMETRIC DIFFUSIONS, AND DUALITY
Authors: FITZSIMMONS P. J.
Published: December 2007

Starting with a symmetric Markov diffusion process X (with symmetry measure m and L2 (m) infinitesimal generator A) and a suitable core [Formula: see text] for the Dirichlet form of X, we describe a class of derivations defined on [Formula: see text]. Associated with each such derivation B is a drift transformation of X, obtained through Girsanov's theorem. The transformed process XB is typically non-symmetric, but we are able to show that if the "divergence" of B is positive, then m is an excessive measure for XB, and the L2 (m) infinitesimal generator of XB is an extension of f ↦ Af + B (f). The methods used are mainly probabilistic, and involve the notions of even and odd continuous additive functionals, and Nakao's stochastic divergence. These methods yield a probabilistic approach to the adjoint of the semigroup of XB, and in particular lead to a solution of a problem of W. Stannat.
INFINITE DIVISIBILITY FOR THE CONDITIONALLY FREE CONVOLUTION
Authors: KRYSTEK ANNA DOROTA
Published: December 2007

Infinite divisibility for the free additive convolution was studied in Ref. 20. A complete characterization of [Formula: see text]-infinitely divisible distributions was given, and it was explained in Ref. 21 that this characterization is an analogue of the classical Lévy–Khintchine characterization. In fact, the analogue of the Gaussian distribution appeared even earlier, when the central limit theorem for free additive convolution was proven in Ref. 19.

In this paper we define the notion of [Formula: see text]-infinitely divisibility and give the description of infinitely divisible compactly supported probability measures relative to the conditionally free convolution. We also show that the Lévy–Khintchine measures associated with a [Formula: see text]-infinitely divisible distribution μ can be calculated, as in the classical or free case, as a weak limit of measures related with the convolution semigroup generated by (μ, φ) for [Formula: see text]-infinitely divisible.
A NEW A PRIORI ESTIMATE FOR THE KOLMOGOROV OPERATOR OF A 2D-STOCHASTIC NAVIER–STOKES EQUATION
Authors: STANNAT WILHELM
Published: December 2007

We prove that the Kolmogorov operator L associated with a 2D-stochastic Navier–Stokes equation with periodic boundary conditions and space-time white noise is m-dissipative for sufficiently large viscosity on finitely based cylindrical test functions in the space L1 w.r.t. the Gaussian measure induced by the enstrophy. The proof is based on a new a priori estimate for the solution of the resolvent equation λF - LF = H.
Transport-dependent calcium signaling in spatially segregated cellular caveolar domains
Authors: Hong Dihui , Jaron Dov , Buerk Donald G. , Barbee Kenneth A.
Published: December 2007

We developed a two-dimensional model of transport-dependent intracellular calcium signaling in endothelial cells (ECs). Our purpose was to evaluate the effects of spatial colocalization of endothelial nitric oxide synthase (eNOS) and capacitative calcium entry (CCE) channels in caveolae on eNOS activation in response to ATP. Caveolae are specialized microdomains of the plasma membrane that contain a variety of signaling molecules to optimize their interactions and regulate their activity. In ECs, these molecules include CCE channels and eNOS. To achieve a quantitative understanding of the mechanisms of microdomain calcium signaling and the preferential sensitivity of eNOS to calcium entering the cell through CCE channels, we constructed a mathematical model incorporating the cell morphology and cellular physiological processes. The model predicts that the spatial segregation of calcium channels in ECs can create transport-dependent sharp gradients in calcium concentration within the cell. The calcium concentration gradient is affected by channel density and cell geometry. This transport-dependent calcium signaling specificity effect is enhanced in ECs by increasing the spatial segregation of the caveolar signaling domains. Our simulation significantly advances the understanding of how Ca2+, despite its many potential actions, can mediate selective activation of signaling pathways. We show that diffusion-limited calcium transport allows functional compartmentalization of signaling pathways based on the spatial arrangements of Ca2+ sources and targets.
Alkaline pH- and cAMP-induced V-ATPase membrane accumulation is mediated by protein kinase A in epididymal clear cells
Authors: Pastor-Soler Núria M. , Hallows Kenneth R. , Smolak Christy , Gong Fan , Brown Dennis , Breton Sylvie
Published: December 2007

In the epididymis, low luminal bicarbonate and acidic pH maintain sperm quiescent during maturation and storage. The vacuolar H+-ATPase (V-ATPase) in epididymal clear cells plays a major role in luminal acidification. We have shown previously that cAMP, luminal alkaline pH, and activation of the bicarbonate-regulated soluble adenylyl cyclase (sAC) induce V-ATPase apical accumulation in these cells, thereby stimulating proton secretion into the epididymal lumen. Here we examined whether protein kinase A (PKA) is involved in this response. Confocal immunofluorescence labeling on rat epididymis perfused in vivo showed that at luminal acidic pH (6.5), V-ATPase was distributed between short apical microvilli and subapical endosomes. The specific PKA activator N6-monobutyryl-3′-5′-cyclic monophosphate (6-MB-cAMP, 1 mM) induced elongation of apical microvilli and accumulation of V-ATPase in these structures. The PKA inhibitor myristoylated-PKI (mPKI, 10 μM) inhibited the apical accumulation of V-ATPase induced by 6-MB-cAMP. Perfusion at pH 6.5 with 8-(4-chlorophenylthio)-2- O-methyl-cAMP (8CPT-2- O-Me-cAMP; 10 μM), an activator of the exchange protein activated by cAMP (Epac), did not induce V-ATPase apical accumulation. When applied at a higher concentration (100 μM), 8CPT-2- O-Me-cAMP induced V-ATPase apical accumulation, but this effect was completely inhibited by mPKI, suggesting crossover effects on the PKA pathway with this compound at high concentrations. Importantly, the physiologically relevant alkaline pH-induced apical V-ATPase accumulation was completely inhibited by pretreatment with mPKI. We conclude that direct stimulation of PKA activity by cAMP is necessary and sufficient for the alkaline pH-induced accumulation of V-ATPase in clear cell apical microvilli.