bluuebunny/crossref_metadata_2025_split huggingface dataset:
Involvement of H-NS in Transpositional Recombination Mediated by IS
1
Authors: Shiga Yasuyuki , Sekine Yasuhiko , Kano Yasunobu , Ohtsubo Eiichi 
Published: July 2002

ABSTRACT

IS
1
, the smallest active transposable element in bacteria, encodes a transposase that promotes inter- and intramolecular transposition. Host-encoded factors, e.g., histone-like proteins HU and integration host factor (IHF), are involved in the transposition reactions of some bacterial transposable elements. Host factors involved in the IS
1
transposition reaction, however, are not known. We show that a plasmid with an IS
1
derivative that efficiently produces transposase did not generate miniplasmids, the products of intramolecular transposition, in mutants deficient in a nucleoid-associated DNA-binding protein, H-NS, but did generate them in mutants deficient in histone-like proteins HU, IHF, Fis, and StpA. Nor did IS
1
transpose intermolecularly to the target plasmid in the H-NS-deficient mutant. The
hns
mutation did not affect transcription from the indigenous promoter of IS
1
for the expression of the transposase gene. These findings show that transpositional recombination mediated by IS
1
requires H-NS but does not require the HU, IHF, Fis, or StpA protein in vivo. Gel retardation assays of restriction fragments of IS
1
-carrying plasmid DNA showed that no sites were bound preferentially by H-NS within the IS
1
sequence. The central domain of H-NS, which is involved in dimerization and/or oligomerization of the H-NS protein, was important for the intramolecular transposition of IS
1
, but the N- and C-terminal domains, which are involved in the repression of certain genes and DNA binding, respectively, were not. The SOS response induced by the IS
1
transposase was absent in the H-NS-deficient mutant strain but was present in the wild-type strain. We discuss the possibility that H-NS promotes the formation of an active IS
1
DNA-transposase complex in which the IS
1
ends are cleaved to initiate transpositional recombination through interaction with IS
1
transposase.
Transcriptional Response of
Pasteurella multocida
to Nutrient Limitation
Authors: Paustian Michael L. , May Barbara J. , Kapur Vivek 
Published: July 2002

ABSTRACT

Bacteria often encounter environments where nutrient availability is limited, and they must adapt accordingly. To identify
Pasteurella multocida
genes that are differentially expressed during nutrient limitation, we utilized whole-genome microarrays to compare levels of gene expression during growth in rich and minimal media. Our analysis showed that the levels of expression of a total of 669 genes, representing approximately one-third of the genome, were detectably altered over the course of the experiment. A large number (
n
= 439) of genes, including those involved in energy metabolism, transport, protein synthesis, and binding, were expressed at higher levels in rich medium, suggesting that, upon exposure to a rich environment,
P. multocida
immediately begins to turn on many energy-intensive biosynthetic pathways or, conversely, turns these genes off when it is exposed to a nutrient-deficient environment. Genes with increased expression in minimal medium (
n
= 230) included those encoding amino acid biosynthesis and transport systems, outer membrane proteins, and heat shock proteins. Importantly, our analysis also identified a large number (
n
= 164) of genes with unknown functions whose expression was altered during nutrient limitation. Overall, the results of our study show that a wide repertoire of genes, many of which have yet to be functionally classified, undergo transcriptional regulation in
P. multocida
in response to growth in minimal medium and provide a strong foundation to investigate the transcriptional response of this multispecies pathogen to growth in a nutrient-limited environment.
The
tra
Region of the Conjugative Plasmid pIP501 Is Organized in an Operon with the First Gene Encoding the Relaxase
Authors: Kurenbach Brigitta , Grothe Dagmar , Farías María Eugenia , Szewzyk Ulrich , Grohmann Elisabeth 
Published: July 2002

ABSTRACT

The
tra
genes
orf1
to
orf11
of pIP501 were shown to be transcribed as a single operon of 11.3 kb in
Enterococcus faecalis
by reverse transcription-PCR. The transcriptional start site of the
tra
mRNA was mapped at 110 bp upstream from the predicted TTG start codon of the first gene of the operon, the
traA
relaxase. The TraA protein (660 amino acids) and a C-terminally truncated version of the TraA protein (293 amino acids) were purified as fusions with glutathione
S
-transferase.
oriT
cleavage activity of both TraA proteins was demonstrated in vitro on supercoiled plasmid pVA2241 DNA containing

oriT
pIP501

. The activity of the DNA relaxase TraA is strictly dependent on the presence of Mg
2+
or Mn
2+
and is highest at temperatures of between 42 and 45°C.
Newly Identified Cytochrome
c
Oxidase Operon in the Nitrogen-Fixing Cyanobacterium
Anabaena
sp. Strain PCC 7120 Specifically Induced in Heterocysts
Authors: Jones Kathryn M. , Haselkorn Robert 
Published: July 2002

ABSTRACT

Two operons have been cloned from
Anabaena
sp. strain PCC 7120 DNA, each of which encodes the three core subunits of distinct mitochondrial-type cytochrome
c
oxidases. The two operons are only 72 to 85% similar to one another at the nucleotide level in the most conserved subunit. One of these,
coxBACII
, is induced >20-fold in the middle to late stages of heterocyst differentiation. Analysis of green fluorescent protein reporters indicates that this operon is expressed specifically in proheterocysts and heterocysts. The other operon,
coxBACI
, is induced only 2.5-fold following nitrogen step-down and is expressed in all cells. Surprisingly, a disruption mutant of
coxAII
, the gene encoding subunit I of the heterocyst-specific oxidase, grows normally in the absence of combined nitrogen. It is likely that
coxBACI
and/or two other putative terminal oxidases present in the
Anabaena
sp. strain PCC 7120 genome are able to compensate for the loss of the heterocyst-specific oxidase in providing ATP for nitrogen fixation and maintaining a low oxygen level in heterocysts.
Rapid Identification of Yeasts in Positive Blood Cultures by a Multiplex PCR Method
Authors: Chang Hsein Chang , Leaw Shiang Ning , Huang Ay Huey , Wu Tsu Lan , Chang Tsung Chain 
Published: July 2002

ABSTRACT

Yeasts are emerging as important etiological agents of nosocomial bloodstream infections. A multiplex PCR method was developed to rapidly identify clinically important yeasts that cause fungemia. The method amplified the internal transcribed spacer 1 (ITS1) region between the 18S and 5.8S rRNA genes and a specific DNA fragment within the ITS2 region of
Candida
albicans
. With this method,
C
.
albicans
produced two amplicons, whereas other species produced only one. Through sequence analysis, the precise lengths of the PCR products were found to be as follows:
C
.
glabrata
(482 or 483 bp),
C
.
guilliermondii
(248 bp),
C
.
parapsilosis
(229 bp),
C
.
albicans
(218 or 219 and 110 bp),
C
.
tropicalis
(218 bp),
Cryptococcus
neoformans
(201 bp), and
C
.
krusei
(182 bp). The PCR products could be effectively separated by disk polyacrylamide gel electrophoresis. The method was used to test 249 positive blood cultures (255 isolates), from which the following species (strain number) were isolated:
C
.
albicans
(128),
C
.
tropicalis
(51),
C
.
glabrata
(28),
C
.
parapsilosis
(23),
C.
neoformans
(9),
C
.
krusei
(5),
C
.
guilliermondii
(3), and other, minor species (8). The test sensitivity of the method was 96.9% (247 of 255 isolates). The eight minor species were either misidentified (one strain) or not identified (seven strains). From the time at which a positive bottle was found, the multiplex PCR could be completed within 8 h; the present method is simpler than any previously reported molecular method for the identification of blood yeasts.
Comparison of IsoCode STIX and FTA Gene Guard Collection Matrices as Whole-Blood Storage and Processing Devices for Diagnosis of Malaria by PCR
Authors: Zhong Kathleen J. Y. , Salas Carola J. , Shafer Robyn , Gubanov Alex , Gasser Robert A. , Magill Alan J. , Forney J. Russ , Kain Kevin C. 
Published: July 2002

ABSTRACT

We compared two collection devices, IsoCode and FTA, with whole blood for the diagnosis of malaria by PCR (
n
= 100). Using whole blood as the reference standard, both devices were sensitive for the detection of single-species malaria infections by PCR (≥96%). However, the detection of mixed infections was suboptimal (IsoCode was 42% sensitive, and FTA was 63% sensitive).
Patterns of Changes in Human Immunodeficiency Virus Type 1 V3 Sequence Populations Late in Infection
Authors: Nelson Julie A. E. , Baribaud Frédéric , Edwards Terri , Swanstrom Ronald 
Published: July 2002

ABSTRACTWe have used a V3-specific heteroduplex tracking assay (V3-HTA) with probes from two different human immunodeficiency virus type 1 (HIV-1) subtypes to examine the extent and pace of HIV-1 evolution late in infection. Twenty-four subjects with advanced HIV-1 infection (CD4+T-cell count, <100/μl) and stable viral loads were studied using blood plasma samples collected over a study period of approximately 9 months, during which time most of the subjects were treated with reverse transcriptase inhibitors. The V3-HTA patterns from the first and last time points were evaluated initially to determine the amounts of change in V3 sequence populations, which were primarily changes in abundance in preexisting sequence populations. Three of the 24 subjects had major changes (greater than 50% total change in the relative abundance of the sequence populations), 11 subjects had intermediate changes (10 to 50% total change), and 10 subjects had minimal changes (less than 10% total change). The average total amount of change was between two- and threefold greater in subjects with X4-like variants, although there was no correlation between average viral load and the presence of X4-like variants. V3-HTA patterns in monthly samples from 11 of the subjects were also compared. In two subjects, the amount of change exceeded 40% in a 1-month period. Overall, the pace of change in V3 populations varied between subjects and was not constant within a subject over time. Sequence analysis of the V3 variants showed that R5-like variants (not containing any X4-associated substitutions) continued to be maintained in three subjects in the presence of X4-like variants, indicating that X4 variants do not always outgrow R5 variants. The coreceptor usage of the V3 sequences from two subjects was determined using a cell fusion assay. One subject had an X4 variant that was maintained at a low level for at least 9 months, during which time the predominant variants were R5X4 (dualtropic), while in the second subject the reverse situation was observed. One of the dualtropic variants had a novel sequence motif in V3, suggesting another evolutionary pathway to altered tropism. These studies begin to probe the complexities and pace of V3 evolution in vivo, revealing dynamic patterns of change among multiple V3 sequence variants in a subset of subjects.
The Intact Retroviral Env Glycoprotein of Human Foamy Virus Is a Trimer
Authors: Wilk Thomas , de Haas Felix , Wagner Andrea , Rutten Twan , Fuller Stephen , Flügel Rolf M. , Löchelt Martin 
Published: July 2002

ABSTRACT
Electron microscopy of negatively stained human foamy virus particles provides direct evidence for the trimeric nature of intact Env surface glycoproteins. Three-dimensional image reconstruction reveals that the Env trimer is a tapering spike 14 nm in length. The spikes were often arranged in hexagonal rings which shared adjacent Env trimers.
Coadministration of Gamma Interferon with DNA Vaccine Expressing Woodchuck Hepatitis Virus (WHV) Core Antigen Enhances the Specific Immune Response and Protects against WHV Infection
Authors: Siegel Felix , Lu Mengji , Roggendorf Michael 
Published: July 2002

ABSTRACTDNA vaccinations are able to induce strong cellular immune responses in mice and confer protection against infectious agents. However, DNA vaccination of large animals appears to be less effective and requires repeated injections of large amounts of plasmid DNA. Enhancement of the efficiency of DNA vaccines may be achieved by coapplication of cytokine-expressing plasmids. Here we investigated, with woodchucks, whether coadministration of an expression plasmid for woodchuck gamma interferon (IFN-γ), pWIFN-γ, can improve DNA vaccination with woodchuck hepatitis virus core antigen (WHcAg). Animals were immunized with pWHcIm (a plasmid expressing WHcAg) alone or with a combination of pWHcIm and pWIFN-γ using a gene gun. Six weeks postimmunization, all animals were challenged with 105genome equivalents of woodchuck hepatitis virus (WHV). The antibody and lymphoproliferative immune responses to WHV proteins were determined after immunization and after challenge. Vaccination with pWHcIm and pWIFN-γ led to a pronounced lymphoproliferative response to WHcAg and protected woodchucks against subsequent virus challenge. Two of three animals vaccinated with pWHcIm alone did not show a detectable lymphoproliferative response to WHcAg. A low-level WHV infection occurred in these woodchucks after challenge, as WHV DNA was detectable in the serum by PCR. None of the pWHcIm-vaccinated animals showed an anti-WHcAg antibody response after DNA vaccination or an anamnestic response after virus challenge. Our results indicate that coadministration of the WIFN-γ gene with pWHcIm enhanced the specific cellular immune response and improved the protective efficacy of WHV-specific DNA vaccines.
Adenovirus Type 9 Fiber Knob Binds to the Coxsackie B Virus-Adenovirus Receptor (CAR) with Lower Affinity than Fiber Knobs of Other CAR-Binding Adenovirus Serotypes
Authors: Kirby Ian , Lord Rosemary , Davison Elizabeth , Wickham Thomas J. , Roelvink Peter W. , Kovesdi Imre , Sutton Brian J. , Santis George 
Published: July 2002

ABSTRACT
The coxsackie B virus and adenovirus (Ad) receptor (CAR) functions as an attachment receptor for multiple Ad serotypes. Here we show that the Ad serotype 9 (Ad9) fiber knob binds to CAR with much reduced affinity compared to the binding by Ad5 and Ad12 fiber knobs as well as the knob of the long fiber of Ad41 (Ad41L). Substitution of Asp222 in Ad9 fiber knob with a lysine that is conserved in Ad5, Ad12, and Ad41L substantially improved Ad9 fiber knob binding to CAR, while the corresponding substitution in Ad5 (Lys442Asp) significantly reduced Ad5 binding. The presence of an aspartic acid residue in Ad9 therefore accounts, at least in part, for the reduced CAR binding affinity of the Ad9 fiber knob. Site-directed mutagenesis of CAR revealed that CAR residues Leu73 and Lys121 and/or Lys123 are critical contact residues, with Tyr80 and Tyr83 being peripherally involved in the binding interaction with the Ad5, Ad9, Ad12, and Ad41L fiber knobs. The overall affinities and the association and dissociation rate constants for wild-type CAR as well as Tyr80 and Tyr83 CAR mutants differed between the serotypes, indicating that their binding modes, although similar, are not identical.
The Leader Protein of Theiler's Virus Inhibits Immediate-Early Alpha/Beta Interferon Production
Authors: van Pesch Vincent , van Eyll Olivier , Michiels Thomas 
Published: July 2002

ABSTRACT
Theiler's virus is a picornavirus responsible for a persistent infection of the central nervous system of the mouse, leading to a chronic demyelinating disease considered to be a model for multiple sclerosis. The leader (L) protein encoded by Theiler's virus is a 76-amino-acid-long peptide containing a zinc-binding motif. This motif is conserved in the L proteins of all cardioviruses, including encephalomyocarditis virus. The L protein of Theiler's virus was suggested to interfere with the alpha/beta interferon (IFN-α/β) response (W.-P. Kong, G. D. Ghadge, and R. P. Roos, Proc. Natl. Acad. Sci. USA 91:1796–1800, 1994). We show that expression of the L protein indeed inhibits the production of alpha/beta interferon by infected L929 cells. The L protein specifically inhibits the transcription of the IFN-α4 and IFN-β genes, which are known to be activated early in response to viral infection. Mutation of the zinc finger was sufficient to block the anti-interferon activity, outlining the importance of this motif in the L protein function. In agreement with the anti-interferon role of the L protein, a virus bearing a mutation in the zinc-binding motif was dramatically impaired in its ability to persist in the central nervous system of SJL/J mice.
Contribution of Vascular Endothelial Growth Factor in the Neovascularization Process during the Pathogenesis of Herpetic Stromal Keratitis
Authors: Zheng Mei , Deshpande Shilpa , Lee Sujin , Ferrara Napoleone , Rouse Barry T. 
Published: July 2002

ABSTRACTThis report analyzes the role of vascular endothelial growth factor (VEGF)-induced angiogenesis in the immunoinflammatory lesion stromal keratitis induced by ocular infection with herpes simplex virus (HSV). Our results show that infection with replication-competent, but not mutant, viruses results in the expression of VEGF mRNA and protein in the cornea. This a rapid event, with VEGF mRNA detectable by 12 h postinfection (p.i.) and proteins detectable by 24 h p.i. VEGF production occurred both in the virus-infected corneal epithelium and in the underlying stroma, in which viral antigens were undetectable. In the stroma, VEGF was produced by inflammatory cells; these initially were predominantly polymorphonuclear leukocytes (PMN), but at later time points both PMN and macrophage-like cells were VEGF producers. In the epithelium, the major site of VEGF-expressing cells in early infection, the infected cells themselves were usually negative for VEGF. Similarly, in vitro infection studies indicated that the cells which produced VEGF were not those which expressed virus. Attesting to the possible role of VEGF-induced angiogenesis in the pathogenesis of herpetic stromal keratitis were experiments showing that VEGF inhibition with mFlt(1–3)-immunoglobulin G diminished angiogenesis and the severity of lesions after HSV infection. These observations are the first to evaluate VEGF-induced angiogenesis in the pathogenesis of stromal keratitis. Our results indicate that the control of angiogenesis represents a useful adjunct to therapy of herpetic ocular disease, an important cause of human blindness.
DDB2 Induces Nuclear Accumulation of the Hepatitis B Virus X Protein Independently of Binding to DDB1
Authors: Nag Alo , Datta Abhishek , Yoo Kyung , Bhattacharyya Dibyendu , Chakrabortty Amit , Wang Xinhi , Slagle Betty L. , Costa Robert H. , Raychaudhuri Pradip 
Published: July 2002

ABSTRACT

The hepatitis B virus (HBV) X protein (HBx) is critical for the life cycle of the virus. HBx associates with several host cell proteins including the DDB1 subunit of the damaged-DNA binding protein DDB. Recent studies on the X protein encoded by the woodchuck hepadnavirus have provided correlative evidence indicating that the interaction with DDB1 is important for establishment of infection by the virus. In addition, the interaction with DDB1 has been implicated in the nuclear localization of HBx. Because the DDB2 subunit of DDB is required for the nuclear accumulation of DDB1, we investigated the role of DDB2 in the nuclear accumulation of HBx. Here we show that expression of DDB2 increases the nuclear levels of HBx. Several C-terminal deletion mutants of DDB2 that fail to bind DDB1 are able to associate with HBx, suggesting that DDB2 may associate with HBx independently of binding to DDB1. We also show that DDB2 enhances the nuclear accumulation of HBx independently of binding to DDB1, since a mutant that does not bind DDB1 is able to enhance the nuclear accumulation of HBx. HBV infection is associated with liver pathogenesis. We show that the nuclear levels of DDB1 and DDB2 are tightly regulated in hepatocytes. Studies with regenerating mouse liver indicate that during late G
1
phase the nuclear levels of both subunits of DDB are transiently increased, followed by a sharp decrease in S phase. Taken together, these results suggest that DDB1 and DDB2 would participate in the nuclear functions of HBx effectively only during the late-G
1
phase of the cell cycle.
In Vivo Inhibition of Anti-Hepatitis B Virus Core Antigen (HBcAg) Immunoglobulin G Production by HBcAg-Specific CD4+Th1-Type T-Cell Clones in a hu-PBL-NOD/SCID Mouse Model
Authors: Cao Tinghua , Meuleman Philip , Desombere Isabelle , Sällberg Matti , Leroux-Roels Geert 
Published: July 2002

ABSTRACTHepatitis B virus (HBV) core antigen (HBcAg)-specific CD4+T-cell responses are believed to play an important role in the control of human HBV infection. In the present study, HBcAg-specific, HLA-DR13*-restricted CD4+Th1-type T-cell clones were generated which secreted both gamma interferon and tumor necrosis factor alpha after in vitro antigen stimulation. These HBcAg-specific CD4+Th1-type T cells were able to lyse HBc peptide-loaded Epstein-Barr virus-transformed lymphoblastoid target cells in vitro. To examine whether these HLA-DR13*-restricted human CD4+Th1 T cells also display the same cytotoxic effects in vivo, we transferred peripheral blood leukocytes (PBL) derived from HBV-infected donors or an HBV-naı̈ve donor sharing the DR13*, together with the HBcAg-specific CD4+Th1-type T cells and HBcAg, directly into the spleen of optimally conditioned Nod/LtSz-Prkdcscid/Prkdcscid(NOD/SCID) mice. The production of both secondary anti-HBc-immunoglobulin G (anti-HBc-IgG) and primary HBcAg-binding IgM in hu-PBL-NOD/SCID mice was drastically inhibited by HBcAg-specific CD4+Th1-type T cells. No inhibition was observed when CD4+Th1 cells and donor PBL did not share an HLA-DR13. These results suggest that HBcAg-specific CD4+Th1 T cells may be able to lyse HBcAg-binding, or -specific, B cells that have taken up and presented HBcAg in a class II-restricted manner. Thus, HBcAg-specific CD4+Th1-type T cells can modulate the function and exert a regulatory role in deleting HBcAg-binding, or -specific, human B cells in vivo, which may be of importance in controlling the infection.
BE VISION, A Package of IBM 7090 FORTRAN Programs to Draw Orthographic Views of Combinations of Plane and Quadric Surfaces
Authors: Weiss Ruth A. 
Published: July 2002

BE VISION is a package of FORTRAN programs for drawing orthographic views of combinations of plane and quadric surfaces. As input, the package takes rectangular coordinate equations specifying the surfaces plus a three-angle specification of the viewing direction. Output is a drawing on the Stromberg Carlson 4020 Microfilm Recorder. Many views of one scene may be obtained simply by changing the viewpoint.
The various subroutines of the package and their functions are described in this paper. It also gives numerous examples of pictures that were produced by BE VISION. The package has been in use since April 1964.