bluuebunny/crossref_metadata_2025 huggingface dataset:
Chondroitin Sulfate Proteoglycan Expression and Binding ofPlasmodium falciparum-Infected Erythrocytes in the Human Placenta during Pregnancy
Authors: Agbor-Enoh Sean T. , Achur Rajeshwara N. , Valiyaveettil Manojkumar , Leke Rose , Taylor Diane W. , Gowda D. Channe
Published: April 2003

A characteristic feature of malaria during pregnancy is the sequestration ofPlasmodium falciparum-infected red blood cells (IRBCs) in the intervillous spaces of the placenta. We have recently shown that unusually low-sulfated chondroitin sulfate proteoglycans (CSPGs) present in the intervillous spaces mediate the adherence of IRBCs in the placenta. In areas of endemicity, the prevalence ofP. falciparuminfection in pregnant women peaks during weeks 13 to 20 and then gradually declines, implying that the placental CSPGs are available for IRBC adhesion early during the pregnancy. However, there is no information on the expression and composition of CSPGs during pregnancy. In this study, the expression pattern of CSPGs during the course of pregnancy was investigated. The CSPGs were purified from placentas of various gestational ages, characterized, and tested for the ability to bind IRBCs. The data demonstrate that the CSPGs are present in the intervillous spaces throughout the second and third trimesters. The levels of CSPGs expressed per unit tissue weight were similar in placentas of various gestational ages. However, the structures of the intervillous-space CSPGs changed considerably during the course of pregnancy. In particular, the molecular weight was decreased, with an accompanying gradual increase in the CSPG size polydispersity, from 16 weeks until 38 weeks. The sulfate content was increased considerably after 24 weeks. Despite these structural changes, the CSPGs of placentas of various gestational ages efficiently supported the binding of IRBCs. These results demonstrate that CSPGs can mediate the sequestration of IRBCs in the intervillous spaces of the placenta during the entire second and third trimesters and possibly during the later part of the first trimester as well.
Mice Genetically Deficient in Immunoglobulin E Are More Permissive Hosts than Wild-Type Mice to a Primary, but Not Secondary, Infection with the Filarial NematodeBrugia malayi
Authors: Spencer L. A. , Porte P. , Zetoff C. , Rajan T. V.
Published: April 2003

Primary and secondary murine and human infections withBrugia malayiare characterized by substantial increases in levels of immunoglobulin E (IgE). To investigate whether this is necessary for worm clearance, IgE−/−mice were subjected to primary- and secondary-infection protocols. Following a primary infection, IgE−/−mice displayed a profound deficit in their ability to clear an intraperitoneal injection of L3 infective-stage larvae in comparison to wild-type counterparts and maintained substantial worm burdens as late as 10 weeks postinfection. Although viable adult parasites were recovered at this late time point from IgE−/−mice, the majority of the mice remained free of microfilariae. IgE−/−cohorts subjected to a secondary-infection protocol were able to clear the challenge inoculation in an accelerated manner, with kinetics similar to that observed in the wild-type animals. Analysis of the humoral response in IgE−/−mice following infection demonstrates a defect in IgG1 and IgG2a production, in addition to the expected lack of IgE. The IgG1 deficiency is no longer evident following a secondary infection. These data imply that deficiencies other than IgE production (i.e., IgG1 production) deficiency may be responsible for the increased permissiveness of IgE−/−mice as hosts following infection withB. malayi.
Inhibition of Response to Alpha Interferon byMycobacterium tuberculosis
Authors: Prabhakar Savita , Qiao Yaming , Hoshino Yoshihiko , Weiden Michael , Canova Antony , Giacomini Elena , Coccia Eliana , Pine Richard
Published: April 2003

We previously reported that infection byMycobacterium tuberculosis, the causative agent of tuberculosis, leads to secretion of alpha/beta interferon (IFN-α/β). While IFN-α/β ordinarily stimulates formation of signal transducer and stimulator of transcription-1 (STAT-1) homodimers and IFN-stimulated gene factor-3 (ISGF-3), only ISGF-3 is found in infected human monocytes and macrophages. We have now investigated the basis for this unusual profile of transcription factor activation and its consequences for regulation of transcription, as well as the impact of infection on response to IFN-α. After infection, IFN-α stimulation of STAT-1 homodimers is inhibited in monocytes and macrophages, while stimulation of ISGF-3 increases in monocytes but tends to decline in macrophages. Effects of infection on the abundance of ISGF-3 subunits, STAT-1, STAT-2, and interferon regulatory factor 9, and on tyrosine phosphorylation of STAT-1 and STAT-2 explain the observed changes in DNA-binding activity, which correlate with increased or inhibited transcription of genes regulated by ISGF-3 and STAT-1. Infection byMycobacterium bovisBCG does not inhibit IFN-α-stimulated tyrosine phosphorylation of STAT-1, formation of homodimers, or transcription of genes regulated by STAT-1 homodimers, suggesting that inhibition of the response to IFN-α/β byM. tuberculosisis an aspect of pathogenicity. Thus, this well-known feature of infection by pathogenic viruses may also be a strategy employed by pathogenic bacteria.
Role of Innate Immune Factors in the Adjuvant Activity of Monophosphoryl Lipid A
Authors: Martin Michael , Michalek Suzanne M. , Katz Jannet
Published: April 2003

Monophosphoryl lipid A (MPL) is a nontoxic derivative of lipopolysaccharide (LPS) that exhibits adjuvant properties similar to those of the parent LPS molecule. However, the mechanism by which MPL initiates its immunostimulatory properties remains unclear. Due to the involvement of Toll-like receptors in recognizing and transducing intracellular signals in response to LPS, the aim of the present study was to determine the ability of MPL to utilize the Toll-like receptor 2 (TLR2) and TLR4. We provide evidence that MPL differentially utilizes TLR2 and TLR4 for the induction of tumor necrosis factor alpha, interleukin 10 (IL-10), and IL-12 by purified human monocytes as well as by human peripheral blood mononuclear cells. Assessment of NF-κB activity demonstrated that MPL utilized TLR2 and especially TLR4 for the activation of NF-κB p65 by human monocytes. In addition, stimulation of human monocytes by MPL led to an up-regulation of the costimulatory molecules CD80 and CD86, an effect that could be reduced by pretreatment of cells with a monoclonal antibody to TLR2 or TLR4. Analysis of MPL-induced activation of the extracellular signal-regulated kinase (ERK) and p38 mitogen-activated protein (MAP) kinases revealed that MPL utilized both TLR2 and TLR4 for the phosphorylation of ERK1/2, while TLR4 was the predominant receptor involved in the ability of MPL to phosphorylate p38. Moreover, using selective inhibitors for MAP kinase kinase (PD98059) and p38 (SB203580), we show that ERK1/2 exhibited differential effects on production of TNF-α and IL-12 p40 by human monocytes, whereas MPL-induced activation of p38 appeared to be predominantly involved in production of IL-10 and IL-12 p40 by MPL-stimulated monocytes. Taken together, these findings aid in understanding the cellular mechanisms by which MPL induces host cell activation and subsequent adjuvant properties.
Staphylococcal Enterotoxin B-Induced Acute Inflammation Is Inhibited by Dexamethasone: Important Role of CXC Chemokines KC and Macrophage Inflammatory Protein 2
Authors: Schramm Rene , Thorlacius Henrik
Published: April 2003

This study was conducted to examine the anti-inflammatory mechanisms of dexamethasone during leukocyte recruitment and expression of the CXC chemokines macrophage inflammatory protein 2 (MIP-2) (CXCL2) and cytokine-induced neutrophil chemoattractant (KC) (CXCL1) in staphylococcal enterotoxin B (SEB)-induced acute inflammation. To do this, SEB was injected into murine air pouches with or without dexamethasone pretreatment for 2 h. SEB induced infiltration of leukocytes in a dose- and time-dependent manner, with the maximal response observed after 4 h of treatment with 10 μg of SEB. The recruited leukocytes comprised more than 77% neutrophils. Moreover, SEB challenge (10 μg) provoked time-dependent secretion of CXC chemokines, which peaked after 1 h. Local administration of antibodies against MIP-2 and KC significantly reduced SEB-triggered neutrophil accumulation by 38 and 59%, respectively. Dexamethasone (10 mg kg−1) significantly decreased neutrophil recruitment by 82% and reduced secretion of MIP-2 and KC by 89 and 85%, respectively, in response to SEB challenge. Our data demonstrate that dexamethasone potently inhibits neutrophil recruitment in SEB-induced inflammation. Moreover, we provide evidence that MIP-2 and KC are key mediators in the neutrophil response to SEB. Furthermore, our findings demonstrate that dexamethasone attenuates SEB-induced expression of MIP-2 and KC. Thus, this study elucidates important signaling pathways of SEB-induced neutrophil recruitment and anti-inflammatory mechanisms of action of dexamethasone.
Cleavage of the Human Immunoglobulin A1 (IgA1) Hinge Region by IgA1 Proteases Requires Structures in the Fc region of IgA
Authors: Chintalacharuvu Koteswara R. , Chuang Philip D. , Dragoman Ashley , Fernandez Christine Z. , Qiu Jiazhou , Plaut Andrew G. , Trinh K. Ryan , Gala Françoise A. , Morrison Sherie L.
Published: April 2003

Secretory immunoglobulin A (IgA) protects the mucosal surfaces against inhaled and ingested pathogens. Many pathogenic bacteria produce IgA1 proteases that cleave in the hinge of IgA1, thus separating the Fab region from the Fc region and making IgA ineffective. Here, we show thatHaemophilus influenzaetype 1 andNeisseria gonorrhoeaetype 2 IgA1 proteases cleave the IgA1 hinge in the context of the constant region of IgA1 or IgA2m(1) but not in the context of IgG2. Both Cα2 and Cα3 but not Cα1 are required for the cleavage of the IgA1 hinge byH. influenzaeandN. gonorrhoeaeproteases. While there was no difference in the cleavage kinetics between wild-type IgA1 and IgA1 containing only the first GalNAc residue of the O-linked glycans, the absence of N-linked glycans in the Fc increased the ability of theN. gonorrhoeaeprotease to cleave the IgA1 hinge. Taken together, these results suggest that, in addition to the IgA1 hinge, structures in the Fc region of IgA are required for the recognition and cleavage of IgA1 by theH. influenzaeandN. gonorrhoeaeproteases.
Interleukin-12 p40- and Fas Ligand-Dependent Apoptotic Pathways Involving STAT-1 Phosphorylation Are Triggered during Infection with a Virulent Strain ofToxoplasma gondii
Authors: Gavrilescu L. Cristina , Denkers Eric Y.
Published: April 2003

Toxoplasma gondiiis an opportunistic intracellular parasite. Infection with the high-virulenceT. gondiistrain RH induces inflammatory cytokine overproduction and uncontrolled apoptosis in lymphoid organs. Here, we show by fluorescent terminal deoxynucleotidyltransferase-mediated dUTP-biotin nick end labeling (TUNEL) assay and binding of fluorescein isothiocyanate-conjugated VAD-FMK, an irreversible pan-caspase inhibitor, that parasite-triggered apoptosis occurs among CD4+, CD8+, B220+, Gr-1+, and NK1.1+splenic populations. Caspases 8 and 9 were activated during infection, implicating cell surface death receptors and mitochondria in apoptosis. Induction of apoptosis was absent among all cell populations in both interleukin-12 (IL-12) p40- and Fas ligand (FasL)-negative mice. STAT-1 phosphorylation correlated with onset of apoptosis during infection, but in the absence of IL-12 p40 and functional FasL, activation of this transcription factor failed to occur. The results demonstrateT. gondii-induced activation of multiple apoptotic pathways, dependent upon both IL-12 p40 and FasL, that may play a role in the lethal pathology of infection.
Changes in Pulmonary Function and Parasite Burden in Rats Infected with
Strongyloides venezuelensis
Concomitant with Induction of Allergic Airway Inflammation
Authors: Negrão-Corrêa Deborah , Silveira Micheline R. , Borges Cynthia M. , Souza Danielle G. , Teixeira Mauro M.
Published: April 2003

The prevalence of allergic diseases such as asthma has increased markedly over the past few decades. To evaluate the possible mutual influence of helminth infection and allergy, the combined effects of experimental allergic airway inflammation and infection with
Strongyloides venezuelensis
on various parasitological and inflammatory indices were evaluated in the rat. A challenge of immunized rats with aerosolized ovalbumin (OVA) resulted in eosinophilic inflammation that peaked 48 h after the challenge and was accompanied by airway hyperresponsiveness (AHR) to an intravenous acetylcholine challenge.
S. venezuelensis
infection concomitant with an OVA challenge of immunized rats resulted in prolonged pulmonary inflammation with increased eosinophil infiltration in bronchoalveolar lavage fluid but not in the lung tissue. These rats also showed a significant parasite burden reduction, especially during parasite migration through the lungs. However, the fecundity rates of worms that reached the intestine were similar in allergic and nonallergic animals. Despite airway inflammation, the increased responsiveness of the airways in the experimental asthma model was suppressed during parasite migration through the lungs (2 days). In contrast, parasite-induced AHR was unchanged 5 days after infection in immunized and challenged rats. In conclusion, infection with
S. venezuelensis
interfered with the onset of AHR following an antigen challenge of immunized rats. The ability of parasites to switch off functional airway responses is therapeutically relevant because we may learn from parasites how to modulate lung function and, hence, the AHR characteristic of asthmatic patients.
Gene Expression Profiling of
Helicobacter pylori
Reveals a Growth-Phase-Dependent Switch in Virulence Gene Expression
Authors: Thompson Lucinda J. , Merrell D. Scott , Neilan Brett A. , Mitchell Hazel , Lee Adrian , Falkow Stanley
Published: April 2003

The global pattern of growth-phase-dependent gene expression of
Helicobacter pylori
during in vitro culture was analyzed by using a high-density DNA microarray. To detect consistent coordinated gene expression in this bacterium, temporal changes in transcription were assessed in two independent time courses. Cluster analysis of the expression profiles highlighted a major switch in gene expression during the late log-to-stationary phase transition that we have termed the Log-Stat switch. Statistical analysis of the genes that were significantly induced or repressed during the Log-Stat switch revealed that many of these genes were related to virulence. Among these, expression of the genes for the neutrophil activating protein (
napA
) and the major flagellin subunit (
flaA
) were significantly induced. Additionally, the expression of a number of genes involved in iron homeostasis changed dramatically at this switch; the gene for the iron-storage protein,
pfr
, was induced, while the genes for two putative iron uptake proteins,
fecA
and
frpB
, were significantly repressed. These data suggest that the late log phase may correspond to the most virulent phase of growth in
H. pylori
and may be intimately related to its pathogenesis. The use of microarrays to analyze the kinetics of the transcriptional response of a bacterial pathogen to a changing environment has enabled the discovery of previously unappreciated relationships between genes by elucidation of coordinated gene expression profiles.
MtsABC Is Important for Manganese and Iron Transport, Oxidative Stress Resistance, and Virulence of
Streptococcus pyogenes
Authors: Janulczyk Robert , Ricci Susanna , Björck Lars
Published: April 2003

MtsABC is a
Streptococcus pyogenes
ABC transporter which was previously shown to be involved in iron and zinc accumulation. In this study, we showed that an
mtsABC
mutant has impaired growth, particularly in a metal-depleted medium and an aerobic environment. In metal-depleted medium, growth was restored by the addition of 10 μM MnCl
2
, whereas other metals had modest or no effect. A characterization of metal radioisotope accumulation showed that manganese competes with iron accumulation in a dose-dependent manner. Conversely, iron competes with manganese accumulation but to a lesser extent. The mutant showed a pronounced reduction (>90%) of
54
Mn accumulation, showing that MtsABC is also involved in Mn transport. Using paraquat and hydrogen peroxide to induce oxidative stress, we show that the mutant has an increased susceptibility to reactive oxygen species. Moreover, activity of the manganese-cofactored superoxide dismutase in the mutant is reduced, probably as a consequence of reduced intracellular availability of manganese. The enzyme functionality was restored by manganese supplementation during growth. The mutant was also attenuated in virulence, as shown in animal experiments. These results emphasize the role of MtsABC and trace metals, especially manganese, for
S. pyogenes
growth, susceptibility to oxidative stress, and virulence.
Amastigote Load and Cell Surface Phenotype of Infected Cells from Lesions and Lymph Nodes of Susceptible and Resistant Mice Infected withLeishmania major
Authors: Muraille Eric , De Trez Carl , Pajak Bernard , Torrentera Fabiola Aguilar , De Baetselier Patrick , Leo Oberdan , Carlier Yves
Published: April 2003

Cells of the dendritic cell (DC) lineage, by their unique ability to stimulate naive T cells, may be of crucial importance in the development of protective immune responses toLeishmaniaparasites. The aim of this study was to compare the impact ofL. majorinfection on DCs in BALB/c (susceptible, developing Th2 responses), C57BL/6 (resistant, developing Th1 responses), and tumor necrosis factor (TNF)−/−C57BL/6 mice (susceptible, developing delayed and reduced Th1 responses). We analyzed by immunohistochemistry the phenotype of infected cells in vivo. Granulocytes (GR1+) and macrophages (CD11b+) appear as the mainly infected cells in primary lesions. In contrast, cells expressing CD11c, a DC specific marker, are the most frequently infected cells in draining lymph nodes of all mice tested. These infected CD11c+cells harbored a particular morphology and cell surface phenotype in infected C57BL/6 and BALB/c mice. CD11c+infected cells from C57BL/6 and TNF−/−C57BL/6 mice displayed a weak parasitic load and a dendritic morphology and frequently expressed CD11b or F4/80 myeloid differentiation markers. In contrast, some CD11c+infected cells from BALB/c mice were multinucleated giant cells. Giant cells presented a dramatic accumulation of parasites and differentiation markers were not detectable at their surface. In all mice, lymph node CD11c+infected cells expressed a low major histocompatibility complex II level and no detectable CD86 expression. Our results suggest that infected CD11c+DC-like cells might constitute a reservoir of parasites in lymph nodes.
Strain-Specific Association of Cytotoxic Activity and Virulence of ClinicalStaphylococcus aureusIsolates
Authors: Krut Oleg , Utermöhlen Olaf , Schlossherr Xenia , Krönke Martin
Published: April 2003

Staphylococcus aureushas been shown to invade and induce the death of various cell types. Here we investigate whether the cytotoxicity of intracellularS. aureusis a general feature or rather characteristic of individualS. aureusstrains. The majority of 23 randomly collected clinicalS. aureusisolates were killed inside keratinocytes and fibroblasts, indicating that the uptake ofS. aureusrepresents an important mechanism of cell-autonomous host defense. However, seven independentS. aureusisolates survived intracellularly and induced significant cytotoxicity for their host cells. Subcloning analysis revealed that the ability or inability to kill host cells is a stable, apparently genetically determined trait of a givenS. aureusisolate. We show that noncytotoxic strains but not cytotoxic strains colocalize with the lysosomal marker LAMP-1, suggesting that only cytotoxic strains escape degradation by the endolysosomal pathway. In a mouse septicemic model, cytotoxicS. aureusisolates produce significantly greater lethality (96%) compared to noncytotoxic strains (41%), which corresponds to 23-, 63-, and 30,000-fold increases of bacterial loads in the liver, spleen, and kidney, respectively. Finally, cytotoxicS. aureusstrains produce clinically apparent arthritis in mice at a greater frequency than compared to noncytotoxicS. aureusstrains. The results of our study unravel a previously unrecognized dichotomy of cytotoxic and noncytotoxicS. aureusisolates, which may play an important role in the dissemination of, and mortality induced by,S. aureusinfection.
Immunization with cDNA Expressed by Amastigotes ofTrypanosoma cruziElicits Protective Immune Response against Experimental Infection
Authors: Boscardin Silvia B. , Kinoshita Sheila S. , Fujimura Adriana E. , Rodrigues Mauricio M.
Published: April 2003

Immunization of mice with plasmids containingTrypanosoma cruzigenes induced specific antibodies, CD4+Th1 and CD8+Tc1 cells, and protective immunity against infection. In most cases, plasmids used for DNA vaccination contained genes encoding antigens expressed by trypomastigotes, the nonreplicative forms of the parasite. In this study, we explored the possibility of using genes expressed by amastigotes, the form of the parasite which replicates inside host cells, for experimental DNA vaccination. For that purpose, we selected a gene related to the amastigote surface protein 2 (ASP-2), an antigen recognized by antibodies and T cells from infected mice and humans, for our study. Using primers specific for theasp-2gene, four distinct groups of genes were amplified from cDNA from amastigotes of the Y strain ofT. cruzi. At the nucleotide level, they shared 82.3 to 89.9% identity with the previously describedasp-2gene. A gene namedclone 9presented the highest degree of identity with theasp-2gene and was selected for immunological studies. Polyclonal antisera raised against the C terminus of the recombinant protein expressed by theclone 9gene reacted with an antigen of approximately 83 kDa expressed in amastigotes ofT. cruzi. Immunization of BALB/c mice with eukaryotic expression plasmids containing theclone 9gene elicited specific antibodies and CD4+T-cell-dependent gamma interferon secretion. Upon challenge with trypomastigotes, mice immunized with plasmids harboring theclone 9gene displayed reduced parasitemia and survived lethal infection. We concluded that amastigote cDNA is an interesting source of antigens that can be used for immunological studies, as well as for vaccine development.
Inhibition of Gamma Interferon Decreases Bacterial Load in Peritonitis by Accelerating Peritoneal Fibrin Deposition and Tissue Repair
Authors: Qiu Gang , Gribbin Elizabeth , Harrison Kathryn , Sinha Neil , Yin Kingsley
Published: April 2003

Bowel perforation can lead to significant bacterial spillage, which may then cause septic peritonitis, characterized by a systemic inflammatory response and organ dysfunction. There are several reports that have shown that the development of peritoneal adhesions is dependent on inflammatory cytokine levels and that these adhesions can reduce bacterial spread, possibly by sealing off the cecum in the cecal ligation and puncture (CLP) model of septic peritonitis. There have not, however, been any studies that have utilized a strategy to accelerate tissue repair in order to seal off the injured cecum and reduce bacterial spread as well as ameliorate systemic inflammation. In the present study, we demonstrate that the administration of anti-gamma interferon (IFN-γ) antibody (1.2 mg/kg of body weight, intravenously) accelerated tissue repair via increased fibrin deposition 12 and 24 h after CLP in rats. This increase in fibrin deposition was associated with peritoneal adhesion 24 h after CLP and a reduction in bacterial load compared to the bacterial load of rats given irrelevant antibody. Plasma fibrin levels, however, were not altered after IFN-γ antibody administration, suggesting that the inhibition of IFN-γ activity specifically increased fibrin deposition to the site of injury. Furthermore, plasma interleukin-6, used as a marker of systemic inflammatory response, was reduced in CLP rats given IFN-γ antibody compared to that found in those given irrelevant antibody. These results suggest that the early inhibition of IFN-γ activity in the CLP model is beneficial by accelerating fibrin deposition in cecal tissue to prevent bacterial spread and reduce the systemic inflammatory response. Importantly, increased fibrin deposition in the ceca was not associated with increased plasma fibrin whereas the latter may have detrimental effects associated with coagulation disorders.
Complete Genome Sequence and Comparative Genomics ofShigella flexneriSerotype 2a Strain 2457T
Authors: Wei J. , Goldberg M. B. , Burland V. , Venkatesan M. M. , Deng W. , Fournier G. , Mayhew G. F. , Plunkett G. , Rose D. J. , Darling A. , Mau B. , Perna N. T. , Payne S. M. , Runyen-Janecky L. J. , Zhou S. , Schwartz D. C. , Blattner F. R.
Published: April 2003

We determined the complete genome sequence ofShigella flexneriserotype 2a strain 2457T (4,599,354 bp).Shigellaspecies cause >1 million deaths per year from dysentery and diarrhea and have a lifestyle that is markedly different from those of closely related bacteria, includingEscherichia coli. The genome exhibits the backbone and island mosaic structure ofE. colipathogens, albeit with much less horizontally transferred DNA and lacking 357 genes present inE. coli. The strain is distinctive in its large complement of insertion sequences, with several genomic rearrangements mediated by insertion sequences, 12 cryptic prophages, 372 pseudogenes, and 195S. flexneri-specific genes. The 2457T genome was also compared with that of a recently sequencedS. flexneri2a strain, 301. Our data are consistent withShigellabeing phylogenetically indistinguishable fromE. coli. TheS. flexneri-specific regions contain many genes that could encode proteins with roles in virulence. Analysis of these will reveal the genetic basis for aspects of this pathogenic organism's distinctive lifestyle that have yet to be explained.
Role of Surface-Exposed Loops ofHaemophilus influenzaeProtein P2 in the Mitogen-Activated Protein Kinase Cascade
Authors: Galdiero Stefania , Capasso Domenica , Vitiello Mariateresa , D'Isanto Marina , Pedone Carlo , Galdiero Massimiliano
Published: April 2003

The outer membrane of gram-negative bacteria contains several proteins, and some of these proteins, the porins, have numerous biological functions in the interaction with the host; porins are involved in the activation of signal transduction pathways and, in particular, in the activation of the Raf/MEK1-MEK2/mitogen-activated protein kinase (MAPK) cascade. The P2 porin is the most abundant outer membrane protein ofHaemophilus influenzaetype b. A three-dimensional structural model for P2 was constructed based on the crystal structures ofKlebsiella pneumoniaeOmpK36 andEscherichia coliPhoE and OmpF. The protein was readily assembled into the β-barrel fold characteristic of porins, despite the low sequence identity with the template proteins. The model provides information on the structural features of P2 and insights relevant for prediction of domains corresponding to surface-exposed loops, which could be involved in the activation of signal transduction pathways. To identify the role of surface-exposed loops, a set of synthetic peptides were synthesized according to the proposed model and were assayed for MEK1-MEK2/MAPK pathway activation. Our results show that synthetic peptides corresponding to surface loops of protein P2 are able to activate the MEK1-MEK2/MAPK pathways like the entire protein, while peptides modeled on internal β strands are unable to induce significant phosphorylation of the MEK1-MEK2/MAPK pathways. In particular, the peptides corresponding to loops L5 (Lys206 to Gly219), L6B (Ser239 to Lys253), and L7 (Thr280 to Lys287) activate, as the whole protein, essentially JNK and p38.
Genome Diversification in
Staphylococcus aureus
: Molecular Evolution of a Highly Variable Chromosomal Region Encoding the Staphylococcal Exotoxin-Like Family of Proteins
Authors: Fitzgerald J. Ross , Reid Sean D. , Ruotsalainen Eeva , Tripp Timothy J. , Liu MengYao , Cole Robert , Kuusela Pentti , Schlievert Patrick M. , Järvinen Asko , Musser James M.
Published: April 2003

Recent genomic studies have revealed extensive variation in natural populations of many pathogenic bacteria. However, the evolutionary processes which contribute to much of this variation remain unclear. A previous whole-genome DNA microarray study identified variation at a large chromosomal region (RD13) of
Staphylococcus aureus
which encodes a family of proteins with homology to staphylococcal and streptococcal superantigens, designated staphylococcal exotoxin-like (SET) proteins. In the present study, RD13 was found in all 63
S. aureus
isolates of divergent clonal, geographic, and disease origins but contained a high level of variation in gene content in different strains. A central variable region which contained from 6 to 10 different
set
genes, depending on the strain, was identified, and DNA sequence analysis suggests that horizontal gene transfer and recombination have contributed to the diversification of RD13. Phylogenetic analysis based on the RD13 DNA sequence of 18 strains suggested that loss of various
set
genes has occurred independently several times, in separate lineages of pathogenic
S. aureus
, providing a model to explain the molecular variation of RD13 in extant strains. In spite of multiple episodes of
set
deletion, analysis of the ratio of silent substitutions in
set
genes to amino acid replacements in their products suggests that purifying selection (selective constraint) is acting to maintain SET function. Further, concurrent transcription in vitro of six of the seven
set
genes in strain COL was detected, indicating that the expression of
set
genes has been maintained in contemporary strains, and Western immunoblot analysis indicated that multiple SET proteins are expressed during the course of human infections. Overall, we have shown that the chromosomal region RD13 has diversified extensively through episodes of gene deletion and recombination. The coexpression of many
set
genes and the production of multiple SET proteins during human infection suggests an important role in host-pathogen interactions.
Coordinate Regulation ofSalmonella entericaSerovar Typhimurium Invasion of Epithelial Cells by the Arp2/3 Complex and Rho GTPases
Authors: Criss Alison K. , Casanova James E.
Published: April 2003

Salmonella entericaserovar Typhimurium can infect epithelial cells via the basolateral surface after breaching the intestinal epithelium, yet little is known about this process. Here, we show that actin polymerization driven by the Arp2/3 complex is critical to both basolateral and apical bacterial invasion of polarized MDCK cells. While there is also a dependence upon toxin B-sensitive Rho GTPases, none of the four GTPases known to be activated byS. entericaserovar Typhimurium SopE are individually required for basolateral internalization. These results underscore that the specific factors required forSalmonellainvasion differ between membrane domains of polarized epithelia.
Expression of a
luxS
Gene Is Not Required for
Borrelia burgdorferi
Infection of Mice via Needle Inoculation
Authors: Hübner Anette , Revel Andrew T. , Nolen Dena M. , Hagman Kayla E. , Norgard Michael V.
Published: April 2003

The
luxS
gene product is an integral component of LuxS/autoinducer-2 (AI-2) quorum-sensing systems in bacteria. A putative
luxS
gene was expressed at comparable levels by
Borrelia burgdorferi
strain 297 cultivated either in vitro or in dialysis membrane chambers implanted in rat peritoneal cavities. Although the borrelial
luxS
gene functionally complemented a LuxS deficiency in
Escherichia coli
DH5α, AI-2-like activity could not be detected within
B. burgdorferi
culture supernatants or concentrated cell lysates. Finally, a
luxS
-deficient mutant of
B. burgdorferi
was infectious at wild-type levels when it was intradermally needle inoculated into mice, indicating that expression of
luxS
probably is not required for infectivity but, at the very least, is not essential for mammalian host adaptation. Our findings also challenge the notion that a LuxS/AI-2 quorum-sensing system is operative in
B. burgdorferi
.
Molecular Patchwork: Chromosomal Recombination between Two
Helicobacter pylori
Strains during Natural Colonization
Authors: Smeets Leonard C. , Arents Nicolaas L. A. , van Zwet Anton A. , Vandenbroucke-Grauls Christina M. J. E. , Verboom Theo , Bitter Wilbert , Kusters Johannes G.
Published: April 2003

Genetic analysis of two
Helicobacter pylori
strains isolated from a single gastric biopsy showed evidence of extensive horizontal gene transfer. Several large recombinations were identified in the
rdxA
gene, which is involved in metronidazole resistance.
fhuAofActinobacillus pleuropneumoniaeEncodes a Ferrichrome Receptor but Is Not Regulated by Iron
Authors: Mikael Leonie G. , Srikumar Ramakrishnan , Coulton James W. , Jacques Mario
Published: April 2003

The swine pathogenActinobacillus pleuropneumoniaepossesses a 75-kDa outer membrane protein (OMP), FhuA, the receptor for ferrichrome, a hydroxamate-type siderophore. Polyclonal serum to FhuA reacted with OMP preparations from 12 serotypes ofA. pleuropneumoniaeunder conditions of iron repletion and restriction. Reverse transcription-PCR confirmed thatA. pleuropneumoniae fhuAexpression is not upregulated in response to low iron levels. AnA. pleuropneumoniae fhuAdeletion mutant was generated and showed abolishment of ferrichrome uptake.
Th1 Cell Development Induced by Cysteine Proteinases A and B in Localized Cutaneous Leishmaniasis Due to
Leishmania guyanensis
Authors: Pascalis Hervé , Lavergne Anne , Bourreau Eliane , Prévot-Linguet Ghislaine , Kariminia Amina , Pradinaud Roger , Rafati Sima , Launois Pascal
Published: April 2003

The cysteine proteinases CPA and CPB from
Leishmania major
induced Th1 responses in patients with leishmaniasis due to
Leishmania guyanensis
. Furthermore, cysteine proteinases induced neither interleukin 4 (IL-4) nor IL-13 and low levels of IL-10 in controls and patients. The results suggest that CPs would be quite good candidates for a vaccine against different
Leishmania
species.
Vγ9Vδ2 T-Cell Anergy and Complementarity-Determining Region 3-Specific Depletion during Paroxysm of Nonendemic Malaria Infection
Authors: Martini Federico , Paglia Maria Grazia , Montesano Carla , Enders Patrick J. , Gentile Marco , Pauza C. David , Gioia Cristiana , Colizzi Vittorio , Narciso Pasquale , Pucillo Leopoldo Paolo , Poccia Fabrizio
Published: April 2003

Vγ9Vδ2 T lymphocytes strongly respond to phosphoantigens fromPlasmodiumparasites. Thus, we analyzed the changes in Vγ9Vδ2 T-cell function and repertoire during the paroxysm phase of nonendemic malaria infection. During malaria paroxysm, Vγ9Vδ2 T cells were early activated but rapidly became anergic and finally loose Jγ1.2 Vγ9 complementarity-determining region 3 transcripts.
Binding of Intimin from EnteropathogenicEscherichia colito Lymphocytes and Its Functional Consequences
Authors: Gonçalves Nathalie S. , Hale Christine , Dougan Gordon , Frankel Gad , MacDonald Thomas T.
Published: April 2003

Intimin-conjugated fluorescent beads bind to spleen CD4 T cells and Peyer's patch, mesenteric lymph node, and cecal follicle lymphocytes, with less binding to lamina propria T cells and intraepithelial lymphocytes. Intimin costimulates proliferation of spleen CD4 T cells and cells from organized lymphoid tissues but does not costimulate cells from the lamina propria of normal or inflamed colon.
A STRATEGY OF DESIGNING ROUTING ALGORITHMS BASED ON IDEAL ROUTINGS
Authors: SHINJO K. , SHIMOGAWA S. , YAMADA J. , OIDA K.
Published: April 2003

This paper proposes a strategy of designing routing algorithms for connectionless packet-switched networks. This strategy consists of three design elements as follows: [A] the notion of ideal routings is introduced to provide the upper performance limits attained by improving routing algorithm and it serves as a standard to measure the performance of other algorithms; [B] a method of constructing simple algorithms is presented under implementation conditions from ideal routings; [C] a method is described to enhance the performance limits of [A]. By using these elements, simple algorithms with a maximum degree of performance attainment are realized. By "degree of performance attainment", we mean that we can see how much room is left for the improvement of algorithms. We develop [A] and [B] with the performance measures of throughput and average packet delay and the M/M/1 queuing network. We decide ideal static routings and their performance limits from [A]. We obtain a new simple algorithm from [B] based on the notion of the ideal routings in implementation conditions. The designed algorithm improves the throughput and the average delay, which are comparable to those from ideal static routings. This improvement is contrasted to the adaptive and distributed OSPF (Open Shortest Path First), a standard Internet routing protocol.
GROWTH OF SURFACES GENERATED BY A PROBABILISTIC CELLULAR AUTOMATION
Authors: BHATTACHARYYA PRATIP
Published: April 2003

A one-dimensional cellular automaton with a probabilistic evolution rule can generate stochastic surface growth in (1+1) dimensions. Two such discrete models of surface growth are constructed from a probabilistic cellular automaton which is known to show a transition from an active phase to an absorbing phase at a critical probability associated with two particular components of the evolution rule. In one of these models, called Model A in this paper, the surface growth is defined in terms of the evolving front of the cellular automaton on the space-time plane. In the other model, called Model B, surface growth takes place by a solid-on-solid deposition process controlled by the cellular automaton configurations that appear in successive time-steps. Both the models show a depinning transition at the critical point of the generating cellular automaton. In addition, Model B shows a kinetic roughening transition at this point. The characteristics of the surface width in these models are derived by scaling arguments from the critical properties of the generating cellular automaton and by Monte Carlo simulations.
DIPOLAR GAY–BERNE LIQUID CRYSTALS: A MONTE CARLO STUDY
Authors: HOUSSA MOHAMMED , RULL LUIS F. , McGROTHER SIMON C.
Published: April 2003

The phase diagrams of several dipolar Gay–Berne systems are generated using Monte Carlo simulations. Particular emphasis is placed upon the location, order and nature of the liquid crystalline phases observed at high fluid densities. The accuracy of the reaction field method is re-affirmed.
SIMULATION OF NEMATIC FREE SURFACES
Authors: DE MIGUEL ENRIQUE , MARTÍN DEL RÍO ELVIRA
Published: April 2003

Molecular dynamics and Monte Carlo methods are applied to study the liquid free surfaces in model liquid crystals. The simulation results suggest that the attractive interactions promote parallel alignment of the molecules at the nematic free surface in the Gay–Berne model, in agreement with theoretical predictions. A change in the orientation from planar to homeotropic is observed and explained in terms of a competing effect between attractive and repulsive interactions. Finally, the simulation results give clear evidence that the hard-core repulsions favor homeotropic orientation at the nematic free surface, in agreement with most theories.
A SIMPLE SOLID-ON-SOLID MODEL OF EPITAXIAL FILM GROWTH: SURFACE MORPHOLOGY ANISOTROPY
Authors: MALARZ K. , MAKSYMOWICZ A. Z.
Published: April 2003

In this paper we present a generalization of a simple solid-on-solid epitaxial model of thin film growth, when surface morphology anisotropy is provoked by anisotropy in the model control parameters of binding energy and/or diffusion barrier. The anisotropy is discussed in terms of the height–height correlation function. It was experimentally confirmed that the difference in diffusion barriers yields anisotropy in morphology of the surface. We obtained antisymmetric correlations in the two in-plane directions for antisymmetric binding.
SIMULATION AND MODELING OF EVOKED RESPONSE ELECTROENCEPHALOGRAPH SIGNAL
Authors: KULKARNI D. R. , PARIKH J. C. , PRATAP R.
Published: April 2003

Electroencephalograph (EEG) data for normal individuals with eyes-closed and under stimuli is analyzed. The stimuli consisted of photo, audio, motor and mental activity. We use several measures from nonlinear dynamics to analyze and characterize the data. We find that the dynamics of the EEG signal is deterministic and chaotic but it is not a low dimensional chaotic system. The evoked responses lead to a redistribution of strengths relative to eyes-closed data. Basically, strength in α waves decreases whereas that in β wave increases. We also carried out simulations separately and in combination for δ, θ, α and β waves to understand the data. From the simulation results, it appears that the characteristics of EEG data are consequences of filtering the data with a relatively small range of frequency (0.5–32 Hz). In view of this, we believe that calculation of known nonlinear measures is not likely to be very useful for studying the dynamics of EEG data. We have also successfully modeled the EEG time series using the concept of state space reconstruction in the framework of artificial neural network. It gives us confidence that one would be able to understand, in a more basic way, how collectivity in EEG signal arises.
TOTALISTIC TWO-DIMENSIONAL CELLULAR AUTOMATA EXHIBITING GLOBAL PERIODIC BEHAVIOR
Authors: BOCCARA N. , ROGER M.
Published: April 2003

We have determined families of two-dimensional deterministic totalistic cellular automaton rules whose stationary density of active sites exhibits a period two in time. Each family of deterministic rules is characterized by an "average probabilistic totalistic rule" exhibiting the same periodic behavior.
INTEGRABILITY, ENTROPY AND QUANTUM COMPUTATION
Authors: KRISHNAMURTHY E. V.
Published: April 2003

The important requirements are stated for the success of quantum computation. These requirements involve coherent preserving Hamiltonians as well as exact integrability of the corresponding Feynman path integrals. Also we explain the role of metric entropy in dynamical evolutionary system and outline some of the open problems in the design of quantum computational systems. Finally, we observe that unless we understand quantum nondemolition measurements, quantum integrability, quantum chaos and the direction of time arrow, the quantum control and computational paradigms will remain elusive and the design of systems based on quantum dynamical evolution may not be feasible.
VESH: A VERTICAL ENERGY SURFACE HOPPING PROCEDURE FOR DETERMINING STABLE ISOMERS OF POLYATOMIC MOLECULAR SYSTEMS
Authors: SÜLZLE D. , CHANG C.
Published: April 2003

We describe a heuristic algorithmic procedure by which a large number of points of minimal energy in configuration space of a polyatomic molecular system (isomers) can be determined. Making use of the intrinsic electronic structure energy scheme of the molecular system, the procedure is initiated from an arbitrary starting configuration and progresses via successive vertical spin, and/or charge state shifts with interposed optimization steps. In this systematic way, a great manifold of stable isomers not only on the ground state potential energy surface but also on excited spin and charge state surfaces can be located. The efficiency and computational practicability of the procedure has been tested on various examples. In these cases, the global minima have been found. Results for singlet and triplet states of the system P 4 are presented in detail.
ADSORPTION OF A SIMPLE FLUID IN A QUENCHED TWO-COMPONENT HARD SPHERE MATRIX REPLICA ORNSTEIN–ZERNIKE EQUATIONS
Authors: MAYORGA MIGUEL , PIZIO OREST , SOKOLOWSKI STEFAN
Published: April 2003

Using the replica Ornstein–Zernike (ROZ) integral equations, we investigate the adsorption of a simple fluid in a hard sphere quenched matrix made of two species. Our main focus is in the dependencies of the density of fluid species on the chemical potential in matrices with different microporosity and for several compositions. The simple fluid is considered by using a hard sphere model. The fluid-matrix interactions are assumed either solely repulsive or attractive of the Yukawa type. The ROZ equations are supplemented by both the Percus–Yevick (PY) and the hypernetted chain (HNC) closures. The PY closure is used to study the model with solely repulsive forces (reference system) and then the contribution of attractive forces into adsorption is included in the mean field approximation. On the other hand, the HNC approximation is used to get insight into the structure of adsorbed fluid and the fluid-matrix correlations in the presence of attractive forces.
"INHERENT STRUCTURES" OF THE ±J ISING SPIN GLASS IN FOUR DIMENSIONS
Authors: CHISHOLM COLIN , LUKEMAN MARK , JAN N. , HUNTER D. L.
Published: April 2003

We measure the "inherent structures" of the ±J Ising spin glass in four dimensions (4D) and find a behavior similar to that seen for the 2D and 3D systems. We are able to determine the transition temperature from the overlap between the quenched states and the equilibrium states. We find that the transition temperature Tsg is 2.07±0.05 which agrees well with the recently reported value of 2.03±0.03 by Maranari and Zuliani. We also find that the ground state energy for the 4D spin glass is near -2.087±0.005, a more precise estimate than the value of -1.83 reported earlier.
NUMERICAL STUDY ON AGING DYNAMICS IN THE 3D ISING SPIN-GLASS MODEL — QUASI-EQUILIBRIUM BEHAVIOR OF SPIN AUTO-CORRELATION FUNCTIONS
Authors: TAKAYAMA H. , YOSHINO H. , KOMORI T.
Published: April 2003

Using Monte Carlo simulations, we have studied aging phenomena in three-dimensional Gaussian Ising spin-glass model focusing on quasi-equilibrium behavior of the spin auto-correlation functions. Weak violation of the time translational invariance in the quasi-equilibrium regime is analyzed in terms of effective stiffness for droplet excitations in the presence of domain walls. The simulation results not only in isothermal aging but also in T-shift aging process. T-shift aging processes exhibit the expected scaling behavior with respect to the characteristic length scales associated with droplet excitations and domain walls in spite of the fact that the growth law for these length scales still shows a pre-asymptotic behavior compared with the asymptotic form proposed by the droplet theory. Implications of our simulational results are also discussed in relation to experimental observations.
NONEQUILIBRIUM RELAXATION METHOD AND ITS APPLICATIONS
Authors: ITO NOBUYASU , OZEKI YUKIYASU
Published: April 2003

Nonequilibrium relaxation (NER) process turns out to be an useful method to study phase transition and critical phenomena. The NER method and its applications are reviewed. Characteristic behavior of the local exponent is analyzed with a simple model.
Topics in the Theory of the Ultracold Dilute Alkali Gases
Authors: Leggett A. J.
Published: April 2003

These lectures address Bose and Fermi ultracold dilute alkali gases. For Bose gases I discuss general BEC concepts, superfluidity, the Josephson effect, and issues related to the establishment of a "phase standard". For Fermi gases I discuss prospects for Cooper pairing and its detection. The four lectures on alkali Bose gases which I actually gave at the School were based on a review paper in preparation for Reviews of Modern Physics. In order to avoid extensive duplication of the contents of that review, what I present here, condensed into three lectures, is a melange of informal commentary on the results presented there and some material which for space and other reasons had to be omitted. This material is ideally read in conjunction with the review. The fourth lecture, on the Fermi alkali gases, is presented here in (nearly) the form in which it was actually given.