bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gene Expression Profiling in AGS Cells Stimulated withHelicobacter pyloriIsogenic Strains (cagAPositive orcagANegative)
Authors: Bach Susanne , Makristathis Athanasios , Rotter Manfred , Hirschl Alexander M. 
Published: July 2002

ABSTRACTTo study host response to CagA, human gastric cancer cell line AGS was infected with aHelicobacter pyloritype I wild-type or isogeniccagA-negative mutant. Differentially expressed genes were identified using cDNA array technology. By Northern blotting, downregulation of focal adhesion kinase and upregulation of LIM kinase mRNA in the presence of CagA were clearly verified. Furthermore, upregulation of LIM kinase, macrophage inflammatory protein-2, c-myc, and bone morphogenetic protein-1 and downregulation of transcription factor Y-box binding protein-1 and focal adhesion kinase mRNA in response toH. pyloritype I infection compared to the uninfected control could be shown by Northern blotting. Hence, these findings identified new targets for further functional studies onH. pylori-associated pathogenesis.
Immune Responses to Recombinant Pneumococcal PspA Antigen Delivered by Live Attenuated
Salmonella enterica
Serovar Typhimurium Vaccine
Authors: Kang Ho Young , Srinivasan Jay , Curtiss Roy 
Published: July 2002

ABSTRACT

Attenuated
Salmonella enterica
serovar Typhimurium expressing recombinant antigens from other pathogens elicits primarily a Th1-type dominant immune response to both recombinant and
Salmonella
antigens. The immunogenicity and appropriate subcellular location of the recombinant antigen in the
Salmonella
vaccine strain may contribute to augmenting immune responses by facilitating adequate exposure of recombinant antigen to antigen-presenting cells for processing. To allow for secretion from gram-negative bacteria and overexpression of antigen, a DNA fragment encoding a highly antigenic α-helical region of PspA (pneumococcal surface protein A) was subcloned downstream from the β-lactamase signal sequence in the multicopy Asd
+
pYA3493 vector to create pYA3494. pYA3493 was derived from a class of Asd
+
vectors with reduced expression of Asd to minimize selective disadvantage and enhance immunization of expressed recombinant antigens. The
S. enterica
serovar Typhimurium vaccine strain was constructed by the introduction of deletion mutations Δ
crp-28
and Δ
asdA16
. Approximately 50% of the recombinant PspA (rPspA) expressed in a
Salmonella
strain harboring pYA3494 was detected in the combined supernatant and periplasmic fractions of broth-grown recombinant
Salmonella
. After a single oral immunization in BALB/c mice with 10
9
CFU of the recombinant
Salmonella
vaccine strain carrying pYA3494, immunoglobulin G (IgG) antibody responses were stimulated to both the heterologous antigen rPspA and
Salmonella
lipopolysaccharide (LPS) and outer membrane proteins (OMPs). About half, and even more at later times after immunization, of the antibodies induced to rPspA were IgG1 (indicating a Th2-type response), whereas 60 to 70% of the antibodies to LPS and 80 to 90% of those to OMPs were IgG2a (indicating a Th1-type response). A sublethal infection with
Streptococcus pneumoniae
WU2 boosted PspA antibody levels and maintained IgG2a/IgG1 ratios similar to those seen before the challenge. Oral immunization with
Salmonella-
PspA vaccine protected 60% of immunized mice from death after intraperitoneal challenge with 50 times the 50% lethal dose of virulent
S. pneumoniae
WU2.
Susceptibility to Experimental Cerebral Malaria Induced byPlasmodium bergheiANKA in Inbred Mouse Strains Recently Derived from Wild Stock
Authors: Bagot S. , Idrissa Boubou M. , Campino S. , Behrschmidt C. , Gorgette O. , Guénet J.-L. , Penha-Gonçalves C. , Mazier D. , Pied S. , Cazenave P.-A. 
Published: July 2002

ABSTRACTThe neurological syndrome caused byPlasmodium bergheiANKA in rodents partially mimics the human disease. Several rodent models of cerebral malaria (CM) exist for the study of the mechanisms that cause the disease. However, since common laboratory mouse strains have limited gene pools, the role of their phenotypic variations causing CM is restricted. This constitutes an obstacle for efficient genetic analysis relating to the pathogenesis of malaria. Most common laboratory mouse strains are susceptible to CM, and the same major histocompatibility complex (MHC) haplotype may exhibit different levels of susceptibility. We analyzed the influence of the MHC haplotype on overcoming CM by using MHC congenic mice with C57BL/10 and C3H backgrounds. No correlation was found between MHC molecules and the development of CM. New wild-derived mouse strains with wide genetic polymorphisms were then used to find new models of resistance to CM. Six of the twelve strains tested were resistant to CM. For two of them, F1progeny and backcrosses performed with the reference strain C57BL/6 showed a high level of heterogeneity in the number and characteristics of the genetic factors associated with resistance to CM.
Lipopolysaccharide-Induced Granule Mobilization and Priming of the Neutrophil Response toHelicobacter pyloriPeptide Hp(2-20), Which Activates Formyl Peptide Receptor-Like 1
Authors: Bylund Johan , Karlsson Anna , Boulay Francois , Dahlgren Claes 
Published: July 2002

ABSTRACTThe cecropin-like bactericidal peptide Hp(2-20) fromHelicobacter pyloriinduces activation of the NADPH oxidase in human neutrophils via formyl peptide receptor-like 1 (FPRL1) (J. Bylund, T. Christophe, F. Boulay, T. Nyström, A. Karlsson, and C. Dahlgren, Antimicrob. Agents Chemother. 45:1700-1704, 2001). Here we investigated the ability of bacterial lipopolysaccharide (LPS) to prime this response. Neutrophils treated with LPS for 30 min at 37°C produced substantially more superoxide anion than control cells upon stimulation with Hp(2-20). Hence, LPS primed the cells for subsequent stimulation through FPRL1. To study the molecular background of this priming phenomenon, we measured the degrees of granule mobilization and concomitant receptor upregulation to the cell surface in LPS-treated cells. Exposure of complement receptors 1 and 3 as well as the formyl peptide receptor (FPR) was markedly increased after LPS treatment. Since approximately 60% of the gelatinase granules were mobilized while the specific granules were retained, we hypothesized that the gelatinase granules were potential stores of FPRL1. The presence of FPRL1 mainly in the gelatinase granules was confirmed by Western blotting of subcellular fractions of resting neutrophils. These results suggest that the mechanism behind the LPS-induced priming of FPRL1-mediated responses lies at the level of granule (receptor) mobilization.
Role of Interleukin-18 in Host Defense against DisseminatedCandida albicansInfection
Authors: Stuyt Rogier J. L. , Netea Mihai G. , Verschueren Ineke , Fantuzzi Giamila , Dinarello Charles A. , Van der Meer Jos W. M. , Kullberg Bart Jan 
Published: July 2002

ABSTRACTIn mice injected intravenously withCandida albicans, administration of anti-interleukin-18 (IL-18) antibodies increased the yeast load in the kidneys. There was no effect on the organ load withCandidawhen gamma interferon (IFN-γ)-deficient mice were treated with anti-IL-18 antibodies, suggesting that the protective effect of IL-18 is mediated through endogenous IFN-γ.
The
Bacillus subtilis
GTP Binding Protein Obg and Regulators of the ς
B
Stress Response Transcription Factor Cofractionate with Ribosomes
Authors: Scott Janelle M. , Ju Jingliang , Mitchell Theresa , Haldenwang W. G. 
Published: July 2002

ABSTRACT

Obg, an essential GTP binding protein of
Bacillus subtilis
, is necessary for stress activation of the ς
B
transcription factor. We investigated Obg's cellular associations by differential centrifugation of crude
B. subtilis
extracts, using an anti-Obg antibody as a probe to monitor Obg during the fractionation, and by fluorescent microscopy of a
B. subtilis
strain in which Obg was fused to green fluorescent protein. The results indicated that Obg is part of a large cytoplasmic complex. In subsequent analyses, Obg coeluted with ribosomal subunits during gel filtration of
B. subtilis
lysates on Sephacryl S-400 and specifically bound to ribosomal protein L13 in an affinity blot assay. Probing the gel filtration fractions with antibodies specific for ς
B
and its coexpressed regulators (Rsb proteins) revealed coincident elution of the upstream components of the ς
B
stress activation pathway (RsbR, -S, and -T) with Obg and the ribosomal subunits. The data implicate ribosome function as a possible mediator of the activity of Obg and the stress induction of ς
B
.
Secretion of Nucleoside Diphosphate Kinase by Mucoid
Pseudomonas aeruginosa
8821: Involvement of a Carboxy-Terminal Motif in Secretion
Authors: Kamath Shilpa , Chen M. L. , Chakrabarty A. M. 
Published: July 2002

ABSTRACT

Nucleoside diphosphate kinase (Ndk) is a ubiquitous enzyme which functions in balancing the nucleotide pool of the cell. We have recently reported that in addition to being intracellular in both mucoid and nonmucoid
Pseudomonas aeruginosa
, Ndk is also secreted into the extracellular environment by mucoid
P. aeruginosa
cells. This secreted Ndk has biochemical activity similar to the intracellular Ndk and is 16 kDa in size. To demonstrate that Ndk is indeed secreted and to localize the secretion motif, we constructed an
ndk
knockout mutant, which lacks both intracellular and extracellular forms of Ndk. In this study, we report the construction of deletion derivatives made from the carboxy-terminal region of Ndk. These deletion derivatives were introduced into the
ndk
::Cm knockout mutant and were examined for the intracellular and extracellular presence of Ndk. It was observed that the carboxy-terminal 8-amino-acid region is required for the secretion of Ndk into the extracellular region. This region has the sequence DXXX, where X is a predominantly hydrophobic residue. Such sequences represent a conserved motif in proteins secreted by the type I secretory pathway in gram-negative microorganisms. To investigate the significance of this motif in the secretion of Ndk, we constructed a fusion protein of Ndk and the blue fluorescent protein (BFP) as well as a fusion protein of mutated Ndk (whose DTEV motif has been changed to AAAA) and the BFP. The presence of extracellular Ndk was detected only in the
ndk
::Cm knockout mutant harboring the wild-type BFP-Ndk protein fusion. We could not detect the presence of extracellular Ndk in the
ndk
::Cm knockout mutant containing the mutated BFP-Ndk protein fusion. In addition, we have also used immunofluorescence microscopy to localize the wild-type and mutated BFP-Ndk proteins in the cell. The significance of these observations is discussed.
Motility and Chemotaxis of Filamentous Cells of
Escherichia coli
Authors: Maki Nazli , Gestwicki Jason E. , Lake Ellen M. , Kiessling Laura L. , Adler Julius 
Published: July 2002

ABSTRACT

Filamentous cells of
Escherichia coli
can be produced by treatment with the antibiotic cephalexin, which blocks cell division but allows cell growth. To explore the effect of cell size on chemotactic activity, we studied the motility and chemotaxis of filamentous cells. The filaments, up to 50 times the length of normal
E. coli
organisms, were motile and had flagella along their entire lengths. Despite their increased size, the motility and chemotaxis of filaments were very similar to those properties of normal-sized cells. Unstimulated filaments of chemotactically normal bacteria ran and stopped repeatedly (while normal-sized bacteria run and tumble repeatedly). Filaments responded to attractants by prolonged running (like normal-sized bacteria) and to repellents by prolonged stopping (unlike normal-sized bacteria, which tumble), until adaptation restored unstimulated behavior (as occurs with normal-sized cells). Chemotaxis mutants that always ran when they were normal sized always ran when they were filament sized, and those mutants that always tumbled when they were normal sized always stopped when they were filament sized. Chemoreceptors in filaments were localized to regions both at the poles and at intervals along the filament. We suggest that the location of the chemoreceptors enables the chemotactic responses observed in filaments. The implications of this work with regard to the cytoplasmic diffusion of chemotaxis components in normal-sized and filamentous
E. coli
are discussed.
Evidence for Multimerization of Neu Proteins Involved in Polysialic Acid Synthesis in
Escherichia coli
K1 Using Improved LexA-Based Vectors
Authors: Daines Dayle A. , Silver Richard P. 
Published: July 2002

ABSTRACT

Recently, M. Dmitrova et al. (Mol. Gen. Genet. 257:205–212, 1998) described a LexA-based genetic system to monitor protein-protein interactions in an
Escherichia coli
background. However, the plasmids used in this system, pMS604 and pDP804, were not readily amenable for general use. In this report, we describe modifications of both plasmids that allow fragments of DNA to be fused to either vector in any reading frame. Homodimerization and heterodimerization of full-length proteins involved in polysialic acid synthesis in
E. coli
K1, as well as heterodimerization between a full-length protein and a protein fragment, demonstrate the usefulness of the modified plasmids for investigating bacterial protein-protein interactions in vivo.
Visualization of Repair of Double-Strand Breaks in the Bacteriophage T7 Genome without Normal DNA Replication
Authors: Lai Ying-Ta , Masker Warren 
Published: July 2002

ABSTRACT

An in vitro system based on extracts of
Escherichia coli
infected with bacteriophage T7 is able to repair double-strand breaks in a T7 genome with efficiencies of 20% or more. To achieve this high repair efficiency it is necessary that the reaction mixtures contain molecules of donor DNA that bracket the double-strand break. Gaps as long as 1,600 nucleotides are repaired almost as efficiently as simple double-strand breaks. DNA synthesis was measured while repair was taking place. It was found that the amount of DNA synthesis associated with repair of a double-strand break was below the level of detection possible with this system. Furthermore, repair efficiencies were the same with or without normal levels of T7 DNA polymerase. However, the repair required the 5′→3′ exonuclease encoded by T7 gene 6. The high efficiency of DNA repair allowed visualization of the repaired product after in vitro repair, thereby assuring that the repair took place in vitro rather than during an in vivo growth step after packaging.
β-Ketoacyl-Acyl Carrier Protein Synthase III (FabH) Is a Determining Factor in Branched-Chain Fatty Acid Biosynthesis
Authors: Choi Keum-Hwa , Heath Richard J. , Rock Charles O. 
Published: July 2002

ABSTRACT

A universal set of genes encodes the components of the dissociated, type II, fatty acid synthase system that is responsible for producing the multitude of fatty acid structures found in bacterial membranes. We examined the biochemical basis for the production of branched-chain fatty acids by gram-positive bacteria. Two genes that were predicted to encode homologs of the β-ketoacyl-acyl carrier protein synthase III of
Escherichia coli
(eFabH) were identified in the
Bacillus subtilis
genome. Their protein products were expressed, purified, and biochemically characterized. Both
B. subtilis
FabH homologs, bFabH1 and bFabH2, carried out the initial condensation reaction of fatty acid biosynthesis with acetyl-coenzyme A (acetyl-CoA) as a primer, although they possessed lower specific activities than eFabH. bFabH1 and bFabH2 also utilized iso- and anteiso-branched-chain acyl-CoA primers as substrates. eFabH was not able to accept these CoA thioesters. Reconstitution of a complete round of fatty acid synthesis in vitro with purified
E. coli
proteins showed that eFabH was the only
E. coli
enzyme incapable of using branched-chain substrates. Expression of either bFabH1 or bFabH2 in
E. coli
resulted in the appearance of a branched-chain 17-carbon fatty acid. Thus, the substrate specificity of FabH is an important determinant of branched-chain fatty acid production.
Dynamic Aspects of the Structured Cell Population in a Swarming Colony of
Proteus mirabilis
Authors: Matsuyama Tohey , Takagi Yuko , Nakagawa Yoji , Itoh Hiroto , Wakita Junichi , Matsushita Mitsugu 
Published: July 2002

ABSTRACT

Proteus mirabilis
forms a concentric-ring colony by undergoing periodic swarming. A colony in the process of such synchronized expansion was examined for its internal population structure. In alternating phases, i.e., swarming (active migration) and consolidation (growth without colony perimeter expansion), phase-specific distribution of cells differing in length, in situ mobility, and migration ability on an agar medium were recognized. In the consolidation phase, the distribution of mobile cells was restricted to the inner part of a new ring and a previous terrace. Cells composing the outer part of the ring were immobile in spite of their ordinary swimming ability in a viscous solution. A sectorial cell population having such an internal structure was replica printed on fresh agar medium. After printing, a transplant which was in the swarming phase continued its ongoing swarming while a transplanted consolidation front continued its scheduled consolidation. This shows that cessation of migration during the consolidation phase was not due to substances present in the underlying agar medium. The ongoing swarming schedule was modifiable by separative cutting of the swarming front or disruption of the ring pattern by random mixing of the pattern-forming cell population. The structured cell population seemed to play a role in characteristic colony growth. However, separation of a narrow consolidation front from a backward area did not induce disturbance in the ongoing swarming schedule. Thus, cells at the frontal part of consolidation area were independent of the internal cell population and destined to exert consolidation and swarming with the ongoing ordinary schedule.
Escherichia coli
DNA Polymerase III τ- and γ-Subunit Conserved Residues Required for Activity In Vivo and In Vitro
Authors: Walker James R. , Hervas Christine , Ross Julie D. , Blinkova Alexandra , Walbridge Michael J. , Pumarega Emilynn J. , Park Mi-Oak , Neely Harold R. 
Published: July 2002

ABSTRACT

The
Escherichia coli
DNA polymerase III τ and γ subunits are single-strand DNA-dependent ATPases (the latter requires the δ and δ′ subunits for significant ATPase activity) involved in loading processivity clamp β. They are homologous to clamp-loading proteins of many organisms from phages to humans. Alignment of 27 prokaryotic τ/γ homologs and 1 eukaryotic τ/γ homolog has refined the sequences of nine previously defined identity and functional motifs. Mutational analysis has defined highly conserved residues required for activity in vivo and in vitro. Specifically, mutations introduced into highly conserved residues within three of those motifs, the P loop, the DExx region, and the SRC region, inactivated complementing activity in vivo and clamp loading in vitro and reduced ATPase catalytic efficiency in vitro. Mutation of a highly conserved residue within a fourth motif, VIc, inactivated clamp-loading activity and reduced ATPase activity in vitro, but the mutant gene, on a multicopy plasmid, retained complementing activity in vivo and the mutant gene also supported apparently normal replication and growth as a haploid, chromosomal allele.
Different Processing of an mRNA Species in
Bacillus subtilis
and
Escherichia coli
Authors: Persson Martin , Glatz Elisabeth , Rutberg Blanka 
Published: July 2002

ABSTRACT

Expression of the
Bacillus subtilis glpD
gene, which encodes glycerol-3-phosphate (G3P) dehydrogenase, is controlled by termination or antitermination of transcription. The untranslated leader sequence of
glpD
contains an inverted repeat that gives rise to a transcription terminator. In the presence of G3P, the antiterminator protein GlpP binds to
glpD
leader mRNA and promotes readthrough of the terminator. Certain mutations in the inverted repeat of the
glpD
leader result in GlpP-independent, temperature-sensitive (TS) expression of
glpD
. The TS phenotype is due to temperature-dependent degradation of the
glpD
mRNA. In the presence of GlpP, the
glpD
mRNA is stabilized.
glpD
leader-
lacZ
fusions were integrated into the chromosomes of
B. subtilis
and
Escherichia coli
. Determination of steady-state levels of fusion mRNA in
B. subtilis
showed that the stability of the fusion mRNA is determined by the
glpD
leader part. Comparison of steady-state levels and half-lives of
glpD
leader-
lacZ
fusion mRNA in
B. subtilis
and
E. coli
revealed significant differences. A
glpD
leader-
lacZ
fusion transcript that was unstable in
B. subtilis
was considerably more stable in
E. coli
. GlpP, which stabilizes the transcript in
B. subtilis
, did not affect its stability in
E. coli
. Primer extension analysis showed that the
glpD
leader-
lacZ
fusion transcript is processed differently in
B. subtilis
and in
E. coli
. The dominating cleavage site in
E. coli
was barely detectable in
B. subtilis
. This site was shown to be a target of
E. coli
RNase III.
Regulation of the
cnr
Cobalt and Nickel Resistance Determinant from
Ralstonia
sp. Strain CH34
Authors: Grass Gregor , Große Cornelia , Nies Dietrich H. 
Published: July 2002

ABSTRACT

Ralstonia
sp. strain CH34 is resistant to nickel and cobalt cations. Resistance is mediated by the
cnr
determinant located on plasmid pMOL28. The
cnr
genes are organized in two clusters,
cnrYXH
and
cnrCBA
. As revealed by reverse transcriptase PCR and primer extension, transcription from these operons is initiated from promoters located upstream of the
cnrY
and
cnrC
genes. These two promoters exhibit conserved sequences at the −10 (CCGTATA) and −35 (CRAGGGGRAG) regions. The CnrH gene product, which is required for expression of both operons, is a sigma factor belonging to the sigma L family, whose activity seems to be governed by the membrane-bound CnrY and CnrX gene products in response to Ni
2+
. Half-maximal activation from the
cnrCBA
operon was determined by using appropriate
lacZ
gene fusions and was shown to occur at an Ni
2+
concentration of about 50 μM.
Distribution of Intervening Sequences in the Genes for 23S rRNA and rRNA Fragmentation among Strains of the
Salmonella
Reference Collection B (SARB) and SARC Sets
Authors: Pabbaraju Kanti , Miller Wayne L. , Sanderson Kenneth E. 
Published: July 2002

ABSTRACT

Intervening sequences (IVSs) occur sporadically in several bacterial genera in the genes for 23S rRNA at relatively conserved locations. They are cleaved after transcription and lead to the presence of fragmented rRNA, which is incorporated into the ribosomes without religation but is nevertheless functional. The fragmentation of rRNA and the number of IVSs in all 72 strains of the
Salmonella
Reference Collection B set and 16 strains of the
Salmonella
Reference Collection C set, which have been established on the basis of multilocus enzyme electrophoresis (MLEE), were analyzed in the present study. Fragmentation of 23S rRNA was restricted to conserved cleavage sites located at bp 550 (helix 25) and bp 1170 (helix 45), locations where IVSs have been reported. Random cleavage at sites where IVSs could not be detected was not seen. Uncleaved IVSs were not detected in any case; thus, the IVSs invariably led to rRNA fragmentation, indicating a strong selection for maintenance of RNase III cleavage sites. The distribution of the number of IVSs carried by the different strains in the seven
rrl
genes is diverse, and the pattern of IVS possession could not be related to the MLEE pattern among the various
Salmonella
strains tested; this indicates that the IVSs are frequently exchanged between strains by lateral transfer. All eight subspecies of the genus
Salmonella
, including subspecies V represented by
Salmonella bongori
, have IVSs in both helix 25 and helix 45; this indicates that IVSs entered the genus after its divergence from
Escherichia coli
(more than 100 million years ago) but before separation of the genus
Salmonella
into many forms or that they were in the ancestor but have been lost from
Escherichia
.