bluuebunny/crossref_metadata_2025 huggingface dataset:
Genetic Loci for Coaggregation Receptor Polysaccharide Biosynthesis inStreptococcus gordonii38
Authors: Xu De-Qi , Thompson John , Cisar John O.
Published: August 2003

The cell wall polysaccharide ofStreptococcus gordonii38 functions as a coaggregation receptor for surface adhesins on other members of the oral biofilm community. The structure of this receptor polysaccharide (RPS) is defined by a heptasaccharide repeat that includes a GalNAcβ1→3Gal-containing recognition motif. The same RPS has now been identified fromS. gordoniiAT, a partially sequenced strain. PCR primers designed from sequences in the genomic database of strain AT were used to identify and partially characterize theS. gordonii38 RPS gene cluster. This cluster includes genes for seven putative glycosyltransferases, a polysaccharide polymerase (Wzy), an oligosaccharide repeating unit transporter (Wzx), and a galactofuranose mutase, the enzyme that promotes synthesis of UDP-Galf, one of five predicted RPS precursors. Genes outside this region were identified for the other four nucleotide-linked sugar precursors of RPS biosynthesis, namely, those for formation of UDP-Glc, UDP-Gal, UDP-GalNAc, and dTDP-Rha. Two genes for putative galactose 4-epimerases were identified. The first, designatedgalE1, was identified as a pseudogene in the galactose operon, and the second, designatedgalE2, was transcribed with three of the four genes for dTDP-Rha biosynthesis (i.e.,rmlA,rmlC, andrmlB). Insertional inactivation ofgalE2abolished (i) RPS production, (ii) growth on galactose, and (iii) both UDP-Gal and UDP-GalNAc 4-epimerase activities in cell extracts. Repair of thegalE1pseudogene in thisgalE2mutant restored growth on galactose but not RPS production. Cell extracts containing functional GalE1 but not GalE2 contained UDP-Gal 4-epimerase but not UDP-GalNAc 4-epimerase activity. Thus, provision of both UDP-Gal and UDP-GalNAc for RPS production byS. gordonii38 depends on the dual specificity of the epimerase encoded bygalE2.
Multiple Regulators Control Capsular Polysaccharide Production in
Vibrio parahaemolyticus
Authors: Güvener Zehra Tüzün , McCarter Linda L.
Published: August 2003

Vibrio parahaemolyticus
, a biofouling marine bacterium and human pathogen, undergoes phase variation displaying translucent (TR) and opaque (OP) colony morphologies. Prior studies demonstrated that OP colonies produce more capsular polysaccharide (CPS) than TR colonies and that opacity is controlled by the
Vibrio harveyi
LuxR-type transcriptional activator OpaR. CPS has also been shown to be regulated by the
scrABC
signaling pathway, which involves a GGDEF-EAL motif-containing sensory protein. The present study identifies
cps
genes and examines their regulation. Transposon insertions in the
cps
locus, which contains 11 genes, abolished opacity. Such mutants failed to produce CPS and were defective in pellicle formation in microtiter wells and in a biofilm attachment assay. Reporter fusions to
cpsA
, the first gene in the locus, showed ∼10-fold-enhanced transcription in the OP (
opaR
+
) strain compared to a TR (Δ
opaR
) strain. Two additional transcriptional regulators were discovered. One potential activator, CpsR, participates in the
scrABC
GGDEF-EAL-signaling pathway; CpsR was required for the increased
cps
expression observed in
scrA
Δ
opaR
strains. CpsR, which contains a conserved module found in members of the AAA+ superfamily of ATP-interacting proteins, is homologous to
Vibrio cholerae
VpsR; however, unlike VpsR, CpsR was not essential for
cps
expression. CpsS, the second newly identified regulator, contains a CsgD-type DNA-binding domain and appears to act as a repressor. Mutants with
cpsS
defects have greatly elevated
cps
transcription; their high level of
cpsA
expression was CpsR dependent in ΤR strains and primarily OpaR dependent in OP strains. Thus, a network of positive and negative regulators modulates CPS production in
V. parahaemolyticus
.
Global Analyses of Transcriptomes and Proteomes of a Parent Strain and an
l
-Threonine-Overproducing Mutant Strain
Authors: Lee Jin-Ho , Lee Dong-Eun , Lee Bheong-Uk , Kim Hak-Sung
Published: August 2003

We compared the transcriptome, proteome, and nucleotide sequences between the parent strain
Escherichia coli
W3110 and the
l
-threonine-overproducing mutant
E
.
coli
TF5015. DNA macroarrays were used to measure mRNA levels for all of the genes of
E
.
coli
, and two-dimensional gel electrophoresis was used to compare protein levels. It was observed that only 54 of 4,290 genes (1.3%) exhibited differential expression profiles. Typically, genes such as
aceA
,
aceB
,
icdA
,
gltA
,
glnA
,
leu
operon,
proA
,
thrA
,
thrC
, and
yigJ
, which are involved in the glyoxylate shunt, the tricarboxylic acid cycle, and amino acid biosynthesis (
l
-glutamine,
l
-leucine, proline, and
l
-threonine), were significantly upregulated, whereas the genes
dadAX
,
hdeA
,
hdeB
,
ompF
,
oppA
,
oppB
,
oppF
,
yfiD
, and many ribosomal protein genes were downregulated in TF5015 compared to W3110. The differential expression such as upregulation of
thr
operon and expression of
yigJ
would result in an accumulation of
l
-threonine in TF5015. Furthermore, two significant mutations,
thrA345
and
ilvA97
, which are essential for overproduction of
l
-threonine, were identified in TF5015 by the sequence analysis. In particular, expression of the mutated
thrABC
(pATF92) in W3110 resulted in a significant incremental effect on
l
-threonine production. Upregulation of
aceBA
and downregulation of b1795,
hdeAB
,
oppA
, and
yfiD
seem to be linked to a low accumulation of acetate in TF5015. Such comprehensive analyses provide information regarding the regulatory mechanism of
l
-threonine production and the physiological consequences in the mutant stain.
TodK, a Putative Histidine Protein Kinase, Regulates Timing of Fruiting Body Morphogenesis inMyxococcus xanthus
Authors: Rasmussen Anders A. , Søgaard-Andersen Lotte
Published: August 2003

In response to starvation,Myxococcus xanthusinitiates a developmental program that results in the formation of spore-filled multicellular fruiting bodies. Fruiting body formation depends on the temporal and spatial coordination of aggregation and sporulation. These two processes are induced by the cell surface-associated C signal, with aggregation being induced after 6 h and sporulation being induced once cells have completed the aggregation process. We report the identification of TodK, a putative histidine protein kinase of two-component regulatory systems that is important for the correct timing of aggregation and sporulation. Loss of TodK function results in early aggregation and early, as well as increased levels of, sporulation. Transcription oftodKdecreases 10-fold in response to starvation independently of the stringent response. Loss of TodK function specifically results in increased expression of a subset of C-signal-dependent genes. Accelerated development in atodKmutant depends on the known components in the C-signal transduction pathway. TodK is not important for synthesis of the C signal. From these results we suggest that TodK is part of a signal transduction system which converges on the C-signal transduction pathway to negatively regulate aggregation, sporulation, and the expression of a subset of C-signal-dependent genes. TodK and the SdeK histidine protein kinase, which is part of a signal transduction system that converges on the C-signal transduction pathway to stimulate aggregation, sporulation, and C-signal-dependent gene expression, act in independent genetic pathways. We suggest that the signal transduction pathways defined by TodK and SdeK act in concert with the C-signal transduction pathway to control the timing of aggregation and sporulation.
Biochemical Characterization of a β-Galactosidase with a Low Temperature Optimum Obtained from an Antarctic
Arthrobacter
Isolate
Authors: Coker James A. , Sheridan Peter P. , Loveland-Curtze Jennifer , Gutshall Kevin R. , Auman Ann J. , Brenchley Jean E.
Published: August 2003

A psychrophilic gram-positive isolate was obtained from Antarctic Dry Valley soil. It utilized lactose, had a rod-coccus cycle, and contained lysine as the diamino acid in its cell wall. Consistent with these physiological traits, the 16S ribosomal DNA sequence showed that it was phylogenetically related to other
Arthrobacter
species. A gene (
bgaS
) encoding a family 2 β-galactosidase was cloned from this organism into an
Escherichia coli
host. Preliminary results showed that the enzyme was cold active (optimal activity at 18°C and 50% activity remaining at 0°C) and heat labile (inactivated within 10 min at 37°C). To enable rapid purification, vectors were constructed adding histidine residues to the BgaS enzyme and its
E. coli
LacZ counterpart, which was purified for comparison. The His tag additions reduced the specific activities of both β-galactosidases but did not alter the other characteristics of the enzymes. Kinetic studies using
o
-nitrophenyl-β-
d
-galactopyranoside showed that BgaS with and without a His tag had greater catalytic activity at and below 20°C than the comparable LacZ β-galactosidases. The BgaS heat lability was investigated by ultracentrifugation, where the active enzyme was a homotetramer at 4°C but dissociated into inactive monomers at 25°C. Comparisons of family 2 β-galactosidase amino acid compositions and modeling studies with the LacZ structure did not mimic suggested trends for conferring enzyme flexibility at low temperatures, consistent with the changes affecting thermal adaptation being localized and subtle. Mutation studies of the BgaS enzyme should aid our understanding of such specific, localized changes affecting enzyme thermal properties.
Influence of Temperature on tRNA Modification in Archaea:
Methanococcoides burtonii
(Optimum Growth Temperature [
T
opt
], 23°C) and
Stetteria hydrogenophila
(
T
opt
, 95°C)
Authors: Noon Kathleen R. , Guymon Rebecca , Crain Pamela F. , McCloskey James A. , Thomm Michael , Lim Julianne , Cavicchioli Ricardo
Published: August 2003

We report the first study of tRNA modification in psychrotolerant archaea, specifically in the archaeon
Methanococcoides burtonii
grown at 4 and 23°C. For comparison, unfractionated tRNA from the archaeal hyperthermophile
Stetteria hydrogenophila
cultured at 93°C was examined. Analysis of modified nucleosides using liquid chromatography-electrospray ionization mass spectrometry revealed striking differences in levels and identities of tRNA modifications between the two organisms. Although the modification levels in
M. burtonii
tRNA are the lowest in any organism of which we are aware, it contains more than one residue per tRNA molecule of dihydrouridine, a molecule associated with maintenance of polynucleotide flexibility at low temperatures. No differences in either identities or levels of modifications, including dihydrouridine, as a function of culture temperature were observed, in contrast to selected tRNA modifications previously reported for archaeal hyperthermophiles. By contrast,
S. hydrogenophila
tRNA was found to contain a remarkable structural diversity of 31 modified nucleosides, including nine methylated guanosines, with eight different nucleoside species methylated at O-2′ of ribose, known to be an effective stabilizing motif in RNA. These results show that some aspects of tRNA modification in archaea are strongly associated with environmental temperature and support the thesis that posttranscriptional modification is a universal natural mechanism for control of RNA molecular structure that operates across a wide temperature range in archaea as well as bacteria.
Characterization of Dominantly Negative Mutant ClyA Cytotoxin Proteins in
Escherichia coli
Authors: Wai Sun Nyunt , Westermark Marie , Oscarsson Jan , Jass Jana , Maier Elke , Benz Roland , Uhlin Bernt Eric
Published: August 2003

We report studies of the subcellular localization of the ClyA cytotoxic protein and of mutations causing defective translocation to the periplasm in
Escherichia coli
. The ability of ClyA to translocate to the periplasm was abolished in deletion mutants lacking the last 23 or 11 amino acid residues of the C-terminal region. A naturally occurring ClyA variant lacking four residues (183 to 186) in a hydrophobic subdomain was retained mainly in the cytosolic fraction. These mutant proteins displayed an inhibiting effect on the expression of the hemolytic phenotype of wild-type ClyA. Studies in vitro with purified mutant ClyA proteins revealed that they were defective in formation of pore assemblies and that their activity in hemolysis assays and in single-channel conductance tests was at least 10-fold lower than that of the wild-type ClyA. Tests with combinations of the purified proteins indicated that mutant and wild-type ClyA interacted and that formation of heteromeric assemblies affected the pore-forming activity of the wild-type protein. The observed protein-protein interactions were consistent with, and provided a molecular explanation for, the dominant negative feature of the mutant ClyA variants.
In Vivo Reconstitution of the FhuA Transport Protein ofEscherichia coliK-12
Authors: Braun Michael , Endriss Franziska , Killmann Helmut , Braun Volkmar
Published: August 2003

The FhuA protein in the outer membrane ofEscherichia coliactively transports ferrichrome and the antibiotics albomycin and rifamycin CGP 4832 and serves as a receptor for the phages T1, T5, and φ80 and for colicin M and microcin J25. The crystal structure reveals a β-barrel with a globular domain, the cork, which closes the channel formed by the barrel. Genetic deletion of the cork resulted in a β-barrel that displays no FhuA activity. A functional FhuA was obtained by cosynthesis of separately encoded cork and the β-barrel domain, each endowed with a signal sequence, which showed that complementation occurs after secretion of the fragments across the cytoplasmic membrane. Inactive complete mutant FhuA and an FhuA fragment containing 357 N-proximal amino acid residues complemented the separately synthesized wild-type β-barrel to form an active FhuA. Previous claims that the β-barrel is functional as transporter and receptor resulted from complementation by inactive complete FhuA and the 357-residue fragment. No complementation was observed between the wild-type cork and complete but inactive FhuA carrying cork mutations that excluded the exchange of cork domains. The data indicate that active FhuA is reconstituted extracytoplasmically by insertion of separately synthesized cork or cork from complete FhuA into the β-barrel, and they suggest that in wild-type FhuA the β-barrel is formed prior to the insertion of the cork.
Moritella
Cold-Active Dihydrofolate Reductase: Are There Natural Limits to Optimization of Catalytic Efficiency at Low Temperature?
Authors: Xu Ying , Feller Georges , Gerday Charles , Glansdorff Nicolas
Published: August 2003

Adapting metabolic enzymes of microorganisms to low temperature environments may require a difficult compromise between velocity and affinity. We have investigated catalytic efficiency in a key metabolic enzyme (dihydrofolate reductase) of
Moritella profunda
sp. nov., a strictly psychrophilic bacterium with a maximal growth rate at 2°C or less. The enzyme is monomeric (
M
r
= 18,291), 55% identical to its
Escherichia coli
counterpart, and displays

T
m

and denaturation enthalpy changes much lower than
E. coli
and
Thermotoga maritima
homologues. Its stability curve indicates a maximum stability above the temperature range of the organism, and predicts cold denaturation below 0°C. At mesophilic temperatures the apparent

K
m

value for dihydrofolate is 50- to 80-fold higher than for
E. coli
,
Lactobacillus casei
, and
T. maritima
dihydrofolate reductases, whereas the apparent

K
m

value for NADPH, though higher, remains in the same order of magnitude. At 5°C these values are not significantly modified. The enzyme is also much less sensitive than its
E. coli
counterpart to the inhibitors methotrexate and trimethoprim. The catalytic efficiency (
k
cat

/K
m

) with respect to dihydrofolate is thus much lower than in the other three bacteria. The higher affinity for NADPH could have been maintained by selection since NADPH assists the release of the product tetrahydrofolate. Dihydrofolate reductase adaptation to low temperature thus appears to have entailed a pronounced trade-off between affinity and catalytic velocity. The kinetic features of this psychrophilic protein suggest that enzyme adaptation to low temperature may be constrained by natural limits to optimization of catalytic efficiency.
Clostridium pasteurianum
F
1
F
o
ATP Synthase: Operon, Composition, and Some Properties
Authors: Das Amaresh , Ljungdahl Lars G.
Published: August 2003

The
atp
operon encoding F
1
F
o
ATP synthase in the fermentative obligate anaerobic bacterium
Clostridium pasteurianum
was sequenced. It consisted of nine genes arranged in the order
atpI
(i),
atpB
(a),
atpE
(c),
atpF
(b),
atpH
(δ),
atpA
(α),
atpG
(γ),
atpD
(β), and
atpC
(ε), which was identical to that found in many bacteria. Reverse transcription-PCR confirmed the presence of the transcripts of all nine genes. The amount of ATPase activity in the membranes of
C
.
pasteurianum
was low compared to what has been found in many other bacteria. The F
1
F
o
complexes solubilized from membranes of
C
.
pasteurianum
and
Escherichia coli
had similar masses, suggesting similar compositions for the F
1
F
o
complexes from the two bacteria. Western blotting experiments with antibodies raised against the purified subunits of F
1
F
o
detected the presence of eight subunits, α, β, γ, δ, ε, a, b, and c, in the F
1
F
o
complex from
C
.
pasteurianum
. The F
1
F
o
complex from
C
.
pasteurianum
was activated by thiocyanate, cyanate, or sulfhydryl compounds; inhibited by sulfite, bisulfite, or bicarbonate; and had tolerance to inhibition by dicyclohexylcarbodiimide. The target of thiol activation of the F
1
F
o
complex from
C
.
pasteurianum
was F
1
. Thiocyanate and sulfite were noncompetitive with respect to substrate Mg ATP but competitive with respect to each other. The F
1
and F
o
parts of the F
1
F
o
complexes from
C
.
pasteurianum
and
E
.
coli
bound to each other, but the hybrid F
1
F
o
complexes were not functionally active.
Interactions of FliJ with the
Salmonella
Type III Flagellar Export Apparatus
Authors: Fraser Gillian M. , González-Pedrajo Bertha , Tame Jeremy R. H. , Macnab Robert M.
Published: August 2003

FliJ, a 17-kDa protein, is a soluble component of the
Salmonella
type III flagellar protein export system that has antiaggregation properties and several other characteristics that suggest it may have a chaperone-like function. We have now examined this protein in detail. Ten-amino-acid scanning deletions covering the entire 147-amino-acid sequence were tested for complementation of a
fliJ
null strain; only the first and last deletions complemented. A few of the deletions, especially towards the C terminus, exerted a dominant negative effect on wild-type cells, indicating that they were actively interfering with function. Two truncated versions of FliJ, representing its N- and C-terminal halves, failed to complement and were not dominant. We tested for FliJ self-association by several techniques. Size-exclusion chromatography (Superdex 200) indicated an apparent molecular mass of around 50 kDa, which could reflect either multimerization or an elongated shape or both. Multiangle light scattering gave a peak value of 20 kDa, close to the molecular mass of the monomer. Analytical ultracentrifugation gave evidence for weak self-association as a trimer or tetramer. It was known from previous studies that FliJ interacts with the N-terminal region of FliH, a negative regulator of the ATPase FliI. Using both truncation and deletion versions of FliJ, we now show that it is its C-terminal region that is responsible for this interaction. We also show that FliJ interacts with the soluble cytoplasmic domain of the largest membrane component of the export apparatus, FlhA; although small deletions in FliJ did not interfere with the association, both truncated versions failed to associate, indicating that a substantial amount of the central region of the FliJ sequence participates in the association. We present a model summarizing these multiple interactions.
Glutathione and Catalase Provide Overlapping Defenses for Protection against Respiration-Generated Hydrogen Peroxide in
Haemophilus influenzae
Authors: Vergauwen Bjorn , Pauwels Frederik , Van Beeumen Jozef J.
Published: August 2003

Glutathione is an abundant and ubiquitous low-molecular-weight thiol that may play a role in many cellular processes, including protection against the deleterious effects of reactive oxygen species. We address here the role of glutathione in protection against hydrogen peroxide (H
2
O
2
) in
Haemophilus influenzae
and show that glutathione and catalase provide overlapping defense systems.
H. influenzae
is naturally glutathione deficient and imports glutathione from the growth medium. Mutant
H. influenzae
lacking catalase and cultured in glutathione-deficient minimal medium is completely devoid of H
2
O
2
scavenging activity and, accordingly, substantial amounts of H
2
O
2
accumulate in the growth medium.
H. influenzae
generates H
2
O
2
at rates similar to those reported for
Escherichia coli
, but the toxicity of this harmful metabolite is averted by glutathione-based H
2
O
2
removal, which appears to be the primary system for protection against H
2
O
2
endogenously generated during aerobic respiration. When H
2
O
2
concentrations exceed low micromolar levels, the
hktE
gene-encoded catalase becomes the predominant scavenger. The requirement for glutathione in protection against oxidative stress is analogous to that in higher and lower eukaryotes but is unlike the situation in other bacteria in which glutathione is dispensable for aerobic growth during both normal and oxidative stress conditions.
Genome Diversification in Phylogenetic Lineages I and II ofListeria monocytogenes: Identification of Segments Unique to Lineage II Populations
Authors: Zhang Chaomei , Zhang Min , Ju Jingliang , Nietfeldt Joseph , Wise John , Terry Philip M. , Olson Michael , Kachman Stephen D. , Wiedmann Martin , Samadpour Mansour , Benson Andrew K.
Published: August 2003

Thirteen different serotypes ofListeria monocytogenescan be distinguished on the basis of variation in somatic and flagellar antigens. Although the known virulence genes are present in all serotypes, greater than 90% of human cases of listeriosis are caused by serotypes 1/2a, 1/2b, and 4b and nearly all outbreaks of food-borne listeriosis have been caused by serotype 4b strains. Phylogenetic analysis of these three common clinical serotypes places them into two different lineages, with serotypes 1/2b and 4b belonging to lineage I and 1/2a belonging to lineage II. To begin examining evolution of the genome in these serotypes, DNA microarray analysis was used to identify lineage-specific and serotype-specific differences in genome content. A set of 44 strains representing serotypes 1/2a, 1/2b, and 4b was probed with a shotgun DNA microarray constructed from the serotype 1/2a strain 10403s. Clones spanning 47 different genes in 16 different contiguous segments relative to the lineage II 1/2a genome were found to be absent in all lineage I strains tested (serotype 4b and 1/2b) and an additional nine were altered exclusively in 4b strains. Southern hybridization confirmed that conserved alterations were, in all but two loci, due to absence of the segments from the genome. Genes within these contiguous segments comprise five functional categories, including genes involved in synthesis of cell surface molecules and regulation of virulence gene expression. Phylogenetic reconstruction and examination of compositional bias in the regions of difference are consistent with a model in which the ancestor of the two lineages had the 1/2 somatic serotype and the regions absent in the lineage I genome arose by loss of ancestral sequences.
Mutations in
rpoBC
Suppress the Defects of a
Sinorhizobium meliloti relA
Mutant
Authors: Wells Derek H. , Long Sharon R.
Published: August 2003

The nitrogen-fixing symbiosis between
Sinorhizobium meliloti
and
Medicago sativa
requires complex physiological adaptation by both partners. One method by which bacteria coordinately control physiological adaptation is the stringent response, which is triggered by the presence of the nucleotide guanosine tetraphosphate (ppGpp). ppGpp, produced by the RelA enzyme, is thought to bind to and alter the ability of RNA polymerase (RNAP) to initiate and elongate transcription and affect the affinity of the core enzyme for various sigma factors. An
S. meliloti relA
mutant which cannot produce ppGpp was previously shown to be defective in the ability to form nodules. This mutant also overproduces a symbiotically necessary exopolysaccharide called succinoglycan (38). The work presented here encompasses the analysis of suppressor mutants, isolated from host plants, that suppress the symbiotic defects of the
relA
mutant. All suppressor mutations are extragenic and map to either
rpoB
or
rpoC
, which encode the β and β′ subunits of RNAP. Phenotypic, structural, and gene expression analyses reveal that suppressor mutants can be divided into two classes; one is specific in its effect on stringent response-regulated genes and shares striking similarity with suppressor mutants of
Escherichia coli
strains that lack ppGpp, and another reduces transcription of all genes tested in comparison to that in the
relA
parent strain. Our findings indicate that the ability to successfully establish symbiosis is tightly coupled with the bacteria's ability to undergo global physiological adjustment via the stringent response.
Physiological Studies of
Escherichia coli
Strain MG1655: Growth Defects and Apparent Cross-Regulation of Gene Expression
Authors: Soupene Eric , van Heeswijk Wally C. , Plumbridge Jacqueline , Stewart Valley , Bertenthal Daniel , Lee Haidy , Prasad Gyaneshwar , Paliy Oleg , Charernnoppakul Parinya , Kustu Sydney
Published: August 2003

Escherichia coli
strain MG1655 was chosen for sequencing because the few mutations it carries (
ilvG rfb-50 rph-1
) were considered innocuous. However, it has a number of growth defects. Internal pyrimidine starvation due to polarity of the
rph-1
allele on
pyrE
was problematic in continuous culture. Moreover, the isolate of MG1655 obtained from the
E. coli
Genetic Stock Center also carries a large deletion around the
fnr
(fumarate-nitrate respiration) regulatory gene. Although studies on DNA microarrays revealed apparent cross-regulation of gene expression between galactose and lactose metabolism in the Stock Center isolate of MG1655, this was due to the occurrence of mutations that increased
lacY
expression and suppressed slow growth on galactose. The explanation for apparent cross-regulation between galactose and
N
-acetylglucosamine metabolism was similar. By contrast, cross-regulation between lactose and maltose metabolism appeared to be due to generation of internal maltosaccharides in lactose-grown cells and may be physiologically significant. Lactose is of restricted distribution: it is normally found together with maltosaccharides, which are starch degradation products, in the mammalian intestine. Strains designated MG1655 and obtained from other sources differed from the Stock Center isolate and each other in several respects. We confirmed that use of other
E
.
coli
strains with MG1655-based DNA microarrays works well, and hence these arrays can be used to study any strain of interest. The responses to nitrogen limitation of two urinary tract isolates and an intestinal commensal strain isolated recently from humans were remarkably similar to those of MG1655.
Rapid Surface Motility in
Bacillus subtilis
Is Dependent on Extracellular Surfactin and Potassium Ion
Authors: Kinsinger Rebecca F. , Shirk Megan C. , Fall Ray
Published: August 2003

Motility on surfaces is an important mechanism for bacterial colonization of new environments. In this report, we describe detection of rapid surface motility in the wild-type
Bacillus subtilis
Marburg strain, but not in several
B. subtilis
168 derivatives. Motility involved formation of rapidly spreading dendritic structures, followed by profuse surface colonies if sufficient potassium ion was present. Potassium ion stimulated surfactin secretion, and the role of surfactin in surface motility was confirmed by deletion of a surfactin synthase gene. Significantly, this motility was independent of flagella. These results demonstrate that wild-type
B. subtilis
strains can use both swimming and sliding-type mechanisms to move across surfaces.
Periodicity of Cell Attachment Patterns during
Escherichia coli
Biofilm Development
Authors: Agladze Konstantin , Jackson Debra , Romeo Tony
Published: August 2003

The complex architecture of bacterial biofilms inevitably raises the question of their design. Microstructure of developing
Escherichia coli
biofilms was analyzed under static and laminar flow conditions. Cell attachment during early biofilm formation exhibited periodic density patterns that persisted during development. Several models for the origination of biofilm microstructure are considered, including an activator-inhibitor or Turing model.
Lactobacillus reuteriCRL1098 Produces Cobalamin
Authors: Taranto María P. , Vera José L. , Hugenholtz Jeroen , De Valdez Graciela F. , Sesma Fernando
Published: August 2003

We found thatLactobacillus reuteriCRL1098, a lactic acid bacterium isolated from sourdough, is able to produce cobalamin. The sugar-glycerol cofermentation in vitamin B12-free medium showed that this strain was able to reduce glycerol through a well-known cobalamin-dependent reaction with the formation of 1,3-propanediol as a final product. The cell extract ofL. reutericorrected the coenzyme B12requirement ofLactobacillus delbrueckiisubsp.lactisATCC 7830 and allowed the growth ofSalmonella entericaserovar Typhimurium (metE cbiB) andEscherichia coli(metE) in minimal medium. Preliminary genetic studies of cobalamin biosynthesis genes fromL. reuteriallowed the identification ofcobgenes which encode the CobA, CbiJ, and CbiK enzymes involved in the cobalamin pathway. The cobamide produced byL. reuteri, isolated in its cyanide form by using reverse-phase high-pressure liquid chromatography, showed a UV-visible spectrum identical to that of standard cyanocobalamin (vitamin B12).
Irp9, Encoded by the High-Pathogenicity Island of
Yersinia enterocolitica
, Is Able To Convert Chorismate into Salicylate, the Precursor of the Siderophore Yersiniabactin
Authors: Pelludat Cosima , Brem Daniela , Heesemann Jürgen
Published: August 2003

The Irp9 protein of
Yersinia enterocolitica
participates in the synthesis of salicylate, the precursor of the siderophore yersiniabactin. In
Pseudomonas
species, salicylate synthesis is mediated by two enzymes: isochorismate synthase and isochorismate pyruvate-lyase. Both enzymes are required for complementation of a Yersinia
irp9
mutant. However,
irp9
is not able to complement
Escherichia coli entC
for the production of enterobactin, which requires isochorismate as a precursor. These results suggest that Irp9 directly converts chorismate into salicylate.
Strictly Polyphosphate-Dependent Glucokinase in a Polyphosphate-Accumulating Bacterium,
Microlunatus phosphovorus
Authors: Tanaka Shotaro , Lee Sun-Og , Hamaoka Kazuhiro , Kato Junichi , Takiguchi Noboru , Nakamura Kazunori , Ohtake Hisao , Kuroda Akio
Published: August 2003

ATP-dependent glucokinase is suggested to have evolved from a hypothetical polyphosphate (polyP)-dependent glucokinase (polyP-GK) via a bifunctional polyP/ATP glucokinase (polyP/ATP-GK). Here we showed that polyP-GK is present in a polyP-accumulating bacterium,
Microlunatus phosphovorus
. The polyP-GK produced glucose-6-P
i
from glucose and polyP, but it could not phosphorylate glucose with ATP. The polyP-GK was most closely related to the polyP/ATP-GK of
Mycobacterium tuberculosis
.
The relative importance of whole body vibration and occupational lifting as risk factors for low-back pain
Authors: Palmer K T , Griffin M J , Syddall H E , Pannett B , Cooper C , Coggon D
Published: September 2003

Aims:To explore the impact of occupational exposure to whole body vibration (WBV) on low back pain (LBP) in the general population and to estimate the burden of LBP attributable to occupational WBV in comparison with that due to occupational lifting.

Methods:A questionnaire including sections on WBV at work, LBP, and potential risk factors was mailed to a community sample of 22 194 men and women of working age. Sources and durations of exposure to occupational WBV were ascertained for the past week and personal vibration doses (eVDV) were estimated. Analysis was confined to subjects reporting exposures in the past week as typical of their work. Associations of LBP with eVDV, driving industrial vehicles, and occupational lifting were explored by logistic regression and attributable numbers were calculated.

Results:Significant associations were found between daily lifting of weights greater than 10 kg at work and LBP, troublesome LBP (which made it difficult to put on hosiery), and sciatica (prevalence ratios 1.3 to 1.7); but the risk of these outcomes in both sexes varied little by eVDV and only weak associations were found with riding on industrial vehicles. Assuming causal associations, the numbers of cases of LBP in Britain attributable to occupational WBV were estimated to be 444 000 in men and 95 000 in women. This compared with an estimated 940 000 male cases and 370 000 female cases of LBP from occupational lifting.

Conclusions:The burden of LBP in Britain from occupational exposure to WBV is smaller than that attributable to lifting at work.
Cardiorespiratory fitness and risk of disability pension: a prospective population based study in Finnish men
Authors: Karpansalo M , Lakka T A , Manninen P , Kauhanen J , Rauramaa R , Salonen J T
Published: September 2003

Background:Early retiring is a major social problem in many western countries.

Aim:To investigate whether good cardiorespiratory fitness prevents disability pensioning in Finnish middle-aged men.

Methods:Subjects were a random population based sample of 1307 men who were 42−60 years old at baseline, had not retired before baseline or died during follow up, and had undergone a cycle ergometer test at baseline. Cardiorespiratory fitness was assessed at baseline with a maximal but symptom limited exercise test on an electrically braked cycle ergometer.

Results:During a follow up of 11 years on average, 790 (60.4%) men were awarded a disability pension, only 254 (19.4%) men reached the old-age pension without previous early pension, and 263 (20.1%) men were still working at the end of follow up. After adjustment for age, body mass index, alcohol consumption, smoking, education, occupation, and baseline chronic diseases, an inverse association was observed between cardiorespiratory fitness and the risk of disability pension. Men with VO2max<25.98 ml/kg/min (lowest fifth) had a 3.28-fold (95% CI 1.70 to 6.32) and men with the duration of exercise test <9.54 minutes (lowest fifth) had a 4.66-fold (95% CI 2.43 to 8.92) risk of disability pension due to cardiovascular diseases compared with men in the highest fifths. Men with lowest fitness level also had an increased risk of disability pension due to musculoskeletal disorders, or all reasons combined.

Conclusions:Physical fitness is inversely associated with the risk of disability pension and especially with the risk of disability due to cardiovascular diseases.
A Methodology for Feature Selection Using Multiobjective Genetic Algorithms for Handwritten Digit String Recognition
Authors: Oliveira L. S. , Sabourin R. , Bortolozzi F. , Suen C. Y.
Published: August 2003

In this paper a methodology for feature selection for the handwritten digit string recognition is proposed. Its novelty lies in the use of a multiobjective genetic algorithm where sensitivity analysis and neural network are employed to allow the use of a representative database to evaluate fitness and the use of a validation database to identify the subsets of selected features that provide a good generalization. Some advantages of this approach include the ability to accommodate multiple criteria such as number of features and accuracy of the classifier, as well as the capacity to deal with huge databases in order to adequately represent the pattern recognition problem. Comprehensive experiments on the NIST SD19 demonstrate the feasibility of the proposed methodology.
Robust Face Detection and Tracking for Real-Life Applications
Authors: Byun Hyeran , Ko Byoungchul
Published: August 2003

In this paper, we propose a new face detection and tracking algorithm for real-life telecommunication applications, such as video conferencing, cellular phone and PDA. We combine template-based face detection and tracking method with color information to track a face regardless of various lighting conditions and complex backgrounds as well as the race. Based on our experiments, we generate robust face templates from wavelet-transformed lowpass and two highpass subimages at the second level low-resolution. However, since template matching is generally sensitive to the change of illumination conditions, we propose a new type of preprocessing method. Tracking method is applied to reduce the computation time and predict precise face candidate region even though the movement is not uniform. Facial components are also detected using k-means clustering and their geometrical properties. Finally, from the relative distance of two eyes, we verify the real face and estimate the size of facial ellipse. To validate face detection and tracking performance of our algorithm, we test our method using six different video categories of QCIF size which are recorded in dynamic environments.
NURBS-Based Segmentation of the Brain in Medical Images
Authors: Meegama Ravinda G. N. , Rajapakse Jagath C.
Published: August 2003

Extracting the human brain from magnetic resonance head scans is difficult because of its highly convoluted and nonuniform geometry. A technique based on Non-Uniform Rational B-Splines (NURBS) surfaces and energy minimizing deformable models to extract and visualize the brain surface patterns accurately from magnetic resonance head scans is presented. The weighting parameter that comes with the NURBS definition is explored to attract the surface into regions showing high curvature. The weight at each control point is adjusted automatically according to the curvature properties of the evolving surface. This process facilitates a deformable model with increased local flexibility that adapts to complex geometrical features of the brain surface. The results show that the proposed model is capable of capturing the correct brain surface with a higher accuracy than the existing techniques.
Energetics and Structure of the Stable and Unstable Biatomic Step Edges of Si(100)
Authors: Van Dijken S. , Zandvliet H. J. W. , Poelsema Bene
Published: August 2003

The atomic geometry of Si(100) with a misorientation of 4.5° towards [110] has been studied with scanning tunneling microscopy. Special attention has been paid to the buckling registry of the dimers and atoms near the biatomic step edge. For the arrangement of the atoms near the steps and at kink positions some simple rules are given. the biatomic step edge formation energies have been determined by analyzing the step edge roughness. The ordering of the various types of step edges is in perfect agreement with total energy calculations performed by Chadi [Phys. Rev. Lett.58, 1691 (1987)]. Finally, the transition from a surface with single steps to a surface with double steps has been calculated to occur at a miscut angle of 1.5°.
Interfacial Modification Induced by Equilibrium Segregation in Ge(S) Bicrystal
Authors: Charaï A. , Fares L. , Alfonso C. , Roussel L. , Rouviere J. L.
Published: August 2003

An original experimental procedure is set up in order to relate unambiguously the equilibrium impurity segregation in a grain boundary to the structural modifications. This is clearly established in the case of the Ge(S) Σ=25 grain boundary. Using HREN, EDS and EELS, we show that the sulfur segregation occurs on the dislocation cores of the grain boundary and that it stabilizes the lowest energy structures of the initial one.
Negative Ion Resonance Evidenced by Vibrationally Resolved Electron Diffraction On the H/Si(111) Surface
Authors: He Y. , Yu L.-M. , Thiry P. A. , Caudano R.
Published: August 2003

The surface vibrations of H-terminated Si(111) are investigated by high resolution electron energy loss spectroscopy (HREELS). Clear evidence is obtained for reassigning the electron resonant scattering from a surface resonance to a negative ion resonance mechanism. Since the electrons emitted from the trapping states show characteristic angular diffraction patterns realated with the geometric and vibrational symmetries of the surface, we suggest the possibility of using this system to investigate vibrationally resolved electron diffraction processes.
Comparison Between the Reaction Mechanisms of Nitridation of Si(100) by a NH3 Molecular Beam and by a $\rm{N}^+_2$ Ion Beam
Authors: Kusunoki I. , Ishidzuka S. , Igari Y. , Takaoka T.
Published: August 2003

Nitridation of a Si(100) surface takes place with NH3 at temperatures higher than 600°C and with a low energy [Formula: see text] ion beam at room temperature, formating a thin film of nitride. The nitridation processes have been studied in situ under ultrahigh vacuum by X-ray photoelectron spectroscopy (XPS). The reaction with NH3 occurs on the surface with Si atoms supplied by out-diffusion from the substrate, producing a nitride film. On the other hand, the N atoms of the low energy [Formula: see text] ion beam (100–1000 eV) penetrate into the bulk by their kinetic energy and form the nitride layer near the surface. The difference of these mechanisms is clearly observed in the evolution of the N1s and Si2p XPS spectra during the reaction.
Photoemission Study of K Doping on a Monolayer of C60 on Clean Si(001)-(2 × 1) Surface
Authors: Pi Tun-Wen , Hong Le-Hong , Wu Rong-Tzong , Cheng Chiu-Ping , Ko May-Ho
Published: August 2003

We present the first valence band photoemission study of a monolayer K x C 60 on a clean Si(001)-(2 × 1) surface. The monolayer C60 which shows weak interaction with the silicon surface reveals clear, but broadened, structures corresponding to bulk C 60. Upon K exposure, the work function drops rapidly due to charge polarization toward the Si surface, considerably affecting then the rate of the Lumo filling. Its centroid initially shown at 0.6 eV shifts to higher binding energy with higher concentration. Moreover, the LUMO always separates 1.5 ± 0.1 eV from the Homo. Features associated with the many-body effect do not appear in the spectra. The Fermi cutoff has never been observed, indicating the insulating nature of the K x C 60 surface.
Structure of Epitaxial CoSi2 Films on Si(111) Studied with Low-Energy Electron Diffraction (LEED)
Authors: Starke U. , Schardt J. , Weiß W. , Rangelov G. , Fauster Th. , Heinz K.
Published: August 2003

Expitaxial films of CoSi 2 on Si(111) were investigated by low-energy electron diffraction. Films of approximately 12 Å thickness were prepared by simultaneous deposition of Co and Si and subsequent annealing. The films were found to crystallize in CaF 2 structure in (111) orientation. Two (1×1) phases of different stoichiometry exist. The surface phase that contains more Co is found to be a CoSi 2(111) bulklike structure terminated by a Si–Co–Si trilayer. The Si-rich phase is terminated by an additional nonrotated silicon bilayer with the lower silicon atoms bound to cobalt in the first CoSi 2 layer. Consequently, these cobalt atoms have an eightfold coordination. Due to the lattice mismatch the silicide films are expanded by 0.5% in the lateral direction and contracted by 1.4% in the vertical direction.
Surfactant-Mediated Growth of Ge/Si(001) Interface Studied by XPD
Authors: Gunnella R. , Castrucci P. , Pinto N. , Cucculelli P. , Davoli I. , Sébilleau D. , De Crescenzi M.
Published: August 2003

The influence of Sb as a surfactant on the formation of Si/Ge interface is studied by means of XPD (X-ray photoelectron diffraction) and AED (Auger electron diffraction) from Ge and Si core levels. The technique employed is particularly suitable for checking the film tetragonal distortion, the growth morphology and the sharpness of the interface. We found a layer by layer growth mode for 3 ML of Ge on Si(001) and related values of strain of the film close to the value predicted by the elastic theory which enforces the use of such a surfactant to obtain high quality and sharp heterostructures. In addition, studying the influence of 3 ML of the Si cap layer on the 3 ML Ge, we obtain no indication of Ge segregation into the Si cap layer. Finally, evidences of quality degradation after high temperature (T > 600° C ) annealing are shown.
The $(\sqrt{3}\times\sqrt{3}){\rm R}30^{\circ}$-Reconstructed 6H–SiC(0001): A Semiconducting Surface
Authors: Forbeaux I. , Themlin J.-M. , Langlais V. , Yu L. M. , Belkhir H. , Debever J.-M.
Published: August 2003

k//-resolved inverse-photoemission spectroscopy of the [Formula: see text] reconstruction of 6H–SiC(0001) reveals a sharp surface state U located 1.10±0.05 eV above the Fermi level at the center of the surface Brillouin zone with a total bandwidth of 0.34±0.05 eV. This value is in good agreement with recent LDA calculations which predict an adatom-induced surface state Σ1 which should be half-filled. In this model, the adatoms are Si atoms occupying the T 4 site above a compact SiC(0001) (Si) termination. In contrast to the predicted metallic behavior, the U state remains completely unoccupied throughout the whole Brillouin zone, and the surface is semiconducting. We propose that some charge transfer from the Si adatoms towards subsituted C atoms in the terminating bilayer stabilizes the reconstruction by moving up the Σ1 state away from the Fermi level.
Atomic Structure of the GaAs(001)-β2(2 × 4) Surface
Authors: Srivastava G. P. , Jenkins S. J.
Published: August 2003

We present detailed results of ab initio pseudopotential calculations for equilibrium atomic geometry and chemical bonding on the arsenic-terminated GaAs(001)-β2(2 × 4) surface. We find that this surface is characterized by the presence of two distinct Ga-As bond lengths between the first and second surface layers. This feature is due to the presence of both threefold- and fourfold-coordinated Ga atoms in the second layer.
Photoemission Investigation of the 2D Electron Gas Created At the InAs(110) Surface
Authors: Yu Aristov V. , Le Lay G. , Soukiassian P. , Zhilin V. M. , Grehk G. M. , Kim H. J. , Johnson R. L. , Giammichele C.
Published: August 2003

On InAs(110) surfaces a downward band bending (BB) was produced either by cleavage defects or by adsorption of very small amounts of Cs atoms. As a consequence the Fermi level was moved high into the conduction band, resulting in the formation of a two-dimensional electron channel (2D-EC). Electron emission arising from this channel was detected by angle-resolved photoelectron spectroscopy near the [Formula: see text] points of the first and second surface Brillouin zones. We present a detailed investigation of the corresponding photoemission characteristics using tunable low energy synchrotron radiation light. We find in particular that the photoemission intensity depends drastically on the photon energy. This effect is interpreted as resulting from the quantization of the 2D electron gas in the direction normal to the surface; it is directly linked to the electron density sampled (i.e. the depth probed) beneath the top surface.
Structural Determination of the InSb(110) Surface by the Automated Tensor LEED Program
Authors: Soares E. A. , De Carvalho V. E. , De Castilho C. M. C.
Published: August 2003

The InSb(110) surface structure has been re-examined using the tensor LEED approach. A refinement of the structure as well as the influence of the Debye temperature on the structure determination is presented.