bluuebunny/crossref_metadata_2025 huggingface dataset:
Effect of Bile on the Cell Surface Permeability Barrier and Efflux System of
Vibrio cholerae
Authors: Chatterjee Arpita , Chaudhuri Sohini , Saha Gargi , Gupta Satadeepa , Chowdhury Rukhsana
Published: October 2004

Gram-negative bacteria are inherently impermeable to hydrophobic compounds, due to the synergistic activity of the permeability barrier imposed by the outer membrane and energy dependent efflux systems. The gram-negative, enteric pathogen
Vibrio cholerae
appears to be deficient in both these activities; the outer membrane is not an effective barrier to hydrophobic permeants, presumably due to the presence of exposed phospholipids on the outer leaflet of the outer membrane, and efflux systems are at best only partially active. When
V. cholerae
was grown in the presence of bile, entry of hydrophobic compounds into the cells was significantly reduced. No difference was detected in the extent of exposed phospholipids on the outer leaflet of the outer membrane between cells grown in the presence or absence of bile. However, in the presence of energy uncouplers, uptake of hydrophobic probes was comparable between cells grown in the presence or absence of bile, indicating that energy-dependent efflux processes may be involved in restricting the entry of hydrophobic permeants into bile grown cells. Indeed, an efflux system(s) is essential for survival of
V. cholerae
in the presence of bile. Expression of
acrAB
, encoding an RND family efflux pump, was significantly increased in
V. cholerae
cells grown in vitro in the presence of bile and also in cells grown in rabbit intestine.
Transcriptional Regulation of the
ant
Operon, Encoding Two-Component Anthranilate 1,2-Dioxygenase, on the Carbazole-Degradative Plasmid pCAR1 of
Pseudomonas resinovorans
Strain CA10
Authors: Urata Masaaki , Miyakoshi Masatoshi , Kai Satoshi , Maeda Kana , Habe Hiroshi , Omori Toshio , Yamane Hisakazu , Nojiri Hideaki
Published: October 2004

The carbazole-degradative plasmid pCAR1 of
Pseudomonas resinovorans
strain CA10 has two gene clusters,
carAaAaBaBbCAcAdDFE
and
antABC
, which are involved in the conversions of carbazole to anthranilate and anthranilate to catechol, respectively. We proved that the
antABC
gene cluster, encoding two-component anthranilate 1,2-dioxygenase, constitutes a single transcriptional unit through Northern hybridization and reverse transcription-PCR (RT-PCR) analyses. The transcription start point of
antA
was mapped at 53 bp upstream point of its translation start point, and the −10 and −35 boxes were homologous to conserved σ
70
recognition sequence. Hence the promoter of the
ant
operon was designated P

ant

. 5′ Deletion analyses using luciferase as a reporter showed that the region up to at least 70 bp from the transcription start point of
antA
was necessary for the activation of P

ant

. Luciferase expression from P

ant

was induced by anthranilate itself, but not by catechol. Two probable AraC/XylS-type regulatory genes found on pCAR1, open reading frame 22 (ORF22) and ORF23, are tandemly located 3.2 kb upstream of the
antA
gene. We revealed that the product of ORF23, designated AntR, is indispensable for the stimulation of P

ant

in
Pseudomonas putida
cells. Northern hybridization and RT-PCR analyses revealed that another copy of P

ant

, which is thought to be translocated about 2.1 kb upstream of the
carAa
gene as a consequence of the transposition of ISPre1, actually drives transcription of the
carAa
gene in the presence of anthranilate, indicating that both
ant
and
car
operons are simultaneously regulated by AntR.
Replicon-Specific Regulation of Small Heat Shock Genes in
Agrobacterium tumefaciens
Authors: Balsiger Sylvia , Ragaz Curdin , Baron Christian , Narberhaus Franz
Published: October 2004

Four genes coding for small heat shock proteins (sHsps) were identified in the genome sequence of
Agrobacterium tumefaciens
, one on the circular chromosome (
hspC
), one on the linear chromosome (
hspL
), and two on the pAT plasmid (
hspAT1
and
hspAT2
). Induction of sHsps at elevated temperatures was revealed by immunoblot analyses. Primer extension experiments and translational
lacZ
fusions demonstrated that expression of the pAT-derived genes and
hspL
is controlled by temperature in a regulon-specific manner. While the sHsp gene on the linear chromosome turned out to be regulated by RpoH (σ
32
), both copies on pAT were under the control of highly conserved ROSE (named for repression of heat shock gene expression) sequences in their 5′ untranslated region. Secondary structure predictions of the corresponding mRNA strongly suggest that it represses translation at low temperatures by masking the Shine-Dalgarno sequence. The
hspC
gene was barely expressed (if at all) and not temperature responsive.
Phosphorylation and RsbX-Dependent Dephosphorylation of RsbR in the RsbR-RsbS Complex ofBacillus subtilis
Authors: Chen Chien-Cheng , Yudkin Michael D. , Delumeau Olivier
Published: October 2004

In the pathway that controls σBactivity, the RsbR-RsbS complex plays an important role by trapping RsbT, a positive regulator of σBofBacillus subtilis. We have proposed that at the onset of stress, RsbR becomes phosphorylated, resulting in an enhanced activity of RsbT towards RsbS. RsbT is then free to interact with and activate RsbU, which in turn ultimately activates σB. In this study with purified proteins, we used mutant RsbR proteins to analyze the role of its phosphorylatable threonine residues. The results show that the phosphorylation of either of the two RsbT-phosphorylatable threonine residues (T171 and T205) in RsbR enhanced the kinase activity of RsbT towards RsbS. However, it appeared that RsbT preferentially phosphorylates T171. We also present in vitro evidence that identifies RsbX as a potential phosphatase for RsbR T205.
Thermophilic, Reversible γ-Resorcylate Decarboxylase from
Rhizobium
sp. Strain MTP-10005: Purification, Molecular Characterization, and Expression
Authors: Yoshida Masahiro , Fukuhara Nobuhiro , Oikawa Tadao
Published: October 2004

We found the occurrence of thermophilic reversible γ-resorcylate decarboxylase (γ-RDC) in the cell extract of a bacterium isolated from natural water,
Rhizobium
sp. strain MTP-10005, and purified the enzyme to homogeneity. The molecular mass of the enzyme was determined to be about 151 kDa by gel filtration, and that of the subunit was 37.5 kDa by sodium dodecyl sulfate-polyacrylamide gel electrophoresis; in other words, the enzyme was a homotetramer. The enzyme was induced specifically by the addition of γ-resorcylate to the medium. The enzyme required no coenzyme and did not act on 2,4-dihydroxybenzoate, 2,5-dihydroxybenzoate, 3,4-dihydroxybenzoate, 3,5-dihydroxybenzoate, 2-hydroxybenzoate, or 3-hydroxybenzoate. It was relatively thermostable to heat treatment, and its half-life at 50°C was estimated to be 122 min; furthermore, it catalyzed the reverse carboxylation of resorcinol. The values of
k
cat
/

K
m

(mΜ
−1
 · s
−1
) for γ-resorcylate and resorcinol at 30°C and pH 7 were 13.4 and 0.098, respectively. The enzyme contains 327 amino acid residues, and sequence identities were found with those of hypothetical protein AGR C 4595p from
Agrobacterium tumefaciens
strain C58 (96% identity), 5-carboxyvanillate decarboxylase from
Sphingomonas paucimobilis
(32%), and 2-amino-3-carboxymuconate-6-semialdehyde decarboxylases from
Bacillus cereus
ATCC 10987 (26%),
Rattus norvegicus
(26%), and
Homo sapiens
(25%). The genes (
graA
[1,230 bp],
graB
[888 bp], and
graC
[1,056 bp]) that are homologous to those in the resorcinol pathway also exist upstream and downstream of the γ-RDC gene. Judging from these results, the resorcinol pathway also exists in
Rhizobium
sp. strain MTP-10005, and γ-RDC probably catalyzes a reaction just before the hydroxylase in it does.
A pH-Sensitive Function and Phenotype: Evidence that EutH Facilitates Diffusion of Uncharged Ethanolamine in
Salmonella enterica
Authors: Penrod Joseph T. , Mace Christopher C. , Roth John R.
Published: October 2004

The
eutH
gene is part of an operon that allows
Salmonella enterica
to use ethanolamine as a sole source of nitrogen, carbon, and energy. Although the sequence of EutH suggests a role in transport,
eutH
mutants use ethanolamine normally under standard conditions (pH 7.0). These mutants fail to use ethanolamine at a low pH. Evidence is presented that protonated ethanolamine (Eth
0
) does not enter cells, while uncharged ethanolamine (Eth
0
) diffuses freely across the membrane. The external concentration of Eth
0
varies with the pH (pK = 9.5). At pH 7.0, the standard ethanolamine concentration (41 mM) provides enough Eth
0
for an influx rate that can support growth with or without EutH. When a lowered pH and/or ethanolamine concentration reduced the Eth
0
concentration below 25 μM, EutH was needed to facilitate diffusion. EutH
+
cells grew normally at Eth
0
concentrations above 3 μM, close to the Km (9 μM) of the first degradative enzyme, ethanolamine ammonia lyase. It is suggested that EutH facilitates diffusion of Eth
0
. As predicted for a transporter, EutH contributed to the toxicity of ethanolamine seen under some conditions; furthermore, fusion of EutH to fluorescent Yfp protein provided evidence that EutH is a membrane protein.
Chemical Structure, Conjugation, and Cross-Reactivity ofBacillus pumilusSh18 Cell Wall Polysaccharide
Authors: Kubler-Kielb Joanna , Coxon Bruce , Schneerson Rachel
Published: October 2004

Bacillus pumilusstrain Sh18 cell wall polysaccharide (CWP), cross-reactive with the capsular polysaccharide ofHaemophilus influenzaetype b, was purified and its chemical structure was elucidated using fast atom bombardment mass spectrometry, nuclear magnetic resonance techniques, and sugar-specific degradation procedures. Two major structures, 1,5-poly(ribitol phosphate) and 1,3-poly(glycerol phosphate), with the latter partially substituted by 2-acetamido-2-deoxy-α-galactopyranose (13%) and 2-acetamido-2-deoxy-α-glucopyranose (6%) on positionO-2, were found. A minor component was established to be a polymer of →3-O-(2-acetamido-2-deoxy-β-glucopyranosyl)-1→4-ribitol-1-OPO3→. The ratios of the three components were 56, 34, and 10 mol%, respectively. The Sh18 CWP was covalently bound to carrier proteins, and the immunogenicity of the resulting conjugates was evaluated in mice. Two methods of conjugation were compared: (i) binding of 1-cyano-4-dimethylaminopyridinium tetrafluoroborate-activated hydroxyl groups of the CWP to adipic acid dihydrazide (ADH)-derivatized protein, and (ii) binding of the carbodiimide-activated terminal phosphate group of the CWP to ADH-derivatized protein. The conjugate-induced antibodies reacted in an enzyme-linked immunosorbent assay with the homologous polysaccharide and with a number of other bacterial polysaccharides containing ribitol and glycerol phosphates, includingH. influenzaetypes a and b and strains ofStaphylococcus aureusandStaphylococcus epidermidis.
Three Parallel Quorum-Sensing Systems Regulate Gene Expression in
Vibrio harveyi
Authors: Henke Jennifer M. , Bassler Bonnie L.
Published: October 2004

In a process called quorum sensing, bacteria communicate using extracellular signal molecules termed autoinducers. Two parallel quorum-sensing systems have been identified in the marine bacterium
Vibrio harveyi
. System 1 consists of the LuxM-dependent autoinducer HAI-1 and the HAI-1 sensor, LuxN. System 2 consists of the LuxS-dependent autoinducer AI-2 and the AI-2 detector, LuxPQ. The related bacterium,
Vibrio cholerae
, a human pathogen, possesses System 2 (LuxS, AI-2, and LuxPQ) but does not have obvious homologues of
V. harveyi
System 1. Rather, System 1 of
V. cholerae
is made up of the CqsA-dependent autoinducer CAI-1 and a sensor called CqsS. Using a
V. cholerae
CAI-1 reporter strain we show that many other marine bacteria, including
V. harveyi
, produce CAI-1 activity. Genetic analysis of
V. harveyi
reveals
cqsA
and
cqsS
, and phenotypic analysis of
V. harveyi cqsA
and
cqsS
mutants shows that these functions comprise a third
V. harveyi
quorum-sensing system that acts in parallel to Systems 1 and 2. Together these communication systems act as a three-way coincidence detector in the regulation of a variety of genes, including those responsible for bioluminescence, type III secretion, and metalloprotease production.
Crystal Structures ofEscherichia coliATP-Dependent Glucokinase and Its Complex with Glucose
Authors: Lunin Vladimir V. , Li Yunge , Schrag Joseph D. , Iannuzzi Pietro , Cygler Miroslaw , Matte Allan
Published: October 2004

Intracellular glucose inEscherichia colicells imported by phosphoenolpyruvate-dependent phosphotransferase system-independent uptake is phosphorylated by glucokinase by using ATP to yield glucose-6-phosphate. Glucokinases (EC 2.7.1.2) are functionally distinct from hexokinases (EC 2.7.1.1) with respect to their narrow specificity for glucose as a substrate. While structural information is available for ADP-dependent glucokinases fromArchaea, no structural information exists for the large sequence family of eubacterial ATP-dependent glucokinases. Here we report the first structure determination of a microbial ATP-dependent glucokinase, that fromE. coliO157:H7. The crystal structure ofE. coliglucokinase has been determined to a 2.3-Å resolution (apo form) and refined to finalRwork/Rfreefactors of 0.200/0.271 and to 2.2-Å resolution (glucose complex) with finalRwork/Rfreefactors of 0.193/0.265.E. coliGlK is a homodimer of 321 amino acid residues. Each monomer folds into two domains, a small α/β domain (residues 2 to 110 and 301 to 321) and a larger α+β domain (residues 111 to 300). The active site is situated in a deep cleft between the two domains.E. coliGlK is structurally similar toSaccharomyces cerevisiaehexokinase and human brain hexokinase I but is distinct from the ADP-dependent GlKs. Bound glucose forms hydrogen bonds with the residues Asn99, Asp100, Glu157, His160, and Glu187, all of which, except His160, are structurally conserved in human hexokinase 1. Glucose binding results in a closure of the small domains, with a maximal Cα shift of ∼10 Å. A catalytic mechanism is proposed that is consistent with Asp100 functioning as the general base, abstracting a proton from the O6 hydroxyl of glucose, followed by nucleophilic attack at the γ-phosphoryl group of ATP, yielding glucose-6-phosphate as the product.
Effect of Dimer Dissociation on Activity and Thermostability of the α-Glucuronidase fromGeobacillus stearothermophilus: Dissecting the Different Oligomeric Forms of Family 67 Glycoside Hydrolases
Authors: Shallom Dalia , Golan Gali , Shoham Gil , Shoham Yuval
Published: October 2004

The oligomeric organization of enzymes plays an important role in many biological processes, such as allosteric regulation, conformational stability and thermal stability. α-Glucuronidases are family 67 glycosidases that cleave the α-1,2-glycosidic bond between 4-O-methyl-d-glucuronic acid and xylose units as part of an array of hemicellulose-hydrolyzing enzymes. Currently, two crystal structures of α-glucuronidases are available, those fromGeobacillus stearothermophilus(AguA) and fromCellvibrio japonicus(GlcA67A). Both enzymes are homodimeric, but surprisingly their dimeric organization is different, raising questions regarding the significance of dimerization for the enzymes' activity and stability. Structural comparison of the two enzymes suggests several elements that are responsible for the different dimerization organization. Phylogenetic analysis shows that the α-glucuronidases AguA and GlcA67A can be classified into two distinct subfamilies of bacterial α-glucuronidases, where the dimer-forming residues of each enzyme are conserved only within its own subfamily. It seems that the different dimeric forms of AguA and GlcA67A represent the two alternative dimeric organizations of these subfamilies. To study the biological significance of the dimerization in α-glucuronidases, we have constructed a monomeric form of AguA by mutating three of its interface residues (W328E, R329T, and R665N). The activity of the monomer was significantly lower than the activity of the wild-type dimeric AguA, and the optimal temperature for activity of the monomer was around 35°C, compared to 65°C of the wild-type enzyme. Nevertheless, the melting temperature of the monomeric protein, 72.9°C, was almost identical to that of the wild-type, 73.4°C. It appears that the dimerization of AguA is essential for efficient catalysis and that the dissociation into monomers results in subtle conformational changes in the structure which indirectly influence the active site region and reduce the activity. Structural and mechanistic explanations for these effects are discussed.
Genomic Studies with
Escherichia coli
MelR Protein: Applications of Chromatin Immunoprecipitation and Microarrays
Authors: Grainger David C. , Overton Timothy W. , Reppas Nikos , Wade Joseph T. , Tamai Eiji , Hobman Jon L. , Constantinidou Chrystala , Struhl Kevin , Church George , Busby Stephen J. W.
Published: October 2004

Escherichia coli
MelR protein is a transcription activator that is essential for melibiose-dependent expression of the
melAB
genes. We have used chromatin immunoprecipitation to study the binding of MelR and RNA polymerase to the
melAB
promoter in vivo. Our results show that MelR is associated with promoter DNA, both in the absence and presence of the inducer melibiose. In contrast, RNA polymerase is recruited to the
melAB
promoter only in the presence of inducer. The MelR DK261 positive control mutant binds to the
melAB
promoter but cannot recruit RNA polymerase. Further analysis of immunoprecipitated DNA, by using an Affymetrix GeneChip array, showed that the
melAB
promoter is the major, if not the sole, target in
E. coli
for MelR. This was confirmed by a transcriptomics experiment to analyze RNA in cells either with or without
melR
.
Use of Fluorescent-Protein Tagging To Determine the Subcellular Localization of
Mycoplasma pneumoniae
Proteins Encoded by the Cytadherence Regulatory Locus
Authors: Kenri Tsuyoshi , Seto Shintaro , Horino Atsuko , Sasaki Yuko , Sasaki Tsuguo , Miyata Makoto
Published: October 2004

Mycoplasma pneumoniae
lacks a cell wall but has internal cytoskeleton-like structures that are assumed to support the attachment organelle and asymmetric cell shape of this bacterium. To explore the fine details of the attachment organelle and the cytoskeleton-like structures, a fluorescent-protein tagging technique was applied to visualize the protein components of these structures. The focus was on the four proteins—P65, HMW2, P41, and P24—that are encoded in the
crl
operon (for “cytadherence regulatory locus”), which is known to be essential for the adherence of
M. pneumoniae
to host cells. When the P65 and HMW2 proteins were fused to enhanced yellow fluorescent protein (EYFP), a variant of green fluorescent protein, the fused proteins became localized at the attachment organelle, enabling visualization of the organelles of living cells by fluorescence microscopy. The leading end of gliding
M. pneumoniae
cells, expressing the EYFP-P65 fusion, was observed as a focus of fluorescence. On the other hand, when the P41 and P24 proteins were labeled with EYFP, the fluorescence signals of these proteins were observed at the proximal end of the attachment organelle. Coexpression of the P65 protein labeled with enhanced cyan fluorescent protein clearly showed that the sites of localization of P41 and P24 did not overlap that of P65. The localization of P41 and P24 suggested that they are also cytoskeletal proteins that function in the formation of unknown structures at the proximal end of the attachment organelle. The fluorescent-protein fusion technique may serve as a powerful tool for identifying components of cytoskeleton-like structures and the attachment organelle. It can also be used to analyze their assembly.
Complete Genome Sequence of the Genetically Tractable Hydrogenotrophic MethanogenMethanococcus maripaludis
Authors: Hendrickson E. L. , Kaul R. , Zhou Y. , Bovee D. , Chapman P. , Chung J. , Conway de Macario E. , Dodsworth J. A. , Gillett W. , Graham D. E. , Hackett M. , Haydock A. K. , Kang A. , Land M. L. , Levy R. , Lie T. J. , Major T. A. , Moore B. C. , Porat I. , Palmeiri A. , Rouse G. , Saenphimmachak C. , Söll D. , Van Dien S. , Wang T. , Whitman W. B. , Xia Q. , Zhang Y. , Larimer F. W. , Olson M. V. , Leigh J. A.
Published: October 2004

The genome sequence of the genetically tractable, mesophilic, hydrogenotrophic methanogenMethanococcus maripaludiscontains 1,722 protein-coding genes in a single circular chromosome of 1,661,137 bp. Of the protein-coding genes (open reading frames [ORFs]), 44% were assigned a function, 48% were conserved but had unknown or uncertain functions, and 7.5% (129 ORFs) were unique toM. maripaludis. Of the unique ORFs, 27 were confirmed to encode proteins by the mass spectrometric identification of unique peptides. Genes for most known functions and pathways were identified. For example, a full complement of hydrogenases and methanogenesis enzymes was identified, including eight selenocysteine-containing proteins, with each being paralogous to a cysteine-containing counterpart. At least 59 proteins were predicted to contain iron-sulfur centers, including ferredoxins, polyferredoxins, and subunits of enzymes with various redox functions. Unusual features included the absence of a Cdc6 homolog, implying a variation in replication initiation, and the presence of a bacterial-like RNase HI as well as an RNase HII typical of theArchaea. The presence of alanine dehydrogenase and alanine racemase, which are uniquely present among theArchaea, explained the ability of the organism to usel- andd-alanine as nitrogen sources. Features that contrasted with the related organismMethanocaldococcus jannaschiiincluded the absence of inteins, even though close homologs of most intein-containing proteins were encoded. Although two-thirds of the ORFs had their highest Blastp hits inMethanocaldococcus jannaschii, lateral gene transfer or gene loss has apparently resulted in genes, which are often clustered, with top Blastp hits in more distantly related groups.
lpt6
, a Gene Required for Addition of Phosphoethanolamine to Inner-Core Lipopolysaccharide of
Neisseria meningitidis
and
Haemophilus influenzae
Authors: Wright J. Claire , Hood Derek W. , Randle Gaynor A. , Makepeace Katherine , Cox Andrew D. , Li Jianjun , Chalmers Ronald , Richards James C. , Moxon E. Richard
Published: October 2004

We previously described a gene,
lpt3
, required for the addition of phosphoethanolamine (PEtn) at the 3 position on the β-chain heptose (HepII) of the inner-core
Neisseria meningitidis
lipopolysaccharide (LPS), but it has long been recognized that the inner-core LPS of some strains possesses PEtn at the 6 position (PEtn-6) on HepII. We have now identified a gene,
lpt6
(NMA0408), that is required for the addition of PEtn-6 on HepII. The
lpt6
gene is located in a region previously identified as Lgt-3 and is associated with other LPS biosynthetic genes. We screened 113 strains, representing all serogroups and including disease and carriage strains, for the
lpt3
and
lpt6
genes and showed that 36% contained both genes, while 50% possessed
lpt3
only and 12% possessed
lpt6
only. The translated amino acid sequence of
lpt6
has a homologue (72.5% similarity) in a product of the
Haemophilus influenzae
Rd genome sequence. Previous structural studies have shown that all
H. influenzae
strains investigated have PEtn-6 on HepII. Consistent with this, we found that, among 70 strains representing all capsular serotypes and nonencapsulated
H. influenzae
strains, the
lpt6
homologue was invariably present. Structural analysis of LPS from
H. influenzae
and
N. meningitidis
strains where
lpt6
had been insertionally inactivated revealed that PEtn-6 on HepII could not be detected. The translated amino acid sequences from the
N. meningitidis
and
H. influenzae lpt6
genes have conserved residues across their lengths and are part of a family of proven or putative PEtn transferases present in a wide range of gram-negative bacteria.
ParB ofPseudomonas aeruginosa: Interactions with Its Partner ParA and Its TargetparSand Specific Effects on Bacterial Growth
Authors: Bartosik Aneta A. , Lasocki Krzysztof , Mierzejewska Jolanta , Thomas Christopher M. , Jagura-Burdzy Grazyna
Published: October 2004

Thepargenes ofPseudomonas aeruginosahave been studied to increase the understanding of their mechanism of action and role in the bacterial cell. Key properties of the ParB protein have been identified and are associated with different parts of the protein. The ParB- ParB interaction domain was mapped in vivo and in vitro to the C-terminal 56 amino acids (aa); 7 aa at the C terminus play an important role. The dimerization domain ofP. aeruginosaParB is interchangeable with the dimerization domain of KorB from plasmid RK2 (IncP1 group). The C-terminal part of ParB is also involved in ParB-ParA interactions. Purified ParB binds specifically to DNA containing a putativeparSsequence based on the consensus sequence found in the chromosomes ofBacillus subtilis, Pseudomonas putida, andStreptomyces coelicolor. The overproduction of ParB was shown to inhibit the function of genes placed nearparS. This “silencing” was dependent on theparSsequence and its orientation. The overproduction ofP. aeruginosaParB or its N-terminal part also causes inhibition of the growth ofP. aeruginosaandP. putidabut notEscherichia colicells. Since this inhibitory determinant is located well away from ParB segments required for dimerization or interaction with the ParA counterpart, this result may suggest a role for the N terminus ofP. aeruginosaParB in interactions with host cell components.
Thirty-Eight C-Terminal Amino Acids of the Coupling Protein TraD of the F-Like Conjugative Resistance Plasmid R1 Are Required and Sufficient To Confer Binding to the Substrate Selector Protein TraM
Authors: Beranek Andreas , Zettl Markus , Lorenzoni Klaus , Schauer Alexandra , Manhart Michael , Koraimann Günther
Published: October 2004

Coupling proteins (CPs) are present in type IV secretion systems of plant, animal, and human pathogens and are essential for DNA transfer in bacterial conjugation systems. CPs connect the DNA-processing machinery to the mating pair-forming transfer apparatus. In this report we present in vitro and in vivo data that demonstrate specific binding of CP TraD of the IncFII R1 plasmid transfer system to relaxosomal protein TraM. With overlay assays and enzyme-linked immunosorbent assays we showed that a truncated version of TraD, termed TraD11 (ΔN155), interacted strongly with TraM. The apparent TraD11-TraM association constant was determined to be 2.6 × 10
7
liters/mol. Electrophoretic mobility shift assays showed that this variant of TraD also strongly bound to TraM when it was in complex with its target DNA. When 38 amino acids were additionally removed from the C terminus of TraD, no binding to TraM was observed. TraD15, comprising the 38 amino-acid-long C terminus of TraD, bound to TraM, indicating that the main TraM interaction domain resides in these 38 amino acids of TraD. TraD15 exerted a dominant negative effect on DNA transfer but not on phage infection by pilus-specific phage R17, indicating that TraM-TraD interaction is important for conjugative DNA transfer but not for phage infection. We also observed that TraD encoded by the closely related F factor bound to TraM encoded by the R1 plasmid. Our results thus provide evidence that substrate selection within the IncF plasmid group is based on TraM's capability to select the correct DNA molecule for transport and not on substrate selection by the CP.
Genome-Wide Transcriptional Analysis of the Cold Shock Response in Wild-Type and Cold-Sensitive, Quadruple-
csp
-Deletion Strains of
Escherichia coli
Authors: Phadtare Sangita , Inouye Masayori
Published: October 2004

A DNA microarray-based global transcript profiling of
Escherichia coli
in response to cold shock showed that in addition to the known cold shock-inducible genes, new genes such as the flagellar operon, those encoding proteins involved in sugar transport and metabolism, and remarkably, genes encoding certain heat shock proteins are induced by cold shock. In the light of strong reduction in metabolic activity of the cell after temperature downshift, the induction of sugar metabolism machinery is unexpected. The deletion of four
csp
s (
cspA
,
cspB
,
cspG
, and
cspE
) affected cold shock induction of mostly those genes that are transiently induced in the acclimation phase, emphasizing that CspA homologues are essential in the acclimation phase. Relevance of these findings with respect to the known RNA chaperone function of CspA homologues is discussed.
Evidence for Polyadenylated mRNA in
Pseudomonas aeruginosa
Authors: Saravanamuthu Senthil Selvan , von Götz Franz , Salunkhe Prabhakar , Chozhavendan Rathinam , Geffers Robert , Buer Jan , Tümmler Burkhard , Steinmetz Ivo
Published: October 2004

In this paper, we report the synthesis of
Pseudomonas aeruginosa
cDNA in the presence of oligo(dT) primers. Hybridization of oligonucleotide DNA microarrays indicates that under the experimental conditions used, at least 43.7% of the expressed genes from
P. aeruginosa
PAO1, representing many different functional classes, can be detected by using oligo(dT)-primed cDNAs.
Treponema pallidumFibronectin-Binding Proteins
Authors: Cameron Caroline E. , Brown Elizabeth L. , Kuroiwa Janelle M. Y. , Schnapp Lynn M. , Brouwer Nathan L.
Published: October 2004

Putative adhesins were predicted by computer analysis of theTreponema pallidumgenome. Two treponemal proteins, Tp0155 and Tp0483, demonstrated specific attachment to fibronectin, blocked bacterial adherence to fibronectin-coated slides, and supported attachment of fibronectin-producing mammalian cells. These results suggest Tp0155 and Tp0483 are fibronectin-binding proteins mediatingT. pallidum-host interactions.
INFLUENCE OF THE INITIAL SOURCE OF EPIDEMIC AND PREVENTIVE VACCINATION ON THE SPREADING PHENOMENA IN A TWO-DIMENSIONAL LATTICE
Authors: KOSIŃSKI R. A. , ADAMOWSKI Ł.
Published: October 2004

The probabilistic model of epidemic in a two-dimensional lattice with an additional random, long range connections characteristic for the small world networks is presented. Relations describing the spreading process of epidemics, like epidemic curve or range of epidemic in time, were found. The influence of the borders of the lattice and the localization of the initial source of epidemic on the epidemic curve is found analytically. The application of the preventive vaccination in the population is discussed.
STRUCTURAL, ELECTRONIC AND MAGNETIC PROPERTIES OF SMALL TinAl (n=1–8) CLUSTERS
Authors: XIANG J. , YAN X. H. , MAO Y. L. , XIAO Y. , WEI S. H.
Published: October 2004

Equilibrium geometries, stabilities, electronic and magnetic properties of Ti n Al (n=1–8) clusters have been studied by using density-functional theory (DFT). The ground-state structures of Ti n Al clusters have been obtained. The resulting geometries show that the aluminum atom remains on the surface of clusters. The evolution of energy difference and gap (HOMO–LUMO) with size of cluster shows Ti 4 Al cluster to be endowed with special stability. The average magnetic moments and the density of states (DOS) are also presented.
RESPONSE FUNCTIONS TO CRITICAL SHOCKS IN SOCIAL SCIENCES: AN EMPIRICAL AND NUMERICAL STUDY
Authors: ROEHNER B. M. , SORNETTE D. , ANDERSEN J. V.
Published: October 2004

We show that, provided one focuses on properly selected episodes, one can apply to the social sciences the same observational strategy that has proved successful in natural sciences such as astrophysics or geodynamics. For instance, in order to probe the cohesion of a society, one can, in different countries, study the reactions to some huge and sudden exogenous shocks, which we call Dirac shocks. This approach naturally leads to the notion of structural (as opposed or complementary to temporal) forecast. Although structural predictions are by far the most common way to test theories in the natural sciences, they have been much less used in the social sciences. The Dirac shock approach opens the way to testing structural predictions in the social sciences. The examples reported here suggest that critical events are able to reveal pre-existing "cracks" because they probe the social cohesion which is an indicator and predictor of future evolution of the system, and in some cases they foreshadow a bifurcation. We complement our empirical work with numerical simulations of the response function ("damage spreading") to Dirac shocks in the Sznajd model of consensus build-up. We quantify the slow relaxation of the difference between perturbed and unperturbed systems, the conditions under which the consensus is modified by the shock and the large variability from one realization to another.
THE ORDERING KINETICS OF ISING SPINS ON THE HONEYCOMB LATTICE
Authors: CHEON MOOKYUNG , CHANG IKSOO
Published: October 2004

We investigate the coarsening dynamics of the Ising model on the honeycomb lattice by Monte Carlo simulation. Although the domain growth law and the persistence exponent at nonzero finite temperature are consistent with the known values of the two-dimensional (2D) Ising model on the square lattice, the nonequilibrium relaxation behavior of this model however shows the interesting and different relaxation properties of two-step relaxation due to the pinning effect and the slow activation process at a low temperature. Multispin heat bath dynamics is used to remove such a pinning effect, which results in the same relaxation behavior of the 2D Ising model as on the square lattice.
SZNAJD OPINION DYNAMICS WITH GLOBAL AND LOCAL NEIGHBORHOOD
Authors: SCHULZE CHRISTIAN
Published: October 2004

In this modification of the Sznajd consensus model on the square lattice, two people of arbitrary distance who agree in their opinions convince their nearest neighbors of this opinion. Similarly to the mean field theory of Slanina and Lavicka, the times needed to reach consensus are distributed exponentially and are quite small. The width of the phase transition vanishes reciprocally to the linear lattice dimension. Advertising has effects independent of the system size. For more than two opinions, three opinions reach a consensus in roughly half of the samples, and four only rarely and only for small lattices. Up to 109 agents were simulated.
ON STABILIZATION OF SOLUTIONS OF COMPLEX COUPLED NONLINEAR SCHRÖDINGER EQUATIONS
Authors: MAHMOUD GAMAL M. , FARGHALY AHMED A. M.
Published: October 2004

We study the stabilization of nonchaotic periodic and quasi-periodic solutions of both integrable (α=1) and nonintegrable (α=2/3) of CCNLS equations of the form: [Formula: see text] where subscripts mean partial derivatives, p(x,t) and q(x,t) are the orthogonal components of an electric field in a glass fiber, [Formula: see text], the defocusing (σ=-1) and focusing (σ=1) cases are distinguished by σ; g1(x) and g2(x) are periodic functions in x and γ; and ω1 and ω2 are parameters. These solutions do not display sensitive dependence on initial conditions. The stabilization of solutions are studied using a feedback control method and their maximal Lyapunov exponents are calculated. Periodic solutions of this system are important in the study of these coupled equations, since they represent stationary or repeatable behavior.
DETERMINATIONS OF UPPER CRITICAL FIELDS IN CONTINUOUS GINZBURG–LANDAU MODEL
Authors: WANG L. , LIM H. S. , ONG C. K.
Published: October 2004

Novel procedures to determine the parallel upper critical field Bc2 (one-dimensional, 1D) have been proposed within a continuous Ginzburg–Landau model. Unlike conventional methods, where Bc2 is obtained through the determination of the smallest eigenvalue of an appropriate eigen equation, the square of the magnetic field is treated as eigenvalue problems by two procedures so that the upper critical field can be directly deduced. The two procedures proposed are extended to determine the upper critical field in the c–a crystal plane (two-dimensional, 2D) with an arbitrary angle θ tilted from the c-axis.

The calculated Bc2 from the two procedures are consistent with each other in both 1D and 2D cases. Moreover, the values of Bc2 near the direction parallel to the layers obtained in the 2D case well approximate the counterparts in the 1D case. The properties of the calculated Bc2 are in reasonably good agreement with existing theories and experiments. The profiles of the order parameters associated with Bc2 for both 1D and 2D cases are Gaussian-like, further validating the methodology proposed.
CHAOS SYNCHRONIZATION OF TWO COUPLED DYNAMOS SYSTEMS WITH UNKNOWN SYSTEM PARAMETERS
Authors: AGIZA H. N.
Published: October 2004

This paper addresses the synchronization problem of two coupled dynamos systems in the presence of unknown system parameters. Based on Lyapunov stability theory, an active control law is derived and activated to achieve the state synchronization of two identical coupled dynamos systems. By using Gerschgorin theorem, a simple generic criterion is derived for global synchronization of two coupled dynamos systems with a unidirectional linear error feedback coupling. This simple criterion is applicable to a large class of chaotic systems, where only a few algebraic inequalities are involved. Numerical simulations results are used to demonstrate the effectiveness of the proposed control methods.
DYNAMIC MOVES IN LATTICE SIMULATION OF PROTEIN FOLDING
Authors: ZHANG LINSEN , CHEN CHANGJUN , HE YI , XIAO YI
Published: October 2004

Lattice simulation is one important method to investigate the universal principle of protein folding. The move set is a basic element in lattice simulation. We used two move sets, dynamic move set and rigid rotation move, to run simulation and compare the thermodynamic and kinetic properties. The results indicate that the dynamic move set has advantage to simulate protein folding.
ON THE STRUCTURAL AND ENERGETIC FEATURES OF SMALL METAL CLUSTERS:Nin,Cun,Pdn,Ptn, ANDPbn; n=3–13
Authors: EL-BAYYARI ZUHEIR , OYMAK HÜSEYIN , KÖKTEN HATICE
Published: October 2004

Using an empirical potential energy function parametrized for each of the Ni , Cu , Pd , Pt , and Pb systems, minimum-energy structures of Nin, Cun, Pdn, Ptn, and Pbn(n=3–13) microclusters have been determined by performing molecular-dynamics simulations. The structural and energetic features of the obtained microclusters have been investigated.
QUASI-VARIATIONAL INEQUALITIES IN TRANSPORTATION NETWORKS
Authors: SCRIMALI LAURA
Published: October 2004

This paper aims to consider user equilibrium problems in transportation networks in the most complete and realistic situations. In fact, the presented model allows for the dependence of data on time, the presence of elastic travel demands, the capacity restrictions and delay effects. The equilibrium conditions for such a model are given and the equivalent formulation in terms of a quasi-variational inequality is discussed. Moreover, a theorem for the existence of solutions is shown and a numerical example is provided. Finally, some questions of stability are studied.
THE LANGEVIN OR KRAMERS APPROACH TO BIOLOGICAL MODELING
Authors: HADELER KARL P. , HILLEN THOMAS , LUTSCHER FRITHJOF
Published: October 2004

In the Langevin or Ornstein–Uhlenbeck approach to diffusion, stochastic increments are applied to the velocity rather than to the space variable. The density of this process satisfies a linear partial differential equation of the general form of a transport equation which is hyperbolic with respect to the space variable but parabolic with respect to the velocity variable, the Klein–Kramers or simply Kramers equation. This modeling approach allows for a more detailed description of individual movement and orientation dependent interaction than the frequently used reaction diffusion framework.

For the Kramers equation, moments are computed, the infinite system of moment equations is closed at several levels, and telegraph and diffusion equations are derived as approximations. Then nonlinearities are introduced such that the semi-linear reaction Kramers equation describes particles which move and interact on the same time-scale. Also for these nonlinear problems a moment approach is feasible and yields nonlinear damped wave equations as limiting cases.

We apply the moment method to the Kramers equation for chemotactic movement and obtain the classical Patlak–Keller–Segel model. We discuss similarities between chemotactic movement of bacteria and gravitational movement of physical particles.
Chronic exposure to β-hydroxybutyrate inhibits glucose-induced insulin release from pancreatic islets by decreasing NADH contents
Authors: Takehiro Mihoko , Fujimoto Shimpei , Shimodahira Makiko , Shimono Dai , Mukai Eri , Nabe Koichiro , Radu Razvan Gheorghe , Kominato Rieko , Aramaki Yo , Seino Yutaka , Yamada Yuichiro
Published: October 2004

To investigate the effects of chronic exposure to ketone bodies on glucose-induced insulin secretion, we evaluated insulin release, intracellular Ca2+and metabolism, and Ca2+efficacy of the exocytotic system in rat pancreatic islets. Fifteen-hour exposure to 5 mM d-β-hydroxybutyrate (HB) reduced high glucose-induced insulin secretion and augmented basal insulin secretion. Augmentation of basal release was derived from promoting the Ca2+-independent and ATP-independent component of insulin release, which was suppressed by the GDP analog. Chronic exposure to HB affected mostly the second phase of glucose-induced biphasic secretion. Dynamic experiments showed that insulin release and NAD(P)H fluorescence were lower, although the intracellular Ca2+concentration ([Ca2+]i) was not affected 10 min after exposure to high glucose. Additionally, [Ca2+]iefficacy in exocytotic system at clamped concentrations of ATP was not affected. NADH content, ATP content, and ATP-to-ADP ratio in the HB-cultured islets in the presence of high glucose were lower, whereas glucose utilization and oxidation were not affected. Mitochondrial ATP production shows that the respiratory chain downstream of complex II is not affected by chronic exposure to HB, and that the decrease in ATP production is due to decreased NADH content in the mitochondrial matrix. Chronic exposure to HB suppresses glucose-induced insulin secretion by lowering the ATP level, at least partly by inhibiting ATP production by reducing the supply of NADH to the respiratory chain. Glucose-induced insulin release in the presence of aminooxyacetate was not reduced, which implies that chronic exposure to HB affects the malate/aspartate shuttle and thus reduces NADH supply to mitochondria.
β-Cell function and islet morphology in normal, obese, and obese β-cell mass-reduced Göttingen minipigs
Authors: Larsen M. O. , Juhl C. B. , Pørksen N. , Gotfredsen C. F. , Carr R. D. , Ribel U. , Wilken M. , Rolin B.
Published: October 2004

Herein, we bridge β-cell function and morphology in minipigs. We hypothesized that different aspects of β-cell dysfunction are present in obesity and obesity with reduced β-cell mass by using pulsatile insulin secretion as an early marker. Measures for β-cell function (glucose and arginine stimulation plus baseline and glucose-entrained pulsatile insulin secretion) and islet morphology were studied in long-term (19–20 mo) obese ( n = 5) and obese β-cell-reduced [nicotinamide + streptozotocin (STZ), n = 5] minipigs and normal controls, representing different stages in the development toward type 2 diabetes. Acute insulin response (AIR) to glucose and arginine were, surprisingly, normal in obese (0.3 g/kg glucose: AIR = 246 ± 119 vs. 255 ± 61 pM in control; 67 mg/kg arginine: AIR = 230 ± 124 vs. 214 ± 85 pM in control) but reduced in obese-STZ animals (0.3 g/kg glucose: AIR = 22 ± 36, P < 0.01; arginine: AIR = 87 ± 92 pM, P < 0.05 vs. control). Baseline pulsatile insulin secretion was reduced in obese (59 ± 16 vs. 76 ± 16% in control, P < 0.05) and more so in obese-STZ animals (43 ± 13%, P < 0.01), whereas regularity during entrainment was increased in obese animals (approximate entropy: 0.85 ± 0.14 vs. 1.13 ± 0.13 in control, P < 0.01). β-Cell mass (mg/kg body wt) was normal in obese and reduced in obese-STZ animals, with pancreatic fat infiltration in both groups. In conclusion, obesity and insulin resistance are not linked with a general reduction of β-cell function, but dynamics of insulin secretion are perturbed. The data suggest a sequence in the development of β-cell dysfunction, with the three groups representing stages in the progression from normal physiology to diabetes, and assessment of pulsatility as the single most sensitive marker of β-cell dysfunction.
Tacrolimus suppresses glucose-induced insulin release from pancreatic islets by reducing glucokinase activity
Authors: Radu Razvan Gheorghe , Fujimoto Shimpei , Mukai Eri , Takehiro Mihoko , Shimono Dai , Nabe Koichiro , Shimodahira Makiko , Kominato Rieko , Aramaki Yo , Nishi Yuichi , Funakoshi Shogo , Yamada Yuichiro , Seino Yutaka
Published: October 2004

Tacrolimus is widely used for immunosuppressant therapy, including various organ transplantations. One of its main side effects is hyperglycemia due to reduced insulin secretion, but the mechanism remains unknown. We have investigated the metabolic effects of tacrolimus on insulin secretion at a concentration that does not influence insulin content. Twenty-four-hour exposure to 3 nM tacrolimus reduced high glucose (16.7 mM)-induced insulin secretion (control 2.14 ± 0.08 vs. tacrolimus 1.75 ± 0.02 ng·islet−1·30 min−1, P < 0.01) without affecting insulin content. In dynamic experiments, insulin secretion and NAD(P)H fluorescence during a 20-min period after 10 min of high-glucose exposure were reduced in tacrolimus-treated islets. ATP content and glucose utilization of tacrolimus-treated islets in the presence of 16.7 mM glucose were less than in control (ATP content: control 9.69 ± 0.99 vs. tacrolimus 6.52 ± 0.40 pmol/islet, P < 0.01; glucose utilization: control 103.8 ± 6.9 vs. tacrolimus 74.4 ± 5.1 pmol·islet−1·90 min−1, P < 0.01). However, insulin release from tacrolimus-treated islets was similar to that from control islets in the presence of 16.7 mM α-ketoisocaproate, a mitochondrial fuel. Glucokinase activity, which determines glycolytic velocity, was reduced by tacrolimus treatment (control 65.3 ± 3.4 vs. tacrolimus 49.9 ± 2.8 pmol·islet−1·60 min−1, P < 0.01), whereas hexokinase activity was not affected. These results indicate that glucose-stimulated insulin release is decreased by chronic exposure to tacrolimus due to reduced ATP production and glycolysis derived from reduced glucokinase activity.
Interactions of TGF-dependent and myogenic oscillations in tubular pressure
Authors: Chon Ki H. , Raghavan Ramakrishna , Chen Yu-Ming , Marsh Donald J. , Yip Kay-Pong
Published: October 2004

We have previously shown that there are two oscillating components in spontaneously fluctuating single-nephron blood flow obtained from Sprague-Dawley rats (Yip K-P, Holstein-Rathlou NH, and Marsh DJ. Am J Physiol Renal Physiol 264: F427–F434, 1993). The slow oscillation (20–30 mHz) is mediated by tubuloglomerular feedback (TGF), whereas the fast oscillation (100 mHz) is probably related to spontaneous myogenic activity. The fast oscillation is rarely detected in spontaneous tubular pressure because of its small magnitude and the fact that tubular compliance filters pressure waves. We detected myogenic oscillation superimposed on TGF-mediated oscillation when ambient tubular flow was interrupted. Two well-defined peaks are present in the mean power spectrum of stop-flow pressure (SFP) centering at 25 and 100 mHz ( n = 13), in addition to a small peak at 125–130 mHz. Bispectral analysis indicates that two of these oscillations (30 and 100 mHz) interact nonlinearly to produce the third oscillation at 125–130 mHz. The presence of nonlinear interactions between TGF and myogenic oscillations indicates that estimates of the relative contribution of each of these mechanisms in renal autoregulation need to account for this interaction. The magnitude of myogenic oscillations was considerably smaller in the SFP measured from spontaneously hypertensive rats (SHR, n = 13); consequently, nonlinear interactions were not observed with bispectral analysis. Reduced augmentation of myogenic oscillations in SFP of SHR might account for the failure in detecting nonlinear interactions in SHR.