bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

ABSTRACTThirteen 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

ABSTRACT

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

ABSTRACT

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

ABSTRACT

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

ABSTRACT

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

ABSTRACTWe 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

ABSTRACT

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

ABSTRACT

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.
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.
Growth of the Organic Molecular Semiconductor PTCDA on Se-Passivated GaAs(100): An STM Study
Authors: Kendrick C. , Kahn A. 
Published: August 2003

We investigate the monolayer and multilayer growth of the organic molecular semiconductor (OMS) 3, 4, 9, 10-perylenetetracarboxylic dianhydride (PTCDA) on the Se-passivated GaAs(100) (2 × 1) surface using STM. Deposition of ~2 ML PTCDA at room temperature results in the formation of clusters, implying good chemical passivation of the substrate. However, we also find a significant number of molecules pinned at high energy defect sites, some of which induce molecular ordering. At higher PTCDA coverage we find that the film invariably orients to the substrate revealing a critical, though weak, molecule-substrate interaction. We present the first molecularly resolved STM images obtained from a thick PTCDA film (~ 60 Å) and show unit cell dimensions and orientation in excellent greement with our previous LEED study.
X-Ray Investigation of the Degradation of Zn-Doped GaInAsP/InP Heterointerface
Authors: Aleksandrov P. A. , Belova N. E. , Nazarov S. A. , Nefedov A. A. , Fanchenko S. S. , Chaplanov V. A. , Yu. Schumilov D. 
Published: August 2003

We report the results of crystal truncation rod study for the following heterostructure: GaInAsP layer grown on Zn-doped InP substrate. Two series of experiments have been performed within 4.5 years. The profiles of coherent (200) polarizability and lattice mismatch have been derived by fitting experimental diffraction intensity data. The comparison of these profiles for two series has shown essential enlargement of the distorted interface region with time. The obtained degradation length value 0.15 μm is consistent with the estimations for the degradation spatial scale due to Zn-induced interdiffusion of In ions through the interface.
Structure of TiO2 Rutile (110) (1 × 1) from Ion Scattering Measurements
Authors: Hird B. , Armstrong R. A. , Seel J. A. 
Published: August 2003

9.22 keV oxygen ion scattering has been used to examine the (110) surface structure of TiO 2 rutile. Peaks in the spectrum of the emitted ions at 45° and at 77° are found at the energies expected for O +– Ti and O +– O collisions by surface atoms. Surface preoparation to optimize the 1 × 1 structure involved annealing a previously sputtered surface to 600°C, first in 10-6 Torr of O 2, and then in UHV. Azimuthal and elevation angular variations of the yields for low incidence angles show shadowing effects. Preliminary analysis seems to be consistent with the (1 × 1) model of a complete surface layer, with rows of oxygen atoms above on the titanium bridge sites. The data suggests that our sample preparation produces incomplete rows of above-surface oxygen atoms, or frequent steps.
In Situ Grazing Incidence X-ray Scattering Study of the Epitaxial Growth of Ag on MgO(001)
Authors: Robach O. , Renaud G. , Barbier A. , Guénard P. 
Published: August 2003

The growth of Ag on MgO(001) was investigated from sub monolayer up to 600 Å coverage. A new method for the preparation of very flat, clean and stoichiometric MgO(001) surfaces is described. The growth is found to be intrinsic, with negligible influence of surface defects. Twins appear at the very first stages of deposition while stacking faults form during the coalescence. A detailed mechanism is proposed for the elastic and plastic misfit relaxation processes. The introduction of a new dislocation within an island is, whatever its size, preceded by a strong deformation of its edges. Plastic relaxation is shown to be a continuous process that starts well before coalescence and the appearance of an interfacial dislocation network.