bluuebunny/crossref_metadata_2025_split huggingface dataset:
Preliminary Testing of an ICT‐Based Learning Support System in Helsinki
Authors: Karaharju‐Suvanto T. , Noponen J. , Pakkanen A. L. 
Published: April 2004

Background and aim:  During dental education, it would be beneficial for the students to be able to combine theoretical teaching with practical work in a logical manner. For this purpose, a Portfolio software has been developed to facilitate ICT‐based learning with DecaMedia Ltd. Test phase had several aims; test the functionality of the software and add necessary refinements, test the flow of information from teachers to students in different forms and to analyse the possible problems in the use of this software and in ICT‐based learning in general.Material and methods:  A group of teachers and students were gathered to test the usefulness of the new software. Prior to this phase, there had been some testing and a questionnaire study on ICT skills and attitudes. During the first period of this project, the software was customized by DecaMedia to meet our demands. Different access levels were created. The students gathered interesting patient cases and took documents in several media forms. The teachers added theoretical material to combine scientific knowledge with practical work either directly or using links.Results and conclusions:  In general, the following areas were noted: this media is good for supporting assessment . When patient files are added, the importance of privacy protection is high as the files are transferred via network. For theoretical material, the copyright has to be considered as well as the size of network‐delivered documents. This program has a user‐friendly interface. Attachment of different file types was straightforward. The operating language of the program is Finnish, which helps less‐experienced students to get started. There are still some limitations, mainly in stability. We found the program useful to support dental education, but more ICT training will be required for both students and teachers. ICT learning can be beneficial addition in dental education.
Do osmotic forces play a role in the uptake of water by human skin?
Authors: Van Kemenade Patricia M. , Houben Mark M. J. , Huyghe Jacques M. , Douven Lucien F. A. 
Published: April 2004

Background/purpose: To describe the water and ion transport through the skin under different conditions, we developed a three‐component mixture model. This model has proven to describe the transient change in transepidermal water loss (TEWL) after a change in relative humidity and the result of damage to the skin. Osmotic forces arc present in the model. To assess the influence of osmotic forces on the water uptake of the skin, we investigated transient TEWL values after 1 h application of salt solutions of different molarities (0, 1, and 4 M NaCl).Methods: Filters saturated with 0, 1, and 4 M NaCl solution were applied for 1 h under occlusion. TEWL was measured 50–90 min after removal of the solution. The transient water loss curves were fit with an exponential function. The area under the fitted curve was calculated and regarded as a measure for the amount of extra water absorbed in the skin.Results: For all molarities, TEWL is increased immediately after removal of the solution. In time, this increase decays until pre‐application values are reached again. The rate of decrease differs significantly for all three molarities. Ninety‐five per cent of the increase has been reversed after 30, 19, and 6 min for the 0, 1, and 4 M case, respectively. The amount of water absorbed differs significantly between the three molarities 7.3±2.0; 3.9±1.0; 2.0±0.5 g/m2, respectively.Conclusions: In all cases, there was an increase in TEWL immediately after removal of the solution. The significant differences in decay time and amount of water absorbed between the three molarities indicate that osmotic forces do play an important role in the water uptake.
In vivo epidermal thickness measurement: ultrasound vs. confocal imaging
Authors: Nouveau‐Richard S. , Monot M. , Bastien P. , De Lacharrière O. 
Published: April 2004

Background/purpose: In this study, in vivo skin imaging methods, ultrasound (US) and confocal microscopy (CM) were compared with regards to their accuracy in measuring the epidermal thickness. In addition an attempt was made to clarify the biological significance of the second echo‐rich line observed on US skin images, i.e. whether it represents the dermal–epidermal junction or the papillar–reticular dermis limit.Methods: US images were obtained with an in‐house device (22 MHz probe) and the CM images with the VivaScope 1000 (Lucid Inc., Rochester, NY, USA). Skin from the dorsal forearm, the back of hand and the palm skin of 11 subjects (25–40 years) were examined. Repeatability of the procedure and reproducibility of the results were evaluated on repeated measurements taken at 1‐month interval.Results: Both techniques are correlated. When a CM measurement is performed from the stratum corneum (SC) surface to the bottom of the papillae, results obtained with US and CM are very similar. Thus, the second echo‐rich line on US skin imaging is likely to reflect a virtual line joining the bottom of the papillae. CM is limited to the measurement of a relative thin epidermis, due to the signal‐to‐noise ratio, which decreases with depth. US technique offers a better repeatability and reproducibility, particularly for SC measurement. This is mainly due to the small size of the investigated field of view in CM.Conclusion: This study confirms the accuracy of US and the feasibility of CM imaging techniques for in vivo epidermal thickness measurement. Echography probably measures a maximal epidermal thickness since it encompasses the bottom of the papillae.
Metabolic Activity of
Staphylococcus epidermidis
Is High during Initial and Low during Late Experimental Foreign-Body Infection
Authors: Vandecasteele Stefaan Johan , Peetermans Willy Eduard , Carbonez An , Van Eldere Johan 
Published: April 2004

ABSTRACT

Foreign-body infection (FBI) is notoriously resistant to eradication by antibiotic treatment. It is hypothesized that reduced bacterial metabolic activity contributes to this resistance. We examined the metabolic activity of
Staphylococcus epidermidis
in 204 samples recovered during in vitro foreign-body colonization and in 424 samples recovered during in vivo FBI in a rat model. Metabolic activity was measured by determining the amount of 16S rRNA per genome by quantitative PCR. The initial foreign-body-associated growth proved to be a metabolically active process, both in vitro and in vivo. The initial 16S rRNA content was similar to that observed during in vitro exponential-growth phase. However, during late in vivo FBI, a 114-fold (
P
≪ 0.0001) decrease in the 16S rRNA content was observed, indicating that there was markedly decreased metabolic activity. This decreased metabolic activity during late FBI can explain at least in part why such infections are so difficult to eradicate with conventional antibiotic treatment.
TheHelicobacter pylori flaA1andwbpBGenes Control Lipopolysaccharide and Flagellum Synthesis and Function
Authors: Merkx-Jacques A. , Obhi R. K. , Bethune G. , Creuzenet C. 
Published: April 2004

ABSTRACTflaA1andwbpBare conserved genes with unknown biological function inHelicobacter pylori.Since both genes are predicted to be involved in lipopolysaccharide (LPS) biosynthesis, flagellum assembly, or protein glycosylation, they could play an important role in the pathogenesis ofH. pylori.To determine their biological role, both genes were disrupted in strain NCTC 11637. Both mutants exhibited altered LPS, with loss of most O-antigen and core modification, and increased sensitivity to sodium dodecyl sulfate compared to wild-type bacteria. These defects could be complemented in a gene-specific manner. Also,flaA1could complement these defects in thewbpBmutant, suggesting a potential redundancy of the reductase activity encoded by both genes. Both mutants were nonmotile, although thewbpBmutant still produced flagella. The defect in the flagellum functionality of this mutant was not due to a defect in flagellin glycosylation since flagellins from wild-type strain NCTC 11637 were shown not to be glycosylated. TheflaA1mutant produced flagellins but no flagellum. Overall, the similar phenotypes observed for both mutants and the complementation of thewbpBmutant byflaA1suggest that both genes belong to the same biosynthesis pathway. The data also suggest thatflaA1andwbpBare at the interface between several pathways that govern the expression of different virulence factors. We propose that FlaA1 and WbpB synthesize sugar derivatives dedicated to the glycosylation of proteins which are involved in LPS and flagellum production and that glycosylation regulates the activity of these proteins.
Transgenic Expression of RecA of the SpirochetesBorrelia burgdorferiandBorrelia hermsiiinEscherichia coliRevealed Differences in DNA Repair and Recombination Phenotypes
Authors: Putteet-Driver Adrienne D. , Zhong Jianmin , Barbour Alan G. 
Published: April 2004

ABSTRACTAfter unsuccessful attempts to recover a viable RecA-deficient mutant of the Lyme borreliosis agentBorrelia burgdorferi, we characterized the functional activities of RecA ofB. burgdorferi, as well as RecA of the relapsing fever spirocheteBorrelia hermsiiand the free-living spirocheteLeptospira biflexa, in arecAmutant ofEscherichia coli. As a control,E. coliRecA was expressed from the same plasmid vector. DNA damage repair activity was assessed after exposure of the transgenic cells to UV light or the radiomimetic chemicals methyl methanesulfonate and mitomycin C. Recombination activity in the cells was assessed by using an assay for homologous recombination between repeats in the chromosome and by measuring the ability of the cells to foster lytic growth byred gammutant bacteriophage λ. Overall, we found that transgenic cells withrecAgenes ofB. burgdorferi,B. hermsii, andL. biflexahad approximately equivalent activities in promoting homologous recombination in thelacZduplication assay, but cells withB. burgdorferi recAand, most notably,B. hermsii recAwere significantly less capable than cells withL. biflexa recAorE. coli recAin responding to DNA damage or in facilitating plaque formation in the phage assay. The comparatively poor function ofBorrelia recAin the latter set of assays may be the consequence of impaired coordination in the loading of the transgenic RecA by RecBCD and/or RecFOR inE. coli.
Pseudomonas aeruginosa
Autoinducer Enters and Functions in Mammalian Cells
Authors: Williams Simon C. , Patterson Erin K. , Carty Nancy L. , Griswold John A. , Hamood Abdul N. , Rumbaugh Kendra P. 
Published: April 2004

ABSTRACT

Quorum sensing (QS) is a cell density-dependent signaling mechanism used by many bacteria to control gene expression. Several recent reports indicate that the signaling molecules (autoinducers) that mediate QS in
Pseudomonas aeruginosa
may also modulate gene expression in host cells; however, the mechanisms are largely unknown. Here we show that two
P. aeruginosa
autoinducers,
N
-3-oxododecanoyl-homoserine lactone and
N
-butyryl-homoserine lactone, can both enter eukaryotic cells and activate artificial chimeric transcription factors based on their cognate transcriptional activators, LasR and RhlR, respectively. The autoinducers promoted nuclear localization of chimeric proteins containing the full LasR or RhlR coding region, and the LasR-based proteins were capable of activating transcription of a LasR-dependent luciferase gene. Responsiveness to autoinducer required the N-terminal autoinducer-binding domains of LasR and RhlR. Truncated proteins consisting of only the C-terminal helix-turn-helix DNA-binding domains of both proteins attached to a nuclear localization signal efficiently translocated to the nucleus in the absence of autoinducer, and truncated LasR-based proteins functioned as constitutively active transcription factors. Chimeric LasR proteins were only activated by their cognate autoinducer ligand and not by
N
-butyryl-
l
-homoserine lactone. These data provide evidence that autoinducer molecules from human pathogens can enter mammalian cells and suggest that autoinducers may influence gene expression in host cells by interacting with and activating as-yet-unidentified endogenous proteins.
The Tp38 (TpMglB-2) Lipoprotein Binds Glucose in a Manner Consistent with Receptor Function in
Treponema pallidum
Authors: Deka Ranjit K. , Goldberg Martin S. , Hagman Kayla E. , Norgard Michael V. 
Published: April 2004

ABSTRACT

A 38-kDa lipoprotein of
Treponema pallidum
(Tp38) was predicted to be a periplasmic sugar-binding protein based on its sequence similarity to the glucose/galactose-binding (MglB) protein of
Escherichia coli
(P. S. Becker, D. R. Akins, J. D. Radolf, and M. V. Norgard, Infect. Immun.
62:
1381-1391, 1994). Inasmuch as glucose is believed to be the principal, if not sole, carbon and energy source for
T. pallidum
and is readily available to the spirochete during its obligate infection of humans, we hypothesized that Tp38 may serve as the organism's requisite glucose receptor. For the present study, a nonacylated recombinant form of Tp38 was coexpressed with GroES and GroEL in
E. coli
to facilitate the isolation of soluble, properly folded Tp38. The highly sensitive method of intrinsic fluorescence spectroscopy, predicated on the manner in which tryptophan residues reside and move within protein microenvironments, was then used to assess sugar binding to Tp38. The intrinsic fluorescence of Tp38 was essentially unaltered when it was exposed to
d
-mannose,
d
-fucose,
d
-ribose,
l
-glucose, or
l
-galactose, but it changed markedly in the presence of
d
-glucose, and to a lesser extent,
d
-galactose, indicating binding. The

K
d

values for
d
-glucose and
d
-galactose binding to Tp38 were 152.2 ± 20.73 nM and 251.2 ± 55.25 nM, respectively. Site-directed mutagenesis of Trp-145, a residue postulated to contribute to the sugar-binding pocket in a manner akin to the essential Trp-183 in
E. coli
MglB, abolished Tp38's conformational change in response to
d
-glucose. The combined data are consistent with Tp38 serving as a glucose receptor for
T. pallidum
. These findings potentially have important implications for syphilis pathogenesis, particularly as they may pertain to glucose-mediated chemotactic responses by
T. pallidum
.
Relationship of Critical Temperature to Macromolecular Synthesis and Growth Yield in
Psychrobacter cryopegella
Authors: Bakermans Corien , Nealson Kenneth H. 
Published: April 2004

ABSTRACT

Most microorganisms isolated from low-temperature environments (below 4°C) are eury-, not steno-, psychrophiles. While psychrophiles maximize or maintain growth yield at low temperatures to compensate for low growth rate, the mechanisms involved remain unknown, as does the strategy used by eurypsychrophiles to survive wide ranges of temperatures that include subzero temperatures. Our studies involve the eurypsychrophilic bacterium
Psychrobacter cryopegella
, which was isolated from a briny water lens within Siberian permafrost, where the temperature is −12°C.
P. cryopegella
is capable of reproducing from −10 to 28°C, with its maximum growth rate at 22°C. We examined the temperature dependence of growth rate, growth yield, and macromolecular (DNA, RNA, and protein) synthesis rates for
P. cryopegella.
Below 22°C, the growth of
P. cryopegella
was separated into two domains at the critical temperature (
T
critical
= 4°C). RNA, protein, and DNA synthesis rates decreased exponentially with decreasing temperatures. Only the temperature dependence of the DNA synthesis rate changed at
T
critical
. When normalized to growth rate, RNA and protein synthesis reached a minimum at
T
critical
, while DNA synthesis remained constant over the entire temperature range. Growth yield peaked at about
T
critical
and declined rapidly as temperature decreased further. Similar to some stenopsychrophiles,
P. cryopegella
maximized growth yield at low temperatures and did so by streamlining growth processes at
T
critical
. Identifying the specific processes which result in
T
critical
will be vital to understanding both low-temperature growth and growth over a wide range of temperatures.
Characterization of
Streptococcus pneumoniae
TrmD, a tRNA Methyltransferase Essential for Growth
Authors: O'Dwyer Karen , Watts Joseph M. , Biswas Sanjoy , Ambrad Jennifer , Barber Michael , Brulé Hervé , Petit Chantal , Holmes David J. , Zalacain Magdalena , Holmes Walter M. 
Published: April 2004

ABSTRACT

Down-regulation of expression of
trmD
, encoding the enzyme tRNA (guanosine-1)-methyltransferase, has shown that this gene is essential for growth of
Streptococcus pneumoniae
. The
S. pneumoniae trmD
gene has been isolated and expressed in
Escherichia coli
by using a His-tagged T7 expression vector. Recombinant protein has been purified, and its catalytic and physical properties have been characterized. The native enzyme displays a molecular mass of approximately 65,000 Da, suggesting that streptococcal TrmD is a dimer of two identical subunits. In fact, this characteristic can be extended to several other TrmD orthologs, including
E. coli
TrmD. Kinetic studies show that the streptococcal enzyme utilizes a sequential mechanism. Binding of tRNA by gel mobility shift assays gives a dissociation constant of 22 nM for one of its substrates,

\batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \(\mathit{tRNA}_{\mathit{CAG}}^{\mathit{Leu}}\) \end{document}

. Other heterologous nonsubstrate tRNA species, like

\batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \(\mathit{tRNA}_{\mathit{GGT}}^{\mathit{Thr}}\) \end{document}

, tRNA
Phe
, and

\batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \(\mathit{tRNA}_{\mathit{TGC}}^{\mathit{Ala}}\) \end{document}

, bind the enzyme with similar affinities, suggesting that tRNA specificity is achieved via a postbinding event(s).
Properties of
Bacillus subtilis
σ
A
Factors with Region 1.1 and the Conserved Arg-103 at the N Terminus of Region 1.2 Deleted
Authors: Hsu Hsin-Hsien , Huang Wei-Cheng , Chen Jia-Perng , Huang Liang-Yin , Wu Chai-Fong , Chang Ban-Yang 
Published: April 2004

ABSTRACT

σ factors in the σ
70
family can be classified into the primary and alternative σ factors according to their physiological functions and amino acid sequence similarities. The primary σ factors are composed of four conserved regions, with the conserved region 1 being divided into two subregions. Region 1.1, which is absent from the alternative σ factor, is poor in conservation; however, region 1.2 is well conserved. We investigated the importance of these two subregions to the function of
Bacillus subtilis
σ
A
, which belongs to a subgroup of the primary σ factor lacking a 254-amino-acid spacer between regions 1 and 2. We found that deletion of not more than 100 amino acid residues from the N terminus of σ
A
, which removed part or all region 1.1, did not affect the overall transcription activity of the truncated σ
A
-RNA polymerase in vitro, indicating that region 1.1 is not required for the functioning of σ
A
in RNA polymerase holoenzyme. This finding is consistent with the complementation data obtained in vivo. However, region 1.1 is able to negatively modulate the promoter DNA-binding activity of the σ
A
-RNA polymerase. Further deletion of the conserved Arg-103 at the N terminus of region 1.2 increased the content of stable secondary structures of the truncated σ
A
and greatly reduced the transcription activity of the truncated σ
A
-RNA polymerase by lowering the efficiency of transcription initiation after core binding of σ
A
. More importantly, the conserved Arg-103 was also demonstrated to be critical for the functioning of the full-length σ
A
in RNA polymerase.
Characterization of a Major
Bacillus anthracis
Spore Coat Protein and Its Role in Spore Inactivation
Authors: Kim Ho-San , Sherman D. , Johnson F. , Aronson A. I. 
Published: April 2004

ABSTRACT

A major
Bacillus anthracis
spore coat protein of 13.4 kDa, designated Cotα, was found only in the
Bacillus cereus
group. A stable ca. 30-kDa dimer of this protein was also present in spore coat extracts. Cotα, which is encoded by a monocistronic gene, was first detected late in sporulation, consistent with a σ
K
-regulated gene. On the basis of immunogold labeling, the protein is in the outer spore coat and absent from the exosporium. In addition, disruption of the gene encoding Cotα resulted in spores lacking a dark-staining outer spore coat in thin-section electron micrographs. The mutant spores were stable upon heating or storage, germinated at the same rate as the wild type, and were resistant to lysozyme. They were, however, more sensitive than the wild type to phenol, chloroform, and hypochlorite but more resistant to diethylpyrocarbonate. In all cases, resistance or sensitivity to these reagents was restored by introducing a clone of the
cot
α gene into the mutant. Since Cotα is an abundant outer spore coat protein of the
B. cereus
group with a prominent role in spore resistance and sensitivity, it is a promising target for the inactivation of
B. anthracis
spores.
Characterization of Virulence Factor Regulation by SrrAB, a Two-Component System in
Staphylococcus aureus
Authors: Pragman Alexa A. , Yarwood Jeremy M. , Tripp Timothy J. , Schlievert Patrick M. 
Published: April 2004

ABSTRACT

Workers in our laboratory have previously identified the staphylococcal respiratory response AB (SrrAB), a
Staphylococcus aureus
two-component system that acts in the global regulation of virulence factors. This system down-regulates production of
agr
RNAIII, protein A, and toxic shock syndrome toxin 1 (TSST-1), particularly under low-oxygen conditions. In this study we investigated the localization and membrane orientation of SrrA and SrrB, transcription of the
srrAB
operon, the DNA-binding properties of SrrA, and the effect of SrrAB expression on
S. aureus
virulence. We found that SrrA is localized to the
S. aureus
cytoplasm, while SrrB is localized to the membrane and is properly oriented to function as a histidine kinase.
srrAB
has one transcriptional start site which results in either an
srrA
transcript or a full-length
srrAB
transcript;
srrB
must be cotranscribed with
srrA
. Gel shift assays of the
agr
P2,
agr
P3, protein A (
spa
), TSST-1 (
tst
), and
srr
promoters revealed SrrA binding at each of these promoters. Analysis of SrrAB-overexpressing strains by using the rabbit model of bacterial endocarditis demonstrated that overexpression of SrrAB decreased the virulence of the organisms compared to the virulence of isogenic strains that do not overexpress SrrAB. We concluded that SrrAB is properly localized and oriented to function as a two-component system. Overexpression of SrrAB, which represses
agr
RNAIII, TSST-1, and protein A in vitro, decreases virulence in the rabbit endocarditis model. Repression of these virulence factors is likely due to a direct interaction between SrrA and the
agr
,
tst
, and
spa
promoters.