bluuebunny/crossref_metadata_2025_split huggingface dataset:
Whole‐body UVB (TL‐01) or UVA‐1 irradiation does not alter the levels of immunomodulatory cytokines in the serum of human volunteers
Authors: Mcloone P. , Man I. , Yule S. , Fluitman A. , Van loveren H. , Norval M. , Gibbs N.K. 
Published: March 2004

Background/Purpose: Ultraviolet (UV) exposure of mammalian skin induces local and systemic immunosuppression. In mice it has been proposed that systemic immunosuppression is mediated by an UV‐induced cytokine cascade involving systemic interleukin (IL)‐4 and IL‐10 and a reduction in IL‐12 activity. To investigate whether there was a parallel mechanism in humans we examined the effect of whole‐body narrowband ultraviolet B (UVB) (311–313 nm; TL‐01) and ultraviolet A (UVA)‐1 (340–400 nm) on serum cytokine levels.Methods/Results: In a first study, five male psoriatic subjects were whole‐body irradiated with three sessions of a standard UVB (TL‐01) phototherapy regimen previously shown to cause downregulation of natural killer cell activity and T helper 1 (Th1) and Th2 cytokine production by peripheral blood mononuclear cells. Enzyme‐linked immunoabsorbent assay (ELISA) of sera taken before and after the third session showed no effect of phototherapy on IL‐10 and tumour necrosis factor‐α (TNF‐α). In a second study, five healthy subjects received three whole‐body exposures of UVB (TL‐01) and five other healthy subjects received three exposures of UVA‐1 on alternate days (total 22 J/cm2). Blood samples were taken before the first irradiation and at 0, 4, 8, 12, 14, 24 and 48 h after the third irradiation. The sera were subsequently analysed for IL‐10, IL‐12, IL‐8, IL‐1β and TNF‐α, by ELISA. The levels of IL‐1β and TNF‐α were below detection limits (<5 pg/ml), while no significant change in the levels of IL‐10, IL‐12 or IL‐8 was detected as a result of either TL‐01 or UVA‐1.Conclusion: It seems unlikely that a modulation in these circulating cytokines assessed in this study accounts for systemic UV‐induced immunosuppression in human subjects.
On Viscoelastic
Compliant Contact-Impact Models
Authors: Atanackovic T. M. , Spasic D. T. 
Published: March 2004

Abstract
We study dynamics of a mass, moving on a straight line, and impacting against the rigid wall through a deformable body, that we model as a straight rod of negligible mass. The chosen constitutive model of the viscoelastic body comprises fractional derivatives of stress and strain and the restrictions on the coefficients that follow from Clausius Duhem inequality. We show that the dynamics of the problem is governed by a single differential equation of real order. The obtained equation was solved numerically. The comparison is made to the solution obtained by the Laplace transform and Post’s inversion formula. The predictions of the model concerning the duration of the impact, maximal values of the impacting force and deformation as well as the restitution coefficient are determined for several values of system parameters.
Surface Instability of
a Semi-Infinite Elastic Body Under Surface van der Waals Forces
Authors: Ru C. Q. 
Published: March 2004

Abstract
It is shown that the surface of a semi-infinite linear elastic body attracted by a rigid flat through van der Waals-like forces is always unstable. The wavelength of the surface wrinkling is finite and decreases with the van der Waals interaction coefficient. In particular, this result implies that the deformation field of the semi-infinite linear elastic body attracted by a rigid flat cannot be determined uniquely.
Crystallographic Comparison of Manganese- and Iron-Dependent Homoprotocatechuate 2,3-Dioxygenases
Authors: Vetting Matthew W. , Wackett Lawrence P. , Que Lawrence , Lipscomb John D. , Ohlendorf Douglas H. 
Published: March 2004

ABSTRACTThe X-ray crystal structures of homoprotocatechuate 2,3-dioxygenases isolated fromArthrobacter globiformisandBrevibacterium fuscumhave been determined to high resolution. These enzymes exhibit 83% sequence identity, yet their activities depend on different transition metals, Mn2+and Fe2+, respectively. The structures allow the origins of metal ion selectivity and aspects of the molecular mechanism to be examined in detail. The homotetrameric enzymes belong to the type I family of extradiol dioxygenases (vicinal oxygen chelate superfamily); each monomer has four βαβββ modules forming two structurally homologous N-terminal and C-terminal barrel-shaped domains. The active-site metal is located in the C-terminal barrel and is ligated by two equatorial ligands, H214NE1and E267OE1; one axial ligand, H155NE1; and two to three water molecules. The first and second coordination spheres of these enzymes are virtually identical (root mean square difference over all atoms, 0.19 Å), suggesting that the metal selectivity must be due to changes at a significant distance from the metal and/or changes that occur during folding. The substrate (2,3-dihydroxyphenylacetate [HPCA]) chelates the metal asymmetrically at sitestransto the two imidazole ligands and interacts with a unique, mobile C-terminal loop. The loop closes over the bound substrate, presumably to seal the active site as the oxygen activation process commences. An “open” coordination sitetransto E267 is the likely binding site for O2. The geometry of the enzyme-substrate complexes suggests that if a transiently formed metal-superoxide complex attacks the substrate without dissociation from the metal, it must do so at the C-3 position. Second-sphere active-site residues that are positioned to interact with the HPCA and/or bound O2during catalysis are identified and discussed in the context of current mechanistic hypotheses.
Transcriptional Analysis of
spo0A
Overexpression in
Clostridium acetobutylicum
and Its Effect on the Cell's Response to Butanol Stress
Authors: Alsaker Keith V. , Spitzer Thomas R. , Papoutsakis Eleftherios T. 
Published: March 2004

ABSTRACT

Spo0A is the regulator of stationary-phase events and is required for transcription of solvent formation genes in
Clostridium acetobutylicum
. In order to elucidate the role of
spo0A
in differentiation, we performed transcriptional analysis of 824(pMSPOA) (a
spo0A
-overexpressing
C. acetobutylicum
strain with enhanced sporulation) against a plasmid control strain. DNA microarray data were contrasted to data from a
spo0A
knockout strain (SKO1) that neither sporulates nor produces solvents. Transcripts of fatty acid metabolism genes, motility and chemotaxis genes, heat shock protein genes, and genes encoding the Fts family of cell division proteins were differentially expressed in the two strains, suggesting that these genes play roles in sporulation and the solvent stress response. 824(pMSPOA) alone showed significant downregulation of many glycolytic genes in stationary phase, which is consistent with metabolic flux analysis data. Surprisingly,
spo0A
overexpression resulted in only nominal transcriptional changes of regulatory genes (
abrB
and
sigF
) whose expression was significantly altered in SKO1. Overexpression of
spo0A
imparted increased tolerance and prolonged metabolism in response to butanol stress. While most of the differentially expressed genes appear to be part of a general stress response (similar to patterns in two plasmid control strains and a
groESL
-overexpressing strain), several genes were expressed at higher levels at early time points after butanol challenge only in 824(pMSPOA). Most of these genes were related to butyryl coenzyme A and butyrate formation and/or assimilation, but they also included the cell division gene
ftsX
, the gyrase subunit-encoding genes
gyrB
and
gyrA
, DNA synthesis and repair genes, and fatty acid synthesis genes, all of which might play a role in the immediate butanol stress response, and thus in enhanced butanol tolerance.
Sortase B, a New Class of Sortase inListeria monocytogenes
Authors: Bierne Hélène , Garandeau Caroline , Pucciarelli M. Graciela , Sabet Christophe , Newton Salete , Garcia-del Portillo Francisco , Cossart Pascale , Charbit Alain 
Published: March 2004

ABSTRACTSortases are transamidases that covalently link proteins to the peptidoglycan of gram-positive bacteria. The genome of the pathogenic bacteriumListeria monocytogenesencodes two sortases genes,srtAandsrtB. ThesrtAgene product anchors internalin and some other LPXTG-containing proteins to the listerial surface. Here, we focus on the role of the second sortase, SrtB. Whereas SrtA acts on most of the proteins in the peptidoglycan fraction, SrtB appears to target minor amounts of surface polypeptides. We identified one of the SrtB-anchored proteins as the virulence factor SvpA, a surface-exposed protein which does not contain the LPXTG motif. Therefore, as inStaphylococcus aureus, the listerial SrtB represents a second class of sortase inL. monocytogenes, involved in the attachment of a subset of proteins to the cell wall, most likely by recognizing an NXZTN sorting motif. The ΔsrtBmutant strain does not have defects in bacterial entry, growth, or motility in tissue-cultured cells and does not show attenuated virulence in mice. SrtB-mediated anchoring could therefore be required to anchor surface proteins involved in the adaptation of this microorganism to different environmental conditions.
Contrasting Effects of σEon Compartmentalization of σFActivity during Sporulation ofBacillus subtilis
Authors: Hilbert David W. , Chary Vasant K. , Piggot Patrick J. 
Published: March 2004

ABSTRACTSpore formation byBacillus subtilisis a primitive form of development. In response to nutrient starvation and high cell density,B. subtilisdivides asymmetrically, resulting in two cells with different sizes and cell fates. Immediately after division, the transcription factor σFbecomes active in the smaller prespore, which is followed by the activation of σEin the larger mother cell. In this report, we examine the role of the mother cell-specific transcription factor σEin maintaining the compartmentalization of gene expression during development. We have studied a strain with a deletion of thespoIIIEgene, encoding a DNA translocase, that exhibits uncompartmentalized σFactivity. We have determined that the deletion ofspoIIIEalone does not substantially impact compartmentalization, but in thespoIIIEmutant, the expression of putative peptidoglycan hydrolases under the control of σEin the mother cell destroys the integrity of the septum. As a consequence, small proteins can cross the septum, thereby abolishing compartmentalization. In addition, we have found that in a mutant with partially impaired control of σF, the activation of σEin the mother cell is important to prevent the activation of σFin this compartment. Therefore, the activity of σEcan either maintain or abolish the compartmentalization of σF, depending upon the genetic makeup of the strain. We conclude that σEactivity must be carefully regulated in order to maintain compartmentalization of gene expression during development.
A Conjugation-Based System for Genetic Analysis of Group II Intron Splicing inLactococcus lactis
Authors: Klein Joanna R. , Chen Yuqing , Manias Dawn A. , Zhuo Jin , Zhou Liang , Peebles Craig L. , Dunny Gary M. 
Published: March 2004

ABSTRACTThe conjugative element pRS01 fromLactococcus lactisencodes the putative relaxase protein LtrB. TheltrBgene is interrupted by the functional group II intron Ll.ltrB. Accurate splicing of the twoltrBexons is required for synthesis of the mRNA encoding the LtrB conjugative relaxase and subsequent plasmid transfer. A conjugation-based genetic assay was developed to identify Ll.ltrB mutations that affect splicing. In this assay a nonsplicing, transfer-defective pRS01 derivative (pM1014) and a shuttle vector carrying theltrBregion, including the Ll.ltrB intron (pCOM9), are used. pCOM9 provides splicing-dependent complementation of the transfer defect of pM1014. Site-directed mutations within Ll.ltrB, either in the catalytic RNA or in the intron-encoded protein geneltrA, were generated in the context of pCOM9. When these mutants were tested in the conjugation-based assay, significantly reduced mating was observed. Quantitative molecular analysis of in vivo splicing activity confirmed that the observed mating defects resulted from reduced splicing. Once the system was validated for the engineered mutants, random mutagenesis of the intron followed by genetic and molecular screening for splicing defects resulted in identification of point mutations that affect splicing.
Sporulation Phenotype of aBacillus subtilisMutant Expressing an Unprocessable but Active σETranscription Factor
Authors: McBride Shonna , Haldenwang W. G. 
Published: March 2004

ABSTRACTσE, a sporulation-specific sigma factor ofBacillus subtilis, is formed from an inactive precursor (pro-σE) by a developmentally regulated processing reaction that removes 27 amino acids from the proprotein's amino terminus. AsigEvariant (sigE335) lacking 15 amino acids of the prosequence is not processed into mature σEbut is active without processing. In the present work, we investigated the sporulation defect insigE335-expressingB. subtilis, asking whether it is the bypass of proprotein processing or a residual inhibition of σEactivity that is responsible. Fluorescence microscopy demonstrated thatsigE335-expressingB. subtilisprogresses further into sporulation (stage III) than do strains lacking σEactivity (stage II). Consistent with its stage III phenotype, and a defect in σEactivity rather than its timing, thesigE335allele did not disturb early sporulation gene expression but did inhibit the expression of late sporulation genes (gerEandsspE). The Spo−phenotype ofsigE335was found to be recessive to wild-typesigE. In vivo assays of σEactivity insigE,sigE335, and merodiploid strains indicate that the residual prosequence on σE335, still impairs its activity to function as a transcription factor. The data suggest that the 11-amino-acid extension on σE335allows it to bind RNA polymerase and direct the resulting holoenzyme to σE-dependent promoters but reduces the enzyme's ability to initiate transcription initiation and/or exit from the promoter.
Hydrogen Peroxide Production in
Streptococcus pyogenes
: Involvement of Lactate Oxidase and Coupling with Aerobic Utilization of Lactate
Authors: Seki Masanori , Iida Ken-ichiro , Saito Mitsumasa , Nakayama Hiroaki , Yoshida Shin-ichi 
Published: March 2004

ABSTRACT

Streptococcus pyogenes
strains can be divided into two classes, one capable and the other incapable of producing H
2
O
2
(M. Saito, S. Ohga, M. Endoh, H. Nakayama, Y. Mizunoe, T. Hara, and S. Yoshida, Microbiology
147:
2469-2477, 2001). In the present study, this dichotomy was shown to parallel the presence or absence of H
2
O
2
-producing lactate oxidase activity in permeabilized cells. Both lactate oxidase activity and H
2
O
2
production under aerobic conditions were detectable only after glucose in the medium was exhausted. Thus, the glucose-repressible lactate oxidase is likely responsible for H
2
O
2
production in
S. pyogenes
. Of the other two potential H
2
O
2
-producing enzymes of this bacterium, NADH and α-glycerophosphate oxidase, only the former exhibited low but significant activity in either class of strains. This activity was independent of the growth phase, suggesting that the protein may serve in vivo as a subunit of the H
2
O
2
-scavenging enzyme NAD(P)H-linked alkylhydroperoxide reductase. The activity of lactate oxidase was associated with the membrane while that of NADH oxidase was in the soluble fraction, findings consistent with their respective physiological roles, i.e., the production and scavenging of H
2
O
2
. Analyses of fermentation end products revealed that the concentration of lactate initially increased with time and decreased on glucose exhaustion, while that of acetate increased during the culture. These results suggest that the lactate oxidase activity of H
2
O
2
-producing cells oxidizes lactate to pyruvate, which is in turn converted to acetate. This latter process proceeds presumably via acetyl coenzyme A and acetyl phosphate with formation of extra ATP.
A DNA Adenine Methyltransferase of
Escherichia coli
That Is Cell Cycle Regulated and Essential for Viability
Authors: Kossykh Valeri G. , Lloyd R. Stephen 
Published: March 2004

ABSTRACT

DNA sequence analysis revealed that the putative
yhdJ
DNA methyltransferase gene of
Escherichia coli
is 55% identical to the
Nostoc
sp. strain PCC7120 gene encoding DNA methyltransferase AvaIII, which methylates adenine in the recognition sequence, ATGCAT. The
yhdJ
gene was cloned, and the enzyme was overexpressed and purified. Methylation and restriction analysis showed that the DNA methyltransferase methylates the first adenine in the sequence ATGCAT. This DNA methylation was found to be regulated during the cell cycle, and the DNA adenine methyltransferase was designated M.EcoKCcrM (for “cell cycle-regulated methyltransferase”). The CcrM DNA adenine methyltransferase is required for viability in
E. coli
, as a strain lacking a functional genomic copy of
ccrM
can be isolated only in the presence of an additional copy of
ccrM
supplied in
trans
. The cells of such a knockout strain stopped growing when expression of the inducible plasmid
ccrM
gene was shut off. Overexpression of M.EcoKCcrM slowed bacterial growth, and the ATGCAT sites became fully methylated throughout the cell cycle; a high proportion of cells with an anomalous size distribution and DNA content was found in this population. Thus, the temporal control of this methyltransferase may contribute to accurate cell cycle control of cell division and cellular morphology. Homologs of M.EcoKCcrM are present in other bacteria belonging to the gamma subdivision of the class
Proteobacteria
, suggesting that methylation at ATGCAT sites may have similar functions in other members of this group.
Effect of
d
-Lactate on the Physiological Activity of the ArcB Sensor Kinase in
Escherichia coli
Authors: Rodriguez Claudia , Kwon Ohsuk , Georgellis Dimitris 
Published: March 2004

ABSTRACT

The Arc two-component system, comprising the ArcB sensor kinase and the ArcA response regulator, modulates the expression of numerous genes in response to the respiratory growth conditions. Under anoxic growth conditions ArcB autophosphorylates and transphosphorylates ArcA, which in turn represses or activates its target operons. The anaerobic metabolite
d
-lactate has been shown to stimulate the in vitro autophosphorylating activity of ArcB. In this study, the in vivo effect of
d
-lactate on the kinase activity of ArcB was assessed. The results demonstrate that
d
-lactate does not act as a direct signal for activation of ArcB, as previously proposed, but acts as a physiologically significant effector that amplifies ArcB kinase activity.
Protective Role for H-NS Protein in IS
1
Transposition
Authors: Rouquette Claudine , Serre Marie-Claude , Lane David 
Published: March 2004

ABSTRACT

The transposase (InsAB′) of the insertion element IS
1
can create breaks in DNA that lead to induction of the SOS response. We have used the SOS response to InsAB′ to screen for host mutations that affect InsAB′ function and thus point to host functions that contribute to the IS
1
transposition mechanism. Mutations in the
hns
gene, which codes for a DNA binding protein with wide-ranging effects on gene expression, abolish the InsAB′-induced SOS response. They also reduce transposition, whether by simple insertion or cointegrate formation, at least 100-fold compared with the frequency seen in

hns
+

cells. Examination of protein profiles revealed that in an
hns
-null mutant, InsAB′ is undetectable under conditions where it constitutes the most abundant protein in

hns
+

cells. Likewise, brief labeling of the
hns
cells with [
35
S]methionine revealed very small amounts of InsAB′, and this was undetectable after a short chase. Transcription from the promoters used to express
insAB
′ was essentially unaltered in
hns
cells, as was the level of
insAB
′ mRNA. A mutation in
lon
, but not in
ftsH
or
clpP
, restored InsAB′ synthesis in the
hns
strain, and a mutation in
ssrA
partially restored it, implying that the absence of H-NS leads to a problem in completing translation of
insAB
′ mRNA and/or degradation of nascent InsAB′ protein.
Restricted Distribution of the Butyrate Kinase Pathway among Butyrate-Producing Bacteria from the Human Colon
Authors: Louis Petra , Duncan Sylvia H. , McCrae Sheila I. , Millar Jacqueline , Jackson Michelle S. , Flint Harry J. 
Published: March 2004

ABSTRACT
The final steps in butyrate synthesis by anaerobic bacteria can occur via butyrate kinase and phosphotransbutyrylase or via butyryl-coenzyme A (CoA):acetate CoA-transferase. Degenerate PCR and enzymatic assays were used to assess the presence of butyrate kinase among 38 anaerobic butyrate-producing bacterial isolates from human feces that represent three different clostridial clusters (IV, XIVa, and XVI). Only four strains were found to possess detectable butyrate kinase activity. These were also the only strains to give PCR products (verifiable by sequencing) with degenerate primer pairs designed within the butyrate kinase gene or between the linked butyrate kinase/phosphotransbutyrylase genes. Further analysis of the butyrate kinase/phosphotransbutyrylase genes of one isolate, L2-50, revealed similar organization to that described previously from different groups of clostridia, along with differences in flanking sequences and phylogenetic relationships. Butyryl-CoA:acetate CoA-transferase activity was detected in all 38 strains examined, suggesting that it, rather than butyrate kinase, provides the dominant route for butyrate formation in the human colonic ecosystem that contains a constantly high concentration of acetate.
A Novel Gene (
narM
) Required for Expression of Nitrate Reductase Activity in the Cyanobacterium
Synechococcus elongatus
Strain PCC7942
Authors: Maeda Shin-ichi , Omata Tatsuo 
Published: March 2004

ABSTRACT

A new class of mutants deficient in nitrate assimilation was obtained from the cyanobacterium
Synechococcus elongatus
strain PCC7942 by means of random insertional mutagenesis. A 0.5-kb genomic region had been replaced by a kanamycin resistance gene cassette in the mutant, resulting in inactivation of two genes, one of which was homologous to the recently characterized
cnaT
gene of
Anabaena
sp. strain PCC7120 (J. E. Frías, A. Herrero, and E. Flores, J. Bacteriol.
185:
5037-5044, 2003). While insertional mutation of the
cnaT
homolog did not affect expression of the nitrate assimilation operon or the activity of the nitrate assimilation enzymes in
S. elongatus
, inactivation of the other gene, designated
narM
, resulted in specific loss of the cellular nitrate reductase activity. The deduced NarM protein is a hydrophilic protein consisting of 161 amino acids.
narM
was expressed constitutively at a low level. The
narM
gene has its homolog only in the cyanobacterial strains that are capable of nitrate assimilation. In most of the cyanobacterial strains,
narM
is located downstream of
narB
, the structural gene of the cyanobacterial nitrate reductase, suggesting the functional link between the two genes. NarM is clearly not the structural component of the cyanobacterial nitrate reductase. The
narM
insertional mutant normally expressed
narB
, indicating that
narM
is not the transcriptional regulator of the structural gene of nitrate reductase. These results suggested that
narM
is required for either synthesis of the prosthetic group of nitrate reductase or assembly of the prosthetic groups to the NarB polypeptide to form functional nitrate reductase in cyanobacteria.