bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect of RyhB Small RNA on Global Iron Use in
Escherichia coli
Authors: Massé Eric , Vanderpool Carin K. , Gottesman Susan 
Published: September 2005

ABSTRACT

RyhB is a noncoding RNA regulated by the Fur repressor. It has previously been shown to cause the rapid degradation of a number of mRNAs that encode proteins that utilize iron. Here we examine the effect of ectopic RyhB production on global gene expression by microarray analysis. Many of the previously identified targets were found, as well as other mRNAs encoding iron-binding proteins, bringing the total number of regulated operons to at least 18, encoding 56 genes. The two major operons involved in Fe-S cluster assembly showed different behavior; the
isc
operon appears to be a direct target of RyhB action, while the
suf
operon does not. This is consistent with previous findings suggesting that the
suf
genes but not the
isc
genes are important for Fe-S cluster synthesis under iron-limiting conditions, presumably for essential iron-binding proteins. In addition, we observed repression of Fur-regulated genes upon RyhB expression, interpreted as due to intracellular iron sparing resulting from reduced synthesis of iron-binding proteins. Our results demonstrate the broad effects of a single noncoding RNA on iron homeostasis.
Characterization of Sporulation Histidine Kinases ofBacillus anthracis
Authors: Brunsing Ryan L. , La Clair Chandra , Tang Sharon , Chiang Christina , Hancock Lynn E. , Perego Marta , Hoch James A. 
Published: September 2005

ABSTRACTThe initiation of sporulation inBacillusspecies is regulated by the phosphorelay signal transduction pathway, which is activated by several histidine sensor kinases in response to cellular and metabolic signals. Comparison of the protein components of the phosphorelay betweenBacillus subtilisandBacillus anthracisrevealed high homology in the phosphorelay orthologs of Spo0F, Spo0B, and Spo0A. The sensor domains of sensor histidine kinases are poorly conserved between species, making ortholog recognition tenuous. Putative sporulation sensor histidine kinases ofB. anthraciswere identified by homology to the HisKA domain ofB. subtilissporulation sensor histidine kinases, which interacts with Spo0F. Nine possible kinases were uncovered, and their genes were assayed for complementation of kinase mutants ofB. subtilis, for ability to drivelacZexpression inB. subtilisandB. anthracis, and for the effect of deletion of each on the sporulation ofB. anthracis. Five of the nine sensor histidine kinases were inferred to be capable of inducing sporulation inB. anthracis. Four of the sensor kinases could not be shown to induce sporulation; however, the genes for two of these were frameshifted in allB. anthracisstrains and one of these was also frameshifted in the pathogenic pXO1-bearingBacillus cereusstrain G9241. It is proposed that acquisition of plasmid pXO1 and pathogenicity may require a dampening of sporulation regulation by mutational selection of sporulation sensor histidine kinase defects. The sporulation ofB. anthracisex vivo appears to result from any one or a combination of the sporulation sensor histidine kinases remaining.
The
lrp
Gene and Its Role in Type I Fimbriation in
Citrobacter rodentium
Authors: Cordone Angela , Mauriello Emilia M. F. , Pickard Derek J. , Dougan Gordon , De Felice Maurilio , Ricca Ezio 
Published: September 2005

ABSTRACT

Citrobacter rodentium
is a murine pathogen that is now widely used as an in vivo model for gastrointestinal infections due to its similarities with human enteropathogens, such as the possession of a locus for enterocyte effacement (the LEE island). We studied the
lrp
gene of
C. rodentium
and found that it encodes a product highly similar to members of the Lrp (leucine-responsive regulatory protein) family of transcriptional regulators, able to recognize leucine as an effector and to repress the expression of its own structural gene. In enterobacteria, Lrp is a global regulator of gene expression, as it controls a large variety of genes, including those coding for cell appendages and other potential virulence factors. Based on the well-established role of Lrp on the expression of pilus genes in
Escherichia coli
, we also studied the role of Lrp in controlling the formation of the type I pilus in
C. rodentium
. Type I pili, produced by the
fim
system, are virulence factors of uropathogens, involved in mediating bacterial adhesion to bladder epithelial cells. Yeast agglutination assays showed that Lrp is needed for type I pilus formation and real-time PCR experiments indicated that Lrp has a strong leucine-mediated effect on the expression of the
fimAICDFGH
operon. Mutant studies indicated that this positive action is exerted mainly through a positive control of Lrp on the phase variation mechanism that regulates
fimAICDFGH
expression. A quantitative analysis of its expression suggested that this operon may also be negatively regulated at the level of transcription.
Analysis of Global Gene Expression and Double-Strand-Break Formation in DNA Adenine Methyltransferase- and Mismatch Repair-DeficientEscherichia coli
Authors: Robbins-Manke Jennifer L. , Zdraveski Zoran Z. , Marinus Martin , Essigmann John M. 
Published: September 2005

ABSTRACTDNA adenine methylation by DNA adenine methyltransferase (Dam) inEscherichia coliplays an important role in processes such as DNA replication initiation, gene expression regulation, and mismatch repair. In addition,E. colistrains deficient in Dam are hypersensitive to DNA-damaging agents. We used genome microarrays to compare the transcriptional profiles ofE. colistrains deficient in Dam and mismatch repair (dam, dam mutS, andmutSmutants). Our results show that >200 genes are expressed at a higher level in thedamstrain, while an additional mutation inmutSsuppresses the induction of many of the same genes. We also show by microarray and semiquantitative real-time reverse transcription-PCR that bothdamanddam mutSstrains show derepression of LexA-regulated SOS genes as well as the up-regulation of other non-SOS genes involved in DNA repair. To correlate the level of SOS induction and the up-regulation of genes involved in recombinational repair with the level of DNA damage, we used neutral single-cell electrophoresis to determine the number of double-strand breaks per cell in each of the strains. We find thatdammutantE. colistrains have a significantly higher level of double-strand breaks than the other strains. We also observe a broad range in the number of double-strand breaks indammutant cells, with a minority of cells showing as many as 10 or more double-strand breaks. We propose that the up-regulation of recombinational repair indammutants allows for the efficient repair of double-strand breaks whose formation is dependent on functional mismatch repair.
Biochemical Properties of a Putative Signal Peptide Peptidase from the Hyperthermophilic Archaeon
Thermococcus kodakaraensis
KOD1
Authors: Matsumi Rie , Atomi Haruyuki , Imanaka Tadayuki 
Published: September 2005

ABSTRACT

We have performed the first biochemical characterization of a putative archaeal signal peptide peptidase (SppA
Tk
) from the hyperthermophilic archaeon
Thermococcus kodakaraensis
KOD1. SppA
Tk
, comprised of 334 residues, was much smaller than its counterpart from
Escherichia coli
(618 residues) and harbored a single predicted transmembrane domain near its N terminus. A truncated mutant protein without the N-terminal 54 amino acid residues (ΔN54SppA
Tk
) was found to be stable against autoproteolysis and was examined further. ΔN54SppA
Tk
exhibited peptidase activity towards fluorogenic peptide substrates and was found to be highly thermostable. Moreover, the enzyme displayed a remarkable stability and preference for alkaline pH, with optimal activity detected at pH 10. ΔN54SppA
Tk
displayed a

K
m

of 240 ± 18 μM and a
V
max
of 27.8 ± 0.7 μmol min
−1
mg
−1
towards Ala-Ala-Phe-4-methyl-coumaryl-7-amide at 80°C and pH 10. The substrate specificity of the enzyme was examined in detail with a FRETS peptide library. By analyzing the cleavage products with liquid chromatography-mass spectrometry, ΔN54SppA
Tk
was found to efficiently cleave peptides with a relatively small side chain at the P-1 position and a hydrophobic or aromatic residue at the P-3 position. The positively charged Arg residue was preferred at the P-4 position, while substrates with negatively charged residues at the P-2, P-3, or P-4 position were not cleaved. When predicted signal sequences from the
T. kodakaraensis
genome sequence were examined, we found that the substrate specificity of ΔN54SppA
Tk
was in good agreement with its presumed role as a signal peptide peptidase in this archaeon.
Nuclear Magnetic Resonance Solution Structure of theEscherichia coliDNA Polymerase III θ Subunit
Authors: Mueller Geoffrey A. , Kirby Thomas W. , DeRose Eugene F. , Li Dawei , Schaaper Roel M. , London Robert E. 
Published: September 2005

ABSTRACTThe catalytic core ofEscherichia coliDNA polymerase III holoenzyme contains three subunits: α, ε, and θ. The α subunit contains the polymerase, and the ε subunit contains the exonucleolytic proofreading function. The small (8-kDa) θ subunit binds only to ε. Its function is not well understood, although it was shown to exert a small stabilizing effect on the ε proofreading function. In order to help elucidate its function, we undertook a determination of its solution structure. In aqueous solution, θ yielded poor-quality nuclear magnetic resonance spectra, presumably due to conformational exchange and/or protein aggregation. Based on our recently determined structure of the θ homolog from bacteriophage P1, named HOT, we constructed a homology model of θ. This model suggested that the unfavorable behavior of θ might arise from exposed hydrophobic residues, particularly toward the end of α-helix 3. In gel filtration studies, θ elutes later than expected, indicating that aggregation is potentially responsible for these problems. To address this issue, we recorded1H-15N heteronuclear single quantum correlation (HSQC) spectra in water-alcohol mixed solvents and observed substantially improved dispersion and uniformity of peak intensities, facilitating a structural determination under these conditions. The structure of θ in 60/40 (vol/vol) water-methanol is similar to that of HOT but differs significantly from a previously reported θ structure. The new θ structure is expected to provide additional insight into its physiological role and its effect on the ε proofreading subunit.
Rejection of Impassable Substrates by
Yersinia
Type III Secretion Machines
Authors: Sorg Joseph A. , Miller Nathan C. , Marketon Melanie M. , Schneewind Olaf 
Published: September 2005

ABSTRACT

Type III machines of pathogenic
Yersinia
spp. transport Yop proteins across the bacterial envelope into host cells. Translational fusions of
yopE
to the dihydrofolate reductase gene (
dhfr
) or the β-galactosidase gene (
lacZ
) generate hybrid proteins that block type III injection of Yop proteins into host cells, consistent with the canonical view that impassable DHFR and LacZ hybrids jam secretion machines. Mutations in repressors of posttranscriptional gene regulation,
Yersinia enterocolitica yscM1
and
yscM2
as well as
Yersinia pestis lcrQ
, relieve the YopE-DHFR-imposed blockade and restore type III injection into host cells. Genetic suppression of the type III blockade does not, however, promote YopE-DHFR secretion. A model is proposed whereby rejection of YopE-DHFR from the secretion pathway inhibits type III gene expression.
Clustered Genes Related to Sulfate Respiration in Uncultured Prokaryotes Support the Theory of Their Concomitant Horizontal Transfer
Authors: Mussmann Marc , Richter Michael , Lombardot Thierry , Meyerdierks Anke , Kuever Jan , Kube Michael , Glöckner Frank Oliver , Amann Rudolf 
Published: September 2005

ABSTRACT
The dissimilatory reduction of sulfate is an ancient metabolic process central to today's biogeochemical cycling of sulfur and carbon in marine sediments. Until now its polyphyletic distribution was most parsimoniously explained by multiple horizontal transfers of single genes rather than by a not-yet-identified “metabolic island.” Here we provide evidence that the horizontal transfer of a gene cluster may indeed be responsible for the patchy distribution of sulfate-reducing prokaryotes (SRP) in the phylogenetic tree. We isolated three DNA fragments (32 to 41 kb) from uncultured, closely related SRP from DNA directly extracted from two distinct marine sediments. Fosmid ws39f7, and partially also fosmids ws7f8 and hr42c9, harbored a core set of essential genes for the dissimilatory reduction of sulfate, including enzymes for the reduction of sulfur intermediates and synthesis of the prosthetic group of the dissimilatory sulfite reductase. Genome comparisons suggest that encoded membrane proteins universally present among SRP are critical for electron transfer to cytoplasmic enzymes. In addition, novel, conserved hypothetical proteins that are likely involved in dissimilatory sulfate reduction were identified. Based on comparative genomics and previously published experimental evidence, a more comprehensive model of dissimilatory sulfate reduction is presented. The observed clustering of genes involved in dissimilatory sulfate reduction has not been previously found. These findings strongly support the hypothesis that genes responsible for dissimilatory sulfate reduction were concomitantly transferred in a single event among prokaryotes. The acquisition of an optimized gene set would enormously facilitate a successful implementation of a novel pathway.
Authorship ignorance: views of researchers in French clinical settings
Authors: Pignatelli B , Maisonneuve H , Chapuis F 
Published: September 2005

Objectives:To assess the knowledge and behaviour of researchers regarding criteria for authorship, and the practices of ghost and gift authorship.Design:Semidirective interviews of senior clinical researchers.Setting:University hospital.Participants:Thirty-nine main investigators of clinical research programmes.Main measurements:Awareness and use of International Committee of Medical Journal Editors (ICMJE) criteria for authorship, and perceptions about ghost and gift authorship.Results:A total of 48 protocols submitted by 42 principal investigators between 1994 and 1996 were identified. Thirty-nine investigators were contacted; 37 (one of whom delegated a co-author) were interviewed between May 2002 and March 2003. Two co-authors of two principal investigators were also interviewed. In all, 42 studies were represented. The interviews lasted for 40–90 minutes and were conducted with openness and respect for confidentiality.The choice of names of co-authors did not follow the ICMJE recommendations. Half of the respondents stated they were aware of criteria for authorship and knew of ICMJE, but most of them did not cite any of the ICMJE criteria among those they applied in deciding authorship. Most of them disagreed with the obligation to meet the three criteria justifying co-authorship because they found these too rigid and inapplicable. Gift authorship was a common practice; 59% of the respondents had been a recipient of gift authorship. Twenty-five (64%) were aware of ghost authorship and the majority considered it questionable and blameworthy.Conclusions:The ICMJE criteria were ignored by clinicians at a university hospital. Ghost and gift authorship were frequent among them. There is a need for French guidelines for authorship to be prepared and implemented.
Stroke patients’ preferences and values about emergency research
Authors: Blixen C E , Agich G J 
Published: September 2005

Background:In the USA, the Food and Drug Administration waiver of informed consent permits certain emergency research only if community consultation occurs. However, uncertainty exists regarding how to define the community(ies) or their representatives.Objective:To collect data on the actual preferences and values of a group—those at risk for stroke—most directly affected by the waiver of informed consent for emergency research.Design:Face to face focused interviews were conducted with 12 patients who were hospitalised with a stroke diagnosis in the previous year. The interviews were audiotaped and a transcript based method was used for their analysis.Results:All 12 participants felt “that it was important that new treatments for stroke be developed”, but they were initially confused about the distinction between “research for stroke” and “emergency research for stroke”. However, after explanation, most (n =  10; 83%) expressed willingness to participate in the latter. In the absence of a surrogate to give informed consent in a stroke emergency situation, the majority (n =  11; 92%) said they would want the physician to “go ahead and enrol them in the trial”.Conclusions:This study is the first to identify the values and concerns of individuals most directly affected by stroke emergency research. Further interviews and focus groups are needed to develop and test a validated questionnaire on the preferences and values surrounding emergency research for stroke.
Production of Chemokines by Perivascular Adipose Tissue
Authors: Henrichot Elvire , Juge-Aubry Cristiana E. , Pernin Agnès , Pache Jean-Claude , Velebit Valdimir , Dayer Jean-Michel , Meda Paolo , Chizzolini Carlo , Meier Christoph A. 
Published: September 2005

Objective—Obesity is associated with an increased risk for cardiovascular disease. Although it is known that white adipose tissue (WAT) produces numerous proinflammatory and proatherogenic cytokines and chemokines, it is unclear whether adipose-derived chemotactic signals affect the chronic inflammation in atherosclerosis.Methods and Results—Histological examination showed that perivascular WAT (pWAT) is in close proximity to vascular walls, particularly at sites that have a tendency to develop atherosclerosis. In rodents, the amount of pWAT is markedly increased by a high-fat diet. At a functional level, supernatant from subcutaneous and pWAT strongly induced the chemotaxis of peripheral blood leukocytes. The migration of granulocytes and monocytes was mostly mediated by interleukin-8 and monocyte chemoattractant protein-1, respectively, whereas both chemokines contributed to the migration of activated T cells. Moreover, pWAT produces these chemokines, as shown by immunohistochemistry and by explant culture. The accumulation of macrophages and T cells at the interface between pWAT and the adventitia of human atherosclerotic aortas may reflect this prochemotactic activity of pWAT.Conclusions—Human pWAT has chemotactic properties through the secretion of different chemokines, and we propose that pWAT might contribute to the progression of obesity-associated atherosclerosis.
The Sinhalese Contribution to Estate Labour in Ceylon, 1881–1891
Authors: Wenzlhuemer Roland 
Published: September 2005

AbstractIt has become a firmly established belief among economic and labour historians that Sri Lanka's plantation industry rested almost exclusively on imported Tamil labour during the 19th century. Although strong evidence countering this "dualistic" viewpoint has been produced since the late 1970s—especially by Éric Meyer—, the contribution of the local Sinhalese peasantry to estate wage labour remains underestimated or, indeed, largely ignored. This article strives to support Meyer's point by bringing together old and new evidence illustrating the at times substantial Sinhalese participation in plantation wage labour. C'est une croyance bien établie parmi les historiens économiques et du travail que l'industrie de la plantation du Sri Lanka reposait presque exclusivement sur le travail de la main-d'čuvre tamoule pendant le 19e siècle. Bien que des indications fortes contre cette perspective "dualiste" aient été produites depuis les années 70—particulièrement par Éric Meyer—, la contribution de la paysannerie locale cinghalaise au travail salarié dans les plantations reste sous-estimée , ou en grande partie ignorée. Cet article tâche de soutenir l'opinion de Meyer en rassemblant des indications vieilles et nouvelles illustrant la participation cinghalaise parfois substantielle au travail salarié dans les plantations.
Some Reflections on Babylonian Exchange during the End of the Third Millennium BC
Authors: Widell Magnus 
Published: September 2005

AbstractFor some products in the Ur III period, a sufficient number of texts provide their silver equivalences, and the ancient value of the products can be estimated. This paper suggests that we should envision two exchange systems in the Ur III period, which operated within two separate and rather different economic spheres. Local exchange took place, at a stated time and place, for the purpose of individual exchange of goods and services. Through this exchange, regular people would obtain a number of different necessities of life that were not provided by the temple and palace households. This was a barter exchange and the silver values encountered in the Ur III texts do not relate to this exchange. Silver was only used in large-scale transactions of goods and in more significant sales of real estate, humans or livestock. Although we may assume that there was a connection between the official silver equivalences and the actual values of the products and commodities in the local exchange, minor fluctuations and changes in the large-scale exchange system would not affect the bartering values in the local exchange. Nous possédons suffisamment de textes nous indiquant quel était l'équivalent en argent de certains produits de la période d'Ur III pour être à même d'estimer la valeur que ces derniers avaient dans l'antiquité. Le présent article suggère qu'il nous faut imaginer, durant la période d'Ur III, deux systèmes d'échange opérant dans le cadre de deux sphères économiques différentes. Les échanges locaux avaient lieu à un moment et à un endroit déterminés, dans le but d'échanger des biens et des services entre particuliers. Ces échanges permettaient aux gens du peuple de se procurer diverses choses nécessaires à l'existence qui ne leur étaient pas fournies par l'intendance du temple et du palais. Il s'agissait d'un simple troc et la valeur en argent mentionnée dans les textes d'Ur III ne concernait pas ces échanges. L'argent n'était utilisé que lors de transactions de biens se traitant sur une grande échelle ou lors de ventes plus importantes de propriétés immobilières, d'hommes ou de bétail. Bien que l'on puisse supposer qu'il y ait eu un rapport entre l'équivalent officiel en argent et la valeur réelle des produits et des matières premières dans les échanges locaux, des fluctuations mineures et des changements dans le système d'échange à grande échelle n'affectaient pas la valeur des produits troqués lors de ces échanges.