bluuebunny/crossref_metadata_2025 huggingface dataset:
Isoleucine Biosynthesis in
Leptospira interrogans
Serotype lai Strain 56601 Proceeds via a Threonine-Independent Pathway
Authors: Xu Hai , Zhang Yuzhen , Guo Xiaokui , Ren Shuangxi , Staempfli Andreas A. , Chiao Juishen , Jiang Weihong , Zhao Guoping
Published: August 2004

Three
leuA
-like protein-coding sequences were identified in
Leptospira interrogans
. One of these, the
cimA
gene, was shown to encode citramalate synthase (EC 4.1.3.-). The other two encoded α-isopropylmalate synthase (EC 4.1.3.12). Expressed in
Escherichia coli
, the citramalate synthase was purified and characterized. Although its activity was relatively low, it was strictly specific for pyruvate as the keto acid substrate. Unlike the citramalate synthase of the thermophile
Methanococcus jannaschii
, the
L. interrogans
enzyme is temperature sensitive but exhibits a much lower

K
m

(0.04 mM) for pyruvate. The reaction product was characterized as (
R
)-citramalate, and the proposed β-methyl-
d
-malate pathway was further confirmed by demonstrating that citraconate was the substrate for the following reaction. This alternative pathway for isoleucine biosynthesis from pyruvate was analyzed both in vitro by assays of leptospiral isopropylmalate isomerase (EC 4.2.1.33) and β-isopropylmalate dehydrogenase (EC 1.1.1.85) in
E. coli
extracts bearing the corresponding clones and in vivo by complementation of
E. coli ilvA
,
leuC
/
D
, and
leuB
mutants. Thus, the existence of a leucine-like pathway for isoleucine biosynthesis in
L. interrogans
under physiological conditions was unequivocally proven. Significant variations in either the enzymatic activities or mRNA levels of the
cimA
and
leuA
genes were detected in
L. interrogans
grown on minimal medium supplemented with different levels of the corresponding amino acids or in cells grown on serum-containing rich medium. The similarity of this metabolic pathway in leptospires and archaea is consistent with the evolutionarily primitive status of the eubacterial spirochetes.
Molecular Characterization of the
eis
Promoter of
Mycobacterium tuberculosis
Authors: Roberts Esteban A. , Clark Amanda , McBeth Sarah , Friedman Richard L.
Published: August 2004

To further understand
Mycobacterium tuberculosis
pathogenesis, the regulation of potential virulence genes needs to be investigated. The
eis
gene of
M. tuberculosis
H37Rv enhances the intracellular survival of
Mycobacterium smegmatis
, which does not contain
eis
, within macrophages (J. Wei, J. L. Dahl, J. W. Moulder, E. A. Roberts, P. O'Gaora, D. B. Young, and R. L. Friedman, J. Bacteriol.
182:
377-384, 2000). Experiments were done to characterize the
eis
promoter in
M. smegmatis
and
M. tuberculosis
H37Ra. The putative −10 and −35 regions matched the
Escherichia coli
σ
70
consensus 67 and 83%, respectively, making it a group A/
SigA
-like mycobacterial promoter. Expression of site-directed variants of the core promoter region, determined by flow cytometry using
gfp
as a reporter, showed that the putative −10 region is essential for
eis
expression. In addition, site-directed alteration of the
eis
promoter to the consensus
E. coli
σ
70
promoter elements increased
gfp
transcription to levels similar to that driven by the heat shock promoter, p
hsp60
, of
Mycobacterium bovis
BCG. Upstream promoter deletion analysis showed that a 200- and 412-bp region of the promoter was necessary for maximum expression of
gfp
in
M. smegmatis
and
M. tuberculosis
H37Ra, respectively. Random mutagenesis of the 412-bp
eis
promoter, using a catechol 2,3-dioxygenase screen and activity assay, defined nucleotides upstream of the core promoter region that are essential to
eis
expression in both
M. smegmatis
and
M. tuberculosis
H37Ra, including a region homologous to a DinR
cis
element.
Differential Regulation of Soluble and Membrane-Bound Inorganic Pyrophosphatases in the Photosynthetic Bacterium
Rhodospirillum rubrum
Provides Insights into Pyrophosphate-Based Stress Bioenergetics
Authors: López-Marqués Rosa L. , Pérez-Castiñeira José R. , Losada Manuel , Serrano Aurelio
Published: August 2004

Soluble and membrane-bound inorganic pyrophosphatases (sPPase and H
+
-PPase, respectively) of the purple nonsulfur bacterium
Rhodospirillum rubrum
are differentially regulated by environmental growth conditions. Both proteins and their transcripts were found in cells of anaerobic phototrophic batch cultures along all growth phases, although they displayed different time patterns. However, in aerobic cells that grow in the dark, which exhibited the highest growth rates, Northern and Western blot analyses as well as activity assays demonstrated high sPPase levels but no H
+
-PPase. It is noteworthy that H
+
-PPase is highly expressed in aerobic cells under acute salt stress (1 M NaCl). H
+
-PPase was also present in anaerobic cells growing at reduced rates in the dark under either fermentative or anaerobic respiratory conditions. Since H
+
-PPase was detected not only under all anaerobic growth conditions but also under salt stress in aerobiosis, the corresponding gene is not invariably repressed by oxygen. Primer extension analyses showed that, under all anaerobic conditions tested, the
R. rubrum
H
+
-PPase gene utilizes two activator-dependent tandem promoters, one with an FNR-like sequence motif and the other with a RegA motif, whereas in aerobiosis under salt stress, the H
+
-PPase gene is transcribed from two further tandem promoters involving other transcription factors. These results demonstrate a tight transcriptional regulation of the H
+
-PPase gene, which appears to be induced in response to a variety of environmental conditions, all of which constrain cell energetics.
Requirements for Nitric Oxide Generation from Isoniazid Activation In Vitro and Inhibition of Mycobacterial Respiration In Vivo
Authors: Timmins Graham S. , Master Sharon , Rusnak Frank , Deretic Vojo
Published: August 2004

Isoniazid (INH), a front-line antituberculosis agent, is activated by mycobacterial catalase-peroxidase KatG, converting INH into bactericidal reactive species. Here we investigated the requirements and the pathway of nitric oxide (NO˙) generation during oxidative activation of INH byMycobacterium tuberculosisKatG in vitro. We also provide in vivo evidence that INH-derived NO˙ can inhibit key mycobacterial respiratory enzymes, which may contribute to the overall antimycobacterial action of INH.
Analysis of the Genome Structure of the Nonpathogenic Probiotic
Escherichia coli
Strain Nissle 1917
Authors: Grozdanov Lubomir , Raasch Carsten , Schulze Jürgen , Sonnenborn Ulrich , Gottschalk Gerhard , Hacker Jörg , Dobrindt Ulrich
Published: August 2004

Nonpathogenic
Escherichia coli
strain Nissle 1917 (O6:K5:H1) is used as a probiotic agent in medicine, mainly for the treatment of various gastroenterological diseases. To gain insight on the genetic level into its properties of colonization and commensalism, this strain's genome structure has been analyzed by three approaches: (i) sequence context screening of tRNA genes as a potential indication of chromosomal integration of horizontally acquired DNA, (ii) sequence analysis of 280 kb of genomic islands (GEIs) coding for important fitness factors, and (iii) comparison of Nissle 1917 genome content with that of other
E. coli
strains by DNA-DNA hybridization. PCR-based screening of 324 nonpathogenic and pathogenic
E. coli
isolates of different origins revealed that some chromosomal regions are frequently detectable in nonpathogenic
E. coli
and also among extraintestinal and intestinal pathogenic strains. Many known fitness factor determinants of strain Nissle 1917 are localized on four GEIs which have been partially sequenced and analyzed. Comparison of these data with the available knowledge of the genome structure of
E. coli
K-12 strain MG1655 and of uropathogenic
E. coli
O6 strains CFT073 and 536 revealed structural similarities on the genomic level, especially between the
E. coli
O6 strains. The lack of defined virulence factors (i.e., alpha-hemolysin, P-fimbrial adhesins, and the semirough lipopolysaccharide phenotype) combined with the expression of fitness factors such as microcins, different iron uptake systems, adhesins, and proteases, which may support its survival and successful colonization of the human gut, most likely contributes to the probiotic character of
E. coli
strain Nissle 1917.
DNA Microarray-Based Genome Comparison of a Pathogenic and a Nonpathogenic Strain of
Xylella fastidiosa
Delineates Genes Important for Bacterial Virulence
Authors: Koide Tie , Zaini Paulo A. , Moreira Leandro M. , Vêncio Ricardo Z. N. , Matsukuma Adriana Y. , Durham Alan M. , Teixeira Diva C. , El-Dorry Hamza , Monteiro Patrícia B. , da Silva Ana Claudia R. , Verjovski-Almeida Sergio , da Silva Aline M. , Gomes Suely L.
Published: August 2004

Xylella fastidiosa
is a phytopathogenic bacterium that causes serious diseases in a wide range of economically important crops. Despite extensive comparative analyses of genome sequences of
Xylella
pathogenic strains from different plant hosts, nonpathogenic strains have not been studied. In this report, we show that
X. fastidiosa
strain J1a12, associated with citrus variegated chlorosis (CVC), is nonpathogenic when injected into citrus and tobacco plants. Furthermore, a DNA microarray-based comparison of J1a12 with 9a5c, a CVC strain that is highly pathogenic and had its genome completely sequenced, revealed that 14 coding sequences of strain 9a5c are absent or highly divergent in strain J1a12. Among them, we found an arginase and a fimbrial adhesin precursor of type III pilus, which were confirmed to be absent in the nonpathogenic strain by PCR and DNA sequencing. The absence of arginase can be correlated to the inability of J1a12 to multiply in host plants. This enzyme has been recently shown to act as a bacterial survival mechanism by down-regulating host nitric oxide production. The lack of the adhesin precursor gene is in accordance with the less aggregated phenotype observed for J1a12 cells growing in vitro. Thus, the absence of both genes can be associated with the failure of the J1a12 strain to establish and spread in citrus and tobacco plants. These results provide the first detailed comparison between a nonpathogenic strain and a pathogenic strain of
X. fastidiosa
, constituting an important step towards understanding the molecular basis of the disease.
spoIVH(ykvV), a Requisite Cortex Formation Gene, Is Expressed in Both Sporulating Compartments ofBacillus subtilis
Authors: Imamura Daisuke , Kobayashi Kazuo , Sekiguchi Junichi , Ogasawara Naotake , Takeuchi Michio , Sato Tsutomu
Published: August 2004

It is well known that theykvU-ykvVoperon is under the regulation of the σE-associated RNA polymerase (EσE). In our study, we observed thatykvVis transcribed together with the upstreamykvUgene by EσEin the mother cell and monocistronically under EσGcontrol in the forespore. Interestingly, alternatively expressedykvVin either the forespore or the mother cell increased the sporulation efficiency in theykvVbackground. Studies show that the YkvV protein is a member of the thioredoxin superfamily and also contains a putative Sec-type secretion signal at the N terminus. We observed efficient sporulation in a mutant strain obtained by replacing the putative signal peptide of YkvV with the secretion signal sequence of SleB, indicating that the putative signal sequence is essential for spore formation. These results suggest that YkvV is capable of being transported by the putative Sec-type signal sequence into the space between the double membranes surrounding the forespore. The ability ofykvVexpression in either compartment to complement is indeed intriguing and further introduces a new dimension to the genetics ofB. subtilisspore formation. Furthermore, electron microscopic observation revealed a defective cortex in theykvVdisruptant. In addition, the expression levels of σK-directed genes significantly decreased despite normal σGactivity in theykvVmutant. However, immunoblotting with the anti-σKantibody showed that pro-σKwas normally processed in theykvVmutant, indicating that YkvV plays an important role in cortex formation, consistent with recent reports. We therefore propose thatykvVshould be renamedspoIVH.
The LuxR Homolog ExpR, in Combination with the Sin Quorum Sensing System, Plays a Central Role in
Sinorhizobium meliloti
Gene Expression
Authors: Hoang Hanh H. , Becker Anke , González Juan E.
Published: August 2004

Quorum sensing, a population density-dependent mechanism for bacterial communication and gene regulation, plays a crucial role in the symbiosis between alfalfa and its symbiont
Sinorhizobium meliloti
. The Sin system, one of three quorum sensing systems present in
S. meliloti
, controls the production of the symbiotically active exopolysaccharide EPS II. Based on DNA microarray data, the Sin system also seems to regulate a multitude of
S. meliloti
genes, including genes that participate in low-molecular-weight succinoglycan production, motility, and chemotaxis, as well as other cellular processes. Most of the regulation by the Sin system is dependent on the presence of the ExpR regulator, a LuxR homolog. Gene expression profiling data indicate that ExpR participates in additional cellular processes that include nitrogen fixation, metabolism, and metal transport. Based on our microarray analysis we propose a model for the regulation of gene expression by the Sin/ExpR quorum sensing system and another possible quorum sensing system(s) in
S. meliloti
.
Comparative Whole-Genome Analysis of Virulent and Avirulent Strains ofPorphyromonas gingivalis
Authors: Chen Tsute , Hosogi Yumiko , Nishikawa Kiyoshi , Abbey Kevin , Fleischmann Robert D. , Walling Jennifer , Duncan Margaret J.
Published: August 2004

We usedPorphyromonas gingivalisgene microarrays to compare the total gene contents of the virulent strain W83 and the avirulent type strain, ATCC 33277. Signal ratios and scatter plots indicated that the chromosomes were very similar, with approximately 93% of the predicted genes in common, while at least 7% of them showed very low or no signals in ATCC 33277. Verification of the array results by PCR indicated that several of the disparate genes were either absent from or variant in ATCC 33277. Divergent features included already reported insertion sequences andragB, as well as additional hypothetical and functionally assigned genes. Several of the latter were organized in a putative operon in W83 and encoded enzymes involved in capsular polysaccharide synthesis. Another cluster was associated with two paralogous regions of the chromosome with a low G+C content, at 41%, compared to that of the whole genome, at 48%. These regions also contained conserved and species-specific hypothetical genes, transposons, insertion sequences, and integrases and were located adjacent to tRNA genes; thus, they had several characteristics of pathogenicity islands. While this global comparative analysis showed the close relationship between W83 and ATCC 33277, the clustering of genes that are present in W83 but divergent in or absent from ATCC 33277 is suggestive of chromosomal islands that may have been acquired by lateral gene transfer.
Tra Proteins Characteristic of F-Like Type IV Secretion Systems Constitute an Interaction Group by Yeast Two-Hybrid Analysis
Authors: Harris Robin L. , Silverman Philip M.
Published: August 2004

Using yeast two-hybrid screens, we have defined an interaction group of six Tra proteins encoded by the F plasmid and required by F+cells to elaborate F pili. The six proteins are TraH, TraF, TraW, TraU, TrbI, and TrbB. Except for TrbI, these proteins were all identified as hallmarks of F-like type IV secretion systems (TFSSs), with no homologues among TFSS genes of P-type or I-type systems (T. Lawley, W. Klimke, M. Gubbins, and L. Frost, FEMS Microbiol. Lett. 224:1-15, 2003). Also with the exception of TrbI, which is an inner membrane protein, the remaining proteins are or are predicted to be periplasmic. TrbI consists of one membrane-spanning segment near its N terminus and an 88-residue, hydrophilic domain that extends into the periplasm. Hence, the proteins of this group probably form a periplasmic cluster inEscherichia coli. The interaction network identifies TraH as the most highly connected node, with two-hybrid links to TrbI, TraU, and TraF. As measured by transcriptional activation oflacZ, the TrbI-TraH interaction inSaccharomyces cerevisiaerequires the TraH amino acid segment from residues 193 to 225. The TraU and TraF interactions are localized to C-terminal segments of TraH (amino acids 315 to 458 for TraF and amino acids 341 to 458 for TraU). The TrbI-TraH interaction with full-length (less the signal peptide) TraH is weak but increases 40-fold with N-terminal TraH deletions; the first 50 amino acids appear to be critical for inhibiting TrbI binding in yeast. Previous studies by others have shown that, with the exception oftrbBmutations, which do not affect the elaboration or function of F pili under laboratory conditions, a mutation in any of the other genes in this interaction group alters the number or length distribution of F pili. We propose a model whereby one function of the TraH interaction group is to control F-pilus extension and retraction.
Identification of the Secretion and Translocation Domain of the Enteropathogenic and EnterohemorrhagicEscherichia coliEffector Cif, Using TEM-1 β-Lactamase as a New Fluorescence-Based Reporter
Authors: Charpentier Xavier , Oswald Eric
Published: August 2004

Enteropathogenic and enterohemorrhagicEscherichia coli(EPEC and EHEC) strains are human and animal pathogens that inject effector proteins into host cells via a type III secretion system (TTSS). Cif is an effector protein which induces host cell cycle arrest and reorganization of the actin cytoskeleton. Cif is encoded by a lambdoid prophage present in most of the EPEC and EHEC strains. In this study, we analyzed the domain that targets Cif to the TTSS by using a new reporter system based on a translational fusion of the effector proteins with mature TEM-1 β-lactamase. Translocation was detected directly in living host cells by using the fluorescent β-lactamase substrate CCF2/AM. We show that the first 16 amino acids (aa) of Cif were necessary and sufficient to mediate translocation into the host cells. Similarly, the first 20 aa of the effector proteins Map, EspF, and Tir, which are encoded in the same region as the TTSS, mediated secretion and translocation in a type III-dependent but chaperone-independent manner. A truncated form of Cif lacking its first 20 aa was no longer secreted and translocated, but fusion with the first 20 aa of Tir, Map, or EspF restored both secretion and translocation. In addition, the chimeric proteins were fully able to trigger host cell cycle arrest and stress fiber formation. In conclusion, our results demonstrate that Cif is composed of a C-terminal effector domain and an exchangeable N-terminal translocation signal and that the TEM-1 reporter system is a convenient tool for the study of the translocation of toxins or effector proteins into host cells.
Multiple-Locus Variable-Number Tandem Repeat Analysis of Dutch
Bordetella pertussis
Strains Reveals Rapid Genetic Changes with Clonal Expansion during the Late 1990s
Authors: Schouls Leo M. , van der Heide Han G. J. , Vauterin Luc , Vauterin Paul , Mooi Frits R.
Published: August 2004

Bordetella pertussis
, the causative agent of whooping cough, has remained endemic in The Netherlands despite extensive nationwide vaccination since 1953. In the 1990s, several epidemic periods have resulted in many cases of pertussis. We have proposed that strain variation has played a major role in the upsurges of this disease in The Netherlands. Therefore, molecular characterization of strains is important in identifying the causes of pertussis epidemiology. For this reason, we have developed a multiple-locus variable-number tandem repeat analysis (MLVA) typing system for
B. pertussis
. By combining the MLVA profile with the allelic profile based on multiple-antigen sequence typing, we were able to further differentiate strains. The relationships between the various genotypes were visualized by constructing a minimum spanning tree. MLVA of Dutch strains of
B. pertussis
revealed that the genotypes of the strains isolated in the prevaccination period were diverse and clearly distinct from the strains isolated in the 1990s. Furthermore, there was a decrease in diversity in the strains from the late 1990s, with a remarkable clonal expansion that coincided with the epidemic periods. Using this genotyping, we have been able to show that
B. pertussis
is much more dynamic than expected.
Escherichia coli
Serogroup O107/O117 Lipopolysaccharide Binds and Neutralizes Shiga Toxin 2
Authors: Gamage Shantini D. , McGannon Colleen M. , Weiss Alison A.
Published: August 2004

The AB
5
toxin Shiga toxin 2 (Stx2) has been implicated as a major virulence factor of
Escherichia coli
O157:H7 and other Shiga toxin-producing
E. coli
strains in the progression of intestinal disease to more severe systemic complications. Here, we demonstrate that supernatant from a normal
E. coli
isolate, FI-29, neutralizes the effect of Stx2, but not the related Stx1, on Vero cells. Biochemical characterization of the neutralizing activity identified the lipopolysaccharide (LPS) of FI-29, a serogroup O107/O117 strain, as the toxin-neutralizing component. LPSs from FI-29 as well as from type strains
E. coli
O107 and
E. coli
O117 were able bind Stx2 but not Stx1, indicating that the mechanism of toxin neutralization may involve inhibition of the interaction between Stx2 and the Gb
3
receptor on Vero cells.
Novel Archaeal Alanine:Glyoxylate Aminotransferase from
Thermococcus litoralis
Authors: Sakuraba Haruhiko , Kawakami Ryushi , Takahashi Hajime , Ohshima Toshihisa
Published: August 2004

A novel alanine:glyoxylate aminotransferase was found in a hyperthermophilic archaeon,
Thermococcus litoralis
. The amino acid sequence of the enzyme did not show a similarity to any alanine:glyoxylate aminotransferases reported so far. Homologues of the enzyme appear to be present in almost all hyperthermophilic archaea whose whole genomes have been sequenced.
Amino Acid Substitutions in Putative Selectivity Filter Regions III and IV in KdpA Alter Ion Selectivity of the KdpFABC Complex from
Escherichia coli
Authors: Bertrand Jessica , Altendorf Karlheinz , Bramkamp Marc
Published: August 2004

When grown under conditions of potassium limitation or high osmolality,
Escherichia coli
synthesizes the K
+
-translocating KdpFABC complex. The KdpA subunit, which has sequence homology to potassium channels of the KcsA type, has been shown to be important for potassium binding and transport. Replacement of the glycine residues in KdpA at positions 345 and 470, members of putative selectivity filter regions III and IV, alters the ion selectivity of the KdpFABC complex.
Complete Genomic Nucleotide Sequence of the Temperate Bacteriophage AaΦ23 of
Actinobacillus actinomycetemcomitans
Authors: Resch Grégory , Kulik Eva M. , Dietrich Fred S. , Meyer Jürg
Published: August 2004

The entire double-stranded DNA genome of the
Actinobacillus actinomycetemcomitans
bacteriophage AaΦ23 was sequenced. Linear DNA contained in the phage particles is circularly permuted and terminally redundant. Therefore, the physical map of the phage genome is circular. Its size is 43,033 bp with an overall molar G+C content of 42.5 mol%. Sixty-six potential open reading frames (ORFs) were identified, including an ORF resulting from a translational frameshift. A putative function could be assigned to 23 of them. Twenty-three other ORFs share homologies only with hypothetical proteins present in several bacteria or bacteriophages, and 20 ORFs seem to be specific for phage AaΦ23. The organization of the phage genome and several genetic functions share extensive similarities to that of the lambdoid phages. However, AaΦ23 encodes a DNA adenine methylase, and the DNA packaging strategy is more closely related to the P22 system. The attachment sites of AaΦ23 (
attP
) and several
A. actinomycetemcomitans
hosts (
attB
) are 49 bp long.
Characterization of Lipoteichoic Acids asLactobacillus delbrueckiiPhage Receptor Components
Authors: Räisänen Liisa , Schubert Karin , Jaakonsaari Tiina , Alatossava Tapani
Published: August 2004

Lipoteichoic acids (LTAs) were purified fromLactobacillus delbrueckiisubsp.lactisATCC 15808 and its LL-H adsorption-resistant mutant, Ads-5, by hydrophobic interaction chromatography.L. delbrueckiiphages (LL-H, the LL-H host range mutant, and JCL1032) were inactivated by these poly(glycerophosphate) type of LTAs in vitro in accordance to their adsorption to intact ATCC 15808 and Ads-5 cells.
Evidence of
bar
Minigene Expression and tRNA
2
Ile
Sequestration as Peptidyl-tRNA
2
Ile
during Lambda Bacteriophage Development
Authors: Oviedo de Anda Norma Angélica , Kameyama Luis , Galindo José Manuel , Guarneros Gabriel , Hernandez-Sanchez Javier
Published: August 2004

Lambda bacteriophage development is impaired in
Escherichia coli
cells defective for peptidyl (pep)-tRNA hydrolase (Pth). Single-base-pair mutations (
bar
−
) that affect translatable two-codon open reading frames named
bar
minigenes (
bar
I or
bar
II) in the lambda phage genome promote the development of this phage in Pth-defective cells (rap cells). When the
bar
I minigene is cloned and overexpressed from a plasmid, it inhibits protein synthesis and cell growth in rap cells by sequestering

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as

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. Either

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or Pth may reverse these effects. In this paper we present evidence that both
bar
I and
bar
II minigenes are translatable elements that sequester

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as

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. In addition, overexpression of the
bar
I minigene impairs the development even of
bar
−
phages in rap cells. Interestingly, tRNA or Pth may reestablish lambda phage development. These results suggest that lambda
bar
minigenes are expressed and

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is sequestered as

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during lambda phage development.
Polymorphic Mutation Frequencies in
Escherichia coli
: Emergence of Weak Mutators in Clinical Isolates
Authors: Baquero María-Rosario , Nilsson Annika I. , del Carmen Turrientes María , Sandvang Dorthe , Galán Juan Carlos , Martínez Jose Luís , Frimodt-Møller Niels , Baquero Fernando , Andersson Dan I.
Published: August 2004

Polymorphisms in the rifampin resistance mutation frequency (
f
) were studied in 696
Escherichia coli
strains from Spain, Sweden, and Denmark. Of the 696 strains, 23% were weakly hypermutable (4 × 10
−8
≤
f
< 4 × 10
−7
), and 0.7% were strongly hypermutable (
f
≥ 4 × 10
−7
). Weak mutators were apparently more frequent in southern Europe and in blood isolates (38%) than in urinary tract isolates (25%) and feces of healthy volunteers (11%).
The RpoS Sigma Factor in the Dissimilatory Fe(III)-Reducing Bacterium
Geobacter sulfurreducens
Authors: Núñez Cinthia , Adams Lorrie , Childers Susan , Lovley Derek R.
Published: August 2004

Geobacter sulfurreducens
RpoS sigma factor was shown to contribute to survival in stationary phase and upon oxygen exposure. Furthermore, a mutation in
rpoS
decreased the rate of reduction of insoluble Fe(III) but not of soluble forms of iron. This study suggests that RpoS plays a role in regulating metabolism of
Geobacter
under suboptimal conditions in subsurface environments.
Erwinia chrysanthemiO Antigen Is Required for Betaine Osmoprotection in High-Salt Media
Authors: Touzé Thierry , Goude Renan , Georgeault Sylvie , Blanco Carlos , Bonnassie Sylvie
Published: August 2004

Cellular components necessary for osmoprotection are poorly known. In this study we show that O antigen is specifically required for the effectiveness of betaines as osmoprotectants forErwinia chrysanthemiin saline media. The phenotype is correlated with the inability ofrfbmutant strains to maintain a high accumulation level of betaines in hypersaline media.
Excision of the
Shigella
Resistance Locus Pathogenicity Island in
Shigella flexneri
Is Stimulated by a Member of a New Subgroup of Recombination Directionality Factors
Authors: Luck Shelley N. , Turner Sally A. , Rajakumar Kumar , Adler Ben , Sakellaris Harry
Published: August 2004

Pathogenicity islands are capable of excision and insertion within bacterial chromosomes. We describe a protein, Rox, that stimulates excision of the
Shigella
resistance locus pathogenicity island in
Shigella flexneri
. Sequence analysis suggests that Rox belongs to a new subfamily of recombination directionality factors, which includes proteins from P4, enterohemorrhagic
Escherichia coli
, and
Yersinia pestis
.
Gaps, conflicts, and consensus in the ethics statements of professional associations, medical groups, and health plans
Authors: Berkman N D , Wynia M K , Churchill L R
Published: August 2004

Background:Patients today interact with physicians, physician groups, and health plans, each of which may follow distinct ethical guidelines.

Method:We systematically compared physician codes of ethics with ethics policies at physician group practices and health plans, using the 1998–99 policies of 38 organisations—18 medical associations (associations), nine physician group practices (groups), and 12 health plans (plans)—selected using random and stratified purposive sampling. A clinician and a social scientist independently abstracted each document, using a 397-item health care ethics taxonomy; a reconciled abstraction form was used for analysis. This study focuses on ethics policies regarding professional obligation towards patients, resource allocation, and care for the vulnerable in society.

Results:A majority in all three groups mention “fiduciary obligations” of one sort or another, but associations generally address physician/patient relations but not health plan obligations, while plans rarely endorse physicians’ obligations of advocacy, beneficence, and non-maleficence. Except for occasional mentions of cost effectiveness or efficiency, ethical considerations in resource allocation rarely arise in the ethics policies of all three organisational types. Very few associations, groups, or plans specifically endorse obligations to vulnerable populations.

Conclusions:With some important exceptions, we found that the ethics policies of associations, groups, and plans are narrowly focused and often ignore important ethical concerns for society, such as resource allocation and care for vulnerable populations. More collaborative work is needed to build integrated sets of ethical standards that address the aims and responsibilities of the major stakeholders in health care delivery.
Ethics of refusing parental requests to withhold or withdraw treatment from their premature baby: Table 1
Authors: Boyle R J , Salter R , Arnander M W
Published: August 2004

In the United Kingdom women have access to termination of pregnancy for maternal reasons until 24 weeks’ completed gestation, but it is accepted practice for children born at or beyond 25 weeks’ gestation to be treated according to the child’s perceived best interests even if this is not in accordance with parental wishes. The authors present a case drawn from clinical practice which highlights the discomfort that parents may feel about such an abrupt change in their rights over their child, and argue that parents should have greater autonomy over treatment decisions regarding their prematurely born children.
Is the clock ticking for terminally ill patients in Israel? Preliminary comment on a proposal for a bill of rights for the terminally ill
Authors: Barilan Y M
Published: August 2004

This paper presents and discusses a recent Israeli proposal to legislate on the rights of the dying patient. A gap exists between elitist biases of the committee proposing the law, and popular values and sentiments. The proposed law divides the dying patients into two groups: “those who wish to go on living” and “those who wish to die”. The former will have a right to life prolonging extraordinary care. It is not clear who would foot the bill for this care. Also it is hard to see how this munificence could fail to discriminate against all other patients. Both the secular ethicists and the rabbis involved in drawing up the proposal accepted the assumption that it is good for some terminal patients to die. The rabbis objected, however, to direct and active interventions that shorten life. The solution arrived at was to install timers in the ventilators so as to allow them to expire automatically unless the patient wishes for their resetting.
The patient who refuses nursing care
Authors: Aveyard H
Published: August 2004

Objectives:The aim of this paper is to examine the way in which nurses manage patients who refuse nursing care procedures.

Design:This paper reports on a qualitative study which was undertaken to explore the way in which nurses obtain consent prior to nursing care procedures. Focus groups were carried out to obtain background data concerning how consent is obtained. Critical incidents were collected through in depth interviews as a means of focusing on specific incidents in clinical practice.

Setting:Two teaching hospitals in England.

Participants:Purposive sample of qualified nurses.

Results:When a patient refuses nursing care, nurses respond by giving information until the patient finally accedes to the procedure. Nurses will go to great lengths to achieve patients’ agreement to the procedure, but the extent to which the agreement remains voluntary cannot be ascertained by the data collected in this study. If the patient does not eventually agree to a procedure, there is evidence that nurses will administer the care in the absence of consent.

Conclusions:Nurses are concerned to obtain the patient’s consent prior to the administration of nursing care but if this cannot be achieved do not regard obtaining consent as an absolute requirement. Consent is preferred, but not considered essential. Nurses have some understanding of the principles of informed consent but do not apply them to everyday clinical nursing practice.
End of life decisions: attitudes of Finnish physicians
Authors: Hildén H-M , Louhiala P , Palo J
Published: August 2004

Objectives:This study investigated Finnish physicians’ experiences of decisions concerning living wills and do not resuscitate (DNR) orders and also their views on the role of patients and family members in these decisions.

Design:A questionnaire was sent to 800 physicians representing the following specialties: general practice (n = 400); internal medicine (n = 207); neurology (n = 100), and oncology (n = 93).

Results:The response rate was 56%. Most of the respondents had a positive attitude toward (92%), and respect for (86%) living wills, and 72% reported situations in which such a will would have been helpful, although experience with their use was limited. The physicians reported both benefits and problems with living wills. Thirteen per cent had completed a living will of their own. Half did not consider living wills to be reliable if they were several years old. Do not resuscitate orders were interpreted in two ways: resuscitation forbidden (70%) or only palliative (symptom oriented) care required (30%). The respondents also documented DNR orders differently. Seventy two per cent discussed DNR decisions always or often with patients able to communicate, and even 76% discussed DNR orders with the family members of patients unable to communicate. Most respondents were able to approach a dying patient without difficulty. They also felt that education in general was needed.

Conclusions:In general Finnish physicians accept living wills, but find they are accompanied by several problems. Many problems could be avoided if physicians and patients conducted progressive discussions about living wills. The differing interpretations of DNR orders are a matter of concern in that they may affect patient treatment. The promotion of patient autonomy with respect to treatment seems rather good, but the limitations of the study need to be kept in mind.
Prescribing cannabis: freedom, autonomy, and values
Authors: Hayry M
Published: August 2004

In many Western jurisdictions cannabis, unlike most other psychoactive drugs, cannot be prescribed to patients even in cases where medical professionals believe that it would ease the patient’s pain or anxiety. The reasons for this prohibition are mostly ideological, although medical and moral arguments have been formulated to support it. In this paper, it is argued that freedom, properly understood, provides a sound ethical reason to allow the use of cannabis in medicine. Scientific facts, appeals to harm and autonomy, and considerations of symbolic value cannot consistently justify prohibitions.
Law and policy in the era of reproductive genetics
Authors: Caulfield T , Knowles L , Meslin E M
Published: August 2004

The extent to which society utilises the law to enforce its moral judgments remains a dominant issue in this era of embryonic stem cell research, preimplantation genetic diagnosis, and human reproductive cloning. Balancing the potential health benefits and diverse moral values of society can be a tremendous challenge. In this context, governments often adopt legislative bans and prohibitions and rely on the inflexible and often inappropriate tool of criminal law. Legal prohibitions in the field of reproductive genetics are not likely to reflect adequately the depth and diversity of competing stakeholder positions. Rather, a comprehensive and readily responsive regulatory policy is required. Such a policy must attend to the evolving scientific developments and ethical considerations. We outline a proposal for effective, responsive, and coherent oversight of new reproductive genetic technologies.
Nicotine conjugate vaccine: is there a right to a smoking future?
Authors: Hasman A , Holm Søren
Published: August 2004

Tobacco consumption is believed to be one of the world’s greatest preventable health problems. According to the World Health Organisation, 1.1 billion people worldwide are addicted to nicotine with tobacco causing an estimated four million premature deaths every year. The development of a nicotine conjugate vaccine suggests that immunisation may hold promise as a future therapeutic and preventive strategy for tobacco smoking and nicotine addiction. Allowing parents to immunise their children against smoking could be an infringement of children’s right to an open future, however, and is not ethically unproblematic
Students’ attitudes and potential behaviour to a competent patient’s request for withdrawal of treatment as they pass through a modern medical curriculum
Authors: Goldie J , Schwartz L , Morrison J
Published: August 2004

Objective:To examine students’ attitudes and potential behaviour to a competent patient’s request for withdrawal of treatment as they pass through a modern medical curriculum.

Design:Cohort design.

Setting:University of Glasgow Medical School, United Kingdom.

Subjects:A cohort of students entering Glasgow University’s new learner centred, integrated medical curriculum in October 1996.

Methods:Students’ responses before and after year 1, after year 3, and after year 5 to the assisted suicide vignette of the Ethics in Health Care Survey instrument, were examined quantitatively and qualitatively. Analysis of students’ multichoice answers enabled measurement of the movement towards professional consensus opinion. Analysis of written justifications helped determine whether their reasoning was consistent with professional consensus and enabled measurement of change in knowledge content and recognition of the values inherent in the vignette. Themes on students’ reasoning behind their decision to withdraw treatment or not were also identified.

Results:Students’ answers were found to be consistent with professional consensus opinion precurriculum and remained so throughout the curriculum. There was an improvement in the knowledge content of the written responses following the first year of the curriculum, which was sustained postcurriculum. However, students were found to analyse the section mainly in terms of autonomy, with few responses considering the other main ethical principles or the wider ethical perspective. Students were unclear on their legal responsibilities.

Conclusions:Students should be encouraged to consider all relevant ethical principles and the wider ethical perspective when deliberating ethical dilemmas. Students should have a clear understanding of their legal responsibilities.
Response to Orr and Siegler—collective intentionality and procreative desires: the permissible view on consent to posthumous conception
Authors: Parker M
Published: August 2004

Orr and Siegler have recently defended a restrictive view concerning posthumous sperm retrieval and conception, which would limit insemination to those cases where the deceased man has provided explicit consent for such a procedure. The restrictive view dominates current law and practice. A permissible view, in contrast, would allow insemination and conception in all but those cases where the posthumous procedure has been explicitly refused, or where there is no reasonable evidence that the deceased person desired children. I describe a phenomenology of procreative desires which supports the permissible view, and which is compatible with requirements concerning the interests of the decedent, concepts of medical infertility, and the welfare of the future child. The account illustrates how our current obsession with individual rights and autonomy can be self-defeating and repressive.
Disability, identity and the “expressivist objection”
Authors: Edwards S D
Published: August 2004

The practice of prenatal screening for disability is sometimes objected to because of the hurt and offence such practices may cause to people currently living with disabilities. This objection is commonly termed “the expressivist objection”. In response to the objection it is standardly claimed that disabilities are analogous to illnesses. And just as it would be implausible to suppose reduction of the incidence of illnesses such as flu sends a negative message to ill people, so it is not plausible to suppose prevention of disability sends a negative message to disabled people. The expressivist objection hinges, however, upon a view of the relationship between disability and self identity which sees disability as part of the identity of the disabled person, in a way in which illnesses such as flu cannot be. This possibility is generally not considered in critiques of the expressivist objection. In this paper, an “identity claim” to the effect that disabilitiescanbe identity constituting is accepted and the force of the expressivist argument is reconsidered in the light of its acceptance. It is concluded that even when such an identity claim is accepted, the expressivist objection is still not morally compelling.
Medical ethics, logic traps, and game theory: an illustrative tale of brain death
Authors: Riggs J E
Published: August 2004

Decision making and choices are frequent themes in medical ethics. Game theory is based upon modelled decision making. Game theory, and associated logic traps, may have relevance to the clinical practice of medicine and medical ethics. The “prisoner’s dilemma” is one logic trap from game theory in which “rational” decision making on the part of participating individuals can lead to “suboptimal” situations. An example of such a situation involving brain death is presented and discussed from the perspective of the prisoner’s dilemma.
Evolutionary ethics: can values change
Authors: Calman K C
Published: August 2004

The hypothesis that values change and evolve is examined by this paper. The discussion is based on a series of examples where, over a period of a few decades, new ethical issues have arisen and values have changed. From this analysis it is suggested that there are a series of core values around which most people would agree. These are unlikely to change over long time periods. There are then a series of secondary or derived values around which there is much more controversy and within which differences of view occur. Such changes need to be documented if we are to understand the process involved in the evolution of differences in ethical views.
Stem cells, embryos, and the environment: a context for both science and ethics
Authors: Towns C R , Jones D G
Published: August 2004

Debate on the potential and uses of human stem cells tends to be conducted by two constituencies—ethicists and scientists. On many occasions there is little communication between the two, with the result that ethical debate is not informed as well as it might be by scientific insights. The aim of this paper is to highlight those scientific insights that may be of relevance for ethical debate.

Environmental factors play a significant role in identifying stem cells and their various subtypes. Research related to the role of the microenvironment has led to emphasis upon “plasticity”, which denotes the ability of one type of stem cell to undergo a transition to cells from other lineages. This could increase the value given to adult stem cells, in comparison with embryonic stem cell research. Any such conclusion should be treated with caution, however, since optimism of this order is not borne out by current research.

The role of the environment is also important in distinguishing between the terms totipotency and pluripotency. We argue that blastocysts (early embryos) and embryonic stem cells are only totipotent if they can develop within an appropriate environment. In the absence of this, they are merely pluripotent. Hence, blastocysts in the laboratory are potentially totipotent, in contrast to their counterparts within the human body which are actually totipotent. This may have implications for ethical debate, suggesting as it does that arguments based on potential for life may be of limited relevance.
A rational cure for prereproductive stress syndrome
Authors: Häyry M
Published: August 2004

Since human reproduction is arguably both irrational and immoral, those who seek help before conceiving could be advised it is all right not to have children.
Woman wants dead fiancé’s baby: who owns a dead man’s sperm
Authors: Spriggs M
Published: August 2004

The Brisbane Supreme Court has denied an Australian woman’s request to harvest and freeze her dead fiancé’s sperm for future impregnation. After she was denied access to the sperm, the woman learnt that her fiancé may have been a sperm donor and she began checking to find out if his sperm was still available. Given what we know, there is a good ethical argument that the woman should have access to the sperm and should be allowed to have her dead fiancé’s child.

Another aspect of this case is that it illustrates the way in which ethics, law, and personal opinion can differ.