bluuebunny/crossref_metadata_2025 huggingface dataset:
Association of the Skn7 and Yap1 Transcription Factors in the Saccharomyces cerevisiae Oxidative Stress Response
Authors: Mulford K. E. , Fassler J. S.
Published: April 2011

Saccharomyces cerevisiae
Skn7p is a stress response transcription factor that undergoes aspartyl phosphorylation by the Sln1p histidine kinase. Aspartyl phosphorylation of Skn7p is required for activation of genes required in response to wall stress, but Skn7p also activates oxidative stress response genes in an aspartyl phosphorylation-independent manner. The presence of binding sites for the Yap1p and Skn7p transcription factors in oxidative stress response promoters and the oxidative stress-sensitive phenotypes of
SKN7
and
YAP1
mutants suggest that these two factors work together. We present here evidence for a DNA-independent interaction between the Skn7 and Yap1 proteins that involves the receiver domain of Skn7p and the cysteine-rich domains of Yap1p. The interaction with Yap1p may help partition the Skn7 protein to oxidative stress response promoters when the Yap1 protein accumulates in the nucleus.
The Major Autolysin of Streptococcus gordonii Is Subject to Complex Regulation and Modulates Stress Tolerance, Biofilm Formation, and Extracellular-DNA Release
Authors: Liu Yaling , Burne Robert A.
Published: April 2011

A gene, designated
atlS
, encoding a major autolysin from
Streptococcus gordonii
, was identified and characterized. The predicted AtlS protein is 1,160 amino acids and 127 kDa and has a conserved β1,4-
N
-acetylmuramidase domain. Zymographic analysis of wild-type
S. gordonii
revealed peptidoglycan hydrolase activities with molecular masses of 130 and 90 kDa that were absent in an
atlS
deletion mutant. Western blotting revealed that the 90-kDa band was derived from the 130-kDa protein. Inactivation of
atlS
resulted in formation of long chains by the cells, markedly decreased autolytic capacity, poor biofilm formation, diminished tolerance of acid and oxidative stress, and decreased production of extracellular DNA (eDNA). The biofilm-forming capacity of the
atlS
mutant could be almost completely restored to that of the wild-type strain by adding purified recombinant AtlA autolysin of
S. mutans
but was only partially restored by addition of eDNA. Autolysis, eDNA release, and
atlS
expression increased sharply when cells entered stationary phase and were greatly enhanced in cells growing with aeration. The LytST and VicRK two-component systems were both required for the induction of
atlS
by aeration, and purified LytT was able to bind to the promoter region of
atlS in vitro
. Thus, AtlS and its associated regulatory cascade dominantly control phenotypes of
S. gordonii
that are critical to colonization, persistence, and competition with other commensal and pathogenic oral bacteria in response to the redox environment and growth domain.
Progesterone Analogs Influence Germination of Clostridium sordellii and Clostridium difficile Spores In Vitro
Authors: Liggins Marc , Ramirez Norma , Magnuson Natiera , Abel-Santos Ernesto
Published: April 2011

Clostridium sordellii
and
Clostridium difficile
are closely related anaerobic Gram-positive, spore-forming human pathogens.
C. sordellii
and
C. difficile
form spores that are believed to be the infectious form of these bacteria. These spores return to toxin-producing vegetative cells upon binding to small molecule germinants. The endogenous compounds that regulate clostridial spore germination are not fully understood. While
C. sordellii
spores require three structurally distinct amino acids to germinate, the occurrence of postpregnancy
C. sordellii
infections suggests that steroidal sex hormones might regulate its capacity to germinate. On the other hand,
C. difficile
spores require taurocholate (a bile salt) and glycine (an amino acid) to germinate. Bile salts and steroid hormones are biosynthesized from cholesterol, suggesting that the common sterane structure can affect the germination of both
C. sordellii
and
C. difficile
spores. Therefore, we tested the effect of sterane compounds on
C. sordellii
and
C. difficile
spore germination. Our results show that both steroid hormones and bile salts are able to increase
C. sordellii
spore germination rates. In contrast, a subset of steroid hormones acted as competitive inhibitors of
C. difficile
spore germination. Thus, even though
C. sordellii
and
C. difficile
are phylogenetically related, the two species' spores respond differently to steroidal compounds.
Molecular Characterization of the Glycerol-Oxidative Pathway of Clostridium butyricum VPI 1718
Authors: Raynaud Céline , Lee Jieun , Sarçabal Patricia , Croux Christian , Meynial-Salles Isabelle , Soucaille Philippe
Published: April 2011

The glycerol oxidative pathway of
Clostridium butyricum
VPI 1718 plays an important role in glycerol dissimilation. We isolated, sequenced, and characterized the region coding for the glycerol oxidation pathway. Five open reading frames (ORFs) were identified:
dhaR
, encoding a putative transcriptional regulator;
dhaD
(1,142 bp), encoding a glycerol dehydrogenase; and
dhaK
(995 bp),
dhaL
(629 bp), and
dhaM
(386 bp), encoding a phosphoenolpyruvate (PEP)-dependent dihydroxyacetone (DHA) kinase enzyme complex. Northern blot analysis demonstrated that the last four genes are transcribed as a 3.2-kb polycistronic operon only in glycerol-metabolizing cultures, indicating that the expression of this operon is regulated at the transcriptional level. The transcriptional start site of the operon was determined by primer extension, and the promoter region was deduced. The glycerol dehydrogenase activity of DhaD and the PEP-dependent DHA kinase activity of DhaKLM were demonstrated by heterologous expression in different
Escherichia coli
mutants. Based on our complementation experiments, we proposed that the HPr phosphoryl carrier protein and His9 residue of the DhaM subunit are involved in the phosphoryl transfer to dihydroxyacetone-phosphate. DhaR, a potential regulator of this operon, was found to contain conserved transmitter and receiver domains that are characteristic of two-component systems present in the AraC family. To the best of our knowledge, this is the first molecular characterization of a glycerol oxidation pathway in a Gram-positive bacterium.
The Interplay of mRNA Stimulatory Signals Required for AUU-Mediated Initiation and Programmed −1 Ribosomal Frameshifting in Decoding of Transposable Element IS
911
Authors: Prère Marie-Françoise , Canal Isabelle , Wills Norma M. , Atkins John F. , Fayet Olivier
Published: April 2011

The IS
911
bacterial transposable element uses −1 programmed translational frameshifting to generate the protein required for its mobility: translation initiated in one gene (
orfA
) shifts to the −1 frame and continues in a second overlapping gene (
orfB
), thus generating the OrfAB transposase. The A-AAA-AAG frameshift site of IS
911
is flanked by two stimulatory elements, an upstream Shine-Dalgarno sequence and a downstream stem-loop. We show here that, while they can act independently, these stimulators have a synergistic effect when combined. Mutagenic analyses revealed features of the complex stem-loop that make it a low-efficiency stimulator. They also revealed the dual role of the upstream Shine-Dalgarno sequence as (i) a stimulator of frameshifting, by itself more potent than the stem-loop, and (ii) a mandatory determinant of initiation of OrfB protein synthesis on an AUU codon directly preceding the A6G motif. Both roles rely on transient base pairing of the Shine-Dalgarno sequence with the 3′ end of 16S rRNA. Because of its effect on frameshifting, the Shine-Dalgarno sequence is an important determinant of the level of transposase in IS
911
-containing cells, and hence of the frequency of transposition.
Roles of Three Transporters, CbcXWV, BetT1, and BetT3, in Pseudomonas aeruginosa Choline Uptake for Catabolism
Authors: Malek Adel A. , Chen Chiliang , Wargo Matthew J. , Beattie Gwyn A. , Hogan Deborah A.
Published: April 2011

Pseudomonas aeruginosauses the quaternary amine choline as a carbon source, osmoprotectant, and macromolecular precursor. The importance of choline inP. aeruginosaphysiology is highlighted by the presence of multiple known and putative choline transporters encoded within its genome. This report describes the relative roles of three choline transporters, the ABC transporter CbcXWV and two symporters, BetT1 and BetT3, inP. aeruginosagrowth on choline under osmotic conditions that are physiologically relevant to eukaryotic hosts. The increased lag phases exhibited by the ΔbetT1and ΔbetT1ΔbetT3mutants relative to the wild type upon transfer to medium with choline as a sole carbon source suggested roles for BetT1 and BetT3 in cells newly exposed to choline. BetT3 and CbcXWV, but not BetT1, were sufficient to support growth on choline.betT1andbetT3expression was regulated by the repressor BetI and choline, whereascbcXWVexpression was induced by the activator GbdR and glycine betaine. The data support a model in which, upon transfer to a choline-based medium, the glycine betaine derived from choline taken up by BetT1 and BetT3 promotes subsequent GbdR-mediatedcbcXWVinduction. Furthermore, growth data indicated that the relative contributions of each transporter varied under different conditions, as BetT1 and CbcXWV were the primary choline transporters under hypo-osmolar conditions whereas BetT3 was the major choline transporter under hyperosmolar conditions. This work represents the first systematic approach to unravel the mechanisms of choline uptake inP. aeruginosa, which has the most complex bacterial choline uptake systems characterized to date.
Membrane-Bound Electron Transport in Methanosaeta thermophila
Authors: Welte Cornelia , Deppenmeier Uwe
Published: April 2011

The obligate aceticlastic methanogen
Methanosaeta thermophila
uses a membrane-bound ferredoxin:heterodisulfide oxidoreductase system for energy conservation. We propose that the system is composed of a truncated form of the F
420
H
2
dehydrogenase, methanophenazine, and the heterodisulfide reductase. Hence, the electron transport chain is distinct from those of well-studied
Methanosarcina
species.
Promoter Recognition and Activation by the Global Response Regulator CbrB in Pseudomonas aeruginosa
Authors: Abdou Laetitia , Chou Han-Ting , Haas Dieter , Lu Chung-Dar
Published: April 2011

In
Pseudomonas aeruginosa
, the CbrA/CbrB two-component system is instrumental in the maintenance of the carbon-nitrogen balance and for growth on carbon sources that are energetically less favorable than the preferred dicarboxylate substrates. The CbrA/CbrB system drives the expression of the small RNA CrcZ, which antagonizes the repressing effects of the catabolite repression control protein Crc, an RNA-binding protein. Dicarboxylates appear to cause carbon catabolite repression by inhibiting the activity of the CbrA/CbrB system, resulting in reduced
crcZ
expression. Here we have identified a conserved palindromic nucleotide sequence that is present in upstream activating sequences (UASs) of promoters under positive control by CbrB and σ
54
RNA polymerase, especially in the UAS of the
crcZ
promoter. Evidence for recognition of this palindromic sequence by CbrB was obtained
in vivo
from mutational analysis of the
crcZ
promoter and
in vitro
from electrophoretic mobility shift assays using
crcZ
promoter fragments and purified CbrB protein truncated at the N terminus. Integration host factor (IHF) was required for
crcZ
expression. CbrB also activated the
lipA
(lipase) promoter, albeit less effectively, apparently by interacting with a similar but less conserved palindromic sequence in the UAS of
lipA
. As expected, succinate caused CbrB-dependent catabolite repression of the
lipA
promoter. Based on these results and previously published data, a consensus CbrB recognition sequence is proposed. This sequence has similarity to the consensus NtrC recognition sequence, which is relevant for nitrogen control.
Regulation of Growth of the Mother Cell and Chromosome Replication during Sporulation of Bacillus subtilis
Authors: Xenopoulos Panagiotis , Piggot Patrick J.
Published: April 2011

During spore formation,
Bacillus subtilis
divides asymmetrically, resulting in two cells with different fates. Immediately after division, the transcription factor σ
F
becomes active in the smaller prespore, followed by activation of σ
E
in the larger mother cell. We recently showed that a delay in σ
E
activation resulted in the novel phenotype of two spores (twins) forming within the same mother cell. Mother cells bearing twins are substantially longer than mother cells with single spores. Here we explore the regulation of the growth and DNA replication of the mother cell. We find that length correlates with chromosome number in the mother cell. We show that replication and growth could occur after asymmetric division in mother cells with no active σ
E
. In contrast, when σ
E
was active, replication and growth ceased. In growing mother cells, with no active σ
E
, Spo0A-directed transcription levels remained low. In the presence of active σ
E
, Spo0A-directed gene expression was enhanced in the mother cells. Artificial Spo0A activation blocked mother cell growth in the absence of σ
E
. Spo0A activation blocked growth even in the absence of SirA, the Spo0A-directed inhibitor of the initiation of replication. Together, the results indicate that the burst of Spo0A-directed expression along with the activation of σ
E
provides mechanisms to block the DNA replication and growth of the mother cell.
Feed-Forward Regulation of Microbisporicin Biosynthesis in Microbispora corallina
Authors: Foulston Lucy , Bibb Mervyn
Published: April 2011

Lantibiotics are ribosomally synthesized, posttranslationally modified peptide antibiotics. Microbisporicin is a potent lantibiotic produced by the actinomycete
Microbispora corallina
and contains unique chlorinated tryptophan and dihydroxyproline residues. The biosynthetic gene cluster for microbisporicin encodes several putative regulatory proteins, including, uniquely, an extracytoplasmic function (ECF) σ factor, σ
MibX
, a likely cognate anti-σ factor, MibW, and a potential helix-turn-helix DNA binding protein, MibR. Here we examine the roles of these proteins in regulating microbisporicin biosynthesis. S1 nuclease protection assays were used to determine transcriptional start sites in the microbisporicin gene cluster and confirmed the presence of the likely ECF sigma factor −10 and −35 sequences in five out of six promoters. In contrast, the promoter of
mibA
, encoding the microbisporicin prepropeptide, has a typical
Streptomyces
vegetative sigma factor consensus sequence. The ECF sigma factor σ
MibX
was shown to interact with the putative anti-sigma factor MibW in
Escherichia coli
using bacterial two-hybrid analysis. σ
MibX
autoregulates its own expression but does not directly regulate expression of
mibA
. On the basis of quantitative reverse transcriptase PCR (qRT-PCR) data, we propose a model for the biosynthesis of microbisporicin in which MibR functions as an essential master regulator and the ECF sigma factor/anti-sigma factor pair, σ
MibX
/MibW, induces feed-forward biosynthesis of microbisporicin and producer immunity.
Complete Genome Sequence of Polymorphum gilvum SL003B-26A1
T
, a Crude Oil-Degrading Bacterium from Oil-Polluted Saline Soil
Authors: Li Shu-Guang , Tang Yue-Qin , Nie Yong , Cai Man , Wu Xiao-Lei
Published: April 2011

Polymorphum gilvum
SL003B-26A1
T
is a type strain of a newly published novel species in the novel genus
Polymorphum
. It was isolated from a crude oil-polluted saline soil in Shengli Oilfield, China, and was able to use the crude oil as the sole carbon source. Here we report the complete genome of SL003B-26A1
T
and the genes likely to be involved in oil degradation and ecological adaption.
Complete Genome Sequencing of Lactobacillus acidophilus 30SC, Isolated from Swine Intestine
Authors: Oh Sejong , Roh Hanseong , Ko Hyeok-Jin , Kim Sujin , Kim Kyoung Heon , Lee Sung Eun , Chang In Seop , Kim Saehun , Choi In-Geol
Published: April 2011

Lactobacillus acidophilus
30SC has been isolated from swine intestines and considered a probiotic strain for dairy products because of its ability to assimilate cholesterol and produce bacteriocins. Here, we report the complete genome sequence of
Lactobacillus acidophilus
30SC (2,078,001 bp) exhibiting strong acid resistance and enhanced bile tolerance.
Genome Sequence of the Spinosyns-Producing Bacterium Saccharopolyspora spinosa NRRL 18395
Authors: Pan Yuanlong , Yang Xi , Li Jing , Zhang Ruifen , Hu Yongfei , Zhou Yuguang , Wang Jun , Zhu Baoli
Published: April 2011

Saccharopolyspora spinosa
is a Gram-positive bacterium that produces spinosad, a well-known biodegradable insecticide that is used for agricultural pest control and has an excellent environmental and mammalian toxicological profile. Here, we present the first draft genome sequence of the type strain
Saccharopolyspora spinosa
NRRL 18395, which consists of 22 scaffolds.
Complete Genome Sequences of Brucella melitensis Strains M28 and M5-90, with Different Virulence Backgrounds
Authors: Wang Fangkun , Hu Sen , Gao Yuzhe , Qiao Zujian , Liu Wenxing , Bu Zhigao
Published: April 2011

Brucella melitensis
is a Gram-negative coccobacillus bacteria belonging to the
Alphaproteobacteria
subclass. It is an important zoonotic pathogen that causes brucellosis, a disease affecting sheep, cattle, and sometimes humans. The
B. melitensis
strain M5-90, a live attenuated vaccine cultured from the
B. melitensis
virulent strain M28, has been an effective tool to control brucellosis in goats and sheep in China. Here we report the complete genome sequences of
B. melitensis
M28 and M5-90, strains with different virulence backgrounds, which will serve as a valuable reference for future studies.
Genome Sequence of Photobacterium mandapamensis Strain
svers.
1.1, the Bioluminescent Symbiont of the Cardinal Fish Siphamia versicolor
Authors: Urbanczyk Henryk , Ogura Yoshitoshi , Hendry Tory A. , Gould Alison L. , Kiwaki Naomi , Atkinson Joshua T. , Hayashi Tetsuya , Dunlap Paul V.
Published: April 2011

Photobacterium mandapamensis
is one of three luminous
Photobacterium
species able to form species-specific bioluminescent symbioses with marine fishes. Here, we present the draft genome sequence of
P. mandapamensis
strain
svers.
1.1, the bioluminescent symbiont of the cardinal fish
Siphamia versicolor
, the first genome of a symbiotic, luminous
Photobacterium
species to be sequenced. Analysis of the sequence provides insight into differences between
P. mandapamensis
and other luminous and symbiotic bacteria in genes involved in quorum-sensing regulation of light production and establishment of symbiosis.
Genome Sequence of the Phototrophic Betaproteobacterium Rubrivivax benzoatilyticus Strain JA2
T
Authors: Mohammed Mujahid , Isukapatla Arvind , Mekala Lakshmi Prasuna , Eedara Veera Venkata Rama Prasad , Chintalapati Sasikala , Chintalapati Venkata Ramana
Published: April 2011

Herein we report the draft genome sequence of a phototrophic bacterium,
Rubrivivax benzoatilyticus
strain JA2
T
, which apparently is the first genome sequence report of a phototrophic member belonging to the class
Betaproteobacteria
. The unique feature of this strain is its capability to synthesize carotenoids through both spirilloxanthin and spheroidenone pathways. Strain JA2
T
produces several novel secondary metabolites, and the genome insights help in understanding the unique machinery that the strain adapted.
Draft Genome Sequence of the Chemolithoheterotrophic, Halophilic Methylotroph Methylophaga thiooxydans DMS010
Authors: Boden Rich , Ferriera Steve , Johnson Justin , Kelly Donovan P. , Murrell J. Colin , Schäfer Hendrik
Published: April 2011

Methylophaga thiooxydansis a mesophilic, obligately halophilic bacterium that is capable of methylotrophic growth on a range of one-carbon compounds as well as chemolithoheterotrophic growth at the expense of thiosulfate. Here we present the draft genome sequence ofMethylophaga thiooxydansDMS010 (DSM 22068T, VKM B2586T), the type strain of the species, which has allowed prediction of the genes involved in one-carbon metabolism, nitrogen metabolism, and other aspects of central metabolism.
Whole-Genome Sequences of Four Mycobacterium bovis BCG Vaccine Strains
Authors: Pan Yuanlong , Yang Xi , Duan Jia , Lu Na , Leung Andrea S. , Tran Vanessa , Hu Yongfei , Wu Na , Liu Di , Wang Zhiming , Yu Xuping , Chen Chen , Zhang Yuanyuan , Wan Kanglin , Liu Jun , Zhu Baoli
Published: April 2011

Mycobacterium bovis
Bacille Calmette-Guérin (BCG) is the only vaccine available against tuberculosis (TB). A number of BCG strains are in use, and they exhibit biochemical and genetic differences. We report the genome sequences of four BCG strains representing different lineages, which will help to design more effective TB vaccines.
Complete Genome Sequence of Burkholderia gladioli BSR3
Authors: Seo Young-Su , Lim Jaeyun , Choi Beom-Soon , Kim Hongsup , Goo Eunhye , Lee Bongsoo , Lim Jong-Sung , Choi Ik-Young , Moon Jae Sun , Kim Jinwoo , Hwang Ingyu
Published: April 2011

We report the complete genome sequence of
Burkholderia gladioli
BSR3, isolated from a diseased rice sheath in South Korea.
Complete Genome Sequence of the Probiotic Strain Lactobacillus casei BD-II
Authors: Ai Lianzhong , Chen Chen , Zhou Fangfang , Wang Lei , Zhang Hao , Chen Wei , Guo Benheng
Published: April 2011

Lactobacillus casei
BD-II, a patented probiotic strain (U.S. patent 7,270,994 B2), was isolated from homemade koumiss in China and has been implemented in the industrial production as starter cultures. Here we report the complete genome sequence of BD-II, which shows high similarity with the well-studied probiotic BL23.
Implications of the Inability of Listeria monocytogenes EGD-e To Grow Anaerobically Due to a Deletion in the Class III NrdD Ribonucleotide Reductase for Its Use as a Model Laboratory Strain
Authors: Ofer Amos , Kreft Jürgen , Logan Derek T. , Cohen Gerald , Borovok Ilya , Aharonowitz Yair
Published: April 2011

Listeria monocytogenesis a Gram-positive facultative intracellular bacterium that causes life-threatening diseases in humans. It grows and survives in environments of low oxygen tension and under conditions of strict anaerobiosis. Oxygen-limiting conditions may be an important factor in determining its pathogenicity.L. monocytogenesserovar 1/2a strain EGD-e has been employed intensively to elucidate the mechanisms of intracellular multiplication and virulence. Listeria possesses genes encoding class I aerobic and class III anaerobic ribonucleotide reductases (RNRs). The class III RNR consists of a catalytic subunit NrdD and an activase NrdG. Surprisingly,L. monocytogenesEGD-e, but not otherL. monocytogenesstrains or other listerial species, is unable to grow under strict anaerobic conditions. Inspection of listerial NrdD amino acid sequences revealed a six-amino acid deletion in the C-terminal portion of the EGD-e protein, next to the essential glycyl radical domain. Nevertheless,L. monocytogenesEGD-e can grow under microaerophilic conditions due to the recruitment of residual class Ia RNR activity. A three-dimensional (3D) model based on the structure of bacteriophage T4 NrdD identified the location of the deletion, which appears in a highly conserved part of the NrdD RNR structure, in the α/β barrel domain near the glycyl radical domain. The deleted KITPFE region is essential either for interactions with the NrdG activase or, indirectly, for the stability of the glycyl radical loop. Given thatL. monocytogenesEGD-e lacks a functional anaerobic RNR, the present findings are relevant to the interpretation of studies of pathogenesis with this strain specifically, in particular under conditions of low oxygen tension.
Defining the Strain-Dependent Impact of the Staphylococcal Accessory Regulator (
sarA
) on the Alpha-Toxin Phenotype of Staphylococcus aureus
Authors: Zielinska Agnieszka K. , Beenken Karen E. , Joo Hwang-Soo , Mrak Lara N. , Griffin Linda M. , Luong Thanh T. , Lee Chia Y. , Otto Michael , Shaw Lindsey N. , Smeltzer Mark S.
Published: April 2011

We demonstrate that mutation of the staphylococcal accessory regulator (
sarA
) limits the accumulation of alpha-toxin and phenol-soluble modulins (PSMs) in
Staphylococcus aureus
isolates of the USA300 clonal lineage. Degradation assays and experiments done with protease inhibitors suggested that this was due to the increased production of extracellular proteases rather than differences associated with the impact of
sarA
on transcription of the target gene (
hla
) or the accessory gene regulator (
agr
). This was confirmed by demonstrating that concomitant mutation of the gene encoding aureolysin (
aur
) reversed the alpha-toxin and PSM-deficient phenotypes of a USA300
sarA
mutant. Mutation of
sarA
had little impact on the alpha-toxin or PSM phenotypes of the commonly studied strain Newman, which is known to have a mutation in
saeS
that results in constitutive activation of the
saeRS
regulatory system, and we also demonstrate that repair of this defect resulted in the increased production of extracellular proteases and reversed both the alpha-toxin and PSM-positive phenotypes of a Newman
sarA
mutant.
Effects of Molybdate and Tungstate on Expression Levels and Biochemical Characteristics of Formate Dehydrogenases Produced by Desulfovibrio alaskensis NCIMB 13491
Authors: Mota Cristiano S. , Valette Odile , González Pablo J. , Brondino Carlos D. , Moura José J. G. , Moura Isabel , Dolla Alain , Rivas Maria G.
Published: April 2011

Formate dehydrogenases (FDHs) are enzymes that catalyze the formate oxidation to carbon dioxide and that contain either Mo or W in a mononuclear form in the active site. In the present work, the influence of Mo and W salts on the production of FDH by
Desulfovibrio alaskensis
NCIMB 13491 was studied. Two different FDHs, one containing W (W-FDH) and a second incorporating either Mo or W (Mo/W-FDH), were purified. Both enzymes were isolated from cells grown in a medium supplemented with 1 μM molybdate, whereas only the W-FDH was purified from cells cultured in medium supplemented with 10 μM tungstate. We demonstrated that the genes encoding the Mo/W-FDH are strongly downregulated by W and slightly upregulated by Mo. Metal effects on the expression level of the genes encoding the W-FDH were less significant. Furthermore, the expression levels of the genes encoding proteins involved in molybdate and tungstate transport are downregulated under the experimental conditions evaluated in this work. The molecular and biochemical properties of these enzymes and the selective incorporation of either Mo or W are discussed.
An HflX-Type GTPase from Sulfolobus solfataricus Binds to the 50S Ribosomal Subunit in All Nucleotide-Bound States
Authors: Blombach Fabian , Launay Helene , Zorraquino Violeta , Swarts Daan C. , Cabrita Lisa D. , Benelli Dario , Christodoulou John , Londei Paola , van der Oost John
Published: April 2011

HflX GTPases are found in all three domains of life, theBacteria,Archaea, andEukarya. HflX fromEscherichia colihas been shown to bind to the 50S ribosomal subunit in a nucleotide-dependent manner, and this interaction strongly stimulates its GTPase activity. We recently determined the structure of an HflX ortholog from the archaeonSulfolobus solfataricus(SsoHflX). It revealed the presence of a novel HflX domain that might function in RNA binding and is linked to a canonical G domain. This domain arrangement is common to all archaeal, bacterial, and eukaryotic HflX GTPases. This paper shows that the archaeal SsoHflX, like its bacterial orthologs, binds to the 50S ribosomal subunit. This interaction does not depend on the presence of guanine nucleotides. The HflX domain is sufficient for ribosome interaction. Binding appears to be restricted to free 50S ribosomal subunits and does not occur with 70S ribosomes engaged in translation. The fingerprint1H-15N heteronuclear correlation nuclear magnetic resonance (NMR) spectrum of SsoHflX reveals a large number of well-resolved resonances that are broadened upon binding to the 50S ribosomal subunit. The GTPase activity of SsoHflX is stimulated by crude fractions of 50S ribosomal subunits, but this effect is lost with further high-salt purification of the 50S ribosomal subunits, suggesting that the stimulation depends on an extrinsic factor bound to the 50S ribosomal subunit. Our results reveal common properties but also marked differences between archaeal and bacterial HflX proteins.
What constitutes consent when parents and daughters have different views about having the HPV vaccine: qualitative interviews with stakeholders: Table 1
Authors: Wood Fiona , Morris Lucy , Davies Myfanwy , Elwyn Glyn
Published: April 2011

Objective

The UK Human Papillomavirus (HPV) vaccine programme commenced in the autumn of 2008 for year 8 (age 12–13 years) schoolgirls. We examine whether the vaccine should be given when there is a difference of opinion between daughters and parents or guardians.

Design

Qualitative study using semi-structured interviews.

Participants

A sample of 25 stakeholders: 14 professionals involved in the development of the HPV vaccination programme and 11 professionals involved in its implementation.

Results

Overriding the parents' wishes was perceived as problematic and could damage the relationship between school and parents. A number of practical problems were raised in relation to establishing whether parents were genuinely against their daughter receiving the vaccine. Although many respondents recognised that the Gillick guidelines were relevant in establishing whether a girl could provide consent herself, they still felt that there were significant problems in establishing whether girls could be assessed as Gillick competent. In some areas school nurses had been advised not to give the vaccine in the absence of parental consent. None of the respondents suggested that a girl should be vaccinated against her consent even if her parents wanted her to have the vaccine.

Conclusions

While the Gillick guidelines provide a legal framework to help professionals make judgements about adolescents consenting to medical treatment, in practice there appears to be variable and confused interpretation of this guidance. Improved legal structures, management procedures and professional advice are needed to support those who are assessing competence and establishing consent to vaccinate adolescents in a school setting.
Should blood-borne virus testing be part of operative consent? When the doctor becomes the patient
Authors: Adams Simon T , Leveson Stephen H
Published: April 2011

Point-of-care testing (POCT) is a sensitive, specific and rapid form of testing for the presence of HIV antibodies. Post-exposure prophylaxis for HIV infection can reduce seroconversion rates by up to 80%. Needlestick injuries are the second commonest cause of occupational injury in the NHS and 20% of these occur during operations. In the NHS, in order to protect staff and patients from the risk of bloodborne viruses such as HIV, it is mandatory to report such injuries; however, numerous studies have shown that many groups, particularly doctors, are reluctant to do so. This article outlines the arguments for and against the introduction of preoperatively seeking consent from patients to have their blood tested for HIV via POCT in order to improve the reporting rates of needlestick injuries incurred during surgery and to protect staff from infection.
Why do parents enrol their children in research: a narrative synthesis
Authors: Fisher Helen R , McKevitt Christopher , Boaz Annette
Published: April 2011

Objective

Recent legislation mandating the inclusion of children in clinical trials has resulted in an increase in the number of children participating in research. We reviewed the literature regarding the reasons parents chose to accept or decline an invitation to enrol their children in clinical research.

Methods

We searched for qualitative studies, written in the English language that considered the experiences of parents who had been invited to enrol their children in research. SCOPUS and Web of Knowledge electronic databases and reference lists of retrieved articles and review papers were searched. Retrieved articles were synthesised using the narrative synthesis method.

Results

16 qualitative studies exploring the experiences of parents living in five countries whose children had a range of health conditions of varying severity were included. The health status of the child appeared to influence parents' reasons for participation. Parents whose children had life threatening conditions often considered they had no choice but to participate and many welcomed the innovation offered through research participation. Such parents also viewed the risks of research less negatively than those whose children were healthy or in the stable stage of a chronic condition. This raises questions regarding the voluntariness of informed consent by such parents.

Conclusions

A tailored approach is needed when discussing research participation with parents of eligible children. While parents of healthy children may be more open to discussions of altruism, those whose children have life threatening illnesses should be given adequate information about the alternatives to, and risks of, research participation.
Achieving online consent to participation in large-scale gene-environment studies: a tangible destination
Authors: Wood Fiona , Kowalczuk Jenny , Elwyn Glyn , Mitchell Clive , Gallacher John
Published: April 2011

Background

Population based genetics studies are dependent on large numbers of individuals in the pursuit of small effect sizes. Recruiting and consenting a large number of participants is both costly and time consuming. We explored whether an online consent process for large-scale genetics studies is acceptable for prospective participants using an example online genetics study.

Methods

We conducted semi-structured interviews with 42 members of the public stratified by age group, gender and newspaper readership (a measure of social status). Respondents were asked to use a website designed to recruit for a large-scale genetic study. After using the website a semi-structured interview was conducted to explore opinions and any issues they would have. Responses were analysed using thematic content analysis.

Results

The majority of respondents said they would take part in the research (32/42). Those who said they would decline to participate saw fewer benefits from the research, wanted more information and expressed a greater number of concerns about the study. Younger respondents had concerns over time commitment. Middle aged respondents were concerned about privacy and security. Older respondents were more altruistic in their motivation to participate. Common themes included trust in the authenticity of the website, security of personal data, curiosity about their own genetic profile, operational concerns and a desire for more information about the research.

Conclusions

Online consent to large-scale genetic studies is likely to be acceptable to the public. The online consent process must establish trust quickly and effectively by asserting authenticity and credentials, and provide access to a range of information to suit different information preferences.
Human dignity and human tissue: a meaningful ethical relationship?
Authors: Kirchhoffer David G , Dierickx Kris
Published: April 2011

Human dignity has long been used as a foundational principle in policy documents and ethical guidelines intended to govern various forms of biomedical research. Despite the vast amount of literature concerning human dignity and embryonic tissues, the majority of biomedical research uses non-embryonic human tissue. Therefore, this contribution addresses a notable lacuna in the literature: the relationship, if any, between human dignity and human tissue. This paper first elaborates a multidimensional understanding of human dignity that overcomes many of the shortcomings associated with the use of human dignity in other ethical debates. Second, it discusses the relationship between such an understanding of human dignity and ‘non-embryonic’ human tissue. Finally, it considers the implications of this relationship for biomedical research and practice involving human tissue. The contribution demonstrates that while human tissue cannot be said to have human dignity, human dignity is nevertheless implicated by human tissue, making what is done with human tissue and how it is done worthy of moral consideration.
Ageing gametes and embryonic death: a response to Bovens
Authors: Kennedy Ashley Graham
Published: April 2011

Luc Bovens, in his 2006 article, argues that it can be shown that the ‘rhythm' method of birth control results in a larger number of embryonic deaths than the IUD, the morning after pill or the combination oral contraceptive pill, just so long as one accepts his three ‘plausible’ assumptions. In this brief response I will argue that Boven's third assumption is not plausible when one takes into account a basic knowledge of human reproductive biology. Thus, his argument, in both of its possible reconstructions, fails.
An empirical study on the preferred size of the participant information sheet in research
Authors: Antoniou Evangelia E , Draper Heather , Reed Keith , Burls Amanda , Southwood Taunton R , Zeegers Maurice P
Published: April 2011

Background

Informed consent is a requirement for all research. It is not, however, clear how much information is sufficient to make an informed decision about participation in research. Information on an online questionnaire about childhood development was provided through an unfolding electronic participant sheet in three levels of information.

Methods

552 participants, who completed the web-based survey, accessed and spent time reading the participant information sheet (PIS) between July 2008 and November 2009. The information behaviour of the participants was investigated. The first level contained less information than might be found on a standard PIS, the second level corresponded to a standard PIS, and the third contained more information than on a standard PIS. The actual time spent on reading the information provided in three incremental levels and the participants' evaluation of the information were calculated.

Results

77% of the participants chose to access the first level of information, whereas 12% accessed the first two levels, 6% accessed all three levels of information and 23% participated without accessing information. The most accessed levels of information were those that corresponded to the average reading times.

Conclusion

The brief information provided in the first level was sufficient for participants to make informed decisions, while a sizeable minority of the participants chose not to access any information at all. This study adds to the debate about how much information is required to make a decision about participation in research and the results may help inform the future development of information sheets by providing data on participants' actual needs when deciding about questionnaire surveys.
Just health: on the conditions for acceptable and unacceptable priority settings with respect to patients' socioeconomic status: Table 1
Authors: Bærøe Kristine , Bringedal Berit
Published: April 2011

It is well documented that the higher the socioeconomic status (SES) of patients, the better their health and life expectancy. SES also influences the use of health services—the higher the patients' SES, the more time and specialised health services provided. This leads to the following question: should clinicians give priority to individual patients with low SES in order to enhance health equity? Some argue that equity is best preserved by physicians who remain loyal to ‘ordinary medical fairness’ in non-ideal circumstances when health disparities persist; ie, doctors should allocate care according to needs only and treat everyone with equal regard by being neutral with respect to patients' SES. This paper furthers a discussion of this view by questioning how equitable needs relate to SES. To clarify, it distinguishes between four versions of ‘healthcare need’ and approaches an acceptable conceptualisation of the notion supported by Norman Daniels' theory on health equity. It concludes that doctors should remain neutral to patients' SES in cases in which several patients require the same health care. However, equitable health care requires considerations of the impact of socioeconomic factors (SEF) on patients' capacity to benefit from the care. Remaining neutral towards patients' SES in this respect does not promote equal regard. It follows that priority setting on the basis of SEF is required in fair clinical distribution of care, eg, through allocating more time to patients with low SES. In order to advance equity accurately, the concept of ordinary medical fairness should be amplified according to this clarification.
The ‘patient's physician one-step removed’: the evolving roles of medical tourism facilitators: Table 1
Authors: Snyder Jeremy , Crooks Valorie A , Adams Krystyna , Kingsbury Paul , Johnston Rory
Published: April 2011

Background

Medical tourism involves patients travelling internationally to receive medical services. This practice raises a range of ethical issues, including potential harms to the patient's home and destination country and risks to the patient's own health. Medical tourists often engage the services of a facilitator who may book travel and accommodation and link the patient with a hospital abroad. Facilitators have the potential to exacerbate or mitigate the ethical concerns associated with medical tourism, but their roles are poorly understood.

Methods

12 facilitators were interviewed from 10 Canadian medical tourism companies.

Results

Three themes were identified: facilitators' roles towards the patient, health system and medical tourism industry. Facilitators' roles towards the patient were typically described in terms of advocacy and the provision of information, but limited by facilitators' legal liability. Facilitators felt they played a positive role in the lives of their patients and the Canadian health system and served as catalysts for reform, although they noted an adversarial relationship with some Canadian physicians. Many facilitators described personally visiting medical tourism sites and forming personal relationships with surgeons abroad, but noted the need for greater regulation of their industry.

Conclusion

Facilitators play a substantial and evolving role in the practice of medical tourism and may be entering a period of professionalisation. Because of the key role of facilitators in determining the effects of medical tourism on patients and public health, this paper recommends a planned conversation between medical tourism stakeholders to define and shape facilitators' roles.
Deadly in pink: the impact of cigarette packaging among young women
Authors: Doxey Juliana , Hammond David
Published: April 2011

Background

This study sought to examine the impact of cigarette packaging on young women, including the impact of ‘plain’ packaging.

Methods

Participants were randomised to view eight cigarette packs designed according to one of four experimental conditions: fully-branded female brands; the same brands without descriptors (eg, ‘slims’); the same brands without brand imagery or descriptors (ie, ‘plain’ packs); and fully branded non-female brands as a control condition. Participants rated packs on perceived appeal, taste, tar, health risks and smoker ‘traits’.

Results

Fully-branded female packs were rated as significantly more appealing than ‘no descriptor’ packs, ‘plain’ packs and non-female branded packs. Female branded packs were associated with a greater number of positive attributes including glamour, slimness and attractiveness, compared to brands without descriptors and ‘plain’ packs. Women who viewed plain packs were less likely to believe that smoking helps people control their appetite—an important predictor of smoking among young women—compared to women who viewed branded female packs.

Conclusions

‘Plain’ packaging—removing colours and design elements—and removing descriptors such as ‘slims’ from packs may reduce brand appeal and thereby susceptibility to smoking among young women.
II.: THE PLANKTON DIATOMS OF THE BAY OF FUNDY.
Authors: Bailey LL.D., F.R. L. W.
Published: April 2011

not available
IV.: A NEW CAPRELLID FROM THE BAY OF FUNDY.
Authors: Huntsman B.A., M.B. A. G.
Published: April 2011

not available
V.: PRELIMINARY NOTES ON THE MOLLUSCA OF ST. ANDREWS AND VICINITY, NEW BRUNSWICK.
Authors: Detweiler B.A. John D.
Published: April 2011

not available
VII.: THE IODINE CONTENT OF THE MARINE FLORA AND FAUNA IN THE NEIGHBOURHOOD OF NANAIMO, VANCOUVER ISLAND, B.C.
Authors: Cameron M.A., B.Sc. A. T.
Published: April 2011

not available
II.: NOTES ON THE ODONATA OF THE VICINITY OF GO HOME BAY, GEORGIAN BAY, ONTARIO.
Authors: Walker B.A., M.B. E. M.
Published: April 2011

not available
Role of substrate on the dendroclimatic response of Scots pine from varying elevations in northern Scotland
Authors: Moir A.K. , Leroy S.A.G. , Helama S.
Published: April 2011

The influence of substrate was evaluated by comparing annual ring widths of Scots pine (Pinus sylvestris L.) with climate data at 13 new sites (five bog, three peat, and five soil), together with 17 previously studied soil sites in northern Scotland. Radial growth rates <1.0 and >1.5 mm·year–1 differentiate well between pine growing on bog and peat, respectively, highlighting the role of pine as a indicator of water levels in these environments. Scots pine chronologies from bog are shown to have a weak temperature–growth response and so limit potential in dendroclimatic reconstructions. However, correlation analysis shows temperature in January–February and July–August to be important determinants of the radial growth of Scots pine on soil. Moving correlation analysis indicates that the relationship between the radial growth of pine on soil near the altitudinal tree line and summer temperature (July–August) is time stable, despite an increase of temperature in northern Scotland. However, winter (January–February) temperature has become less limiting since the 1920s. Scots pine at some soil, bog, and peat sites have increased or developed correlation with October temperature since the 1940s, suggesting an extension of the growth season, particularly on the western coast of Scotland.
Impact of primary and secondary machinery tracks on fine root growth of sugar maple after selection cutting
Authors: Malo Catherine , Messier Christian
Published: April 2011

Selection cutting, where approximately 30% of the trees are removed every 30 years, is the main silvicultural treatment used in temperate deciduous forests of Quebec (Canada). Concerns have been raised that the use of heavy machinery is creating soil disturbances that are negatively affecting the growth and survival of remaining trees. The aim of the study was to determine if heavy machinery is affecting the growth, morphology, and architecture of sugar maple (Acer saccharum Marsh.) fine roots in and around machinery tracks left after selection logging. The study site, a sugar maple dominated stand, was located in southern Quebec. Root ingrowth bags and standard root cores were used to compare fine root growth, morphology, and architecture in and around machinery tracks one year after logging. Fine root growth of maple was reduced fivefold in both primary (multiple trip) and secondary (only one trip) machinery tracks compared with the control. There was a nonstatistical reduction in fine root growth within 1 m of the tracks. Because machinery tracks cover between 15% and 25% of a stand after selection logging, such reduction in fine root growth could be significant for the growth and survival of the remaining mature maple trees.