bluuebunny/crossref_metadata_2025 huggingface dataset:
Quantification of the Effect of Culturing Temperature on Salt-Induced Heat Resistance of
Bacillus
Species
Authors: den Besten Heidy M. W. , van der Mark Eric-Jan , Hensen Lonneke , Abee Tjakko , Zwietering Marcel H.
Published: May 2010

Short- and long-term exposure to mild stress conditions can activate stress adaptation mechanisms in pathogens, resulting in a protective effect toward otherwise lethal stresses. The mesophilic strains
Bacillus cereus
ATCC 14579 and ATCC 10987 and the psychrotolerant strain
B. weihenstephanensis
KBAB4 were cultured at 12°C and 30°C until the exponential growth phase (i) in the absence of salt, (ii) in the presence of salt, and (iii) with salt shock after they reached the exponential growth phase and subsequently heat inactivated. Both the first-order model and the Weibull model were fitted to the inactivation kinetics, and statistical indices were calculated to select for each condition the most appropriate model to describe the inactivation data. The third-decimal reduction times (which reflected the times needed to reduce the initial number of microorganisms by three decimal powers) were determined for quantitative comparison. The heat resistance of both mesophilic strains increased when cells were salt cultured and salt shocked at 30°C, whereas these salt-induced effects were not significant for the psychrotolerant strain. In contrast, only the psychrotolerant strain showed salt-induced heat resistance when cells were cultured at 12°C. Therefore, culturing temperature and strain diversity are important aspects to address when adaptive stress responses are quantified. The activated adaptive stress response had an even larger impact on the number of surviving microorganisms when the stress factor (i.e., salt) was still present during inactivation. These factors should be considered when stress-integrated predictive models are developed that can be used in the food industry to balance and optimize processing conditions of minimally processed foods.
Verotoxin 2 Enhances Adherence of Enterohemorrhagic
Escherichia coli
O157:H7 to Intestinal Epithelial Cells and Expression of β1-Integrin by IPEC-J2 Cells
Authors: Liu Bianfang , Yin Xianhua , Feng Yanni , Chambers James R. , Guo Aiguang , Gong Joshua , Zhu Jing , Gyles Carlton L.
Published: May 2010

Verotoxin (VT) has been implicated in the promotion of adherence to and colonization of intestinal epithelial cells by enterohemorrhagic
Escherichia coli
(EHEC) O157:H7. The present study investigated the effect of VT2 on the adherence of EHEC O157:H7 strain 86-24 to porcine jejunal (IPEC-J2), human colon (CaCo-2), and human laryngeal carcinoma (HEp-2) cell lines and on the expression in IPEC-J2 cells of synthases for β1-integrin and nucleolin, both of which are implicated in bacterial adherence. The effect on expression of globotriaosylceramide (Gb3) synthase, the receptor for VT, was also examined. Data were obtained by adherence assays and quantitative reverse transcriptase PCR, using EHEC O157 strain 86-24, a
vt2
deletion mutant, a
vt2
phage-negative strain, and complemented mutants in which the
vt2
gene was restored. Compared with the adherence of the parent and complemented mutant strains, the
vt2
-negative strains adhered significantly less to all three types of cells. Adherence of the wild-type EHEC strain to IPEC-J2 cells was accompanied by increased expression of β1-integrin, nucleolin, and Gb3 synthase. IPEC-J2 cells in association with wild-type EHEC O157:H7 or the complemented mutants expressed higher levels of β1-integrin than did cells in association with the
vt2
-negative strains or with no bacteria. Expression of nucleolin was decreased by association with the
vt2
-negative mutant, but complementation failed to restore wild-type expression. The data indicate that VT2 plays a role in the adherence of EHEC O157:H7 to intestinal epithelial cells, possibly by increasing the expression of the host receptor β1-integrin.
Adsorption of Extracellular Chromosomal DNA and Its Effects on Natural Transformation of
Azotobacter vinelandii
Authors: Lu Nanxi , Zilles Julie L. , Nguyen Thanh H.
Published: May 2010

To better understand the influence of environmental conditions on the adsorption of extracellular chromosomal DNA and its availability for natural transformation, the amount and conformation of adsorbed DNA were monitored under different conditions in parallel with transformation assays using the soil bacterium
Azotobacter vinelandii
. DNA adsorption was monitored using the technique of quartz crystal microbalance with dissipation (QCM-D). Both silica and natural organic matter (NOM) surfaces were evaluated in solutions containing either 100 mM NaCl or 1 mM CaCl
2
. The QCM-D data suggest that DNA adsorbed to silica surfaces has a more compact and rigid conformation in Ca
2+
solution than in Na
+
solution and that the reverse is true when DNA is adsorbed to NOM surfaces. While the amounts of DNA adsorbed on a silica surface were similar for Ca
2+
and Na
+
solutions, the amount of DNA adsorbed on an NOM-coated surface was higher in Ca
2+
solution than in Na
+
solution. Transformation frequencies for dissolved DNA and DNA adsorbed to silica and to NOM were 6 × 10
−5
, 5 × 10
−5
, and 2.5 × 10
−4
, respectively. For NOM-coated surfaces, transformation frequencies from individual experiments were 2- to 50-fold higher in the presence of Ca
2+
than in the presence of Na
+
. The results suggest that groundwater hardness (i.e., Ca
2+
concentration) will affect the amount of extracellular DNA adsorbed to the soil surface but that neither adsorption nor changes in the conformation of the adsorbed DNA will have a strong effect on the frequency of natural transformation of
A. vinelandii
.
Fluorescent Reporters for Studies of Cellular Localization of Proteins in
Staphylococcus aureus
Authors: Pereira Pedro M. , Veiga Helena , Jorge Ana M. , Pinho Mariana G.
Published: May 2010

We have constructed a set of plasmids that allow expression, from their native chromosomal loci, of
Staphylococcus aureus
proteins fused to one of four different fluorescent proteins (green fluorescent protein [GFP], cyan fluorescent protein [CFP], yellow fluorescent protein [YFP], and mCherry), using two different resistance markers (kanamycin and erythromycin). We have also constructed a plasmid that allows expression of proteins from the ectopic
spa
locus in the
S. aureus
chromosome. This toolbox can be used for studies of the localization of proteins in
S. aureus
, a prominent pathogen in both health care and community settings.
Inactivation and Augmentation of the Primary 3-Ketosteroid-Δ
1
- Dehydrogenase in
Mycobacterium neoaurum
NwIB-01: Biotransformation of Soybean Phytosterols to 4-Androstene- 3,17-Dione or 1,4-Androstadiene-3,17-Dione
Authors: Wei Wei , Wang Feng-qing , Fan Shu-yue , Wei Dong-zhi
Published: May 2010

3-Ketosteroid-Δ
1
-dehydrogenase, KsdD
M
, was identified by targeted gene disruption and augmentation from
Mycobacterium neoaurum
NwIB-01, a newly isolated strain. The difficulty of separating 4-androstene-3,17-dione (AD) from 1,4-androstadiene-3,17-dione (ADD) is a key bottleneck to the microbial transformation of phytosterols in industry. This problem was tackled via genetic manipulation of the KsdD-encoding gene. Mutants in which KsdD
M
was inactivated or augmented proved to be good AD(D)-producing strains.
Pilot-Scale Production of Fatty Acid Ethyl Esters by an Engineered
Escherichia coli
Strain Harboring the p(Microdiesel) Plasmid
Authors: Elbahloul Yasser , Steinbüchel Alexander
Published: May 2010

Fatty acid ethyl esters (FAEEs) were produced in this study by the use of an engineered
Escherichia coli
p(Microdiesel) strain. Four fed-batch pilot scale cultivations were carried out by first using glycerol as sole carbon source for biomass production before glucose and oleic acid were added as carbon sources. Cultivations yielded a cell density of up to 61 ± 3.1 g of cell dry mass (CDM) per liter and a maximal FAEE content of 25.4% ± 1.1% (wt/wt) of CDM.
Cloning and Characterization of a Gene Cluster for Hatomarubigin Biosynthesis in
Streptomyces
sp. Strain 2238-SVT4
Authors: Kawasaki Takashi , Hirashima Reiko , Maruta Tomoka , Sato Haruka , Maeda Ayumi , Yamada Yuki , Takeda Maho , Hayakawa Yoichi
Published: May 2010

Streptomyces
sp. strain 2238-SVT4 produces hatomarubigins A, B, C, and D, which belong to the angucycline family. Among them, hatomarubigin D has a unique dimeric structure with a methylene linkage. PCR using aromatase and cyclase gene-specific primers identified the
hrb
gene cluster for angucycline biosynthesis in
Streptomyces
sp. 2238-SVT4. The cluster consisted of 30 open reading frames, including those for the minimal polyketide synthase, ketoreductase, aromatase, cyclase,
O
-methyltransferase, oxidoreductase, and oxygenase genes. Expression of a part of the gene cluster containing
hrbR1
to
hrbX
in
Streptomyces lividans
TK23 resulted in the production of hatomarubigins A, B, and C. Hatomarubigin D was obtained from the conversion of hatomarubigin C by a purified enzyme encoded by
hrbY
, among the remaining genes.
Fluorescence
In Situ
Hybridization Method Using a Peptide Nucleic Acid Probe for Identification of
Salmonella
spp. in a Broad Spectrum of Samples
Authors: Almeida C. , Azevedo N. F. , Fernandes R. M. , Keevil C. W. , Vieira M. J.
Published: May 2010

A fluorescence
in situ
hybridization (FISH) method for the rapid detection of
Salmonella
spp. using a novel peptide nucleic acid (PNA) probe was developed. The probe theoretical specificity and sensitivity were both 100%. The PNA-FISH method was optimized, and laboratory testing on representative strains from the
Salmonella
genus subspecies and several related bacterial species confirmed the predicted theoretical values of specificity and sensitivity. The PNA-FISH method has been successfully adapted to detect cells in suspension and is hence able to be employed for the detection of this bacterium in blood, feces, water, and powdered infant formula (PIF). The blood and PIF samples were artificially contaminated with decreasing pathogen concentrations. After the use of an enrichment step, the PNA-FISH method was able to detect 1 CFU per 10 ml of blood (5 × 10
9
± 5 × 10
8
CFU/ml after an overnight enrichment step) and also 1 CFU per 10 g of PIF (2 × 10
7
± 5 × 10
6
CFU/ml after an 8-h enrichment step). The feces and water samples were also enriched according to the corresponding International Organization for Standardization methods, and results showed that the PNA-FISH method was able to detect
Salmonella
immediately after the first enrichment step was conducted. Moreover, the probe was able to discriminate the bacterium in a mixed microbial population in feces and water by counter-staining with 4′,6-diamidino-2-phenylindole (DAPI). This new method is applicable to a broad spectrum of samples and takes less than 20 h to obtain a diagnosis, except for PIF samples, where the analysis takes less than 12 h. This procedure may be used for food processing and municipal water control and also in clinical settings, representing an improved alternative to culture-based techniques and to the existing
Salmonella
PNA probe, Sal23S10, which presents a lower specificity.
NtcA from
Microcystis aeruginosa
PCC 7806 Is Autoregulatory and Binds to the Microcystin Promoter
Authors: Ginn H. P. , Pearson L. A. , Neilan B. A.
Published: May 2010

NtcA is a transcription factor that has been found in a diverse range of cyanobacteria. This nitrogen-controlled factor was focused on as a key component in the yet-to-be-deciphered regulatory network controlling microcystin production. Adaptor-mediated PCR was utilized to isolate the
ntcA
gene from
Microcystis aeruginosa
PCC 7806. This gene was cloned, and the recombinant (His-tagged) protein was overexpressed and purified for use in mobility shift assays to analyze NtcA binding to putative sites identified in the microcystin
mcyA
/
D
promoter region. Autoregulation of NtcA in
M. aeruginosa
was shown via NtcA binding in the upstream
ntcA
promoter region. The observation of binding of NtcA to the
mcyA
/
D
promoter region has direct relevance for the regulation of microcystin biosynthesis, as transcription of the
mcyABCDEFGHIJ
gene cluster appears to be under direct control of nitrogen.
Characterization of the NifA-RpoN Regulon in
Rhizobium etli
in Free Life and in Symbiosis with
Phaseolus vulgaris
Authors: Salazar Emmanuel , Díaz-Mejía J. Javier , Moreno-Hagelsieb Gabriel , Martínez-Batallar Gabriel , Mora Yolanda , Mora Jaime , Encarnación Sergio
Published: May 2010

The NifA-RpoN complex is a master regulator of the nitrogen fixation genes in alphaproteobacteria. Based on the complete
Rhizobium etli
genome sequence, we constructed an
R. etli
CFN42 oligonucleotide (70-mer) microarray and utilized this tool, reverse transcription (RT)-PCR analysis (transcriptomics), proteomics, and bioinformatics to decipher the NifA-RpoN regulon under microaerobic conditions (free life) and in symbiosis with bean plants. The
R. etli
NifA-RpoN regulon was determined to contain 78 genes, including the genes involved in nitrogen fixation, and the analyses revealed 42 new NifA-RpoN-dependent genes. More importantly, this study demonstrated that the NifA-RpoN regulon is composed of genes and proteins that have very diverse functions, that play fundamental and previously less appreciated roles in regulating the normal physiology of the cell, and that have important functions in providing adequate conditions for efficient nitrogen fixation in symbiosis. The
R. etli
NifA-RpoN regulon defined here has some components in common with other NifA-RpoN regulons described previously, but the vast majority of the components have been found only in the
R. etli
regulon, suggesting that they have a specific role in this bacterium and particular requirements during nitrogen fixation compared with other symbiotic bacterial models.
Enhancement of Survival and Electricity Production in an Engineered Bacterium by Light-Driven Proton Pumping
Authors: Johnson Ethan T. , Baron Daniel B. , Naranjo Belén , Bond Daniel R. , Schmidt-Dannert Claudia , Gralnick Jeffrey A.
Published: May 2010

Microorganisms can use complex photosystems or light-dependent proton pumps to generate membrane potential and/or reduce electron carriers to support growth. The discovery that proteorhodopsin is a light-dependent proton pump that can be expressed readily in recombinant bacteria enables development of new strategies to probe microbial physiology and to engineer microbes with new light-driven properties. Here, we describe functional expression of proteorhodopsin and light-induced changes in membrane potential in the bacteriumShewanella oneidensisstrain MR-1. We report that there were significant increases in electrical current generation during illumination of electrochemical chambers containingS. oneidensisexpressing proteorhodopsin. We present evidence that an engineered strain is able to consume lactate at an increased rate when it is illuminated, which is consistent with the hypothesis that proteorhodopsin activity enhances lactate uptake by increasing the proton motive force. Our results demonstrate that there is coupling of a light-driven process to electricity generation in a nonphotosynthetic engineered bacterium. Expression of proteorhodopsin also preserved the viability of the bacterium under nutrient-limited conditions, providing evidence that fulfillment of basic energy needs of organisms may explain the widespread distribution of proteorhodopsin in marine environments.
Enhanced Surface Colonization by
Escherichia coli
O157:H7 in Biofilms Formed by an
Acinetobacter calcoaceticus
Isolate from Meat-Processing Environments
Authors: Habimana Olivier , Heir Even , Langsrud Solveig , Åsli Anette Wold , Møretrø Trond
Published: May 2010

A meat factory commensal bacterium,
Acinetobacter calcoaceticus
, affected the spatial distribution of
Escherichia coli
O157:H7 surface colonization. The biovolume of
E. coli
O157:H7 was 400-fold higher (1.2 × 10
6
μm
3
) in a dynamic cocultured biofilm than in a monoculture (3.0 × 10
3
μm
3
), and
E. coli
O157:H7 colonized spaces between
A. calcoaceticus
cell clusters.
Domains III and I-2α, at the Entrance of the Binding Cleft, Play an Important Role in Cold Adaptation of the Periplasmic Dipeptide-Binding Protein (DppA) from the Deep-Sea Psychrophilic Bacterium
Pseudoalteromonas
sp. Strain SM9913
Authors: Zhang Wei-Xin , Xie Bin-Bin , Chen Xiu-Lan , Dong Sheng , Zhang Xi-Ying , Zhou Bai-Cheng , Zhang Yu-Zhong
Published: May 2010

The peptide transporter from a cold-adapted bacterium has never been reported. In the present study, the
dpp
operon from the psychrophilic bacterium
Pseudoalteromonas
sp. strain SM9913 was cloned and analyzed. The dipeptide binding protein DppA of SM9913 was overexpressed in
Escherichia coli
, and its cold adaptation characteristics were studied. The recombinant DppA of SM9913 (
Ps
DppA) displayed the highest ligand-binding affinity at 15°C, whereas the recombinant DppA of
E. coli
(
Ec
DppA) displayed the highest ligand-binding affinity at 35°C. Thermal and guanidium hydrochloride unfolding analyses indicated that
Ps
DppA has more structural instability than
Ec
DppA. Six domain-exchanged mutants of
Ps
DppA were expressed and purified. Analyses of these mutants indicated that domains III, I-2, and I-3 of
Ps
DppA were less stable than those from
Ec
DppA and that domains III and I-2 made a significant contribution to the high binding affinity of
Ps
DppA at low temperatures. Structural and sequence analyses suggested that the state transition-involved regions in domain III and the α part of domain I-2 are the hot spots of optimization during cold adaptation and that decreasing the side-chain size in these regions is an important strategy for the cold adaptation of
Ps
DppA.
Regulation of Neurotoxin Production and Sporulation by a Putative
agrBD
Signaling System in Proteolytic
Clostridium botulinum
Authors: Cooksley Clare M. , Davis Ian J. , Winzer Klaus , Chan Weng C. , Peck Michael W. , Minton Nigel P.
Published: May 2010

A significant number of genome sequences of
Clostridium botulinum
and related species have now been determined.
In silico
analysis of these data revealed the presence of two distinct
agr
loci (
agr
-
1
and
agr
-
2
) in all group I strains, each encoding putative proteins with similarity to AgrB and AgrD of the well-studied
Staphylococcus aureus agr
quorum sensing system. In
S. aureus
, a small diffusible autoinducing peptide is generated from AgrD in a membrane-located processing event that requires AgrB. Here the characterization of both
agr
loci in the group I strain
C. botulinum
ATCC 3502 and of their homologues in a close relative,
Clostridium sporogenes
NCIMB 10696, is reported. In
C. sporogenes
NCIMB 10696,
agr
-
1
and
agr
-
2
appear to form transcriptional units that consist of
agrB
,
agrD
, and flanking genes of unknown function. Several of these flanking genes are conserved in
Clostridium perfringens
. In agreement with their proposed role in quorum sensing, both loci were maximally expressed during late-exponential-phase growth. Modulation of
agrB
expression in
C. sporogenes
was achieved using antisense RNA, whereas in
C. botulinum
, insertional
agrD
mutants were generated using ClosTron technology. In comparison to the wild-type strains, these strains exhibited drastically reduced sporulation and, for
C. botulinum
, also reduced production of neurotoxin, suggesting that both phenotypes are controlled by quorum sensing. Interestingly, while
agr
-
1
appeared to control sporulation,
agr
-
2
appeared to regulate neurotoxin formation.
Application of Whole-Cell Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry for Rapid Identification and Clustering Analysis ofPantoeaSpecies
Authors: Rezzonico Fabio , Vogel Guido , Duffy Brion , Tonolla Mauro
Published: May 2010

Pantoea agglomeransis an ecologically diverse taxon that includes commercially important plant-beneficial strains and opportunistic clinical isolates. Standard biochemical identification methods in diagnostic laboratories were repeatedly shown to run into false-positive identifications ofP. agglomerans, a fact which is also reflected by the high number of 16S rRNA gene sequences in public databases that are incorrectly assigned to this species. More reliable methods for rapid identification are required to ascertain the prevalence of this species in clinical samples and to evaluate the biosafety of beneficial isolates. Whole-cell matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) methods and reference spectra (SuperSpectrum) were developed for accurate identification ofP. agglomeransand related bacteria and used to detect differences in the protein profile within variants of the same strain, including a ribosomal point mutation conferring streptomycin resistance. MALDI-TOF MS-based clustering was shown to generally agree with classification based ongyrBsequencing, allowing rapid and reliable identification at the species level.
Chromatin-Mediated Epigenetic Regulation in the Malaria Parasite Plasmodium falciparum
Authors: Cui Liwang , Miao Jun
Published: May 2010

Malaria is a major public health problem in many developing countries, with the malignant tertian parasitePlasmodium falciparumcausing the most malaria-associated mortality. Extensive research, especially with the advancement of genomics and transfection tools, has highlighted the fundamental importance of chromatin-mediated gene regulation in the developmental program of this early-branching eukaryote. ThePlasmodiumparasite genomes reveal the existence of both canonical and variant histones that make up the nucleosomes, as well as a full collection of conserved enzymes for chromatin remodeling and histone posttranslational modifications (PTMs). Recent studies have identified a wide array of both conserved and novel histone PTMs inP. falciparum, indicating the presence of a complex and divergent “histone code.” Genome-wide analysis has begun to decipher the nucleosome landscape and histone modifications associated with the dynamic organization of chromatin structures during the parasite's life cycle. Focused studies on malaria-specific phenomena such as antigenic variation and red cell invasion pathways shed further light on the involvement of epigenetic mechanisms in these processes. Here we review our current understanding of chromatin-mediated gene regulation in malaria parasites, with specific reference to exemplar studies on antigenic variation and host cell invasion.
Oligomeric Sensor Kinase DcuS in the Membrane of
Escherichia coli
and in Proteoliposomes: Chemical Cross-linking and FRET Spectroscopy
Authors: Scheu Patrick D. , Liao Yun-Feng , Bauer Julia , Kneuper Holger , Basché Thomas , Unden Gottfried , Erker Wolfgang
Published: May 2010

DcuS is the membrane-integral sensor histidine kinase of the DcuSR two-component system in
Escherichia coli
that responds to extracellular C
4
-dicarboxylates. The oligomeric state of full-length DcuS was investigated
in vitro
and in living cells by chemical cross-linking and by

f

luorescence

r

esonance

e

nergy

t

ransfer (FRET) spectroscopy. The FRET results were quantified by an improved method using background-free spectra of living cells for determining FRET efficiency (
E
) and donor fraction {

f
D

= (donor)/[(donor) + (acceptor)]}. Functional fusions of cyan fluorescent protein (CFP) and yellow fluorescent protein (YFP) variants of green fluorescent protein to DcuS were used for
in vivo
FRET measurements. Based on noninteracting membrane proteins and perfectly interacting proteins (a CFP-YFP fusion), the results of FRET of cells coexpressing DcuS-CFP and DcuS-YFP were quantitatively evaluated. In living cells and after reconstitution of purified recombinant DcuS in proteoliposomes, DcuS was found as a dimer or higher oligomer, independent of the presence of an effector. Chemical cross-linking with disuccinimidyl suberate showed tetrameric, in addition to dimeric, DcuS in proteoliposomes and in membranes of bacteria, whereas purified DcuS in nondenaturing detergent was mainly monomeric. The presence and amount of tetrameric DcuS
in vivo
and in proteoliposomes was not dependent on the concentration of DcuS. Only membrane-embedded DcuS (present in the oligomeric state) is active in (auto)phosphorylation. Overall, the FRET and cross-linking data demonstrate the presence in living cells, in bacterial membranes, and in proteoliposomes of full-length DcuS protein in an oligomeric state, including a tetramer.
Evidence that Regulatory Protein MarA of
Escherichia coli
Represses
rob
by Steric Hindrance
Authors: McMurry Laura M. , Levy Stuart B.
Published: May 2010

The MarA protein of
Escherichia coli
can both activate and repress the initiation of transcription, depending on the position and orientation of its degenerate 20-bp binding site (“marbox”) at the promoter. For all three known repressed genes, the marbox overlaps the promoter. It has been reported that MarA represses the
rob
promoter via an RNA polymerase (RNAP)-DNA-MarA ternary complex. Under similar conditions, we found a ternary complex for the repressed
purA
promoter also. These findings, together with the backwards orientation of repressed marboxes, suggested a unique interaction of MarA with RNAP in repression. However, no repression-specific residues of MarA could be found among 38 single-alanine replacement mutations previously shown to retain activation function or among mutants from random mutagenesis. Mutations Thr12Ala, Arg36Ala, Thr95Ile, and Pro106Ala were more damaging for activation than for repression, some up to 10-fold, so these residues may play a specific role in activation. We found that nonspecific binding of RNAP to promoterless regions of DNA was presumably responsible for the ternary complexes seen previously. When RNAP binding was promoter specific, MarA reduced RNAP access to the
rob
promoter; there was little or no ternary complex. These findings strongly implicate steric hindrance as the mechanism of repression of
rob
by MarA.
The Hyperthermophilic Euryarchaeon
Archaeoglobus fulgidus
Repairs Uracil by Single-Nucleotide Replacement
Authors: Knævelsrud Ingeborg , Moen Marivi N. , Grøsvik Kristin , Haugland Gyri T. , Birkeland Nils-Kåre , Klungland Arne , Leiros Ingar , Bjelland Svein
Published: May 2010

Hydrolytic deamination of cytosine to uracil in cellular DNA is a major source of C-to-T transition mutations if uracil is not repaired by the DNA base excision repair (BER) pathway. Since deamination increases rapidly with temperature, hyperthermophiles, in particular, are expected to succumb to such damage. There has been only one report of crenarchaeotic BER showing strong similarities to that in most eukaryotes and bacteria for hyperthermophilic
Archaea
. Here we report a different type of BER performed by extract prepared from cells of the euryarchaeon
Archaeoglobus fulgidus
. Although immunodepletion showed that the monofunctional family 4 type of uracil-DNA glycosylase (UDG) is the principal and probably only UDG in this organism, a β-elimination mechanism rather than a hydrolytic mechanism is employed for incision of the abasic site following uracil removal. The resulting 3′ remnant is removed by efficient 3′-phosphodiesterase activity followed by single-nucleotide insertion and ligation. The finding that repair product formation is stimulated similarly by ATP and ADP
in vitro
raises the question of whether ADP is more important
in vivo
because of its higher heat stability.
Identification of a Novel Arsenite Oxidase Gene,
arxA
, in the Haloalkaliphilic, Arsenite-Oxidizing Bacterium
Alkalilimnicola ehrlichii
Strain MLHE-1
Authors: Zargar Kamrun , Hoeft Shelley , Oremland Ronald , Saltikov Chad W.
Published: May 2010

Although arsenic is highly toxic to most organisms, certain prokaryotes are known to grow on and respire toxic metalloids of arsenic (i.e., arsenate and arsenite). Two enzymes are known to be required for this arsenic-based metabolism: (i) the arsenate respiratory reductase (ArrA) and (ii) arsenite oxidase (AoxB). Both catalytic enzymes contain molybdopterin cofactors and form distinct phylogenetic clades (ArrA and AoxB) within the dimethyl sulfoxide (DMSO) reductase family of enzymes. Here we report on the genetic identification of a “new” type of arsenite oxidase that fills a phylogenetic gap between the ArrA and AoxB clades of arsenic metabolic enzymes. This “new” arsenite oxidase is referred to as ArxA and was identified in the genome sequence of the Mono Lake isolate
Alkalilimnicola ehrlichii
MLHE-1, a chemolithoautotroph that can couple arsenite oxidation to nitrate reduction. A genetic system was developed for MLHE-1 and used to show that
arxA
(gene locus ID
mlg
_
0216
) was required for chemoautotrophic arsenite oxidation. Transcription analysis also showed that
mlg
_
0216
was only expressed under anaerobic conditions in the presence of arsenite. The
mlg
_
0216
gene is referred to as
arxA
because of its greater homology to
arrA
relative to
aoxB
and previous reports that implicated Mlg_0216 (ArxA) of MLHE-1 in reversible arsenite oxidation and arsenate reduction
in vitro
. Our results and past observations support the position that ArxA is a distinct clade within the DMSO reductase family of proteins. These results raise further questions about the evolutionary relationships between arsenite oxidases (AoxB) and arsenate respiratory reductases (ArrA).
Regulation of an Auxiliary, Antibiotic-Resistant Tryptophanyl-tRNA Synthetase Gene via Ribosome-Mediated Transcriptional Attenuation
Authors: Vecchione James J. , Sello Jason K.
Published: May 2010

cis
-Acting RNA elements in the leaders of bacterial mRNA often regulate gene transcription, especially in the context of amino acid metabolism. We determined that the transcription of the auxiliary, antibiotic-resistant tryptophanyl-tRNA synthetase gene (
trpRS1
) in
Streptomyces coelicolor
is regulated by a ribosome-mediated attenuator in the 5′ leader of its mRNA region. This regulatory element controls gene transcription in response to the physiological effects of indolmycin and chuangxinmycin, two antibiotics that inhibit bacterial tryptophanyl-tRNA synthetases. By mining streptomycete genome sequences, we found several orthologs of
trpRS1
that share this regulatory element; we predict that they are regulated in a similar fashion. The validity of this prediction was established through the analysis of a
trpRS1
ortholog (SAV4725) in
Streptomyces avermitilis
. We conclude that the
trpRS1
locus is a widely distributed and self-regulating antibiotic resistance cassette. This study provides insights into how auxiliary aminoacyl-tRNA synthetase genes are regulated in bacteria.
Complete Genome Sequences of
Yersinia pestis
from Natural Foci in China
Authors: Shen Xiaona , Wang Qi , Xia Lianxu , Zhu Xiaoyu , Zhang Zhikai , Liang Ying , Cai Hong , Zhang Enmin , Wei Jianchun , Chen Chen , Song Zhizhong , Zhang Hongtao , Yu Dongzheng , Hai Rong
Published: May 2010

Yersinia pestis
, the causative agent of plague, is a deadly bacterium that affects humans. Strain D106004 was isolated from a new plague focus in Yulong County, China, in 2006. To gain insights into the epidemic origin, we have sequenced the genomes of D106004 and strains Z176003 and D182038, isolated from neighboring regions.
Mutagenesis and Chemical Cross-Linking Suggest that Wzz Dimer Stability and Oligomerization Affect Lipopolysaccharide O-Antigen Modal Chain Length Control
Authors: Papadopoulos Magdalene , Morona Renato
Published: May 2010

In
Shigella flexneri
, the polysaccharide copolymerase (PCP) protein Wzz
SF
confers a modal length of 10 to 17 repeat units (RUs) to the O-antigen (Oag) component of lipopolysaccharide (LPS). PCPs form oligomeric structures believed to be related to their function. To identify functionally important regions within Wzz
SF
, random in-frame linker mutagenesis was used to create mutants with 5-amino-acid insertions (termed Wzz
i
proteins), and DNA sequencing was used to locate the insertions. Analysis of the resulting LPS conferred by Wzz
i
proteins identified five mutant classes. The class I mutants were inactive, resulting in nonregulated LPS Oag chains, while classes II and III conferred shorter LPS Oag chains of 2 to 10 and 8 to 14 RUs, respectively. Class IV mutants retained near-wild-type function, and class V mutants increased the LPS Oag chain length to 16 to 25 RUs
. In vivo
formaldehyde cross-linking indicated class V mutants readily formed high-molecular-mass oligomers; however, class II and III Wzz
i
mutants were not effectively cross-linked. Wzz dimer stability was also investigated by heating cross-linked oligomers at 100°C in the presence of SDS. Unlike the Wzz
SF
wild type and class IV and V Wzz
i
mutants, the class II and III mutant dimers were not detectable. The location of each insertion was mapped onto available PCP three-dimensional (3D) structures, revealing that class V mutations were most likely located within the inner cavity of the PCP oligomer. These data suggest that the ability to produce stable dimers may be important in determining Oag modal chain length.
Improved neurological function in a paediatric patient following Onyx embolization of a cervical glomus arteriovenous malformation
Authors: Kitamura Gene , Jacobson J Paul , Zouros Alexander , Neglio Holly
Published: May 2010

Spinal cord intramedullary arteriovenous malformations (AVMs) pose a therapeutic challenge. Because of their complex angioanatomy, surgical excision of these lesions is difficult at best. Over the past decade, endovascular therapy has been established as an alternative treatment modality. As an embolic agent,N-butyl cyanoacrylate (NBCA) posed several problems such as difficulty of use and unpredictable performance. Onyx (ev3, Irvine, California, USA), an alternative liquid embolic agent, possesses several advantageous properties, such as increased control of agent delivery, over previous embolic agents like NBCA. However, reports of Onyx use in treating spinal intramedullary AVMs are still rare, especially in paediatric patients. We report a paediatric patient with glomus-type spinal intramedullary AVM treated successfully with Onyx with intermediate-term outcome.
Bilateral mirror aneurysms at the origin of the posteroinferior cerebellar artery: case report and review of the literature
Authors: Mariniello Giuseppe , Briganti Francesco , Tortora Fabio , Marseglia Mariano , Maiuri Francesco
Published: May 2010

We report an exceptional case of symmetrical mirror aneurysms at the origin of the posterior inferior cerebellar arteries treated by endovascular occlusion. Questions related to a correct diagnosis and treatment at this localization are discussed.
NBCA embolization of a ruptured intraventricular distal anterior choroidal artery aneurysm in a patient with moyamoya disease
Authors: Choulakian Armen , Drazin Doniel , Alexander Michael J
Published: May 2010

Occasionally an aneurysm is the cause of hemorrhage in patients with moyamoya disease (MMD). We present a case of a ruptured intraventricular distal anterior choroidal artery (AChA) aneurysm treated withn-butyl cyanoacrylic acid (nBCA) (Trufill nBCA Liquid Embolic, Codman Neurovascular, Raynham, Massachusetts, USA) embolization in a patient with MMD. There were no procedural complications and at 6 month follow-up she remained neurologically normal. Six month follow-up cerebral angiography showed no residual aneurysm. The endovascular route is an attractive option for many aneurysms associated with MMD as the lesions can be treated without disturbing the moyamoya collaterals. nBCA, delivered through a flow-guided microcatheter, is a good embolic agent choice when the lesion is distal on a small vessel and when distal parent artery occlusion can be tolerated. Intraventricular AChA aneurysms are well suited for this treatment strategy.
Preindustrial reconstruction of a perhumid midboreal landscape, Anticosti Island, Quebec
Authors: Barrette Martin , Bélanger Louis , De Grandpré Louis
Published: May 2010

The knowledge of natural disturbance dynamics and preindustrial landscapes is essential to implement sustainable forest management. Recent findings identify the lack of a forest dynamics model, different from the standard cyclic model of Baskerville (1975. For. Chron. 51: 138–140), for balsam fir ( Abies balsamea (L.) Mill.) ecosystems of maritime eastern Canada. With the use of historical forest maps and dendrochronology, we reconstructed the range of variability of the preindustrial landscape (6798 km2) and inferred on the natural disturbance dynamics of the balsam fir forest of Anticosti Island. The preindustrial landscape was characterized by a forest matrix of overmature softwood stands with inclusions of younger softwood stands ranging from 0.1 to 7837 ha in size. Widespread stand-initiating events were apparently rare in the preindustrial landscape over the last 160 years. Since our results were not well represented by the cyclic model, which predicts the occurrence of a mosaic of stands in different age classes, we proposed an alternative forest dynamics model for eastern balsam fir ecosystems near the Gulf of St. Lawrence. Forest management inspired by this alternative model may be more appropriate to maintain or restore ecological characteristics of balsam fir forests of this region within their range of natural variability.
Density estimation based on k-tree sampling and point pattern reconstruction
Authors: Nothdurft Arne , Saborowski Joachim , Nuske Robert S. , Stoyan Dietrich
Published: May 2010

In k-tree sampling, also referred to as point-to-tree distance sampling, the k nearest trees are measured. The problem associated with k-tree sampling is its lack of unbiased density estimators. The presented density estimator based on point pattern reconstruction remedies that shortcoming. It requires the coordinates of all k trees. These coordinates are translated into a simulation window where they remain unchanged. Empirical cumulative distribution functions of intertree and location-to-tree distances estimated from the sample plots are set as target characteristics. Using the idea of simulated annealing, an optimal new tree pattern is constructed in the simulation window outside the k-tree samples. The reconstruction of the point pattern minimizes the contrast between the empirical cumulative distribution functions and their analogs for the simulated pattern. The density estimator is simply the tree density of the optimum pattern in the simulation window. The performance of the reconstruction-based density estimator is assessed for k = 6 and k = 4 based on systematic sampling grids regarding its potential application in forest inventories. Simulations are carried out using real stem maps (covering different stand densities and different types of spatial point patterns, such as regular, clustered, and random) as well as completely random patterns. The new density estimator proves to be empirically superior in terms of bias and root mean squared error compared with commonly used estimators. The reconstruction-based density estimator has biases smaller than 2%.
ASSESSMENT ON SECURITY RISKS OF CUSTOMER RELATIONSHIP MANAGEMENT SYSTEMS
Authors: KIM SANGKYUN
Published: May 2010

To adapt to the firm's environmental changes continuously, the customer relationship management system is a key which monitors external changes and adapts internal cultures and processes in response to external challenges. Increasing use of customer relationship management systems in competitive business environments has given rise to various kinds of security problems. This paper reviews previous studies on customer relationship management systems, protection of customer information, and evaluation of information security systems. Finally, considering the characteristics of customer relationship management systems and security evaluation methodology, this paper suggests the assessment criteria for security risks of customer relationship management systems.
INDEPENDENCE AND CONDITIONAL DECOMPOSABLE INFORMATION MEASURES
Authors: BUSANELLO GIUSEPPE , COLETTI GIULIANELLA , VANTAGGI BARBARA
Published: May 2010

We deal with conditional decomposable information measures, directly defined as functions on a suitable set of conditional events satisfying a class of axioms. For these general measures we introduce a notion of independence and study its main properties in order to compare it with classical definitions present in the literature. The particular case of Wiener-Shannon information measure is taken in consideration and the links between the provided independence for information measures and the independence for the underlying probability are analyzed.
TESTING EQUIVALENCE OF PURE QUANTUM STATES AND GRAPH STATES UNDER SLOCC
Authors: D'SOUZA ADAM G. , BRIËT JOP , FEDER DAVID L.
Published: May 2010

A set of necessary and sufficient conditions are derived for the equivalence of an arbitrary pure state and a graph state on n qubits under stochastic local operations and classical communication (SLOCC), using the stabilizer formalism. Because all stabilizer states are equivalent to graph states by local unitary transformations, these conditions constitute a classical algorithm for the determination of SLOCC-equivalence of pure states and stabilizer states. This algorithm provides a distinct advantage over the direct solution of the SLOCC-equivalence condition |ψ〉 = S|g〉 for an unknown invertible local operator S, as it usually allows for easy detection of states that are not SLOCC-equivalent to graph states.
QUANTUM LOGIC BETWEEN DISTANT TRAPPED IONS
Authors: OLMSCHENK S. , HAYES D. , MATSUKEVICH D. N. , MAUNZ P. , MOEHRING D. L. , MONROE C.
Published: May 2010

Trapped atomic ions have proven to be one of the most promising candidates for the realization of quantum computation due to their long trapping times, excellent coherence properties, and exquisite control of the internal atomic states. Integrating ions (quantum memory) with photons (distance link) offers a unique path to large-scale quantum computation and long-distance quantum communication. In this article, we present a detailed review of the experimental implementation of a heralded photon-mediated quantum gate between remote ions, and the employment of this gate to perform a teleportation protocol between two ions separated by a distance of about one meter.
DISTRIBUTED QUANTUM COMPUTATION ARCHITECTURE USING SEMICONDUCTOR NANOPHOTONICS
Authors: VAN METER RODNEY , LADD THADDEUS D. , FOWLER AUSTIN G. , YAMAMOTO YOSHIHISA
Published: May 2010

In a large-scale quantum computer, the cost of communications will dominate the performance and resource requirements, place many severe demands on the technology, and constrain the architecture. Unfortunately, fault-tolerant computers based entirely on photons with probabilistic gates, though equipped with "built-in" communication, have very large resource overheads; likewise, computers with reliable probabilistic gates between photons or quantum memories may lack sufficient communication resources in the presence of realistic optical losses. Here, we consider a compromise architecture, in which semiconductor spin qubits are coupled by bright laser pulses through nanophotonic waveguides and cavities using a combination of frequent probabilistic and sparse determinstic entanglement mechanisms. The large photonic resource requirements incurred by the use of probabilistic gates for quantum communication are mitigated in part by the potential high-speed operation of the semiconductor nanophotonic hardware. The system employs topological cluster-state quantum error correction for achieving fault-tolerance. Our results suggest that such an architecture/technology combination has the potential to scale to a system capable of attacking classically intractable computational problems.
DIFFUSION OF INFORMATION COMMUNICATION TECHNOLOGY (ICT) THROUGH THE RURAL INTERNET CENTRE: THE MALAYSIAN EXPERIENCE
Authors: SULAIMAN AININ , JAAFAR NOOR ISMAWATI , JANI ROHANA
Published: May 2010

This paper focuses on examining the ICT diffusion by studying an initiative of the Malaysian government to bridge the digital divide that exists across the country's urban and rural communities. This is achieved through investigating the operation and the experience of a typical Rural Internet Centre. The findings of this study showed that there is keen interest among the community to learn and sharpen their ICT-related skills. The Internet Centre serves to provide an avenue for the realisation of this goal. The study showed that despite some operational snags, the Internet Centre performed well. One of the by-products of the centre was that its activities fostered closer relationships among users; it provided an avenue for disparate community members to interact and share their new skills. Bringing the ICT usage and appreciation to the rural areas was successful. About half of the centre users made weekly visits during which they searched for information on the internet, sent and received e-mail and attended the Internet Centre's regular IT classes. They also saw it as a valuable communication channel and a potential leveller of the technological capability gap.
Crystal tuff in the Stoer Group, Torridonian Supergroup, NW Scotland
Authors: Batchelor Richard A. , Prave Anthony R.
Published: May 2010

Synopsis

One thin bed in sandstones belonging to the Stoer Group (Torridonian Supergroup) contains feldspar and quartz grains showing deep concave embayments which are interpreted as corrosion features, and are all embedded in a fine-grained illitic or sericitic matrix. Its bulk chemical composition is similar to that of Phanerozoic metabentonites but it differs from the overlying Stac Fada Member which is believed to represent either a volcanogenic deposit or an impact ejecta blanket. Field relationships, petrographic and chemical characteristics point to this bed having a volcanic origin. This thin bed represents a crystal tuff and is the earliest example of a volcanogenic deposit in the Torridonian Supergroup in Scotland.
Nitric oxide synthase 3 contributes to ventilator-induced lung injury
Authors: Vaporidi Katerina , Francis Roland C. , Bloch Kenneth D. , Zapol Warren M.
Published: May 2010

Nitric oxide synthase (NOS) depletion or inhibition reduces ventilator-induced lung injury (VILI), but the responsible mechanisms remain incompletely defined. The aim of this study was to elucidate the role of endothelial NOS, NOS3, in the pathogenesis of VILI in an in vivo mouse model. Wild-type and NOS3-deficient mice were ventilated with high-tidal volume (HVT; 40 ml/kg) for 4 h, with and without adding NO to the inhaled gas. Additional wild-type mice were pretreated with tetrahydrobiopterin and ascorbic acid, agents that can prevent NOS-generated superoxide production. Arterial blood gas tensions, histology, and lung mechanics were evaluated after 4 h of HVTventilation. The concentration of protein, IgM, cytokines, malondialdehyde, and 8-isoprostane were measured in bronchoalveolar lavage fluid (BALF). Myeloperoxidase activity, total and oxidized glutathione levels, and NOS-derived superoxide production were measured in lung tissue homogenates. HVTventilation induced VILI in wild-type mice, as reflected by decreased lung compliance, increased concentrations of protein and cytokines in BALF, and oxidative stress. All indices of VILI were ameliorated in NOS3-deficient mice. Augmenting pulmonary NO levels by breathing NO during mechanical ventilation did not increase lung injury in NOS3-deficient mice. HVTventilation increased NOS-inhibitable superoxide production in lung extracts from wild-type mice but not in those from NOS3-deficient mice. Administration of tetrahydrobiopterin and ascorbic acid ameliorated VILI in wild-type mice. Our results indicate that NOS3 contributes to ventilator-induced lung injury via increased production of superoxide.
Positive Approximation and Interpolation Using Compactly Supported Radial Basis Functions
Authors: Wu Jinming , Zhang Xiaolei , Peng Lihui
Published: May 2010

We discuss the problem of constrained approximation and interpolation of scattered data by using compactly supported radial basis functions, subjected to the constraint of preserving positivity. The approaches are presented to compute positive approximation and interpolation by solving the two corresponding optimization problems. Numerical experiments are provided to illustrate that the proposed method is flexible.