bluuebunny/crossref_metadata_2025 huggingface dataset:
Design, Development, Testing and Qualification of Diverse Safety Rod and Its Drive Mechanism for a Prototype Fast Breeder Reactor
Authors: Vijayashree R. , Veerasamy R. , Patri Sudheer , Chellapandi P. , Vaidyanathan G. , Chetal S. C. , Raj Baldev
Published: July 2010

Prototype fast breeder reactor is U–PuO2 fueled sodium cooled pool type fast reactor and it is currently under construction at Kalpakkam, India. Prototype fast breeder reactor is equipped with two independent fast acting and diverse shutdown systems. A shutdown system comprises of sensors, logic circuits, drive mechanisms, and neutron absorbing rods. The two shutdown systems of prototype fast breeder reactor are capable of bringing down the reactor to cold shutdown state independent of the other. The absorber rods of the second shutdown system of prototype fast breeder reactor are called as diverse safety rods (DSRs) and their drive mechanisms are called as diverse safety rod drive mechanisms (DSRDMs). DSRs are normally parked above active core by DSRDMs. On receiving scram signal, the electromagnet of DSRDM is de-energized and it facilitates fast shutdown of the reactor by dropping the DSR into the active core. For the development of prototypes of DSR and DSRDM, three phases of testing, namely, individual component testing, integrated functional testing in room temperature, and endurance testing at high temperature sodium, were done. The electromagnet of DSRDM has been separately tested at room temperature, in furnace, and in sodium. Specimens simulating the contact conditions between electromagnet and armature of DSR have been tested to rule out self-welding possibility. The prototype of DSR has been tested in flowing water to determine the pressure drop and drop time. The functional testing of the integrated prototype DSRDM and DSR in aligned and misaligned conditions in air/water has been completed. The performance testing of the integrated system in sodium has been done in three campaigns. During the third campaign of sodium testing, the performance of the system has been verified with 30 mm misalignment at various temperatures. The third campaign has qualified the system for 10 years of operation in reactor. This paper presents design, development, testing, and qualification of the prototype DSR and DSRDM. Salient design specifications for both DSRDM and DSR are listed initially. The conceptual and detailed design features are explained with the help of figures. Details on material of construction are given at appropriate places. Test plans and criteria for endurance testing in sodium for qualification of DSRDM and DSR for operation in reactor are briefed. Brief explanation of test setups and typical test results are also given.
Study on the Coupled Neutronic and Thermal-Hydraulic Characteristics of the New Concept Molten Salt Reactor
Authors: Wang Peng , Qian Libo , Zhang Dalin , Tian Wenxi , Su Guanghui , Qiu Suizheng
Published: July 2010

The new concept molten salt reactor is the only liquid-fuel reactor of the six Generation IV advanced nuclear energy systems. The liquid molten salt serves as the fuel and coolant simultaneously and causes one important feature: the delayed neutron precursors are drifted by the fuel flow, which leads the spread of delayed neutrons’ distribution to noncore parts of the primary circuit, and it also results in reactivity variation depending on the flow condition of the fuel salt. Therefore, the neutronic and thermal-hydraulic characteristics of the molten salt reactor are quite different from the conventional nuclear reactors using solid fissile materials. Besides, there is no other reactor design theory and safety analysis methodologies can be used for reference. The neutronic model is derived based on the conservation of particles considering the flow effect of the fuel salt in the molten salt reactor, while the thermal-hydraulic model applies the fundamental conservation laws: the mass, momentum, and energy conservation equations. Then, the neutronic and thermal-hydraulic calculations are coupled and the influences of inflow temperature and flow velocity on the reactor physical properties are obtained. The calculated results show that the flow effect on the distributions of thermal and fast neutron fluxes is very weak, as well as on the effective multiplication factor keff, while the flow effect on the distribution of delayed neutron precursors is much stronger. The inflow temperature influences the distribution of neutron fluxes and delayed neutron precursors slightly, and makes a significant negative reactivity. Coupled calculation also reveals that the flow velocity of molten salt has little effect on the distribution of neutron fluxes in the steady-state, but affects the delayed neutron precursors’ distribution significantly.
Core Melt Solidification Characteristics in PRV Lower Head-Experimental Results From LIVE Tests
Authors: Gaus-Liu Xiaoyang , Miassoedov Alexei , Cron Thomas , Foit Jerzy , Wenz Thomas , Schmidt-Stiefel Silke
Published: July 2010

Core melt solidification phenomena in the lower plenum of pressurized reactor vessel during external reactor vessel cooling is investigated in late in-vessel phase experiment tests under different external cooling conditions and melt pouring positions. The melt solidification behavior, which has not yet been given sufficient attention, is an important issue since it influences not only the transient but also the steady state of melt pool thermal hydraulics. A noneutectic melt (80 mol %KNO3–20 mol %NaNO3) was used to simulate the core melt. It has been found out that when the vessel is cooled with water during the whole test period (water cooling), the cooling is more effective than the case that the vessel lower head is first cooled with air and flooded by water (air/water cooling). Water cooling at the beginning leads to faster buildup of crust layer on the vessel inner wall and lower crust thermal conductivity compared with air/water cooling. In comparison with the air/water cooling, the water cooling also achieves shorter time period of crust growth. During the solidification period in all tests, the constitutional supercooling condition is fulfilled. Pouring position near the vessel wall results in considerable asymmetry in the heat flux distribution through the vessel wall.
Comparing Nonsynergistic Gamma Models with Interaction Models To Predict Growth of EmeticBacillus cereuswhen Using Combinations of pH and Individual Undissociated Acids as Growth-Limiting Factors
Authors: Biesta-Peters Elisabeth G. , Reij Martine W. , Gorris Leon G. M. , Zwietering Marcel H.
Published: July 2010

A combination of multiple hurdles to limit microbial growth is frequently applied in foods to achieve an overall level of protection. Quantification of hurdle technology aims at identifying synergistic or multiplicative effects and is still being developed. The gamma hypothesis states that inhibitory environmental factors aiming at limiting microbial growth rates combine in a multiplicative manner rather than synergistically. Its validity was tested here with respect to the use of pH and various concentrations of undissociated acids, i.e., acetic, lactic, propionic, and formic acids, to control growth ofBacillus cereusin brain heart infusion broth. The key growth parameter considered was the maximum specific growth rate, μmax, as observed by determination of optical density. A variety of models from the literature describing the effects of various pH values and undissociated acid concentrations on μmaxwere fitted to experimental data sets and compared based on a predefined set of selection criteria, and the best models were selected. The cardinal model developed by Rosso (for pH dependency) and the model developed by Luong (for undissociated acid) were found to provide the best fit and were combined in a gamma model with good predictive performance. The introduction of synergy factors into the models was not able to improve the quality of the prediction. On the contrary, inclusion of synergy factors led to an overestimation of the growth boundary, with the inherent possibility of leading to underestimation of the risk under the conditions tested in this research.
Antimicrobial Activity of Simulated Solar Disinfection against Bacterial, Fungal, and Protozoan Pathogens and Its Enhancement by Riboflavin
Authors: Heaselgrave Wayne , Kilvington Simon
Published: July 2010

Riboflavin significantly enhanced the efficacy of simulated solar disinfection (SODIS) at 150 watts per square meter (W m
−2
) against a variety of microorganisms, including
Escherichia coli
,
Fusarium solani
,
Candida albicans
, and
Acanthamoeba polyphaga
trophozoites (>3 to 4 log
10
after 2 to 6 h;
P
< 0.001). With
A. polyphaga
cysts, the kill (3.5 log
10
after 6 h) was obtained only in the presence of riboflavin and 250 W m
−2
irradiance.
Community Structure of Subsurface Biofilms in the Thermal Sulfidic Caves of Acquasanta Terme, Italy
Authors: Jones D. S. , Tobler D. J. , Schaperdoth I. , Mainiero M. , Macalady J. L.
Published: July 2010

We performed a microbial community analysis of biofilms inhabiting thermal (35 to 50°C) waters more than 60 m below the ground surface near Acquasanta Terme, Italy. The groundwater hosting the biofilms has 400 to 830 μM sulfide, <10 μM O
2
, pH of 6.3 to 6.7, and specific conductivity of 8,500 to 10,500 μS/cm. Based on the results of 16S rRNA gene cloning and fluorescent
in situ
hybridization (FISH), the biofilms have low species richness, and lithoautotrophic (or possibly mixotrophic)
Gamma
- and
Epsilonproteobacteria
are the principle biofilm architects.
Deltaproteobacteria
sequences retrieved from the biofilms have <90% 16S rRNA similarity to their closest relatives in public databases and may represent novel sulfate-reducing bacteria. The Acquasanta biofilms share few species in common with Frasassi cave biofilms (13°C, 80 km distant) but have a similar community structure, with representatives in the same major clades. The ecological success of
Sulfurovumales
-group
Epsilonproteobacteria
in the Acquasanta biofilms is consistent with previous observations of their dominance in sulfidic cave waters with turbulent water flow and high dissolved sulfide/oxygen ratios.
Diffusion Measurements inside Biofilms by Image-Based Fluorescence Recovery after Photobleaching (FRAP) Analysis with a Commercial Confocal Laser Scanning Microscope
Authors: Waharte François , Steenkeste Karine , Briandet Romain , Fontaine-Aupart Marie-Pierre
Published: July 2010

Research about the reactional and structural dynamics of biofilms at the molecular level has made great strides, owing to efficient fluorescence imaging methods in terms of spatial resolution and fast acquisition time but also to noninvasive conditions of observation consistent with
in situ
biofilm studies. In addition to conventional fluorescence intensity imaging, the fluorescence recovery after photobleaching (FRAP) module can now be routinely implemented on commercial confocal laser scanning microscopes (CLSMs). This method allows measuring of local diffusion coefficients in biofilms and could become an alternative to fluorescence correlation spectroscopy (FCS). We present here an image-based FRAP protocol to improve the accuracy of FRAP measurements inside “live” biofilms and the corresponding analysis. An original kymogram representation allows control of the absence of perturbing bacterial movement during image acquisition. FRAP data analysis takes into account molecular diffusion during the bleach phase and uses the image information to extract molecular diffusion coefficients. The fluorescence spatial intensity profile analysis used here for the first time with biofilms is supported both by our own mathematical model and by a previously published one. This approach was validated to FRAP experiments on fluorescent-dextran diffusion inside
Lactoccocus lactis
and
Stenotrophomonas maltophilia
biofilms, and the results were compared to previously published FCS measurements.
Rapidly Growing Nontuberculous Mycobacteria Cultured from Home Tap and Shower Water
Authors: van Ingen Jakko , Blaak Hetty , de Beer Jessica , de Roda Husman Ana Maria , van Soolingen Dick
Published: July 2010

Tap and shower water at two locations in the Netherlands was examined for the presence of rapidly growing nontuberculous mycobacteria. Cultures yielded
Mycobacterium peregrinum
,
M. salmoniphilum
,
M. llatzerense
,
M. septicum
, and three potentially novel species, a distribution different from that in clinical samples.
Cloning and Expression of a Novel NADP(H)-Dependent Daidzein Reductase, an Enzyme Involved in the Metabolism of Daidzein, from Equol-Producing
Lactococcus
Strain 20-92
Authors: Shimada Yoshikazu , Yasuda Setsuko , Takahashi Masayuki , Hayashi Takashi , Miyazawa Norihiro , Sato Ikutaro , Abiru Yasuhiro , Uchiyama Shigeto , Hishigaki Haretsugu
Published: July 2010

Equol is a metabolite produced from daidzein by enteric microflora, and it has attracted a great deal of attention because of its protective or ameliorative ability against several sex hormone-dependent diseases (e.g., menopausal disorder and lower bone density), which is more potent than that of other isoflavonoids. We purified a novel NADP(H)-dependent daidzein reductase (L-DZNR) from
Lactococcus
strain 20-92 (
Lactococcus
20-92; S. Uchiyama, T. Ueno, and T. Suzuki, international patent WO2005/000042) that is involved in the metabolism of soy isoflavones and equol production and converts daidzein to dihydrodaidzein. Partial amino acid sequences were determined from purified L-DZNR, and the gene encoding L-DZNR was cloned. The nucleotide sequence of this gene consists of an open reading frame of 1,935 nucleotides, and the deduced amino acid sequence consists of 644 amino acids. L-DZNR contains two cofactor binding motifs and an 4Fe-4S cluster. It was further suggested that L-DZNR was an NAD(H)/NADP(H):flavin oxidoreductase belonging to the
o
ld
y
ellow
e
nzyme (OYE) family. Recombinant histidine-tagged L-DZNR was expressed in
Escherichia coli
. The recombinant protein converted daidzein to (
S
)-dihydrodaidzein with enantioselectivity. This is the first report of the isolation of an enzyme related to daidzein metabolism and equol production in enteric bacteria.
Genomic Island TnSmu2 of
Streptococcus mutans
Harbors a Nonribosomal Peptide Synthetase-Polyketide Synthase Gene Cluster Responsible for the Biosynthesis of Pigments Involved in Oxygen and H
2
O
2
Tolerance
Authors: Wu Chenggang , Cichewicz Robert , Li Yihong , Liu Jinman , Roe Bruce , Ferretti Joseph , Merritt Justin , Qi Fengxia
Published: July 2010

The oral biofilm community consists of >800 microbial species, among which
Streptococcus mutans
is considered a primary pathogen for dental caries. The genomic island TnSmu2 of
S. mutans
comprises >2% of the genome. In this study, we demonstrate that TnSmu2 harbors a gene cluster encoding nonribosomal peptide synthetases (NRPS), polyketide synthases (PKS), and accessory proteins and regulators involved in nonribosomal peptide (NRP) and polyketide (PK) biosynthesis. Interestingly, the sequences of these genes and their genomic organizations and locations are highly divergent among different
S. mutans
strains, yet each TnSmu2 region encodes NRPS/PKS and accessory proteins. Mutagenesis of the structural genes and putative regulatory genes in strains UA159, UA140, and MT4653 resulted in colonies that were devoid of their yellow pigmentation (for strains UA140 and MT4653). In addition, these mutant strains also displayed retarded growth under aerobic conditions and in the presence of H
2
O
2
. High-performance liquid chromatography profiling of cell surface extracts identified unique peaks that were missing in the mutant strains, and partial characterization of the purified product from UA159 demonstrated that it is indeed a hybrid NRP/PK, as predicted. A genomic survey of 94 clinical
S. mutans
isolates suggests that the TnSmu2 gene cluster may be more prevalent than previously recognized.
Response of Porcine Intestinal
In Vitro
Organ Culture Tissues following Exposure to
Lactobacillus plantarum
JC1 and
Salmonella enterica
Serovar Typhimurium SL1344
Authors: Collins J. W. , Coldham N. G. , Salguero F. J. , Cooley W. A. , Newell W. R. , Rastall R. A. , Gibson G. R. , Woodward M. J. , La Ragione R. M.
Published: July 2010

The development of novel intervention strategies for the control of zoonoses caused by bacteria such as
Salmonella
spp. in livestock requires appropriate experimental models to assess their suitability. Here, a novel porcine intestinal
in vitro
organ culture (IVOC) model utilizing cell crown (CC) technology (CCIVOC) (Scaffdex) was developed. The CCIVOC model was employed to investigate the characteristics of association of
S. enterica
serovar Typhimurium strain SL1344 with porcine intestinal tissue following exposure to a
Lactobacillus plantarum
strain. The association of bacteria to host cells was examined by light microscopy and electron microscopy (EM) after appropriate treatments and staining, while changes in the proteome of porcine jejunal tissues were investigated using quantitative label-free proteomics. Exposure of porcine intestinal mucosal tissues to
L. plantarum
JC1 did not reduce the numbers of
S.
Typhimurium bacteria associating to the tissues but was associated with significant (
P
< 0.005) reductions in the percentages of areas of intestinal IVOC tissues giving positive staining results for acidic mucins. Conversely, the quantity of neutrally charged mucins present within the goblet cells of the IVOC tissues increased significantly (
P
< 0.05). In addition, tubulin-α was expressed at high levels following inoculation of jejunal IVOC tissues with
L. plantarum
. Although
L. plantarum
JC1 did not reduce the association of
S.
Typhimurium strain SL1344 to the jejunal IVOC tissues, detection of increased acidic mucin secretion, host cytoskeletal rearrangements, and proteins involved in the porcine immune response demonstrated that this strain of
L. plantarum
may contribute to protecting the pig from infections by
S.
Typhimurium or other pathogens.
Candida albicans Cyclin Clb4 Carries S-Phase Cyclin Activity
Authors: Ofir Ayala , Kornitzer Daniel
Published: July 2010

Cyclin-dependent kinases (CDKs) are key regulators of eukaryotic cell cycle progression. The cyclin subunit activates the CDK and also imparts to the complex, at least in some cases, substrate specificity.
Saccharomyces cerevisiae
, an organism in which the roles of individual cyclins are best studied, contains nine cyclins (three G
1
cyclins and six B-type cyclins) capable of activating the main cell cycle CDK, Cdc28. Analysis of the genome of the pathogenic yeast
Candida albicans
revealed only two sequences corresponding to B-type cyclins,
C. albicans
Clb2 (CaClb2) and CaClb4. Notably, no homolog of the
S. cerevisiae
S-phase-specific cyclins, Clb5/Clb6, could be detected. Here, we performed an
in vitro
analysis of the activity of CaClb2 and CaClb4 and of three G
1
cyclins, as well as an analysis of the phenotype of
S. cerevisiae
cells expressing CaClb2 or CaClb4 instead of Clb5. Remarkably, replacement of
CLB5
by Ca
CLB4
caused rapid diploidization of
S. cerevisiae.
In addition, both
in vivo
and
in vitro
analyses indicate that, in spite of the higher sequence similarity of CaClb2 to Clb5/Clb6, CaClb4 is the functional homolog of Clb5/Clb6. The activity of a CaClb2/CaClb4 cyclin hybrid suggests that the cyclin box domain of CaClb4 carries the functional specificity of the protein. These results have implications for our understanding of the evolution of specificity of the cell cycle cyclins.
Multiple Promoters Contribute to Swarming and the Coordination of Transcription with Flagellar Assembly in
Salmonella
Authors: Wozniak Christopher E. , Chevance Fabienne F. V. , Hughes Kelly T.
Published: July 2010

In
Salmonella
, there are three classes of promoters in the flagellar transcriptional hierarchy. This organization allows genes needed earlier in the construction of flagella to be transcribed before genes needed later. Four operons (
fliAZY
,
flgMN
,
fliDST
, and
flgKL
) are expressed from both class 2 and class 3 promoters. To investigate the purpose for expressing genes from multiple flagellar promoters, mutants were constructed for each operon that were defective in either class 2 transcription or class 3 transcription. The mutants were checked for defects in swimming through liquids, swarming over surfaces, and transcriptional regulation. The expression of the hook-associated proteins (FlgK, FlgL, and FliD) from class 3 promoters was found to be important for swarming motility. Both
flgMN
promoters were involved in coordinating class 3 transcription with the stage of assembly of the hook-basal body. Finally, the
fliAZY
class 3 promoter lowered class 3 transcription in stationary phase. These results indicate that the multiple flagellar promoters respond to specific environmental conditions and help coordinate transcription with flagellar assembly.
Characterization of the Structure and Biological Functions of a Capsular Polysaccharide Produced by
Staphylococcus saprophyticus
Authors: Park Sunny , Kelley Kathryn A. , Vinogradov Evgeny , Solinga Robert , Weidenmaier Christopher , Misawa Yoshiki , Lee Jean C.
Published: July 2010

Staphylococcus saprophyticus
is a common cause of uncomplicated urinary tract infections in women.
S. saprophyticus
strain ATCC 15305 carries two staphylococcal cassette chromosome genetic elements, SCC
15305RM
and SCC
15305cap
. The SCC
15305cap
element carries 13 open reading frames (ORFs) involved in capsular polysaccharide (CP) biosynthesis, and its G+C content (26.7%) is lower than the average G+C content (33.2%) for the whole genome.
S. saprophyticus
strain ATCC 15305
capD
,
capL
, and
capK
(

capD
Ssp

,

capL
Ssp

, and

capK
Ssp

) are homologous to genes encoding UDP-FucNAc biosynthesis, and
gtaB
and

capI
Ssp

show homology to genes involved in UDP-glucuronic acid synthesis.
S. saprophyticus
ATCC 15305 CP, visualized by immunoelectron microscopy, was extracted and purified using anionic-exchange and size exclusion chromatography. Analysis of the purified CP by
1
H and
13
C nuclear magnetic resonance (NMR) spectroscopy and gas-liquid chromatography revealed two types of branched tetrasaccharide repeating units composed of the following:

\batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \[\begin{array}{c}\mathbf{-4)-{\beta}-Glc}-\mathbf{(1-3)-Sug}-\mathbf{(1-4)-{\beta}-GlcA}-(\mathbf{1-}\\\mathbf{{\vert}}\\\mathbf{{\beta}-GlcNAc}-\mathbf{(1-2)}\end{array}\] \end{document}

Sug represents two stereoisomers of 2-acetamido-2,6-dideoxy-hexos-4-ulose residues, one of which has an
arabino
configuration. The encapsulated ATCC 15305 strain was resistant to complement-mediated opsonophagocytic killing by human neutrophils, whereas the acapsular mutant C1 was susceptible. None of 14 clinical isolates reacted with antibodies to the ATCC 15305 CP. However, 11 of the 14
S. saprophyticus
isolates were phenotypically encapsulated based on their resistance to complement-mediated opsonophagocytic killing and their failure to hemagglutinate when cultivated aerobically. Ten of the 14 clinical strains carried homologues of the conserved staphylococcal
capD
gene or the
S. saprophyticus gtaB
gene, or both. Our results suggest that some strains of
S. saprophyticus
are encapsulated and that more than one capsular serotype exists.
Posttranscriptional Regulation of Glutamine Synthetase in the Filamentous Cyanobacterium
Anabaena
sp. PCC 7120: Differential Expression between Vegetative Cells and Heterocysts
Authors: Galmozzi Carla V. , Saelices Lorena , Florencio Francisco J. , Muro-Pastor M. Isabel
Published: July 2010

Genes homologous to those implicated in glutamine synthetase (GS) regulation by protein-protein interaction in the cyanobacterium
Synechocystis
sp. strain PCC 6803 are conserved in several cyanobacterial sequenced genomes. We investigated this GS regulatory mechanism in
Anabaena
sp. strain PCC 7120. In this strain the system operates with only one GS inactivation factor (inactivation factor 7A [IF7A]), encoded by open reading frame (ORF)
asl2329
(
gifA
). Following addition of ammonium, expression of
gifA
is derepressed, leading to the synthesis of IF7A, and consequently, GS is inactivated. Upon ammonium removal, the GS activity returns to the initial level and IF7A becomes undetectable. The global nitrogen control protein NtcA binds to the
gifA
promoter. Constitutive high expression levels of
gifA
were found in an
Anabaena ntcA
mutant (CSE2), indicating a repressor role for NtcA.
In vitro
studies demonstrate that
Anabaena
GS is not inactivated by
Synechocystis
IFs (IF7 and IF17), indicating the specificity of the system. We constructed an
Anabaena
strain expressing a second inactivating factor, containing the amino-terminal part of IF17 from
Synechocystis
fused to IF7A. GS inactivation in this strain is more effective than that in the wild type (WT) and resembles that observed in
Synechocystis
. Finally we found differential expression of the IF system between heterocysts and vegetative cells of
Anabaena
.
Aromatic Acid Metabolites of
Escherichia coli
K-12 Can Induce the
marRAB
Operon
Authors: Chubiz Lon M. , Rao Christopher V.
Published: July 2010

MarR is a key regulator of the
marRAB
operon involved in antibiotic resistance and solvent stress tolerance in
Escherichia coli
. We show that two metabolic intermediates, 2,3-dihydroxybenzoate and anthranilate, involved in enterobactin and tryptophan biosynthesis, respectively, can activate
marRAB
transcription. We also found that a third intermediate involved in ubiquinone biosynthesis, 4-hydroxybenzoate, activates
marRAB
transcription in the absence of TolC. Of the three, however, only 2,3-dihydroxybenzoate directly binds MarR and affects its activity.
Molecular Cloning, Expression, and Characterization of a Ca
2+
-Dependent, Membrane-Associated Nuclease of
Mycoplasma genitalium
Authors: Li Linbo , Krishnan Manickam , Baseman Joel B. , Kannan T. R.
Published: July 2010

In this study, we identified and characterized the enzymatic properties of MG_186, a calcium-dependent
Mycoplasma genitalium
nuclease. MG_186 displays the hallmarks of nucleases, as indicated by its amino acid sequence similarity to other nucleases. We cloned, UGA corrected, expressed, purified, and demonstrated that recombinant MG_186 (rMG_186) exhibits nuclease activity similar to that of typical sugar-nonspecific endonucleases and exonucleases. Biochemical characterization indicated that Ca
2+
alone enhances its activity, which was inhibited by divalent cations, such as Zn
2+
and Mn
2+
. Chelating agents EGTA and EDTA also inhibited nuclease activity. Mycoplasma membrane fractionation and Triton X-114 phase separation showed that MG_186 was a membrane-associated lipoprotein, and electron microscopy revealed its surface membrane location. Incubation of purified human endometrial cell nuclei with rMG_186 resulted in DNA degradation and morphological changes typical of apoptosis. Further, immunofluorescence analysis of rMG_186-treated nuclei indicated that morphological changes were linked to the disintegration of lamin and the internalization of rMG_186. Since
M. genitalium
has the capacity to invade eukaryotic cells and localize to the perinuclear and nuclear region of parasitized target cells, MG_186 has the potential to provide
M. genitalium
, which possesses the smallest genome of any self-replicating cell, with the ability to degrade host nucleic acids both as a source of nucleotide precursors for growth and for pathogenic purposes.
Expressed Genome of
Methylobacillus flagellatus
as Defined through Comprehensive Proteomics and New Insights into Methylotrophy
Authors: Hendrickson Erik L. , Beck David A. C. , Wang Tiansong , Lidstrom Mary E. , Hackett Murray , Chistoserdova Ludmila
Published: July 2010

In recent years, techniques have been developed and perfected for high-throughput identification of proteins and their accurate partial sequencing by shotgun nano-liquid chromatography-tandem mass spectrometry (nano-LC-MS/MS), making it feasible to assess global protein expression profiles in organisms with sequenced genomes. We implemented comprehensive proteomics to assess the expressed portion of the genome of
Methylobacillus flagellatus
during methylotrophic growth. We detected a total of 1,671 proteins (64% of the inferred proteome), including all the predicted essential proteins. Nonrandom patterns observed with the nondetectable proteins appeared to correspond to silent genomic islands, as inferred through functional profiling and genome localization. The protein contents in methylamine- and methanol-grown cells showed a significant overlap, confirming the commonality of methylotrophic metabolism downstream of the primary oxidation reactions. The new insights into methylotrophy include detection of proteins for the
N
-methylglutamate methylamine oxidation pathway that appears to be auxiliary and detection of two alternative enzymes for both the 6-phosphogluconate dehydrogenase reaction (GndA and GndB) and the formate dehydrogenase reaction (FDH1 and FDH4). Mutant analysis revealed that GndA and FDH4 are crucial for the organism's fitness, while GndB and FDH1 are auxiliary.
The ABC Transporter HrtAB Confers Resistance to Hemin Toxicity and Is Regulated in a Hemin-Dependent Manner by the ChrAS Two-Component System inCorynebacterium diphtheriae
Authors: Bibb Lori A. , Schmitt Michael P.
Published: July 2010

Corynebacterium diphtheriae, the causative agent of the severe respiratory disease diphtheria, utilizes hemin and hemoglobin as iron sources for growth in iron-depleted environments. Because of the toxicity of high levels of hemin and iron, these compounds are often tightly regulated in bacterial systems. In this report, we identify and characterize theC. diphtheriae hrtABgenes, which encode a putative ABC type transporter involved in conferring resistance to the toxic effects of hemin. Deletion of thehrtABgenes inC. diphtheriaeproduced increased sensitivity to hemin, which was complemented by a plasmid harboring the clonedhrtABlocus. The HrtAB system was not involved in the uptake and use of hemin as an iron source. ThehrtABgenes are located on theC. diphtheriaegenome upstream from thechrSAoperon, which encodes a previously characterized two-component signal transduction system that regulates gene expression in a heme-dependent manner. ThehrtBpromoter is activated by the ChrAS system in the presence of hemin or hemoglobin, and mutations in thechrSAgenes abolish heme-activated expression from thehrtBpromoter. It was also observed that transcription from thehrtBpromoter is reduced in adtxRdeletion mutant, suggesting that DtxR is required for optimal expression ofhrtAB. Previous studies proposed that the ChrS sensor kinase may be responsive to an environmental signal, such as hemin. We show that specific point mutations in the ChrS N-terminal transmembrane domain result in a reduced ability to activate thehrtBpromoter in the presence of a heme source, suggesting that this putative sensor region is essential for the detection of a signal produced in response to hemin exposure. This study shows that the HrtAB system is required for protection from hemin toxicity and that expression of thehrtABgenes is regulated by the ChrAS two-component system. This study demonstrates a direct correlation between the detection of heme or a heme-associated signal by the N-terminal sensor domain of ChrS and the transcriptional activation of thehrtABgenes.
Massive Gene Duplication Event among Clinical Isolates of the
Mycobacterium tuberculosis
W/Beijing Family
Authors: Domenech Pilar , Kolly Gaëlle S. , Leon-Solis Lizbel , Fallow Ashley , Reed Michael B.
Published: July 2010

As part of our effort to uncover the molecular basis for the phenotypic variation among clinical
Mycobacterium tuberculosis
isolates, we have previously reported that isolates belonging to the W/Beijing lineage constitutively overexpress the DosR-regulated transcriptional program. While generating
dosR
knockouts in two independent W/Beijing sublineages, we were surprised to discover that they possess two copies of
dosR
. This
dosR
amplification is part of a massive genomic duplication spanning 350 kb and encompassing >300 genes. In total, this equates to 8% of the genome being present as two copies. The presence of I
S6110
elements at both ends of the region of duplication, and in the novel junction region, suggests that it arose through unequal homologous recombination of sister chromatids at the IS
6110
sequences. Analysis of isolates representing the major
M. tuberculosis
lineages has revealed that the 350-kb duplication is restricted to the most recently evolved sublineages of the W/Beijing family. Within these isolates, the duplication is partly responsible for the constitutive
dosR
overexpression phenotype. Although the nature of the selection event giving rise to the duplication remains unresolved, its evolution is almost certainly the result of specific selective pressure(s) encountered inside the host. A preliminary
in vitro
screen has failed to reveal a role of the duplication in conferring resistance to common antitubercular drugs, a trait frequently associated with W/Beijing isolates. Nevertheless, this first description of a genetic remodeling event of this nature for
M. tuberculosis
further highlights the potential for the evolution of diversity in this important global pathogen.
In-Depth Profiling of the LiaR Response ofBacillus subtilis
Authors: Wolf Diana , Kalamorz Falk , Wecke Tina , Juszczak Anna , Mäder Ulrike , Homuth Georg , Jordan Sina , Kirstein Janine , Hoppert Michael , Voigt Birgit , Hecker Michael , Mascher Thorsten
Published: July 2010

The Lia system, a cell envelope stress response module ofBacillus subtilis, is comprised of the LiaRS two-component system and a membrane-anchored inhibitor protein, LiaF. It is highly conserved in theFirmicutesbacteria, and all orthologs investigated so far are activated by cell wall antibiotics. In response to envelope stress, the systems inFirmicutescocci induce the expression of a number of genes that are involved in conferring resistance against its inducers. In contrast, a complete picture of the LiaR regulon ofB. subtilisis still missing and no phenotypes could be associated with mutants lacking LiaRS. Here, we performed genome-wide transcriptomic, proteomic, and in-depth phenotypic profiling of constitutive “Lia ON” and “Lia OFF” mutants to obtain a comprehensive picture of the Lia response ofBacillus subtilis. In addition to the known targetsliaIHandyhcYZ-yhdA, we identifiedydhEas a novel gene affected by LiaR-dependent regulation. The results of detailed follow-up gene expression studies, together with proteomic analysis, demonstrate that theliaIHoperon represents the only relevant LiaR target locusin vivo. It encodes a small membrane protein (LiaI) and a phage shock protein homolog (LiaH). LiaH forms large oligomeric rings reminiscent of those described forEscherichia coliPspA orArabidopsis thalianaVipp1. The results of comprehensive phenotype studies demonstrated that the gene products of theliaIHoperon are involved in protecting the cell against oxidative stress and some cell wall antibiotics. Our data suggest that the LiaFSR system ofB. subtilisand, presumably, otherFirmicutesbacilli coordinates a phage shock protein-like response.
Separate DNA Pol II- and Pol IV-Dependent Pathways of Stress-Induced Mutation during Double-Strand-Break Repair in
Escherichia coli
Are Controlled by RpoS
Authors: Frisch Ryan L. , Su Yang , Thornton P. C. , Gibson Janet L. , Rosenberg Susan M. , Hastings P. J.
Published: July 2010

Previous work showed that about 85% of stress-induced mutations associated with DNA double-strand break repair in carbon-starved
Escherichia coli
result from error-prone DNA polymerase IV (Pol IV) (DinB) and that the mutagenesis is controlled by the RpoS stress response, which upregulates
dinB
. We report that the remaining mutagenesis requires high-fidelity Pol II, and that this component also requires RpoS. The results identify a second DNA polymerase contributing to stress-induced mutagenesis and show that RpoS promotes mutagenesis by more than the simple upregulation of
dinB
.
Complete Genome Sequence of
Lactobacillus fermentum
CECT 5716, a Probiotic Strain Isolated from Human Milk
Authors: Jiménez Esther , Langa Susana , Martín Virginia , Arroyo Rebeca , Martín Rocío , Fernández Leónides , Rodríguez Juan M.
Published: July 2010

Lactobacillus fermentum
is a heterofermentative lactic acid bacterium and is frequently isolated from mucosal surfaces of healthy humans.
Lactobacillus fermentum
CECT 5716 is a well-characterized probiotic strain isolated from human milk and, at present, is used in commercial infant formulas. Here, we report the complete and annotated genome sequence of this strain.
Complete Genome Sequence of
Croceibacter atlanticus
HTCC2559
T
Authors: Oh Hyun-Myung , Kang Ilnam , Ferriera Steve , Giovannoni Stephen J. , Cho Jang-Cheon
Published: July 2010

Here we announce the complete genome sequence of
Croceibacter atlanticus
HTCC2559
T
, which was isolated by high-throughput dilution-to-extinction culturing from the Bermuda Atlantic Time Series station in the Western Sargasso Sea. Strain HTCC2559
T
contained genes for carotenoid biosynthesis, flavonoid biosynthesis, and several macromolecule-degrading enzymes. The genome confirmed physiological observations of cultivated
Croceibacter atlanticus
strain HTCC2559
T
, which identified it as an obligate chemoheterotroph.
Predicting Coating Failure using the Central Limit Theorem and Physical Modeling
Authors: Hinderliter Brian , Croll Stuart
Published: July 2010

In service, coatings are assaulted by huge numbers of ultraviolet photons, moisture molecules, pollutant molecules, thermal or other stresses with additional, occasional insults. Individually, these arrive at indeterminate times and locations so either Monte Carlo simulations or the statistics of random processes can be used to estimate the accumulation of damage. These damage results can then be used to calculate the deterioration in coating properties using well-known and robust physical models. In this way, not only can appearance properties like gloss and yellowing be modelled, but also the coating integrity via its fracture toughness or barrier properties, via electrochemical impedance. Additional physical detail or processes may be included, at several points, to produce a more complete predictive simulation or interpretative scheme. Simple calculations of how accelerated weathering affects coating service lifetime also demonstrate how inconsistencies may easily arise between accelerated testing and natural exposure.
A 'Smart' Corrosion-Inhibiting Pigment Based on a Chemical Reaction
Authors: Kendig Martin , Cunningham Michael , Evans Ryan
Published: July 2010

Results show that a solid corrosion inhibitor composed of a mixture of permanganate-containing hydrotalcite and environmentally benign Cr(III) oxide potentially forms the key component of a 'smart' corrosion protective paint. In the presence of a neutral electrolytic environment the solid inhibitor releases the permanganate through an ion exchange mechanism. The permanganate then reacts with the Cr(III) oxide to form soluble Cr(VI) compounds. The activity of Cr(VI) in the aqueous phase slows the oxygen reduction half of corrosion reaction, thereby inhibiting corrosion. A paint made from this pigment contains no hazardous hexavalent chromium unless it is exposed to a corrosive environment.
A Novel Anti-corrosion Calcium Magnesium Polyphosphate Pigment and Its Performance in Aqueous Solutions on Mild Steel
Authors: Yang Y. F. , Scantlebury J. D. , Koroleva E. , Ogawa O. , Tanabe H.
Published: July 2010

A novel calcium magnesium polyphosphate pigment has been compared with a conventional zinc phosphate pigment and examined in two aqueous solutions, a 3.5% sodium chloride solution and a simulated acid rain water. From a variety of techniques it was determined that the novel pigment acted as an effective corrosion inhibitor and its mode of action was probably a mixed cathodic and anodic type. Evidence for a thin protective film on the steel surface was obtained.
A Mathematical Model to Study the Effect of Different Variables on the Potential Distribution in a Damaged Metal/Organic Coating System Using FEM
Authors: Montoya Rodrigo , Barranco Violeta , Carmona Noemi , Galvan Juan C.
Published: July 2010

On the basis of a system formed by mild steel coated with a thin sol-gel coating, a computer program was developed to solve the numerical system obtained from the application of the finite element method (FEM) to the variational formulation of the Laplace bidimensional equation with the proper boundary conditions. The aim was to obtain the potential distribution on a damaged metal/organic coating system after an accelerated cathodic delamination test.
Ways of Increasing the Effectiveness of the Electrochemical Noise Method for Assessment of Organic Coatings on Metal
Authors: Jamali Sina , Mills Douglas J. , Woodcock Christopher
Published: July 2010

The most practically useful arrangement for making Electrochemical Noise Measurements is NOCS. Previously reported work using NOCS suggested that the arrangement had somewhat increased sensitivity to error (drift, spikes etc) in the value of noise resistance (Rn) that was calculated. The current work looked to address this by using an improved data analysis approach using a drift removal programme. Also Rsn (spectral noise resistance at 0.002Hz) has been calculated using either the MEM or FFT methods and compared with (Rn)To investigate possible ambiguity arising from interrogating three separate areas, samples with known values of resistance (high, medium and low) were joined in combinations and Rn measured. It was found that the cell connected to the reference input tended to dominate ie potential noise prevails over current noise. With some refinement, the NOCS method should soon be a practical method for field application.
Failure Mechanisms of PVD Films on Organic Coatings
Authors: Bao Yuqing , Gao Jiming , Gawne David T.
Published: July 2010

Physical vapour deposited (PVD) films have many benefits as coatings on metals but provide little corrosion resistance or surface levelling of the underlying substrate. This research investigates the use of epoxy undercoats for PVD films as a means of overcoming these deficiencies. Experimental trials showed that sputtered titanium films and the epoxy undercoats both cracked severely as a result of the PVD process. A quantitative model has been developed for the calculation of residual stress in a three-layer film-epoxy-substrate system. The model and experimental trials showed that cracking originated from thermal stresses developed in the titanium-epoxy-aluminium system as a result of PVD. Instability and cracking initiated where pores intersected the film-coating interface. Increasing the baking temperature to 210oC raised the tensile strength of the epoxy sufficiently to avoid instability due to residual stress and produce crack-free PVD titanium films.
A Novel Anti-corrosion Calcium Magnesium Polyphosphate Pigment and Its Performance in Aqueous Solutions on Mild Steel when Coupled to Metallic Zinc
Authors: Yang Y. F. , Scantlebury J. D. , Koroleva E. , Ogawa O. , Tanabe H.
Published: July 2010

A novel calcium magnesium polyphosphate pigment has been studied as a corrosion inhibitor for mild steel in two aqueous solutions, a 3.5% sodium chloride solution and an artificial acid rain water. To simulate the situation where the novel pigment was added to a zinc pigmented coating, the mild steel samples were connected to a pure zinc sheet. A significant improvement in performance was observed compared with no zinc. It was shown that the effect of the zinc was a synergistic combination of lowered potential and the presence of zinc ions which enhanced the cathodic inhibitive properties of the pigment system.
Biotic Sol-Gel Coating for the Inhibition of Corrosion in Seawater
Authors: Gittens Jeanette E. , Wang Heming , Smith Thomas J. , Akid Robert , Greenfield David
Published: July 2010

In marine environments corrosion is exacerbated by formation of destructive biofilms containing sulphate-reducing bacteria, which promote corrosion by forming corrosive species, such as H2S. Corrosion-causing biofilms are often resistant to inactivation by biocides since the biofilm bacteria are protected by a matrix of exopolymeric substances (EPS). Paradoxically, a biofilm of the endospore-forming Paenibacillus polymyxa can actually inhibit corrosion. Sol gel technology and immobilized microorganisms have been combined in a unique coating that inhibits corrosion on aluminium alloys, being low-cost, effective and environmentally friendly. Viability studies show that P. polymyxa endospores can withstand solvent concentration of up to 50% and an acid concentration of up to 1.5M and germinate within a biotic sol-gel coating. Electrochemical impedance spectroscopy and linear polarization resistance tests, in addition to an extended field trial, have shown that the endospore-loaded coatings show resistance to corrosion and biofilm formation relative to coatings without added endospores.
On the Oxidation Products in Mg-Rich Primers: I. the Case of Pure Mg Pigment
Authors: Wang Jinhai , Bierwagen Gordon P. , Xu Hong , Battocchi Dante
Published: July 2010

As a complement to the mechanism study of Mg-rich primer protecting aerospace Al alloys (especially AA 2024-T3) from corrosion, the oxidation products produced during Prohesion exposure as well as their distribution in primer films were analyzed by multiple surface analysis approaches. On cross-section samples prepared with a microtome technique, the major Mg oxidation/corrosion product was identified as hydromagnesite (Mg5(CO3)4(OH)2•5H2O) by XPS and Raman spectroscopy. Furthermore, through SEM and confocal microscopy, it was observed that the oxidation products were mainly accumulated in the voids presented in coating film. Based on these results obtained, the possible corrosion protection mechanism of Mg-rich primer was suggested.
Tailored Sol-Gel Coatings as Environmentally Friendly Pre-Treatments for Corrosion Protection
Authors: Barranco Violeta , Carmona Noemi , Villegas Maria A. , Galvan Juan C.
Published: July 2010

Concerning the development of new alternatives for replacement of the toxic chromate surface treatments, the aim of the present study is to design and produce new electrochemically active sol-gel thin films of different composition in the ZrO2-SiO2 system, to act as first chemically active layer for pre-treatments of metallic painted surfaces. For its evaluation, a new methodology combining accelerated test, and global and localised electrochemical impedance spectroscopy (EIS) is proposed. For the localised measurements, a new mini-cell system (MCS) is introduced. An active protection mechanism at the cathodic sites underneath the sol-gel thin film was observed. This inhibitor effect is associated with a self-sealing mechanism by the hydrolysis of Zr4+-ions chemically incorporated in the sol-gel network. After the accelerated test, these Zr4+-ions tend to form links different from Si-O-Zr (i.e. zirconium hydroxides and/or oxides). Such new insoluble compounds plug the pores and defects in the sol-gel coatings increasing the low frequency impedance during immersion in NaCl aqueous solutions.