bluuebunny/crossref_metadata_2025 huggingface dataset:
Stress-Time-Temperature-Humidity Effects on Demination of Graphite/Epoxy Laminates
Authors: Garg Amar C.
Published: September 2009

The effect of sustained load and hygrothermal environments on Mode I delamination behavior of T300/934 unidirectional graphite/epoxy laminates has been studied. Several double cantilever beam specimens were subjected to constant load in presence of various hygrothermal conditions either for short duration (a few minutes to a few hours) or for long duration (several months). The pre-loaded specimens were then tested to determine delamination behavior. It is indicated that the crack growth does not occur as a result of exposure to load and environment. On the contrary, an increase in fracture toughness around the crack tip is observed for pre-loaded specimens and the increase is seen to depend on exposure duration and environment. In general, the loaded specimens exposed to water show a significant increase in fracture toughness. The failed specimens were examined by SEM and topographical features are noted. The crack tip exposed to high stresses in presence of environment show distinguishable features.
Evaluation of Bodner-Partom Model Parameters at High Strain Rate
Authors: Rajendran A. M. , Bless S. J. , Dawicke D. S.
Published: September 2009

The objective of this paper is to model the high strain rate material behavior of metals using Bodner-Partom visco-plastic constitutive model. A unique algorithm has been developed to evaluate the model parameters from the split Hopkinson Bar and plane plate impact tests data. The model parameters were successfully determined for the 6061-T6 aluminum, 1020 steel, and HY 100 steel. Using the evaluated model parameters, the test data obtained from an unusually wide range of stress states for these three metals were successfully modeled.
Complexity in Transcription Control at the Activation Domain–Mediator Interface
Authors: Balamotis Michael A. , Pennella Mario A. , Stevens Jennitte L. , Wasylyk Bohdan , Belmont Andrew S. , Berk Arnold J.
Published: September 2009

Transcriptional activation kinetics varies in different cell types in part because related transcription factors make alternative mediator interactions.
Novel p47

phox

-Related Organizers Regulate Localized NADPH Oxidase 1 (Nox1) Activity
Authors: Gianni Davide , Diaz Begoña , Taulet Nicolas , Fowler Bruce , Courtneidge Sara A. , Bokoch Gary M.
Published: September 2009

Tks proteins, which are Src substrates, control the localized production of reactive oxygen species by Nox.
AIMing 2 Detect Foreign DNA
Authors: Krieg Arthur M.
Published: September 2009

AIM2 is a receptor for cytoplasmic double-stranded DNA and induces the formation of an IL-1β–secreting inflammasome.
Calcium Oxalate Biomineralization by
Piloderma fallax
in Response to Various Levels of Calcium and Phosphorus
Authors: Tuason Melissa Marie S. , Arocena Joselito M.
Published: September 2009

Piloderma fallax
is an ectomycorrhizal fungus commonly associated with several conifer and hardwood species. We examined the formation of calcium oxalate crystals by
P. fallax
in response to calcium (0.0, 0.1, 0.5, 1, and 5 mM) and phosphorus (0.1 and 6 mM) additions in modified Melin-Norkrans agar medium. Both calcium and phosphorus supplementation significantly affected the amount of calcium oxalate formed. More calcium oxalate was formed at high P levels. Concentrations of soluble oxalate in the fungus and medium were higher at low P levels. There was a strong positive linear relationship between Ca level and calcium oxalate but only under conditions of phosphorus limitation. Calcium oxalate crystals were identified as the monohydrate form (calcium oxalate monohydrate [COM] whewellite) by X-ray diffraction analysis. Prismatic, styloid, and raphide forms of the crystals, characteristic COM, were observed on the surface of fungal hyphae by scanning electron microscopy.
P. fallax
may be capable of dissolving hyphal calcium oxalate under conditions of limited Ca. The biomineralization of calcium oxalate by fungi may be an important step in the translocation and cycling of Ca and P in soil.
Rumen Microbiome Composition Determined Using Two Nutritional Models of Subacute Ruminal Acidosis
Authors: Khafipour Ehsan , Li Shucong , Plaizier Jan C. , Krause Denis O.
Published: September 2009

Subacute ruminal acidosis (SARA) is a metabolic disease in dairy cattle that occurs during early and mid-lactation and has traditionally been characterized by low rumen pH, but lactic acid does not accumulate as in acute lactic acid acidosis. It is hypothesized that factors such as increased gut permeability, bacterial lipopolysaccharides, and inflammatory responses may have a role in the etiology of SARA. However, little is known about the nature of the rumen microbiome during SARA. In this study, we analyzed the microbiome of 64 rumen samples taken from eight lactating Holstein dairy cattle using terminal restriction fragment length polymorphisms (TRFLP) of 16S rRNA genes and real-time PCR. We used rumen samples from two published experiments in which SARA had been induced with either grain or alfalfa pellets. The results of TRFLP analysis indicated that the most predominant shift during SARA was a decline in gram-negative
Bacteroidetes
organisms. However, the proportion of
Bacteroidetes
organisms was greater in alfalfa pellet-induced SARA than in mild or severe grain-induced SARA (35.4% versus 26.0% and 16.6%, respectively). This shift was also evident from the real-time PCR data for
Prevotella albensis
,
Prevotella brevis
, and
Prevotella ruminicola
, which are members of the
Bacteroidetes
. The real-time PCR data also indicated that severe grain-induced SARA was dominated by
Streptococcus bovis
and
Escherichia coli
, whereas mild grain-induced SARA was dominated by
Megasphaera elsdenii
and alfalfa pellet-induced SARA was dominated by
P. albensis
. Using discriminant analysis, the severity of SARA and degree of inflammation were highly correlated with the abundance of
E. coli
and not with lipopolysaccharide in the rumen. We thus suspect that
E. coli
may be a contributing factor in disease onset.
Acyl-Homoserine Lactones Can Induce Virus Production in Lysogenic Bacteria: an Alternative Paradigm for Prophage Induction
Authors: Ghosh Dhritiman , Roy Krishnakali , Williamson Kurt E. , Srinivasiah Sharath , Wommack K. Eric , Radosevich Mark
Published: September 2009

Prophage typically are induced to a lytic cycle under stressful environmental conditions or when the host's survival is threatened. However, stress-independent, spontaneous induction also occurs in nature and may be cell density dependent, but the in vivo signal(s) that can trigger induction is unknown. In the present study, we report that acyl-homoserine lactones (AHL), the essential signaling molecules of quorum sensing in many gram-negative bacteria, can trigger phage production in soil and groundwater bacteria. This phenomenon also was operative in a λ lysogen of
Escherichia coli
. In model coculture systems, we monitored the real-time AHL production from
Pseudomonas aeruginosa
PAO1 using an AHL bioluminescent sensor and demonstrated that λ-prophage induction in
E. coli
was correlated with AHL production. As a working model in
E. coli
, we show that the induction responses of λ with AHL remained unaffected when
recA
was deleted, suggesting that this mechanism does not involve an SOS response. In the same λ lysogen we also demonstrated that
sdiA
, the AHL receptor, and
rcsA
, a positive transcriptional regulator of exopolysaccharide synthesis, are involved in the AHL-mediated induction process. These findings relate viral reproduction to chemical signals associated with high host cell abundance, suggesting an alternative paradigm for prophage induction.
Role of the
Streptococcus mutans irvA
Gene in GbpC-Independent, Dextran-Dependent Aggregation and Biofilm Formation
Authors: Zhu Min , Ajdić Dragana , Liu Yuan , Lynch David , Merritt Justin , Banas Jeffrey A.
Published: September 2009

Dextran-dependent aggregation (DDAG) of
Streptococcus mutans
is an in vitro phenomenon that is believed to represent a property of the organism that is beneficial for sucrose-dependent biofilm development. GbpC, a cell surface glucan-binding protein, is responsible for DDAG in
S. mutans
when cultured under defined stressful conditions. Recent reports have described a putative transcriptional regulator gene,
irvA
, located just upstream of
gbpC
, that is normally repressed by the product of an adjacent gene,
irvR
. When repression of
irvA
is relieved, there is a resulting increase in the expression of GbpC and decreases in competence and synthesis of the antibiotic mutacin I. This study examined the role of
irvA
in DDAG and biofilm formation by engineering strains that overexpressed
irvA
(IrvA+) on an extrachromosomal plasmid. The IrvA+ strain displayed large aggregation particles that did not require stressful growth conditions. A novel finding was that overexpression of
irvA
in a
gbpC
mutant background retained a measure of DDAG, albeit very small aggregation particles. Biofilms formed by the IrvA+ strain in the parental background possessed larger-than-normal microcolonies. In a
gbpC
mutant background, the overexpression of
irvA
reversed the fragile biofilm phenotype normally associated with loss of GbpC. Real-time PCR and Northern blot analyses found that expression of
gbpC
did not change significantly in the IrvA+ strain but expression of
spaP
, encoding the major surface adhesin P1, increased significantly. Inactivation of
spaP
eliminated the small-particle DDAG. The results suggest that IrvA promotes DDAG not only by GbpC, but also via an increase in P1.
Molecular Characterization of Potential Nitrogen Fixation by Anaerobic Methane-Oxidizing Archaea in the Methane Seep Sediments at the Number 8 Kumano Knoll in the Kumano Basin, Offshore of Japan
Authors: Miyazaki Junichi , Higa Ryosaku , Toki Tomohiro , Ashi Juichiro , Tsunogai Urumu , Nunoura Takuro , Imachi Hiroyuki , Takai Ken
Published: September 2009

The potential for microbial nitrogen fixation in the anoxic methane seep sediments in a mud volcano, the number 8 Kumano Knoll, was characterized by molecular phylogenetic analyses. A total of 111 of thenifH(a gene coding a nitrogen fixation enzyme, Fe protein) clones were obtained from different depths of the core sediments, and the phylogenetic analysis of the clones indicated the genetic diversity ofnifHgenes. The predominant group detected (methane seep group 2), representing 74% of clonal abundance, was phylogenetically related to thenifHsequences obtained from theMethanosarcinaspecies but was most closely related to thenifHsequences potentially derived from the anoxic methanotrophic archaea (ANME-2 archaea). The recovery of thenifgene clusters including thenifHsequences of the methane seep group 2 and the subsequent reverse transcription-PCR detection of thenifDandnifHgenes strongly suggested that the genetic components of the gene clusters would be operative for the in situ assimilation of molecular nitrogen (N2) by the host microorganisms. DNA-based quantitative PCR of the archaeal 16S rRNA gene, the group-specificmcrA(a gene encoding the methyl-coenzyme M reductase α subunit) gene, and thenifDandnifHgenes demonstrated the similar distribution patterns of the archaeal 16S rRNA gene, themcrAgroups c-d and e, and thenifDandnifHgenes through the core sediments. These results supported the idea that the anoxic methanotrophic archaea ANME-2c could be the microorganisms hosting thenifgene clusters and could play an important role in not only the in situ carbon (methane) cycle but also the nitrogen cycle in subseafloor sediments.
Effect of Carbohydrate Composition in Barley and Oat Cultivars on Microbial Ecophysiology and Proliferation of
Salmonella enterica
in an In Vitro Model of the Porcine Gastrointestinal Tract
Authors: Pieper Robert , Bindelle Jérôme , Rossnagel Brian , Van Kessel Andrew , Leterme Pascal
Published: September 2009

The influence of the carbohydrate (CHO) composition of cereal cultivars on microbial ecophysiology was studied using an in vitro model of the porcine gastrointestinal tract. Ten hull-less barley cultivars, six barley cultivars with hulls, six oat cultivars, and six oat groats that differed in β-glucan, nonstarch polysaccharide (NSP), and starch contents and starch type were hydrolyzed enzymatically and incubated for 72 h with pig feces. Fermentation kinetics were modeled, and microbial compositions and short-chain fatty acid (SCFA) profiles were analyzed using terminal restriction fragment length polymorphism and gas chromatography. Cluster analysis and canonical ordination revealed different effects on fermentation and microbial ecology depending on the type of CHO and cultivar. First, in cultivars of barley with hulls and oats, the cellulose and insoluble NSP contents (i) increased
Ruminococcus flavefaciens
-like and
Clostridium xylanolyticum
-like phylotypes, (ii) increased acetate production, and (iii) decreased fermentation activity. Second, in hull-less barley cultivars the β-glucan, amylose, amylopectin, crude protein, and soluble NSP contents determined the microbial community composition and activity as follows: (i) the amylose contents of the hull-less barley varieties increased the butyrate production and the abundance of
Clostridium
butyricum
-like phylotypes, (ii) the β-glucan content determined the total amounts of SCFA, and (iii) the amylopectin and starch contents affected the abundance of
Clostridium
ramosum
-like phylotypes, members of
Clostridium
cluster XIVa, and
Bacteroides
-like bacteria. Finally, the effect of CHO on proliferation of
Salmonella enterica
in the model was determined.
Salmonella
cell counts were not affected, but the relative proportion of
Salmonella
decreased with hull-less barley cultivars and increased with oat cultivars as revealed by quantitative PCR. Our results shed light on the complex interactions of cereal CHO with intestinal bacterial ecophysiology and the possible impact on host health.
Comparison of Bacterioneuston and Bacterioplankton Dynamics during a Phytoplankton Bloom in a Fjord Mesocosm
Authors: Cunliffe Michael , Whiteley Andrew S. , Newbold Lindsay , Oliver Anna , Schäfer Hendrik , Murrell J. Colin
Published: September 2009

The bacterioneuston is the community of
Bacteria
present in surface microlayers, the thin surface film that forms the interface between aquatic environments and the atmosphere. In this study we compared bacterial cell abundances and bacterial community structures of the bacterioneuston and the bacterioplankton (from the subsurface water column) during a phytoplankton bloom mesocosm experiment. Bacterial cell abundance, determined by flow cytometry, followed a typical bacterioplankton response to a phytoplankton bloom, with
Synechococcus
and high-nucleic acid content (HNA) bacterial cell numbers initially falling, probably due to selective protist grazing. Subsequently HNA and low-nucleic acid content bacterial cells increased in abundance, but
Synechococcus
cells did not. There was no significant difference between bacterioneuston and bacterioplankton cell abundances during the experiment. Conversely, distinct and consistent differences between the bacterioneuston and the bacterioplankton community structures were observed. This was monitored simultaneously by
Bacteria
16S rRNA gene terminal restriction fragment length polymorphism and denaturing gradient gel electrophoresis. The conserved patterns of community structure observed in all of the mesocosms indicate that the bacterioneuston is distinctive and nonrandom.
Impact of Host Developmental Age on the Transcriptome of the Symbiotic Bacterium
Buchnera aphidicola
in the Pea Aphid (
Acyrthosiphon pisum
)
Authors: Bermingham John , Rabatel Andréane , Calevro Federica , Viñuelas José , Febvay Gérard , Charles Hubert , Douglas Angela , Wilkinson Tom
Published: September 2009

Of the 617 genes from
Buchnera aphidicola
, the obligate bacterial symbiont of the pea aphid, 23% were differentially expressed in embryos compared to adults. Genes involved in flagellar apparatus and riboflavin synthesis exhibited particularly robust upregulation in embryos, suggesting functional differences between the symbiosis in the adult and embryo insect.
Population Structure of the Lyme Borreliosis Spirochete
Borrelia burgdorferi
in the Western Black-Legged Tick (
Ixodes pacificus
) in Northern California
Authors: Girard Yvette A. , Travinsky Bridgit , Schotthoefer Anna , Fedorova Natalia , Eisen Rebecca J. , Eisen Lars , Barbour Alan G. , Lane Robert S.
Published: September 2009

Factors potentially contributing to the lower incidence of Lyme borreliosis (LB) in the far-western than in the northeastern United States include tick host-seeking behavior resulting in fewer human tick encounters, lower densities of
Borrelia burgdorferi
-infected vector ticks in peridomestic environments, and genetic variation among
B. burgdorferi
spirochetes to which humans are exposed. We determined the population structure of
B. burgdorferi
in over 200 infected nymphs of the primary bridging vector to humans,
Ixodes pacificus
, collected in Mendocino County, CA. This was accomplished by sequence typing the spirochete lipoprotein
ospC
and the 16S-23S rRNA intergenic spacer (IGS). Thirteen
ospC
alleles belonging to 12 genotypes were found in California, and the two most abundant,
ospC
genotypes H3 and E3, have not been detected in ticks in the Northeast. The most prevalent
ospC
and IGS biallelic profile in the population, found in about 22% of ticks, was a new
B. burgdorferi
strain defined by
ospC
genotype H3. Eight of the most common
ospC
genotypes in the northeastern United States, including genotypes I and K that are associated with disseminated human infections, were absent in Mendocino County nymphs.
ospC
H3 was associated with hardwood-dominated habitats where western gray squirrels, the reservoir host, are commonly infected with LB spirochetes. The differences in
B. burgdorferi
population structure in California ticks compared to the Northeast emphasize the need for a greater understanding of the genetic diversity of spirochetes infecting California LB patients.
Gene Cloning, Protein Characterization, and Alteration of Product Selectivity for the Trehalulose Hydrolase and Trehalulose Synthase from “
Pseudomonas mesoacidophila
” MX-45
Authors: Watzlawick Hildegard , Mattes Ralf
Published: September 2009

The naturally occurring structural isomer of sucrose, trehalulose, is produced by sucrose isomerase (SI). Screening of chromosomal DNA from “
Pseudomonas mesoacidophila
” MX-45 with an SI-specific probe facilitated the cloning of two adjacent gene homologs,
mutA
and
mutB
. Both genes were expressed separately in
E
scherichia
c
oli
, and their enzyme products were characterized. MutA hydrolyzed the substrates trehalulose, isomaltulose, and sucrose into glucose and fructose. Due to its highest activity on trehalulose, MutA was referred to as trehalulase.
m
utB
encodes the SI (trehalulose synthase) and catalyzes the isomerization of sucrose to mainly trehalulose. From Northern blot analysis it is apparent that the
mutB
gene is not transcribed as part of an operon and was transcriptionally upregulated when
P. mesoacidophila
MX-45 cells were grown in sucrose medium, whereas under investigated conditions no transcript for
mut
A
was detected. Mutants of
mutB
were created by a random mutagenesis approach in order to alter the product specificity of MutB. Two types of mutants have emerged, one type that prefers the hydrolytic reaction on sucrose and another type that still acts as an SI but with a significant shift in the product from trehalulose to isomaltulose. The hydrolytic character of MutB R311C was demonstrated through its higher catalytic efficiency for glucose production over trehalulose production. MutB D442N favored the transfer reaction, with an isomer preference for isomaltulose.
Deformed Wing Virus Implicated in Overwintering Honeybee Colony Losses
Authors: Highfield Andrea C. , El Nagar Aliya , Mackinder Luke C. M. , Noël Laure M.-L. J. , Hall Matthew J. , Martin Stephen J. , Schroeder Declan C.
Published: September 2009

The worldwide decline in honeybee colonies during the past 50 years has often been linked to the spread of the parasitic mite
Varroa destructor
and its interaction with certain honeybee viruses. Recently in the United States, dramatic honeybee losses (colony collapse disorder) have been reported; however, there remains no clear explanation for these colony losses, with parasitic mites, viruses, bacteria, and fungal diseases all being proposed as possible candidates. Common characteristics that most failing colonies share is a lack of overt disease symptoms and the disappearance of workers from what appears to be normally functioning colonies. In this study, we used quantitative PCR to monitor the presence of three honeybee viruses, deformed wing virus (DWV), acute bee paralysis virus (ABPV), and black queen cell virus (BQCV), during a 1-year period in 15 asymptomatic, varroa mite-positive honeybee colonies in Southern England, and 3 asymptomatic colonies confirmed to be varroa mite free. All colonies with varroa mites underwent control treatments to ensure that mite populations remained low throughout the study. Despite this, multiple virus infections were detected, yet a significant correlation was observed only between DWV viral load and overwintering colony losses. The long-held view has been that DWV is relatively harmless to the overall health status of honeybee colonies unless it is in association with severe varroa mite infestations. Our findings suggest that DWV can potentially act independently of varroa mites to bring about colony losses. Therefore, DWV may be a major factor in overwintering colony losses.
Suggestive Evidence for Darwinian Selection against Asparagine-Linked Glycans of Plasmodium falciparum and Toxoplasma gondii
Authors: Bushkin G. Guy , Ratner Daniel M. , Cui Jike , Banerjee Sulagna , Duraisingh Manoj T. , Jennings Cameron V. , Dvorin Jeffrey D. , Gubbels Marc-Jan , Robertson Seth D. , Steffen Martin , O'Keefe Barry R. , Robbins Phillips W. , Samuelson John
Published: September 2009

We are interested in asparagine-linked glycans (N-glycans) ofPlasmodium falciparumandToxoplasma gondii, because their N-glycan structures have been controversial and because we hypothesize that there might be selection against N-glycans in nucleus-encoded proteins that must pass through the endoplasmic reticulum (ER) prior to threading into the apicoplast. In support of our hypothesis, we observed the following. First, in protists with apicoplasts, there is extensive secondary loss of Alg enzymes that make lipid-linked precursors to N-glycans.Theileriamakes no N-glycans, andPlasmodiummakes a severely truncated N-glycan precursor composed of one or two GlcNAc residues. Second, secreted proteins ofToxoplasma, which uses its own 10-sugar precursor (Glc3Man5GlcNAc2) and the host 14-sugar precursor (Glc3Man9GlcNAc2) to make N-glycans, have very few sites for N glycosylation, and there is additional selection against N-glycan sites in its apicoplast-targeted proteins. Third, while the GlcNAc-bindingGriffonia simplicifolialectin II labels ER, rhoptries, and surface of plasmodia, there is no apicoplast labeling. Similarly, the antiretroviral lectin cyanovirin-N, which binds to N-glycans ofToxoplasma, labels ER and rhoptries, but there is no apicoplast labeling. We conclude that possible selection against N-glycans in protists with apicoplasts occurs by eliminating N-glycans (Theileria), reducing their length (Plasmodium), or reducing the number of N-glycan sites (Toxoplasma). In addition, occupation of N-glycan sites is markedly reduced in apicoplast proteins versus some secretory proteins in bothPlasmodiumandToxoplasma.
Mapping of the
Saccharomyces cerevisiae
Oxa1-Mitochondrial Ribosome Interface and Identification of MrpL40, a Ribosomal Protein in Close Proximity to Oxa1 and Critical for Oxidative Phosphorylation Complex Assembly
Authors: Jia Lixia , Kaur Jasvinder , Stuart Rosemary A.
Published: September 2009

The Oxa1 protein plays a central role in facilitating the cotranslational insertion of the nascent polypeptide chains into the mitochondrial inner membrane. Mitochondrially encoded proteins are synthesized on matrix-localized ribosomes which are tethered to the inner membrane and in physical association with the Oxa1 protein. In the present study we used a chemical cross-linking approach to map the
Saccharomyces cerevisiae
Oxa1-ribosome interface, and we demonstrate here a close association of Oxa1 and the large ribosomal subunit protein, MrpL40. Evidence to indicate that a close physical and functional relationship exists between MrpL40 and another large ribosomal protein, the Mrp20/L23 protein, is also provided. MrpL40 shares sequence features with the bacterial ribosomal protein L24, which like Mrp20/L23 is known to be located adjacent to the ribosomal polypeptide exit site. We propose therefore that MrpL40 represents the
Saccharomyces cerevisiae
L24 homolog. MrpL40, like many mitochondrial ribosomal proteins, contains a C-terminal extension region that bears no similarity to the bacterial counterpart. We show that this C-terminal mitochondria-specific region is important for MrpL40's ability to support the synthesis of the correct complement of mitochondrially encoded proteins and their subsequent assembly into oxidative phosphorylation complexes.
A Point Mutation in the Sensor Histidine Kinase SaeS of
Staphylococcus aureus
Strain Newman Alters the Response to Biocide Exposure
Authors: Schäfer Daniel , Lâm Thiên-Trí , Geiger Tobias , Mainiero Markus , Engelmann Susanne , Hussain Muzaffar , Bosserhoff Armin , Frosch Matthias , Bischoff Markus , Wolz Christiane , Reidl Joachim , Sinha Bhanu
Published: September 2009

Staphylococcus aureus
reacts to changing environmental conditions such as heat, pH, and chemicals through global regulators such as the
sae
(
S. aureus
exoprotein expression) two-component signaling system. Subinhibitory concentrations of some antibiotics were shown to increase virulence factor expression. Here, we investigated the
S. aureus
stress response to sublethal concentrations of a commonly used biocide (Perform), by real-time quantitative PCR (qRT-PCR), promoter activity assay, sodium dodecyl sulfate (SDS)-polyacrylamide gel electrophoresis, and a flow cytometric invasion assay. Perform, acting through the production of reactive oxygen species, generally downregulated expression of extracellular proteins in strains 6850, COL, ISP479C but upregulated these proteins in strain Newman. Upregulated proteins were
sae
dependent. The Perform component SDS, but not paraquat (another oxygen donor), mimicked the biocide effect. Eap (extracellular adherence protein) was most prominently augmented. Upregulation of
eap
and
sae
was confirmed by qRT-PCR. Promoter activity of
sae
P1 was increased by Perform and SDS. Both substances enhanced cellular invasiveness, by 2.5-fold and 3.2-fold, respectively. Increased invasiveness was dependent on Eap and the
sae
system, whereas
agr
,
sarA
,
sigB
, and fibronectin-binding proteins had no major effect in strain Newman. This unique response pattern was due to a point mutation in SaeS (the sensor histidine kinase), as demonstrated by allele swapping. Newman
saePQRS
ISP479C
behaved like ISP479C, whereas
saePQRS
Newman
rendered ISP479C equally responsive as Newman. Taken together, the findings indicate that a point mutation in SaeS of strain Newman was responsible for increased expression of Eap upon exposure to sublethal Perform and SDS concentrations, leading to increased Eap-dependent cellular invasiveness. This may be important for understanding the regulation of virulence in
S. aureus
.
LuxS-Based Quorum Sensing Does Not Affect the Ability ofSalmonella entericaSerovar Typhimurium To Express the SPI-1 Type 3 Secretion System, Induce Membrane Ruffles, or Invade Epithelial Cells
Authors: Perrett Charlotte A. , Karavolos Michail H. , Humphrey Suzanne , Mastroeni Pietro , Martinez-Argudo Isabel , Spencer Hannah , Bulmer David , Winzer Klaus , McGhie Emma , Koronakis Vassilis , Williams Paul , Khan C. M. Anjam , Jepson Mark A.
Published: September 2009

Bacterial species can communicate by producing and sensing small autoinducer molecules by a process known as quorum sensing.Salmonella entericaproduces autoinducer 2 (AI-2) via theluxSsynthase gene, which is used by some bacterial pathogens to coordinate virulence gene expression with population density. We investigated whether theluxSgene might affect the ability ofSalmonella entericaserovar Typhimurium to invade epithelial cells. No differences were found between the wild-type strain ofS. Typhimurium, SL1344, and its isogenicluxSmutant with respect to the number and morphology of the membrane ruffles induced or their ability to invade epithelial cells. The dynamics of the ruffling process were also similar in the wild-type strain (SL1344) and theluxSmutant. Furthermore, comparing the Salmonella pathogenicityisland 1 (SPI-1) type 3 secretion profiles of wild-type SL1344 and theluxSmutant by Western blotting and measuring the expression of a single-copy green fluorescent protein fusion to theprgH(an essential SPI-1 gene) promoter indicated that SPI-1 expression and activity are similar in the wild-type SL1344 andluxSmutant. Genetic deletion ofluxSdid not alter the virulence ofS. Typhimurium in the mouse model, and therefore, it appears thatluxSdoes not play a significant role in regulating invasion ofSalmonellain vitro or in vivo.
The Catalase-Peroxidase KatG Is Required for Virulence of
Xanthomonas campestris
pv. campestris in a Host Plant by Providing Protection against Low Levels of H
2
O
2
Authors: Jittawuttipoka Thichakorn , Buranajitpakorn Sarinya , Vattanaviboon Paiboon , Mongkolsuk Skorn
Published: September 2009

Xanthomonas campestris
pv. campestris
katG
encodes a catalase-peroxidase that has a role in protecting the bacterium against micromolar concentrations of H
2
O
2
. A knockout mutation in
katG
that causes loss of catalase-peroxidase activity correlates with increased susceptibility to H
2
O
2
and a superoxide generator and is avirulent in a plant model system.
katG
expression is induced by oxidants in an OxyR-dependent manner.
Comparative Genomics of Ethanolamine Utilization
Authors: Tsoy Olga , Ravcheev Dmitry , Mushegian Arcady
Published: September 2009

Ethanolamine can be used as a source of carbon and nitrogen by phylogenetically diverse bacteria. Ethanolamine-ammonia lyase, the enzyme that breaks ethanolamine into acetaldehyde and ammonia, is encoded by the gene tandem
eutBC
. Despite extensive studies of ethanolamine utilization in
Salmonella enterica
serovar Typhimurium, much remains to be learned about EutBC structure and catalytic mechanism, about the evolutionary origin of ethanolamine utilization, and about regulatory links between the metabolism of ethanolamine itself and the ethanolamine-ammonia lyase cofactor adenosylcobalamin. We used computational analysis of sequences, structures, genome contexts, and phylogenies of ethanolamine-ammonia lyases to address these questions and to evaluate recent data-mining studies that have suggested an association between bacterial food poisoning and the diol utilization pathways. We found that EutBC evolution included recruitment of a TIM barrel and a Rossmann fold domain and their fusion to N-terminal α-helical domains to give EutB and EutC, respectively. This fusion was followed by recruitment and occasional loss of auxiliary ethanolamine utilization genes in
Firmicutes
and by several horizontal transfers, most notably from the firmicute stem to the
Enterobacteriaceae
and from
Alphaproteobacteria
to
Actinobacteria
. We identified a conserved DNA motif that likely represents the EutR-binding site and is shared by the ethanolamine and cobalamin operons in several enterobacterial species, suggesting a mechanism for coupling the biosyntheses of apoenzyme and cofactor in these species. Finally, we found that the food poisoning phenotype is associated with the structural components of metabolosome more strongly than with ethanolamine utilization genes or with paralogous propanediol utilization genes per se.
Characterization of the Sporulation Initiation Pathway of
Clostridium difficile
and Its Role in Toxin Production
Authors: Underwood Sarah , Guan Shuang , Vijayasubhash Vinod , Baines Simon D. , Graham Luke , Lewis Richard J. , Wilcox Mark H. , Stephenson Keith
Published: September 2009

Clostridium difficile
is responsible for significant mortality and morbidity in the hospitalized elderly.
C. difficile
spores are infectious and are a major factor contributing to nosocomial transmission. The Spo0A response regulator is the master regulator for sporulation initiation and can influence many other cellular processes. Using the ClosTron gene knockout system, we inactivated genes encoding Spo0A and a putative sporulation-associated sensor histidine kinase in
C. difficile
. Inactivation of
spo0A
resulted in an asporogeneous phenotype, whereas inactivation of the kinase reduced
C. difficle
sporulation capacity by 3.5-fold, suggesting that this kinase also has a role in sporulation initiation. Furthermore, inactivation of either
spo0A
or the kinase resulted in a marked defect in
C. difficile
toxin production. Therefore, Spo0A and the signaling pathway that modulates its activity appear to be involved in regulation of toxin synthesis in
C. difficile
. In addition, Spo0A was directly phosphorylated by a putative sporulation-associated kinase, supporting the hypothesis that sporulation initiation in
C. difficile
is controlled by a two-component signal transduction system rather than a multicomponent phosphorelay. The implications of these findings for
C. difficile
sporulation, virulence, and transmission are discussed.
Evolutionary Dynamics ofompA, the Gene Encoding theChlamydia trachomatisKey Antigen
Authors: Nunes Alexandra , Borrego Maria J. , Nunes Baltazar , Florindo Carlos , Gomes João P.
Published: September 2009

Chlamydia trachomatisis the trachoma agent and causes most bacterial sexually transmitted infections worldwide. Its major outer membrane protein (MOMP) is a well-known porin and adhesin and is the dominant antigen. So far, investigation of MOMP variability has been focused mainly on molecular epidemiological surveys. In contrast, we aimed to evaluate the impact of the host pressure on this key antigen by analyzing its evolutionary dynamics in 795 isolates from urogenital infections, taking into account the MOMP secondary structure and the sizes/positions of antigenic regions. One-third of the specimens showed a mutational drift from the corresponding genotype, where ∼42% of the mutations had never been described. Amino acid alterations were sixfold more frequent within B-cell epitopes than in the remaining protein (P= 0.027), and some mutations were also found within or close to T-cell antigenic clusters. Interestingly, the two most ecologically successful genotypes, E and F, showed a mutation rate 60.3-fold lower than that of the other genotypes (P< 10−8), suggesting that their efficacy may be the result of a better fitness in dealing with the host immune system rather than of specific virulence factors. Furthermore, the variability exhibited by some genetic variants involved residues that are known to play a critical role during the membrane mechanical movements, contributing to a more stable and flexible porin conformation, which suggests some plasticity to deal with environmental pressure. Globally, these MOMP mutational trends yielded no mosaic structures or important phylogenetic changes, but instead yielded point mutations on specific protein domains, which may enhance pathogen's infectivity, persistence, and transmission.
Distribution and Phylogeny of Light-Oxygen-Voltage-Blue-Light-Signaling Proteins in the Three Kingdoms of Life
Authors: Krauss Ulrich , Minh Bui Quang , Losi Aba , Gärtner Wolfgang , Eggert Thorsten , von Haeseler Arndt , Jaeger Karl-Erich
Published: September 2009

Plants and fungi respond to environmental light stimuli via the action of different photoreceptor modules. One such class, responding to the blue region of light, is constituted by photoreceptors containing so-called
l
ight-
o
xygen-
v
oltage (LOV) domains as sensor modules. Four major LOV families are currently identified in eukaryotes: (i) the plant phototropins, regulating various physiological effects such as phototropism, chloroplast relocation, and stomatal opening; (ii) the aureochromes, mediating photomorphogenesis in photosynthetic stramenopile algae; (iii) the plant circadian photoreceptors of the zeitlupe (ZTL)/adagio (ADO)/flavin-binding Kelch repeat F-box protein 1 (FKF1) family; and (iv) the fungal circadian photoreceptors white-collar 1 (WC-1). Blue-light-sensitive LOV signaling modules are also widespread throughout the prokaryotic world, and physiological responses mediated by bacterial LOV photoreceptors were recently reported. Thus, the question arises as to the evolutionary relationship between the pro- and eukaryotic LOV photoreceptor systems. We used Bayesian and maximum-likelihood tree reconstruction methods to infer evolutionary scenarios that might have led to the widespread appearance of LOV domains among the pro- and eukaryotes. The phylogenetic study presented here suggests a bacterial origin for the LOV domains of the four major eukaryotic LOV photoreceptor families, whereas the LOV sensor domains were most likely recruited from the bacteria in the course of plastid and mitochondrial endosymbiosis.
Dynamics of Two Phosphorelays Controlling Cell Cycle Progression inCaulobacter crescentus
Authors: Chen Y. Erin , Tsokos Christos G. , Biondi Emanuele G. , Perchuk Barrett S. , Laub Michael T.
Published: September 2009

InCaulobacter crescentus, progression through the cell cycle is governed by the periodic activation and inactivation of the master regulator CtrA. Two phosphorelays, each initiating with the histidine kinase CckA, promote CtrA activation by driving its phosphorylation and by inactivating its proteolysis. Here, we examined whether the CckA phosphorelays also influence the downregulation of CtrA. We demonstrate that CckA is bifunctional, capable of acting as either a kinase or phosphatase to drive the activation or inactivation, respectively, of CtrA. By identifying mutations that uncouple these two activities, we show that CckA's phosphatase activity is important for downregulating CtrA prior to DNA replication initiation in vivo but that other phosphatases may exist. Our results demonstrate that cell cycle transitions inCaulobacterrequire and are likely driven by the toggling of CckA between its kinase and phosphatase states. More generally, our results emphasize how the bifunctional nature of histidine kinases can help switch cells between mutually exclusive states.
Comparative Genome Analysis ofListeriaBacteriophages Reveals Extensive Mosaicism, Programmed Translational Frameshifting, and a Novel Prophage Insertion Site
Authors: Dorscht Julia , Klumpp Jochen , Bielmann Regula , Schmelcher Mathias , Born Yannick , Zimmer Markus , Calendar Richard , Loessner Martin J.
Published: September 2009

The genomes of sixListeriabacteriophages were sequenced and analyzed. Phages A006, A500, B025, P35, and P40 are members of theSiphoviridaeand contain double-stranded DNA genomes of between 35.6 kb and 42.7 kb. Phage B054 is a unique myovirus and features a 48.2-kb genome. Phage B025 features 3′ overlapping single-stranded genome ends, whereas the other viruses contain collections of terminally redundant, circularly permuted DNA molecules. Phages P35 and P40 have a broad host range and lack lysogeny functions, correlating with their virulent lifestyle. Phages A500, A006, and B025 integrate into bacterial tRNA genes, whereas B054 targets the 3′ end of translation elongation factor genetsf. This is the first reported case of phage integration into such an evolutionarily conserved genetic element. Peptide fingerprinting of viral proteins revealed that both A118 and A500 utilize +1 and −1 programmed translational frameshifting for generating major capsid and tail shaft proteins with C termini of different lengths. In both cases, the unusual +1 frameshift at the 3′ ends of thetshcoding sequences is induced by overlapping proline codons andcis-acting shifty stops. AlthoughListeriaphage genomes feature a conserved organization, they also show extensive mosaicism within the genome building blocks. Of particular interest is B025, which harbors a collection of modules and sequences with relatedness not only to otherListeriaphages but also to viruses infecting other members of theFirmicutes. In conclusion, our results yield insights into the composition and diversity ofListeriaphages and provide new information on their function, genome adaptation, and evolution.
Multiple Two-Component Systems Modulate Alkali Generation inStreptococcus gordoniiin Response to Environmental Stresses
Authors: Liu Yaling , Burne Robert A.
Published: September 2009

The oral commensalStreptococcus gordoniimust adapt to constantly fluctuating and often hostile environmental conditions to persist in the oral cavity. The arginine deiminase system (ADS) ofS. gordoniienables cells to produce, ornithine, ammonia, CO2, and ATP from arginine hydrolysis, augmenting the acid tolerance of the organism. The ADS genes are substrate inducible and sensitive to catabolite repression, mediated through ArcR and CcpA, respectively, but the system also requires low pH and anaerobic conditions for optimal activation. Here, we demonstrate that the CiaRH and ComDE two-component systems (TCS) are required for low-pH-dependent expression of ADS genes inS. gordonii. Further, the VicRK TCS is required for optimal ADS gene expression under anaerobic conditions and enhances the sensitivity of the operon to repression by oxygen. The known anaerobic activator of the ADS, Fnr-like protein (Flp), appeared to act independently of the Vic TCS. Mutants ofS. gordoniilacking components of the CiaRH, ComDE, or VicRK grew more slowly in acidified media and were more sensitive to killing at lethal pH values and to agents that induce oxidative stress. This study provides the first evidence that TCS can regulate the ADS of bacteria in response to specific environmental signals and reveals some notable differences in the contribution of CiaRH, ComDE, and VicRK to viability and stress tolerance between the oral commensalS. gordoniiand the oral pathogenStreptococcus mutans.
Multipole Moments of the Hydrogen Molecule
Authors: Karl G. , Poll J. D. , Wolniewicz L.
Published: September 2009

For small internuclear distances, the quadrupole moment of the hydrogen molecule is quadratic in the internuclear distance, with a coefficient determined by the quadrupole shielding factor of the helium atom. Similarly the hexadecapole moment is quartic in the internuclear distance for small internuclear distances, with a coefficient which is determined by the properties of the helium atom. We give the results of a machine computation of the hexadecapole moment of the hydrogen molecule using up to 54 term variational wave functions and its matrix elements between rotational and vibrational states of the molecule. The intensity of the ΔJ = 4 induced spectrum of hydrogen gas is also discussed.
The Distortion Moment Microwave Spectrum of 12CH4 in the Ground Vibronic State
Authors: Holt C. W. , Gerry M. C. L. , Ozier I.
Published: September 2009

Seven Q branch transitions between 7.8 and 20 GHz have been observed in the distortion moment pure rotational spectrum of 12CH4 in its ground vibronic state. The spectrum was obtained using a conventional Stark modulated microwave spectrometer specially modified for the detection of very weak lines. From the frequencies of these seven transitions, along with the ortho–para splitting known for the (J = 2) state and two Q branch splittings measured earlier by infrared–microwave double resonance, we have determined the one quartic tensor distortion constant DT, the two sextic constants H4T and H6T, and the three octic constants L4T, L6T, and L8T. These are (in Hz): DT = (132 943.41 ± 0.71); H4T = −(16.9839 ± 0.0076); H6T = (11.0342 ± 0.0086); L4T = (20.27 ± 0.24) × 10−4; L6T = −(26.77 ± 0.35) × 10−4; L8T = −(30.0 ± 1.8) × 10−4. The errors are the standard deviations resulting from a least squares analysis. Estimates are also given of the absolute errors. These results consitute the first measurement of the octic distortion constants. The values for DT, H4T, and H6T are compared to earlier determinations. The theoretical considerations that affect the observation of these transitions are reviewed and a detailed description of the special experimental techniques used is given. The method of analysis is described. Finally, as an aid to other high resolution studies of methane and to possible astrophysical detection of the molecule, the Q branch splittings are tabulated up to J = 21.
The Resonance Fluorescence Spectrum of Cl2 in the Vacuum Ultraviolet
Authors: Douglas A. E. , Hoy A. R.
Published: September 2009

The resonance fluorescence spectrum of Cl2 first observed by Rao and Venkateswarlu in 1962, has been photographed at high resolution and analyzed. The assignments of the lines have been revised and new resonance series have been observed. It is shown that the ground state of Cl2, dissociates into Cl atoms with no potential hill and that the dissociation energy isD0 = 19 997.28 cm−1.Vibrational and rotational constants and the R.K.R. curve of the ground state of Cl2 have been determined. The long-range portion of the ground state potential of Cl2 has been examined and shown to be consistent with the predictions of theory and measurements from the B3Π0 potential.
The Spectrum of CuO: Rotational Analysis of a 2Σ−–X2Πi Transition
Authors: Appelblad O. , Lagerqvist A.
Published: September 2009

A blue band system of CuO, a 2Σ−–X2Πi transition, has been rotationally analyzed. The relative branch intensities differ from those of a pure 2Σ–2Π transition. The molecular constants of all the known states of CuO are given.
THE TWO-ENVELOPE PROBLEM REVISITED
Authors: ABBOTT DEREK , DAVIS BRUCE R. , PARRONDO JUAN M. R.
Published: September 2009

The two-envelope problem has intrigued mathematicians for decades, and is a question of choice between two states in the presence of uncertainty. The problem so far, is considered open and there has been no agreed approach or framework for its analysis. In this paper we outline an elementary approach based on Cover's switching function that, in essence, makes a biased random choice where the bias is conditioned on the observed value of one of the states. We argue that the resulting symmetry breaking introduced by this process results in a gain counter to naive expectation. Finally, we discuss a number of open questions and new lines of enquiry that this discovery opens up.