bluuebunny/crossref_metadata_2025 huggingface dataset:
Development of a Blood Flow Model and Validation Against Experiments and Analytical Models
Authors: van Geel M. H. A. , Giannopapa C. G. , van der Linden B. J.
Published: January 2011

In cardiovascular research, FSI is expressed by the interaction of the blood with the vessel or the heart. FSI plays a crucial role when the deformation of the boundary, in this case the vessel wall, cannot be neglected. Arterial blood flow and wave propagation in liquid filled vessels has been investigated by many researchers. Their work comprises computational, theoretical and experimental investigations and will be outlined below. This paper presents the development and validation of an arterial blood flow model. The model has been developed using finite elements and the fluid and the solid are coupled using the ALE method. This method allows moving boundaries without the need for the mesh movement to follow the material. In this paper both straight and tapered aortic analogues are included in the investigation. The pressure, pressure gradient, fluid flow and wall distension obtained from the finite element model is compared with an unique experimental data set and analytical theory. There is a good agreement between the computational, analytical and experimental results.
Effects of Initial Tube-Tubesheet Clearance and Grooves on Axial and Hoop Residual Stresses of Roller Expanded Joints
Authors: Shuaib A. N. , Duffuaa O. M. , Merah N. , Al-Nassar Y.
Published: January 2011

An axisymmetric finite element model is used to evaluate the effect of large initial tube-tubesheet radial clearance and the effect of grooves machined in the tubesheet hole on the distributions and magnitudes of the radial deformation of expanded tube walls, residual contact stress, residual hoop stress, and residual axial stress along the expanded length of the tube and in the transition zone. The results have revealed the presence of residual axial stresses and residual hoop stresses in the inside and outside surfaces of the tubes with various degrees of severity. These tensile residual stresses may cause crack initiation and propagation and may lead stress corrosion cracking in corrosive environments.
Analysis of Contact Pressure Distribution on a Pass Partition Gasket in Conjunction With a Double-Tapered Seal in a High Pressure Heat Exchanger Closure
Authors: Gardner Christopher , Madazhy Rajeev , Howard Erik
Published: January 2011

This paper describes the use of a partition gasket in addition to a self-energized, double-tapered, metal seal in a high pressure heat exchanger. For over 30 years a single gasket was used to seal the heat exchanger partitions against the closure. Although designed to standard code, it often resulted in leaks. Over the past five years, the double-tapered seal has been used extensively to replace welded diaphragms in high pressure heat exchangers in refineries with great success. In this design a tapered-seal is introduced in conjunction with a pass partition gasket for multiple pass heat exchanger, to address problems associated with leaks. Finite Element Analysis (FEA) was performed on the assembly at bolt-up and during internal pressure operation, and contact pressure distribution was analyzed. A 12″ scaled model of the actual heat exchanger closure assembly was designed and hydrostatic pressure tested to ensure relative pressures were held. Actual working-plant applications will be discussed as well.
Moving Beyond NDE to Proactive Management of Materials Degradation
Authors: Bond Leonard J.
Published: January 2011

There is growing interest in life extensions to enable longer term operation (LTO) for both existing nuclear power plants (NPPs) and proposed new NPPs. In order to justify an initial license extension for the 40–60 year period, new non-destructive examination (NDE) approaches have been developed and deployed by NPP operators in their Aging Management Programs (AMPs). However, to achieve the goals of even longer term operation, and specifically for the USA in looking at methodologies to support subsequent license renewal periods (i.e., 60–80 years, and beyond), it is necessary to understand the capabilities of current NDE methods to detect, monitor and trend degradation and hence enable timely implementation of appropriate corrective actions. This paper discusses insights from past experience, the state-of-the-art, and current activities in the move towards providing a capacity for proactive management of materials degradation (PMMD) to support NPP LTO.
Design Rules for Pipe Systems Subject to Internal Explosions: Part 2
Authors: Smeulers Jan P. M. , Pape Gersom
Published: January 2011

In this part 2 various causes of dynamic stress amplification are discussed that are generated by internal explosion waves. The stress increase is expressed in an amplification factor that relates the increased stress to the hoop stress that would result if the detonation pressure is applied as a static load on the pipe. Also the induced stresses in piping components are analyzed.
Thiostrepton and Derivatives Exhibit Antimalarial and Gametocytocidal Activity by Dually Targeting Parasite Proteasome and Apicoplast
Authors: Aminake Makoah N. , Schoof Sebastian , Sologub Ludmilla , Leubner Monika , Kirschner Marc , Arndt Hans-Dieter , Pradel Gabriele
Published: January 2011

Ribosome-targeting antibiotics exert their antimalarial activity on the apicoplast of the malaria parasite, an organelle of prokaryote origin having essential metabolic functions. These antibiotics typically cause a delayed-death phenotype, which manifests in parasite killing during the second replication cycle following administration. As an exception, treatment with the antibiotic thiostrepton results in an immediate killing. We recently demonstrated that thiostrepton and its derivatives interfere with the eukaryotic proteasome, a multimeric protease complex that is important for the degradation of ubiquitinated proteins. Here, we report that the thiostrepton-based compounds are active against chloroquine-sensitive and -resistant
Plasmodium falciparum
, where they rapidly eliminate parasites before DNA replication. The minor parasite fraction that escapes the fast killing of the first replication cycle is arrested in the schizont stage of the following cycle, displaying a delayed-death phenotype. Thiostrepton further exhibits gametocytocidal activity by eliminating gametocytes, the sexual precursor cells that are crucial for parasite transmission to the mosquito. Compound treatment results in an accumulation of ubiquitinated proteins in the blood stages, indicating an effect on the parasite proteasome. In accordance with these findings, expression profiling revealed that the proteasome is present in the nucleus and cytoplasm of trophozoites, schizonts, and gametocytes. In conclusion, thiostrepton derivatives represent promising candidates for malaria therapy by dually acting on two independent targets, the parasite proteasome and the apicoplast, with the capacity to eliminate both intraerythrocytic asexual and transmission stages of the parasite.
In Vitro
and
In Vivo
Properties of BAL30376, a β-Lactam and Dual β-Lactamase Inhibitor Combination with Enhanced Activity against Gram-Negative Bacilli That Express Multiple β-Lactamases
Authors: Page Malcolm G. P. , Dantier Clothilde , Desarbre Eric , Gaucher Bérangère , Gebhardt Klaus , Schmitt-Hoffmann Anne
Published: January 2011

BAL30376 is a triple combination comprising a siderophore monobactam,
BAL19764
; a novel bridged monobactam,
BAL29880
, which specifically inhibits class C β-lactamases; and clavulanic acid, which inhibits many class A and some class D β-lactamases. The MIC
90
was ≤4 μg/ml (expressed as the concentration of
BAL19764
) for most species of the
Enterobacteriaceae
family, including strains that produced metallo-β-lactamases and were resistant to all of the other β-lactams tested. The MIC
90
for
Stenotrophomonas maltophilia
was 2 μg/ml, for multidrug-resistant (MDR)
Pseudomonas aeruginosa
it was 8 μg/ml, and for MDR
Acinetobacter
and
Burkholderia
spp. it was 16 μg/ml. The presence of the class C β-lactamase inhibitor
BAL29880
contributed significantly to the activity of
BAL30376
against strains of
Citrobacter freundii
,
Enterobacter
species,
Serratia marcescens
, and
P. aeruginosa
. The presence of clavulanic acid contributed significantly to the activity against many strains of
Escherichia coli
and
Klebsiella pneumoniae
that produced class A extended-spectrum β-lactamases. The activity of
BAL30376
against strains with metallo-β-lactamases was largely attributable to the intrinsic stability of the monobactam
BAL19764
toward these enzymes. Considering its three components,
BAL30376
was unexpectedly refractory toward the development of stable resistance.
Seasonal Changes of Freshwater Ammonia-Oxidizing Archaeal Assemblages and Nitrogen Species in Oligotrophic Alpine Lakes
Authors: Auguet Jean-Christophe , Nomokonova Natalya , Camarero Lluis , Casamayor Emilio O.
Published: January 2011

The annual changes in the composition and abundance of ammonia-oxidizing archaea (AOA) were analyzed monthly in surface waters of three high mountain lakes within the Limnological Observatory of the Pyrenees (LOOP; northeast Spain) using both 16S rRNA and functional (ammonia monooxygenase gene,
amoA
) gene sequencing as well as quantitative PCR amplification. The set of biological data was related to changes in nitrogen species and to other relevant environmental variables. The whole archaeal assemblage was dominated by phylotypes closely related to the crenarchaeal 1.1a group (58% ± 18% of total 16S rRNA gene sequences), and consistent structural changes were detected during the study. Water temperature was the environmental variable that better explained spring, summer, and winter (ice-covered lakes) archaeal assemblage structure. The
amoA
gene was detected year round, and seasonal changes in
amoA
gene composition were well correlated with changes in the archaeal 16S rRNA gene pool. In addition, copy numbers of both the specific 1.1a group 16 rRNA and archaeal
amoA
genes were well correlated, suggesting that most freshwater 1.1a
Crenarchaeota
had the potential to carry out ammonia oxidation. Seasonal changes in the diversity and abundance of AOA (i.e.,
amoA
) were better explained by temporal changes in ammonium, the substrate for nitrification, and mostly nitrite, the product of ammonia oxidation. Lacustrine
amoA
gene sequences grouped in coherent freshwater phylogenetic clusters, suggesting that freshwater habitats harbor typical
amoA
-containing ecotypes, which is different from soils and seas. We observed within the freshwater
amoA
gene sequence pool a high genetic divergence (translating to up to 32% amino acid divergence) between the spring and the remaining AOA assemblages. This suggests that different AOA ecotypes are adapted to different temporal ecological niches in these lakes.
Diversity of Multidrug-Resistant
Salmonella enterica
Strains Associated with Cattle at Harvest in the United States
Authors: Brichta-Harhay Dayna M. , Arthur Terrance M. , Bosilevac Joseph M. , Kalchayanand Norasak , Shackelford Steven D. , Wheeler Tommy L. , Koohmaraie Mohammad
Published: January 2011

The prevalence and diversity of multidrug-resistant (MDR)
Salmonella enterica
strains associated with cattle at harvest in the United States were examined. Hides and carcasses of cattle were sampled at processing plants (
n
= 6) located in four geographically distant regions from July 2005 to April 2006. The mean prevalences of
Salmonella
on hides, preevisceration carcasses (immediately after hide removal), and postintervention carcasses (in the chiller and after the full complement of interventions) were 89.6%, 50.2%, and 0.8%, respectively. The values for MDR
Salmonella enterica
strains (defined as those resistant to two or more antimicrobials) as percentages of
Salmonella
prevalence were 16.7% (95% confidence interval [CI], 8.3 to 25.1%; median percent prevalence, 6.9%), 11.7% (95% CI, 4.4 to 19.0%; median, 4.8%), and 0.33% (95% CI, −0.3 to 0.70%; median, 0%), respectively. In this study, 16,218
Salmonella
hide and carcass isolates were screened for antimicrobial resistance. Of these, 978 (6.0%) unique MDR
S. enterica
isolates were identified and serotyped and their XbaI pulsed-field gel electrophoresis (PFGE) profiles determined. The predominant MDR
S. enterica
serotypes observed were Newport (53.1%), Typhimurium (16.6%), and Uganda (10.9%). Differences in MDR
S. enterica
prevalence were detected, and PFGE analysis revealed both epidemic clusters (profiles found in plants in multiple regions/seasons) and endemic clusters (profiles observed in plants in limited regions/seasons) within several of the MDR serotypes examined. Despite these differences, multiple-hurdle processing interventions employed at all plants were found to be quite effective and decreased
Salmonella
carcass contamination by 98.4% (95% CI, 97.6 to 99.7%).
Abundance, Diversity, and Activity of Ammonia-Oxidizing Prokaryotes in the Coastal Arctic Ocean in Summer and Winter
Authors: Christman Glenn D. , Cottrell Matthew T. , Popp Brian N. , Gier Elizabeth , Kirchman David L.
Published: January 2011

Ammonia oxidation, the first step in nitrification, is performed by certain
Beta
- and
Gammaproteobacteria
and
Crenarchaea
to generate metabolic energy. Ammonia monooxygenase (
amoA
) genes from both
Bacteria
and
Crenarchaea
have been found in a variety of marine ecosystems, but the relative importance of
Bacteria
versus
Crenarchaea
in ammonia oxidation is unresolved, and seasonal comparisons are rare. In this study, we compared the abundance of betaproteobacterial and crenarchaeal
amoA
genes in the coastal Arctic Ocean during summer and winter over 2 years. Summer and winter betaproteobacterial
amoA
clone libraries were significantly different, although the gene sequences were similar to those found in temperate and polar environments. Betaproteobacterial and crenarchaeal
amoA
genes were 30- to 115-fold more abundant during the winter than during the summer in both years of the study. Archaeal
amoA
genes were more abundant than betaproteobacterial
amoA
genes in the first year, but betaproteobacterial
amoA
was more abundant than archaeal
amoA
the following year. The ratio of archaeal
amoA
gene copies to marine group I crenarchaeal 16S rRNA genes averaged 2.9 over both seasons and years, suggesting that ammonia oxidation was common in
Crenarchaea
at this location. Potential nitrification rates, as well as the total
amoA
gene abundance, were highest in the winter when competition with phytoplankton was minimal and ammonium concentrations were the highest. These results suggest that ammonium concentrations were important in determining the rates of ammonia oxidation and the abundance of ammonia-oxidizing
Betaproteobacteria
and
Crenarchaea
.
Molecular Epidemiology of
Salmonella enterica
Serovar Typhimurium Isolates from Cattle in Hokkaido, Japan: Evidence of Clonal Replacement and Characterization of the Disseminated Clone
Authors: Tamamura Yukino , Uchida Ikuo , Tanaka Kiyoshi , Okazaki Hizuru , Tezuka Satoru , Hanyu Hideki , Kataoka Natsumi , Makino Sou-ichi , Kishima Masato , Kubota Takayuki , Kanno Toru , Hatama Shinichi , Ishihara Ryoko , Hata Eiji , Yamada Hironari , Nakaoka Yuuji , Akiba Masato
Published: January 2011

The molecular epidemiology of 545
Salmonella enterica
serovar Typhimurium isolates collected between 1977 and 2009 from cattle in Hokkaido, Japan, was investigated using pulsed-field gel electrophoresis (PFGE). Nine main clusters were identified from 116 PFGE patterns. Cluster I comprised 248 isolates, 243 of which possessed a sequence specific to definitive phage type 104 (DT104) or U302. The cluster I isolates were dominant in 1993 to 2003, but their numbers declined beginning in 2004. Beginning in 2002, an increase was observed in the number of cluster VII isolates, consisting of 21 PFGE patterns comprising 165 isolates. A total of 116 isolates representative of the 116 PFGE profiles were analyzed by multilocus variable-number tandem-repeat analysis (MLVA). Other than two drug-sensitive isolates, 19 isolates within cluster VII were classified in the same cluster by MLVA. Among the cluster VII isolates, an antibiotic resistance type showing resistance to ampicillin, chloramphenicol, streptomycin, sulfonamides, tetracycline, kanamycin, cefazolin, and sulfamethoxazole-trimethoprim and a resistance type showing resistance to ampicillin, streptomycin, sulfonamides, tetracycline, and kanamycin were found in 23 and 125 isolates, respectively. In the 19 isolates representative of cluster VII, the
bla
TEM-1
gene was found on a
Salmonella
serotype Typhimurium virulence plasmid, which was transferred to
Escherichia coli
by electroporation along with resistance to two to four other antimicrobials. Genomic analysis by subtractive hybridization and plasmid analysis suggested that the
bla
TEM-1
-carrying virulence plasmid has a mosaic structure composed of elements of different origin. These results indicate an emerging multidrug-resistant
S
. Typhimurium clone carrying a virulence-resistance plasmid among cattle in Hokkaido, Japan.
Gene Cluster Conferring Streptomycin, Sulfonamide, and Tetracycline Resistance in
Escherichia coli
O157:H7 Phage Types 23, 45, and 67
Authors: Ziebell K. , Johnson R. P. , Kropinski A. M. , Reid-Smith R. , Ahmed R. , Gannon V. P. , Gilmour M. , Boerlin P.
Published: January 2011

Multidrug resistance to streptomycin, sulfonamide, and tetracycline (AMR-SSuT) was identified in 156 of 171 isolates of
Escherichia coli
O157:H7 of phage types 23, 45, and 67. In 154 AMR-SSuT isolates, resistance was encoded by
strA
,
strB
,
sul2
, and
tet
(B), which in 59 of 63 tested isolates were found clustered together on the chromosome within the
cdiA
locus.
Inhibition of
Streptococcus mutans
Biofilm Formation by
Streptococcus salivarius
FruA
Authors: Ogawa Ayako , Furukawa Soichi , Fujita Shuhei , Mitobe Jiro , Kawarai Taketo , Narisawa Naoki , Sekizuka Tsuyoshi , Kuroda Makoto , Ochiai Kuniyasu , Ogihara Hirokazu , Kosono Saori , Yoneda Saori , Watanabe Haruo , Morinaga Yasushi , Uematsu Hiroshi , Senpuku Hidenobu
Published: January 2011

The oral microbial flora consists of many beneficial species of bacteria that are associated with a healthy condition and control the progression of oral disease. Cooperative interactions between oral streptococci and the pathogens play important roles in the development of dental biofilms in the oral cavity. To determine the roles of oral streptococci in multispecies biofilm development and the effects of the streptococci in biofilm formation, the active substances inhibiting
Streptococcus mutans
biofilm formation were purified from
Streptococcus salivarius
ATCC 9759 and HT9R culture supernatants using ion exchange and gel filtration chromatography. Matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry analysis was performed, and the results were compared to databases. The
S. salivarius
HT9R genome sequence was determined and used to indentify candidate proteins for inhibition. The candidates inhibiting biofilms were identified as
S. salivarius
fructosyltransferase (FTF) and exo-beta-
d
-fructosidase (FruA). The activity of the inhibitors was elevated in the presence of sucrose, and the inhibitory effects were dependent on the sucrose concentration in the biofilm formation assay medium. Purified and commercial FruA from
Aspergillus niger
(31.6% identity and 59.6% similarity to the amino acid sequence of FruA from
S. salivarius
HT9R) completely inhibited
S. mutans
GS-5 biofilm formation on saliva-coated polystyrene and hydroxyapatite surfaces. Inhibition was induced by decreasing polysaccharide production, which is dependent on sucrose digestion rather than fructan digestion. The data indicate that
S. salivarius
produces large quantities of FruA and that FruA alone may play an important role in multispecies microbial interactions for sucrose-dependent biofilm formation in the oral cavity.
Detection of Shiga Toxin-Producing
Escherichia coli
Serotypes O26:H11, O103:H2, O111:H8, O145:H28, and O157:H7 in Raw-Milk Cheeses by Using Multiplex Real-Time PCR
Authors: Madic Jordan , Vingadassalon Noémie , de Garam Carine Peytavin , Marault Muriel , Scheutz Flemming , Brugère Hubert , Jamet Emmanuel , Auvray Frédéric
Published: January 2011

Shiga toxin (Stx)-producing
Escherichia coli
(STEC) strains are a diverse group of food-borne pathogens with various levels of virulence for humans. In this study, we describe the use of a combination of multiple real-time PCR assays for the screening of 400 raw-milk cheeses for the five main pathogenic STEC serotypes (O26:H11, O103:H2, O111:H8, O145:H28, and O157:H7). The prevalences of samples positive for
stx
, intimin-encoding gene (
eae
), and at least one of the five O group genetic markers were 29.8%, 37.3%, and 55.3%, respectively. The H2, H7, H8, H11, and H28
fliC
alleles were highly prevalent and could not be used as reliable targets for screening. Combinations of
stx
,
eae
variants, and O genetic markers, which are typical of the five targeted STEC serotypes, were detected by real-time PCR in 6.5% of the cheeses (26 samples) and included
stx-wzx
O26
-
eae-
β
1
(4.8%; 19 samples),
stx
-
wzx
O103
-
eae-
ε (1.3%; five samples),
stx
-
ihp1
O145
-
eae-
γ
1
(0.8%; three samples), and
stx
-
rfbE
O157
-
eae
-γ
1
(0.3%; one sample). Twenty-eight immunomagnetic separation (IMS) assays performed on samples positive for these combinations allowed the recovery of seven
eae
β
1
-positive STEC O26:H11 isolates, whereas no STEC O103:H2, O145:H28, or O157:H7 strains could be isolated. Three
stx
-negative and
eae
β
1
-positive
E. coli
O26:[H11] strains were also isolated from cheeses by IMS. Colony hybridization allowed us to recover STEC from
stx
-positive samples for 15 out of 45 assays performed, highlighting the difficulties encountered in STEC isolation from dairy products. The STEC O26:H11 isolates shared the same virulence genetic profile as enterohemorrhagic
E. coli
(EHEC) O26:H11, i.e., they carried the virulence-associated genes EHEC-
hlyA
,
katP
, and
espP
, as well as genomic O islands 71 and 122. Except for one strain, they all contained the
stx1
variant only, which was reported to be less frequently associated with human cases than
stx2
. Pulsed-field gel electrophoresis (PFGE) analysis showed that they displayed high genetic diversity; none of them had patterns identical to those of human O26:H11 strains investigated here.
Fate ofMycobacterium aviumsubsp.paratuberculosisafter Application of Contaminated Dairy Cattle Manure to Agricultural Soils
Authors: Salgado M. , Collins M. T. , Salazar F. , Kruze J. , Bölske G. , Söderlund R. , Juste R. , Sevilla I. A. , Biet F. , Troncoso F. , Alfaro M.
Published: January 2011

Details regarding the fate ofMycobacterium aviumsubsp.paratuberculosis(basonym,Mycobacterium paratuberculosis) after manure application on grassland are unknown. To evaluate this, intact soil columns were collected in plastic pipes (lysimeters) and placed under controlled conditions to test the effect of a loamy or sandy soil composition and the amount of rainfall on the fate ofM. paratuberculosisapplied to the soil surface with manure slurry. The experiment was organized as a randomized design with two factors and three replicates.M. paratuberculosis-contaminated manure was spread on the top of the 90-cm soil columns. After weekly simulated rainfall applications, water drainage samples (leachates) were collected from the base of each lysimeter and cultured forM. paratuberculosisusing Bactec MGIT ParaTB medium and supplements. Grass was harvested, quantified, and tested from each lysimeter soil surface. The identity of all probableM. paratuberculosisisolates was confirmed by PCR for IS900and F57 genetic elements. There was a lag time of 2 months after each treatment beforeM. paratuberculosiswas found in leachates. The greatest proportions ofM. paratuberculosis-positive leachates were from sandy-soil lysimeters in the manure-treated group receiving the equivalent of 1,000 mm annual rainfall. Under the higher rainfall regimen (2,000 mm/year),M. paratuberculosiswas detected more often from lysimeters with loamy soil than sandy soil. Among all lysimeters,M. paratuberculosiswas detected more often in grass clippings than in lysimeter leachates. At the end of the trial, lysimeters were disassembled and soil cultured at different depths, and we found thatM. paratuberculosiswas recovered only from the uppermost levels of the soil columns in the treated group. Factors associated withM. paratuberculosispresence in leachates were soil type and soil pH (P< 0.05). ForM. paratuberculosispresence in grass clippings, only manure application showed a significant association (P< 0.05). From these findings we conclude that this pathogen tends to move slowly through soils (faster through sandy soil) and tends to remain on grass and in the upper layers of pasture soil, representing a clear infection hazard for grazing livestock and a potential for the contamination of runoff after heavy rains.
Persistent Infection or Successive Reinfection of Deer Mice withBartonella vinsoniisubsp.arupensis
Authors: Bai Ying , Calisher Charles H. , Kosoy Michael Y. , Root J. Jeffrey , Doty Jeffrey B.
Published: January 2011

Bartonella infections are common in rodents. From 1994 to 2006, longitudinal studies of a rodent community, consisting mainly of deer mice (Peromyscus maniculatus), were conducted in southwestern Colorado to study hantaviruses. Blood samples from deer mice captured one or more times during the period 2003 to 2006 (n= 737) were selected to study bartonellae in deer mice. Bartonellae were found to be widely distributed in that population, with an overall prevalence of 82.4% (607/737 mice). No correlation was found between bartonella prevalence and deer mouse weight or sex. Persistent or successive infections with bartonellae were observed in deer mice captured repeatedly, with a prevalence of 83.9% (297/354), and the infection appeared to last for more than 1 year in some of them. Persistent infection with bartonellae may explain the high prevalence of these bacteria in deer mice at this site and, perhaps, elsewhere. Genetic analysis demonstrated that deer mouse-borne bartonella isolates at this site belong to the same species,B. vinsoniisubsp.arupensis, demonstrating a specific relationship betweenB. vinsoniisubsp.arupensisand deer mice.
Comprehensive Approaches to Molecular Biomarker Discovery for Detection and Identification of
Cronobacter
spp. (
Enterobacter sakazakii
) and
Salmonella
spp
Authors: Yan Xianghe , Gurtler Joshua , Fratamico Pina , Hu Jing , Gunther Nereus W. , Juneja Vijay , Huang Lihan
Published: January 2011

Cronobacter
spp. (formerly
Enterobacter sakazakii
) and
Salmonella
spp. are increasingly implicated internationally as important microbiological contaminants in low-moisture food products, including powdered infant formula. Estimates indicate that 40 to 80% of infants infected with
Cronobacter sakazakii
and/or
Salmonella
in the United States may not survive the illness. A systematic approach, combining literature-based data mining, comparative genome analysis, and the direct sequencing of PCR products of specific biomarker genes, was used to construct an initial collection of genes to be targeted. These targeted genes, particularly genes encoding virulence factors and genes responsible for unique phenotypes, have the potential to function as biomarker genes for the identification and differentiation of
Cronobacter
spp. and
Salmonella
from other food-borne pathogens in low-moisture food products. In this paper, a total of 58 unique
Salmonella
gene clusters and 126 unique potential
Cronobacter
biomarkers and putative virulence factors were identified. A chitinase gene, a well-studied virulence factor in fungi, plants, and bacteria, was used to confirm this approach. We found that the chitinase gene has very low sequence variability and/or polymorphism among
Cronobacter
,
Citrobacter
, and
Salmonella
, while differing significantly in other food-borne pathogens, either by sequence blasting or experimental testing, including PCR amplification and direct sequencing. This computational analysis for
Cronobacter
and
Salmonella
biomarker identification and the preliminary laboratory studies are only a starting point; thus, PCR and array-based biomarker verification studies of these and other food-borne pathogens are currently being conducted.
The EIIABManPhosphotransferase System Permease Regulates Carbohydrate Catabolite Repression inStreptococcus gordonii
Authors: Tong Huichun , Zeng Lin , Burne Robert A.
Published: January 2011

Commensal oral streptococci play critical roles in oral biofilm formation and promote dental health by competing with, and antagonizing the growth of, pathogenic organisms, such asStreptococcus mutans. Efficient utilization of the spectrum of carbohydrates in the oral cavity by commensal streptococci is essential for their persistence, and yet very little is known about the regulation of carbohydrate catabolism by these organisms. Carbohydrate catabolite repression (CCR) in the abundant oral commensalStreptococcus gordoniistrain DL-1 was investigated using the exo-β-d-fructosidase gene (fruA) and a fructose/mannose sugar:phosphotransferase (PTS) enzyme II operon (levDEFG) as model systems. Functional studies confirmed the predicted roles of FruA and LevD inS. gordonii. ManL, the AB domain of a fructose/mannose-type enzyme II PTS permease, contributed to utilization of glucose, mannose, galactose, and fructose and exerted primary control over CCR of thefruAandlevDoperons. Unlike inS. mutans, ManL-dependent CCR was not sugar specific, and galactose was very effective at eliciting CCR inS. gordonii. Inactivation of the apparentccpAhomologue ofS. gordoniiactually enhanced CCR offruAandlevD, an effect likely due to its demonstrated role in repression ofmanLexpression. Thus, there are some similarities and fundamental differences in CCR control mechanisms between the oral pathogenS. mutansand the oral commensalS. gordoniithat may eventually be exploited to enhance the competitiveness of health-associated commensals in oral biofilms.
Detection of
Cryptosporidium molnari
Oocysts from Fish by Fluorescent-Antibody Staining Assays for
Cryptosporidium
spp. Affecting Humans
Authors: Barugahare Rona , Dennis Michelle M. , Becker Joy A. , Šlapeta Jan
Published: January 2011

Three direct fluorescent-antibody staining assay kits for the detection of zoonotic
Cryptosporidium
species were used to detect
Cryptosporidium molnari
from Murray cod, and the cryptosporidia were characterized by using small-subunit (SSU) ribosomal DNA (rDNA). To facilitate rapid diagnosis of infection, this study demonstrated that all three kits detected fresh
C. molnari
and two kits detected formalin-fixed oocysts.
Ammonium Availability Affects the Ratio of Ammonia-Oxidizing Bacteria to Ammonia-Oxidizing Archaea in Simulated Creek Ecosystems
Authors: Herrmann Martina , Scheibe Andrea , Avrahami Sharon , Küsel Kirsten
Published: January 2011

The ammonia-oxidizing microbial community colonizing clay tiles in flow channels changed in favor of ammonia-oxidizing bacteria during a 12-week incubation period even at originally high ratios of ammonia-oxidizing archaea to ammonia-oxidizing bacteria (AOB). AOB predominance was established more rapidly in flow channels incubated at 350 μM NH
4
+
than in those incubated at 50 or 20 μM NH
4
+
. Biofilm-associated potential nitrification activity was first detected after 28 days and was positively correlated with bacterial but not archaeal
amoA
gene copy numbers.
Role of Glucose in the Expression of Cryptococcus neoformans Antiphagocytic Protein 1, App1
Authors: Williams Virginia , Del Poeta Maurizio
Published: January 2011

The cryptococcus-specific protein antiphagocytic protein 1 (App1) regulates
Cryptococcus neoformans
virulence by controlling macrophage-driven fungal phagocytosis. This is accomplished through complement receptors (CR), specifically CR3. When inhaled,
C. neoformans
can cause a life-threatening meningoencephalitis in immunocompromised patients. Because glucose starvation can significantly change the gene expression and virulence of
C. neoformans
and because App1 is critical for phagocytosis in the lung—a low-glucose environment—we investigated the role of glucose in App1 expression. We found that App1 was upregulated dramatically under low-glucose conditions, and it was upregulated when
C. neoformans
cells were incubated in bronchoalveolar lavage (BAL) fluid, serum, and cerebrospinal fluid, which are low-glucose environments. Characterization of App1's regulation based on mammalian lung physiology revealed that App1 is upregulated via both increases in transcription and increases in mRNA stability. Our data provide new insights regarding
C. neoformans
adaptations to low-glucose environments.
Nhe1 Is Essential for Potassium but Not Calcium Facilitation of Cell Motility and the Monovalent Cation Requirement for Chemotactic Orientation in Dictyostelium discoideum
Authors: Lusche Daniel F. , Wessels Deborah , Ryerson Daniel E. , Soll David R.
Published: January 2011

InDictyostelium discoideum, extracellular K+or Ca2+at a concentration of 40 or 20 mM, respectively, facilitates motility in the absence or presence of a spatial gradient of chemoattractant. Facilitation results in maximum velocity, cellular elongation, persistent translocation, suppression of lateral pseudopod formation, and myosin II localization in the posterior cortex. A lower threshold concentration of 15 mM K+or Na or 5 mM Ca2+is required for chemotactic orientation. Although the common buffer solutions used byD. discoideumresearchers to study chemotaxis contain sufficient concentrations of cations for chemotactic orientation, the majority contain insufficient levels to facilitate motility. Here it has been demonstrated that Nhe1, a plasma membrane protein, is required for K+but not Ca2+facilitation of cell motility and for the lower K+but not Ca2+requirement for chemotactic orientation.
Bistability in
myo
-Inositol Utilization by
Salmonella enterica
Serovar Typhimurium
Authors: Kröger Carsten , Srikumar Shabarinath , Ellwart Joachim , Fuchs Thilo M.
Published: January 2011

The capability of
Salmonella enterica
serovar Typhimurium strain 14028 (
S
. Typhimurium 14028) to utilize
myo
-inositol (MI) is determined by the genomic island GEI4417/4436 carrying the
iol
genes that encode enzymes, transporters, and a repressor responsible for the MI catabolic pathway. In contrast to all bacteria investigated thus far,
S
. Typhimurium 14028 growing on MI as the sole carbon source is characterized by a remarkable long lag phase of 40 to 60 h. We report here that on solid medium with MI as the sole carbon source, this human pathogen exhibits a bistable phenotype characterized by a dissection into large colonies and a slow-growing bacterial background. This heterogeneity is reversible and therefore not caused by mutation, and it is not observed in the absence of the
iol
gene repressor IolR nor in the presence of at least 0.55% CO
2
. Bistability is correlated with the activity of the
iolE
promoter (P

iolE

), but not of P

iolC

or P

iolD

, as shown by promoter-
gfp
fusions. On the single-cell level, fluorescence microscopy and flow cytometry analysis revealed a gradual switch of P

iolE

from the “off” to the “on” status during the late lag phase and the transition to the log phase. Deletion of
iolR
or the addition of 0.1% NaHCO
3
induced an early growth start of
S
. Typhimurium 14028 in minimal medium with MI. The addition of ethoxyzolamide, an inhibitor of carboanhydrases, elongated the lag phase in the presence of bicarbonate. The positive-feedback loop via repressor release and positive induction by bicarbonate-CO
2
might allow
S
. Typhimurium 14028 to adapt to rapidly changing environments. The phenomenon described here is a novel example of bistability in substrate degradation, and, to our knowledge, is the first demonstration of gene regulation by bicarbonate-CO
2
in
Salmonella
.
Sulfate-Driven Elemental Sparing Is Regulated at the Transcriptional and Posttranscriptional Levels in a Filamentous Cyanobacterium
Authors: Gutu Andrian , Alvey Richard M. , Bashour Sami , Zingg Daniel , Kehoe David M.
Published: January 2011

Sulfur is an essential nutrient that can exist at growth-limiting concentrations in freshwater environments. The freshwater cyanobacterium
Fremyella diplosiphon
(also known as
Tolypothrix
sp. PCC 7601) is capable of remodeling the composition of its light-harvesting antennae, or phycobilisomes, in response to changes in the sulfur levels in its environment. Depletion of sulfur causes these cells to cease the accumulation of two forms of a major phycobilisome protein called phycocyanin and initiate the production of a third form of phycocyanin, which possesses a minimal number of sulfur-containing amino acids. Since phycobilisomes make up approximately 50% of the total protein in these cells, this elemental sparing response has the potential to significantly influence the fitness of this species under low-sulfur conditions. This response is specific for sulfate and occurs over the physiological range of sulfate concentrations likely to be encountered by this organism in its natural environment.
F. diplosiphon
has two separate sulfur deprivation responses, with low sulfate levels activating the phycobilisome remodeling response and low sulfur levels activating the chlorosis or bleaching response. The phycobilisome remodeling response results from changes in RNA abundance that are regulated at both the transcriptional and posttranscriptional levels. The potential of this response, and the more general bleaching response of cyanobacteria, to provide sulfur-containing amino acids during periods of sulfur deprivation is examined.
Two DNA Translocases Synergistically Affect Chromosome Dimer Resolution inBacillus subtilis
Authors: Kaimer Christine , Schenk Katrin , Graumann Peter L.
Published: January 2011

InBacillus subtilis, chromosome dimers that block complete segregation of sister chromosomes arise in about 15% of exponentially growing cells. Two dedicated recombinases, RipX and CodV, catalyze the resolution of dimers by site-specific recombination at thedifsite, which is located close to the terminus region on the chromosome. We show that the two DNA translocases inB. subtilis, SftA and SpoIIIE, synergistically affect dimer resolution, presumably by positioning thedifsites in close proximity, before or after completion of cell division, respectively. Furthermore, we observed that both recombinases, RipX and CodV, assemble on the chromosome at thedifsite throughout the cell cycle. The preassembly of recombinases probably ensures that dimer resolution can occur rapidly within a short time window around cell division.
Core and Panmetabolism in
Escherichia coli
Authors: Vieira Gilles , Sabarly Victor , Bourguignon Pierre-Yves , Durot Maxime , Le Fèvre François , Mornico Damien , Vallenet David , Bouvet Odile , Denamur Erick , Schachter Vincent , Médigue Claudine
Published: January 2011

Escherichia coli
exhibits a wide range of lifestyles encompassing commensalism and various pathogenic behaviors which its highly dynamic genome contributes to develop. How environmental and host factors shape the genetic structure of
E. coli
strains remains, however, largely unknown. Following a previous study of
E. coli
genomic diversity, we investigated its diversity at the metabolic level by building and analyzing the genome-scale metabolic networks of 29
E. coli
strains (8 commensal and 21 pathogenic strains, including 6
Shigella
strains). Using a tailor-made reconstruction strategy, we significantly improved the completeness and accuracy of the metabolic networks over default automatic reconstruction processes. Among the 1,545 reactions forming
E. coli
panmetabolism, 885 reactions were common to all strains. This high proportion of core reactions (57%) was found to be in sharp contrast to the low proportion (13%) of core genes in the
E. coli
pangenome, suggesting less diversity of metabolic functions compared to that of all gene functions. Core reactions were significantly overrepresented among biosynthetic reactions compared to the more variable degradation processes. Differences between metabolic networks were found to follow
E. coli
phylogeny rather than pathogenic phenotypes, except for
Shigella
networks, which were significantly more distant from the others. This suggests that most metabolic changes in non-
Shigella
strains were not driven by their pathogenic phenotypes. Using a supervised method, we were yet able to identify small sets of reactions related to pathogenicity or commensalism. The quality of our reconstructed networks also makes them reliable bases for building metabolic models.
Absence of Diauxie during Simultaneous Utilization of Glucose and Xylose bySulfolobus acidocaldarius
Authors: Joshua Chijioke J. , Dahl Robert , Benke Peter I. , Keasling Jay D.
Published: January 2011

Sulfolobus acidocaldariusutilizes glucose and xylose as sole carbon sources, but its ability to metabolize these sugars simultaneously is not known. We report the absence of diauxie during growth ofS. acidocaldariuson glucose and xylose as co-carbon sources. The presence of glucose did not repress xylose utilization. The organism utilized a mixture of 1 g/liter of each sugar simultaneously with a specific growth rate of 0.079 h−1and showed no preference for the order in which it utilized each sugar. The organism grew faster on 2 g/liter xylose (0.074 h−1) as the sole carbon source than on an equal amount of glucose (0.022 h−1). When grown on a mixture of the two carbon sources, the growth rate of the organism increased from 0.052 h−1to 0.085 h−1as the ratio of xylose to glucose increased from 0.25 to 4.S. acidocaldariusappeared to utilize a mixture of glucose and xylose at a rate roughly proportional to their concentrations in the medium, resulting in complete utilization of both sugars at about the same time. Gene expression in cells grown on xylose alone was very similar to that in cells grown on a mixture of xylose and glucose and substantially different from that in cells grown on glucose alone. The mechanism by which the organism utilized a mixture of sugars has yet to be elucidated.
The
Escherichia coli
K-12 MntR Miniregulon Includes
dps
, Which Encodes the Major Stationary-Phase DNA-Binding Protein
Authors: Yamamoto Kaneyoshi , Ishihama Akira , Busby Stephen J. W. , Grainger David C.
Published: January 2011

Escherichia coli
MntR protein is the Mn
2+
-responsive transcriptional repressor of the MntH manganese transporter. We have used chromatin immunoprecipitation to determine the distribution of Mn
2+
-MntR across the entire
E. coli
chromosome
in vivo
, and we report that MntR binds to only four targets, adjacent to the
mntH
,
mntR
,
yebN
, and
dps
genes. Unexpectedly, we found that
dps
expression is directly repressed by Mn
2+
-MntR.
Effects of Metal on the Biochemical Properties of
Helicobacter pylori
HypB, a Maturation Factor of [NiFe]-Hydrogenase and Urease
Authors: Sydor Andrew M. , Liu Jenny , Zamble Deborah B.
Published: January 2011

The biosyntheses of the [NiFe]-hydrogenase and urease enzymes in
Helicobacter pylori
require several accessory proteins for proper construction of the nickel-containing metallocenters. The hydrogenase accessory proteins HypA and HypB, a GTPase, have been implicated in the nickel delivery steps of both enzymes. In this study, the metal-binding properties of
H. pylori
HypB were characterized, and the effects of metal binding on the biochemical behavior of the protein were examined. The protein can bind stoichiometric amounts of Zn(II) or Ni(II), each with nanomolar affinity. Mutation of Cys106 and His107, which are located between two major GTPase motifs, results in undetectable Ni(II) binding, and the Zn(II) affinity is weakened by 2 orders of magnitude. These two residues are also required for the metal-dependent dimerization observed in the presence of Ni(II) but not Zn(II). The addition of metals to the protein has distinct impacts on GTPase activity, with zinc significantly reducing GTP hydrolysis to below detectable levels and nickel only slightly altering the
k
cat
and

K
m

of the reaction. The regulation of HypB activities by metal binding may contribute to the maturation of the nickel-containing enzymes.
The Sporulation Protein SirA Inhibits the Binding of DnaA to the Origin of Replication by Contacting a Patch of Clustered Amino Acids
Authors: Rahn-Lee Lilah , Merrikh Houra , Grossman Alan D. , Losick Richard
Published: January 2011

Bacteria regulate the frequency and timing of DNA replication initiation by controlling the activity of the replication initiator protein DnaA. SirA is a recently discovered regulator of DnaA in
Bacillus subtilis
whose synthesis is turned on at the start of sporulation. Here, we demonstrate that SirA contacts DnaA at a patch of 3 residues located on the surface of domain I of the replication initiator protein, corresponding to the binding site used by two unrelated regulators of DnaA found in other bacteria. We show that the interaction of SirA with domain I inhibits the ability of DnaA to bind to the origin of replication. DnaA mutants containing amino acid substitutions of the 3 residues are functional in replication initiation but are immune to inhibition by SirA.
Structural and Mechanical Properties ofKlebsiella pneumoniaeType 3 Fimbriae
Authors: Chen Feng-Jung , Chan Chia-Han , Huang Ying-Jung , Liu Kuo-Liang , Peng Hwei-Ling , Chang Hwan-You , Liou Gunn-Guang , Yew Tri-Rung , Liu Cheng-Hsien , Hsu Ken Y. , Hsu Long
Published: January 2011

This study investigated the structural and mechanical properties ofKlebsiella pneumoniaetype 3 fimbriae, which constitute a known virulence factor for the bacterium. Transmission electron microscopy and optical tweezers were used to understand the ability of the bacterium to survive flushes. An individualK. pneumoniaetype 3 fimbria exhibited a helix-like structure with a pitch of 4.1 nm and a three-phase force-extension curve. The fimbria was first nonlinearly stretched with increasing force. Then, it started to uncoil and extended several micrometers at a fixed force of 66 ± 4 pN (n= 22). Finally, the extension of the fimbria shifted to the third phase, with a characteristic force of 102 ± 9 pN (n= 14) at the inflection point. Compared with the P fimbriae and type 1 fimbriae of uropathogenicEscherichia coli,K. pneumoniaetype 3 fimbriae have a larger pitch in the helix-like structure and stronger uncoiling and characteristic forces.
Gene Expression Profiling of
Corynebacterium glutamicum
during Anaerobic Nitrate Respiration: Induction of the SOS Response for Cell Survival
Authors: Nishimura Taku , Teramoto Haruhiko , Inui Masayuki , Yukawa Hideaki
Published: January 2011

The gene expression profile of
Corynebacterium glutamicum
under anaerobic nitrate respiration revealed marked differences in the expression levels of a number of genes involved in a variety of cellular functions, including carbon metabolism and respiratory electron transport chain, compared to the profile under aerobic conditions using DNA microarrays. Many SOS genes were upregulated by the shift from aerobic to anaerobic nitrate respiration. An elongated cell morphology, similar to that induced by the DivS-mediated suppression of cell division upon cell exposure to the DNA-damaging reagent mitomycin C, was observed in cells subjected to anaerobic nitrate respiration. None of these transcriptional and morphological differences were observed in a
recA
mutant strain lacking a functional RecA regulator of the SOS response. The
recA
mutant cells additionally showed significantly reduced viability compared to wild-type cells similarly grown under anaerobic nitrate respiration. These results suggest a role for the RecA-mediated SOS response in the ability of cells to survive any DNA damage that may result from anaerobic nitrate respiration in
C. glutamicum
.