bluuebunny/crossref_metadata_2025_split huggingface dataset:
Selenate-Dependent Anaerobic Arsenite Oxidation by a Bacterium from Mono Lake, California
Authors: Fisher Jenny C. , Hollibaugh James T. 
Published: March 2008

ABSTRACT

Arsenate was produced when anoxic Mono Lake water samples were amended with arsenite and either selenate or nitrate. Arsenite oxidation did not occur in killed control samples or live samples with no added terminal electron acceptor. Potential rates of anaerobic arsenite oxidation with selenate were comparable to those with nitrate (∼12 to 15 μmol·liter
−1
h
−1
). A pure culture capable of selenate-dependent anaerobic arsenite oxidation (strain ML-SRAO) was isolated from Mono Lake water into a defined salts medium with selenate, arsenite, and yeast extract. This strain does not grow chemoautotrophically, but it catalyzes the oxidation of arsenite during growth on an organic carbon source with selenate. No arsenate was produced in pure cultures amended with arsenite and nitrate or oxygen, indicating that the process is selenate dependent. Experiments with washed cells in mineral medium demonstrated that the oxidation of arsenite is tightly coupled to the reduction of selenate. Strain ML-SRAO grows optimally on lactate with selenate or arsenate as the electron acceptor. The amino acid sequences deduced from the respiratory arsenate reductase gene (
arrA
) from strain ML-SRAO are highly similar (89 to 94%) to those from two previously isolated Mono Lake arsenate reducers. The 16S rRNA gene sequence of strain ML-SRAO places it within the
Bacillus
RNA group 6 of gram-positive bacteria having low G+C content.
Mechanism for Oxidation of High-Molecular-Weight Substrates by a Fungal Versatile Peroxidase, MnP2
Authors: Tsukihara Takahisa , Honda Yoichi , Sakai Ryota , Watanabe Takahito , Watanabe Takashi 
Published: March 2008

ABSTRACTUnlike general peroxidases,Pleurotus ostreatusMnP2 was reported to have a unique property of direct oxidization of high-molecular-weight compounds, such as Poly R-478 and RNase A. To elucidate the mechanism for oxidation of polymeric substrates by MnP2, a series of mutant enzymes were produced by using a homologous gene expression system, and their reactivities were characterized. A mutant enzyme with an Ala substituting for an exposing Trp (W170A) drastically lost oxidation activity for veratryl alcohol (VA), Poly R-478, and RNase A, whereas the kinetic properties for Mn2+and H2O2were substantially unchanged. These results demonstrated that, in addition to VA, the high-molecular-weight substrates are directly oxidized by MnP2 at W170. Moreover, in the mutants Q266F and V166/168L, amino acid substitution(s) around W170 resulted in a decreased activity only for the high-molecular-weight substrates. These results, along with the three-dimensional modeling of the mutants, suggested that the mutations caused a steric hindrance to access of the polymeric substrates to W170. Another mutant, R263N, contained a newly generated N glycosylation site and showed a higher molecular mass in sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis. Interestingly, the R263N mutant exhibited an increased reactivity with VA and high-molecular-weight substrates. The existence of an additional carbohydrate modification and the catalytic properties in this mutant are discussed. This is the first study of a direct mechanism for oxidation of high-molecular-weight substrates by a fungal peroxidase using a homologous gene expression system.
Taxonomic and Strain-Specific Identification of the Probiotic Strain
Lactobacillus rhamnosus
35 within the
Lactobacillus casei
Group
Authors: Coudeyras Sophie , Marchandin Hélène , Fajon Céline , Forestier Christiane 
Published: March 2008

ABSTRACT

Lactobacilli are lactic acid bacteria that are widespread in the environment, including the human diet and gastrointestinal tract. Some
Lactobacillus
strains are regarded as probiotics because they exhibit beneficial health effects on their host. In this study, the long-used probiotic strain
Lactobacillus rhamnosus
35 was characterized at a molecular level and compared with seven reference strains from the
Lactobacillus casei
group. Analysis of
rrn
operon sequences confirmed that
L. rhamnosus
35 indeed belongs to the
L. rhamnosus
species, and both temporal temperature gradient gel electrophoresis and ribotyping showed that it is closer to the probiotic strain
L. rhamnosus
ATCC 53103 (also known as
L. rhamnosus
GG) than to the species type strain. In addition,
L. casei
ATCC 334 gathered in a coherent cluster with
L. paracasei
type strains, unlike
L. casei
ATCC 393, which was closer to
L. zeae
; this is evidence of the lack of relatedness between the two
L. casei
strains. Further characterization of the eight strains by pulsed-field gel electrophoresis repetitive DNA element-based PCR identified distinct patterns for each strain, whereas two isolates of
L. rhamnosus
35 sampled 40 years apart could not be distinguished. By subtractive hybridization using the
L. rhamnosus
GG genome as a driver, we were able to isolate five
L. rhamnosus
35-specific sequences, including two phage-related ones. The primer pairs designed to amplify these five regions allowed us to develop rapid and highly specific PCR-based identification methods for the probiotic strain
L. rhamnosus
35.
Development of a Microbial Time/Temperature Indicator Prototype for Monitoring the Microbiological Quality of Chilled Foods
Authors: Vaikousi Hariklia , Biliaderis Costas G. , Koutsoumanis Konstantinos P. 
Published: March 2008

ABSTRACT

A time/temperature indicator (TTI) system based on the growth and metabolic activity of a
Lactobacillus sakei
strain was developed for monitoring food quality throughout the chilled-food chain. In the designed system, an irreversible color change of a chemical chromatic indicator (from red to yellow) progressively occurs due to the pH decline that results from microbial growth and metabolism in a selected medium. The relation of the TTI response (color change) to the growth and metabolic activity (glucose consumption, lactic acid production, pH decrease) of
L. sakei
was studied. In addition, the temperature dependence of the TTI kinetics was investigated isothermally in the range of 0 to 16°C and modeled with a system of differential equations. At all temperatures tested, the pH and color changes of the TTI system followed closely the growth of
L. sakei
, with the endpoint (the time at which a distinct visual color change to the final yellow was observed) of the TTI coinciding with a population level of 10
7
to 10
8
CFU/ml. The endpoint decreased from 27 days at 0°C to 2.5 days at 16°C, yielding an activation energy of 97.7 kJ/mol, which was very close to the activation energy of the
L. sakei
growth rate in the TTI substrate (103.2 kJ/mol). Furthermore, experiments conducted on the effect of the inoculum level showed a negative linear relationship between the level of
L. sakei
inoculated in the system medium and the endpoint of the TTI. For example, the endpoint at 8°C ranged from 6 to 2 days for inoculum levels of 10
1
and 10
6
CFU/ml, respectively. This relationship allows the easy adjustment of the TTI endpoint at a certain temperature according to the shelf life of the food product of concern by using an appropriate inoculum level of
L. sakei
. The microbial TTI prototype developed in the present study could be used as an effective tool for monitoring shelf life during the distribution and storage of food products that are spoiled primarily by lactic acid bacteria or other bacteria exhibiting similar kinetic responses and spoilage potentials. Apart from the low cost, the main advantage of the proposed TTI is that its response closely matches the loss of the quality of a food product by simulating the microbial spoilage process in particular environments.
The Type III Secretion System of
Xanthomonas fuscans
subsp.
fuscans
Is Involved in the Phyllosphere Colonization Process and in Transmission to Seeds of Susceptible Beans
Authors: Darsonval A. , Darrasse A. , Meyer D. , Demarty M. , Durand K. , Bureau C. , Manceau C. , Jacques M.-A. 
Published: March 2008

ABSTRACT

Understanding the survival, multiplication, and transmission to seeds of plant pathogenic bacteria is central to study their pathogenesis. We hypothesized that the type III secretion system (T3SS), encoded by
hrp
genes, could have a role in host colonization by plant pathogenic bacteria. The seed-borne pathogen
Xanthomonas fuscans
subsp.
fuscans
causes common bacterial blight of bean (
Phaseolus vulgaris
). Directed mutagenesis in strain CFBP4834-R of
X. fuscans
subsp.
fuscans
and bacterial population density monitoring on bean leaves showed that strains with mutations in the
hrp
regulatory genes,
hrpG
and
hrpX
, were impaired in their phyllospheric growth, as in the null interaction with
Escherichia coli
C600 and bean. In the compatible interaction, CFBP4834-R reached high phyllospheric population densities and was transmitted to seeds at high frequencies with high densities. Strains with mutations in structural
hrp
genes maintained the same constant epiphytic population densities (1 × 10
5
CFU g
−1
of fresh weight) as in the incompatible interaction with
Xanthomonas campestris
pv. campestris ATCC 33913 and the bean. Low frequencies of transmission to seeds and low bacterial concentrations were recorded for CFBP4834-R
hrp
mutants and for ATCC 33913, whereas
E. coli
C600 was not transmitted. Moreover, unlike the wild-type strain, strains with mutations in
hrp
genes were not transmitted to seeds by vascular pathway. Transmission to seeds by floral structures remained possible for both. This study revealed the involvement of the
X. fuscans
subsp.
fuscans
T3SS in phyllospheric multiplication and systemic colonization of bean, leading to transmission to seeds. Our findings suggest a major contribution of
hrp
regulatory genes in host colonization processes.
IS
6110
, a
Mycobacterium tuberculosis
Complex-Specific Insertion Sequence, Is Also Present in the Genome of
Mycobacterium smegmatis
, Suggestive of Lateral Gene Transfer among Mycobacterial Species
Authors: Coros Abbie , DeConno Erin , Derbyshire Keith M. 
Published: March 2008

ABSTRACT

IS
6110
is an insertion element found exclusively within the members of the
Mycobacterium tuberculosis
complex (MTBC), and because of this exclusivity, it has become an important diagnostic tool in the identification of MTBC species. The restriction of IS
6110
to the MTBC is hypothesized to arise from the inability of these bacteria to exchange DNA. We have identified an IS
6110
-related element in a strain of
Mycobacterium smegmatis.
The presence of IS
6110
indicates that lateral gene transfer has occurred among mycobacterial species, suggesting that the mycobacterial gene pool is larger than previously suspected.
Influence of the σBStress Factor andyxaB, the Gene for a Putative Exopolysaccharide Synthase under σBControl, on Biofilm Formation
Authors: Nagórska Krzysztofa , Hinc Krzysztof , Strauch Mark A. , Obuchowski Michał 
Published: March 2008

ABSTRACTBacillus subtilisforms structured communities of biofilms encased in an exopolysaccharide matrix on solid surfaces and at the air-liquid interface. It is postulated that nonoptimal growth conditions induce this multicellular behavior. We showed that under laboratory conditions a strain deleted forsigBwas unable to form a floating pellicle on the surface of a liquid medium. However, overexpression ofyxaB, encoding a putative exopolysaccharide synthase, from a pSpacpromoter in asigB-deleted strain resulted in partial recovery of the wild-type phenotype, indicating the participation of the YxaB protein in this multicellular process. We present data concerning the regulation of transcription of genesyxaBandyxaA, encoding a putative glycerate kinase. Both genes are cotranscribed as a single transcription unit from a σA-dependent promoter during vegetative growth of a liquid bacterial culture. The promoter driving transcription of theyxaABoperon is regulated by AbrB. In addition, the second gene in the operon,yxaB, possesses its own promoter, which is recognized by RNA polymerase containing the σBsubunit. This transcription start site is used under general stress conditions, resulting in increased expression.
ATP-Induced Shrinkage of DNA with MukB Protein and the MukBEF Complex of
Escherichia coli
Authors: Chen Ning , Zinchenko Anatoly A. , Yoshikawa Yuko , Araki Sumiko , Adachi Shun , Yamazoe Mitsuyoshi , Hiraga Sota , Yoshikawa Kenichi 
Published: March 2008

ABSTRACT

Fluorescence microscopic observation of individual T4 DNA molecules revealed that the MukBEF complex (bacterial condensin) and its subunit, the MukB (a member of the SMC [structural maintenance of chromosomes] superfamily) homodimer, of
Escherichia coli
markedly shrunk large DNA molecules in the presence of hydrolyzable ATP. In contrast, in the presence of ADP or ATP-γS, the conformation of DNA was almost not changed. This suggests that the ATPase activity of subunit MukB is essential for shrinking large DNA molecules. Stretching experiments on the shrunken DNA molecules in the presence of ATP and MukBEF indicated a cross-bridging interaction between DNA molecules.
Inclusion of specific water volume within an elasto-plastic model for unsaturated soil
Authors: Wheeler S J 
Published: March 2008

Existing elasto-plastic critical state constitutive models for unsaturated soil provide no information on the variation of water content or degree of saturation. These models cannot therefore, for example, be used to predict unsaturated soil behaviour during undrained loading, when the variation of suction is determined by the requirement that water content remains constant. This problem has been tackled by extending an existing elasto-plastic model to include relationships describing the variation of specific water volume (the volume of water and solids in an element of soil containing unit volume of solids). The proposed form of the variation of specific water volume was based on consideration of the soil fabric, resulting in a coupled form of elasto-plastic behaviour. Predictions from the elasto-plastic model showed good agreement with the experimental results from suction-controlled triaxial tests on unsaturated samples of compacted speswhite kaolin. Normal compression lines for specific water volume at different values of suction were well predicted, as was the variation of specific water volume during wetting. Critical state values of specific water volume were slightly underestimated, but test paths for both drained and undrained shearing were predicted with reasonable success. Key words: compacted clays, constitutive model, critical state, elasto-plasticity, triaxial tests, unsaturated.
In situ soil flushing using prefabricated vertical drains
Authors: Gabr M A , Bowders J J , Wang J , Quaranta J 
Published: March 2008

The use of prefabricated vertical drains (PVDs) for enhanced soil flushing was investigated using a bench scale experimental setup. Soil samples were prepared and saturated in contaminant recovery cells (CRC). The PVDs were installed in rectangular and circular configurations, and a vacuum was applied to recover subsurface water. A predictive model for contaminant transport using the PVD-enhanced soil flushing was developed and presented. Results from the CRC tests using four PVDs in a rectangular arrangement indicated that the volume of the retrieved fluid increased as a function of the vacuum level and was approximately 0.55 mL/s at a vacuum level of 9.0 kPa. This represented a recovery efficiency of approximately 100%, since the base inflow through the sample was 0.55 mL/s. Using six PVDs in a circular configuration with a spacing of 14 mm from the center of the circle, a flow rate of approximately 6 mL/s was recovered under 6.8 kPa of vacuum. The average drawdown under a vacuum of 8.6 kPa ranged from 15 to 45 mm, and the zone of effective drawdown was measured to be approximately 200 mm in diameter. This value is approximately 10 times the effective diameter of the PVDs. An injectionextraction test indicated that, under an applied injection pressure of 3.5 kPa, an injection flow rate of approximately 6.5 mL/s was measured. At a vacuum pressure of 6 kPa and using the cicular configuration, the injection and recovery flow rates were approximately balanced. Such balance is essential to avoid decreasing the flushing rate due to the compression of the soil voids as well as to avoid the desaturation of soil profile. Key words: contaminant transport, injection, model, prefabricated vertical drains, retardation, soil flushing, vacuum.
Application of pipe temperature simulator for Norman Wells oil pipeline
Authors: Nixon JF (Derick) , MacInnes Kaye L 
Published: March 2008

The Norman Wells oil pipeline has been operating successfully for 10 years, transporting crude oil from the Norman Wells field in the Northwest Territories to southern markets. The temparatures of the oil in the pipeline have been closely monitored at several locations, and a detailed record of the thermal performance of the pipeline and the response of the surrounding permafrost soils is available. Recently, a geothermal program has been developed to predict the temparature profiles along a buried pipeline in more detail than has hitherto been attempted. The recently developed simulator accounts for freezing and thawing around the pipeline, while accounting for the heat losses from the pipeline to the ground as the contents flow through the line. The Norman Wells oil pipeline has provided an opportunity to test and calibrate the new model. Comparaisons between observed temperatures along the line and predictions from the simulator have been made, and the agreement is generally extremely good. The downstream effects of recent changes to the operating temperatures at Norman Wells were accurately predicted, illustrating the potential applications of model. The simulator will allow the effects of future planned changes in operating conditions to be more accurately evaluated, as well as playing an important part in design engineering studies for future oil, water, and gas pipeline projects elsewhere. Key words: pipeline, geothermal, oil temperatures. permafrost, thaw, Norman Wells.
Microstructure of a compacted silt
Authors: Delage Pierre , Audiguier Martine , Cui Yu-Jun , Howat Michael D 
Published: March 2008

This paper presents a qualitative and quantitative study of the microstructure of a compacted silt, carried out using a scanning electron microscope and mercury intrusion pore size distribution measurements. Samples have been statically compacted at three water contents: on the dry side of the standard Proctor optimum water content, at the optimum, and on the wet side. The wet sample has a matrix type structure, with a clayey fraction filling the voids and adhering to the silt-sized grains, whereas the other samples display a structure characterized by a skeleton made of silt grain aggregates linked together by clayey bidges. The distribution of water and air within the microstructure of the compacted soil is described for each of the three compaction states. Key words: compacted soil, microstructure, scanning electron microscope, pore size distribution, mercury intrusion, clay hydration.
High-bandwidth data dissemination for large-scale distributed systems
Authors: Kostić Dejan , Snoeren Alex C. , Vahdat Amin , Braud Ryan , Killian Charles , Anderson James W. , Albrecht Jeannie , Rodriguez Adolfo , Vandekieft Erik 
Published: March 2008

This article focuses on the multireceiver data dissemination problem. Initially, IP multicast formed the basis for efficiently supporting such distribution. More recently, overlay networks have emerged to support point-to-multipoint communication. Both techniques focus on constructing trees rooted at the source to distribute content among all interested receivers. We argue, however, that trees have two fundamental limitations for data dissemination. First, since all data comes from a single parent, participants must often continuously probe in search of a parent with an acceptable level of bandwidth. Second, due to packet losses and failures, available bandwidth is monotonically decreasing down the tree.To address these limitations, we present Bullet, a data dissemination mesh that takes advantage of the computational and storage capabilities of end hosts to create a distribution structure where a node receives data in parallel from multiple peers. For the mesh to deliver improved bandwidth and reliability, we need to solve several key problems: (i) disseminating disjoint data over the mesh, (ii) locating missing content, (iii) finding who to peer with (peering strategy), (iv) retrieving data at the right rate from all peers (flow control), and (v) recovering from failures and adapting to dynamically changing network conditions. Additionally, the system should be self-adjusting and should have few user-adjustable parameter settings. We describe our approach to addressing all of these problems in a working, deployed system across the Internet. Bullet outperforms state-of-the-art systems, including BitTorrent, by 25-70% and exhibits strong performance and reliability in a range of deployment settings. In addition, we find that, relative to tree-based solutions, Bullet reduces the need to perform expensive bandwidth probing.
Host Nuclear Factor-κB Activation Potentiates Lung Cancer Metastasis
Authors: Stathopoulos Georgios T. , Sherrill Taylor P. , Han Wei , Sadikot Ruxana T. , Yull Fiona E. , Blackwell Timothy S. , Fingleton Barbara 
Published: March 2008

Abstract
Epidemiologic and experimental evidence suggests that a link exists between inflammation and cancer, although this relationship has only recently begun to be elucidated for lung cancer, the most frequently fatal human tumor. Nuclear factor-κB (NF-κB), a transcription factor that controls innate immune responses in the lungs, has been implicated as an important determinant of cancer cell proliferative and metastatic potential; however, its role in lung tumorigenesis is uncertain. Here, we specifically examine the role of NF-κB–induced airway inflammation in lung cancer metastasis using a model of intravenous injection of Lewis lung carcinoma cells into immunocompetent C57Bl/6 mice. Induction of lung inflammation by direct and specific NF-κB activation in airway epithelial cells potentiates lung adenocarcinoma metastasis. Moreover, we identify resident lung macrophages as crucial effectors of lung susceptibility to metastatic cancer growth. We conclude that NF-κB activity in host tissue is a significant factor in the development of lung metastasis. (Mol Cancer Res 2008;6(3):364–71)