bluuebunny/crossref_metadata_2025 huggingface dataset:
Iron plaque enhances phosphorus uptake by rice (Oryza sativa) growing under varying phosphorus and iron concentrations
Authors: Liang Y. , Zhu Y.‐G. , Xia Y. , Li Z. , Ma Y.
Published: November 2006

Both solution culture and pot experiments were performed to investigate (a) the effects of external Fe (II) concentrations and forms on the formation of iron plaque on the roots of rice (Oryza sativa) and subsequent P adsorption on iron plaque and shoot P concentrations and (b) the effects of soil moisture regimes on the formation of iron plaque and P adsorption on root surfaces and P accumulation in shoots. The results showed that iron plaque was significantly increased with increasing Fe2+ concentrations in the solution culture. The amounts of P adsorbed on the iron plaque were increased significantly with external Fe2+ concentrations. Although shoot P concentration was not significantly affected by Fe2+ treatment after incubation for 2 days, it was significantly increased in the Fe‐treated plants compared with Fe‐deprived ones after incubation for 4 days. Soil culture experiment showed that the formation of iron plaque on root surfaces was promoted by exogenous iron, with greater amount of iron plaque being formed by addition of ferric hydroxide than of ferric oxide. Phosphorus adsorption on iron plaque also increased with the addition of iron oxides, and increasing soil P increased the amounts of P associated with the iron plaque and shoot P concentration. The amounts of iron plaque were almost sixfold higher under flooding condition than under field capacity condition. Plants pretreated under flooding condition generally had higher shoot P concentrations when they were transplanted to solutions with varying P levels, and this was most pronounced in the treatment with highest solution P concentration. The results suggest that iron plaque acts as a nutrient reservoir for phosphorus in the rhizosphere and helps enhance P acquisition by rice.
Quality assurance and system stability of a clinical MRI‐guided focused ultrasound system: Four‐year experience
Authors: McDannold Nathan , Hynynen Kullervo
Published: November 2006

To retrospectively evaluate the four‐year experience of a quality assurance method for a MRI‐guided focused ultrasound system that uses temperature maps acquired during heating in an ultrasound/MRI phantom. This quality assurance method was performed before 148 clinical uterine fibroid thermal ablation treatments. The stability of the peak temperature rise, the targeting accuracy, the shape of the heated zone, and the noise level in the imaging was evaluated. The peak temperature rise was mostly stable for the first three years. An increase in heating was observed when the system was replaced after year three. Detection of this increase was taken into account in the subsequent clinical treatments. A small secondary hotspot was detected by the temperature maps and was seen to be resolved after system calibration. The average standard deviation in unheated regions of the phantom in the temperature maps was 0.5±0.2 °C; it was less than 1 °C in all but one procedure. The average initial targeting error was 2.8±1.8 and 2.8±2.1 mm in two radial directions and 7.7±2.9 mm along the ultrasound beam direction. The width of the heating profile was consistent over the four years. This simple method to evaluate the performance appeared to be sensitive to small changes in system performance, which was adequately stable over a four‐year time period.
The response of prototype plane‐parallel ionization chambers in small megavoltage x‐ray fields
Authors: McNiven Andrea L. , Mulligan Matt , Kron Tomas , Battista Jerry J.
Published: November 2006

Accurate small‐field dosimetry has become important with the use of multiple small fields in modern radiotherapy treatments such as IMRT and stereotactic radiosurgery. In this study, we investigate the response of a set of prototype plane‐parallel ionization chambers, based upon the Exradin T11 chamber, with active volume diameters of 2, 4, 10, and , exposed to stereotactic radiotherapy x‐ray fields. Our goal was to assess their usefulness for accurate small x‐ray field dose measurements. The relative ionization response was measured in circular fields (0.5 to diameter) as compared to a reference field. A large discrepancy was found between the relative response in the smallest plane‐parallel chamber and other small volume dosimeters (radiochromic film, micro‐metal‐oxide‐semiconductor field‐effect transistor and diode) used for comparison. Monte Carlo BEAMnrc simulations were used to simulate the experimental setup in order to investigate the cause of the under‐response and to calculate appropriate correction factors that could be applied to experimental measurements. It was found that in small fields, the air cavity of these custom‐made research chambers perturbed the secondary electron fluence profile significantly, resulting in decreased fluence within the active volume, which in turn produces a chamber under‐response. It is demonstrated that a large correction to the correction factor would be required to improve dosimetric accuracy in small fields, and that these factors could be derived using Monte Carlo simulations.
Dual system approach to computer‐aided detection of breast masses on mammograms
Authors: Wei Jun , Chan Heang‐Ping , Sahiner Berkman , Hadjiiski Lubomir M. , Helvie Mark A. , Roubidoux Marilyn A. , Zhou Chuan , Ge Jun
Published: November 2006

In this study, our purpose was to improve the performance of our mass detection system by using a new dual system approach which combines a computer‐added detection (CAD) system optimized with “average” masses with another CAD system optimized with “subtle” masses. The two single CAD systems have similar image processing steps, which include prescreening, object segmentation, morphological and texture feature extraction, and false positive (FP) reduction by rule‐based and linear discriminant analysis (LDA) classifiers. A feed‐forward backpropagation artificial neural network was trained to merge the scores from the LDA classifiers in the two single CAD systems and differentiate true masses from normal tissue. For an unknown test mammogram, the two single CAD systems are applied to the image in parallel to detect suspicious objects. A total of three data sets were used for training and testing the systems. The first data set of 230 current mammograms, referred to as the average mass set, was collected from 115 patients. We also collected 264 mammograms, referred to as the subtle mass set, which were one to two years prior to the current exam from these patients. Both the average and the subtle mass sets were partitioned into two independent data sets in a cross validation training and testing scheme. A third data set containing 65 cases with 260 normal mammograms was used to estimate the FP marker rates during testing. When the single CAD system trained on the average mass set was applied to the test set with average masses, the FP marker rates were 2.2, 1.8, and 1.5 per image at the case‐based sensitivities of 90%, 85%, and 80%, respectively. With the dual CAD system, the FP marker rates were reduced to 1.2, 0.9, and 0.7 per image, respectively, at the same case‐based sensitivities. Statistically significantimprovements on the free response receiver operating characteristic curves were observed when the dual system and the single system were compared using the test sets with either average masses or subtle masses.
The impact of hypofractionation on simultaneous dose‐boosting to hypoxic tumor subvolumes
Authors: Ruggieri Ruggero , Nahum Alan E.
Published: November 2006

In a previous study, the dependence of the therapeutic ratio on the number of fractions , including both acute and chronic hypoxia, was investigated for homogeneously irradiated tumors. The present study further develops the model to include simultaneous dose‐boosting to the hypoxic tumour subvolumes. The acutely hypoxic tumor subvolume was partitioned into a large number of oxygenation subvolumes, modelled through rectangular waves all with the same frequency and fractional time spent below the hypoxic threshold, but with randomly distributed phases. Three quite different assumptions were considered for the effect of prolonged hypoxia on the radiosensitivity of the chronically hypoxic clonogens, ranging from equal radiosensitivity to that of the a‐cells to an even greater radiosensitivity than that of the well‐oxygenated cells. The linear‐quadratic model, including tumor repopulation, intertumor ‐heterogeneity, and dependence of the oxygen enhancement ratio on the dose per fraction, was adopted for tumor control probability (TCP) computation. To include a consideration of therapeutic ratio, lung irradiation was considered and the mean normalized total lung dose was used as a risk indicator. For those schedules yielding 50% TCP with homogeneous irradiation (our reference benchmark), we estimated the gain in TCP and the corresponding from dose boosting only the ‐subvolume, both the ‐ and the ch‐subvolumes, or 50% of the pretreatment tumor volume without specific targeting to tumor hypoxia. For two of the three assumptions for the radiosensitivity of the ch‐clonogens, dose‐boosting the ch‐subvolume was associated with a substantial gain in TCP, and with a trend including minima in , for severely hypofractionated schedules only, whereas when dose‐boosting both the ‐ and the ch‐subvolumes a substantial gain in TCP was always obtained for multifractionated schedules. By contrast, the “blind” dose‐boosting strategy was generally inferior, although an appreciable gain in TCP for severely hypofractionated schedules was obtained. In conclusion, a strategy of dose‐boosting tumor hypoxia, guided by nuclear medicine techniques that substantially map chronic hypoxia, is expected to yield optimal gains in TCP via severely hypofractionated delivery.
In vivo dosimetry by an aSi‐based EPID
Authors: Piermattei Angelo , Fidanzio Andrea , Stimato Gerardina , Azario Luigi , Grimaldi Luca , D'Onofrio Guido , Cilla Savino , Balducci Mario , Gambacorta Maria Antonietta , Di Napoli Nicola , Cellini Numa
Published: November 2006

A method for the in vivo determination of the isocenter dose, , and mid‐plane dose, , using the transmitted signal measured by 25 central pixels of an aSi‐based EPID is here reported. The method has been applied to check the conformal radiotherapy of pelvic tumors and supplies accurate in vivo dosimetry avoiding many of the disadvantages associated with the use of two diode detectors (at the entrance and exit of the patient) as their periodic recalibration and their positioning. Irradiating water‐equivalent phantoms of different thicknesses, a set of correlation functions were obtained by the ratio between and as a function of the phantom thickness, , for a different field width, . For the in vivo determination of and values, the water‐equivalent thickness of the patients (along the beam central axis) was evaluated by means of the treatment planning system that uses CT scans calibrated in terms of the electron densities. The and values experimentally determined were compared with the stated doses and , determined by the treatment planning system for ten pelvic treatments. In particular, for each treatment four fields were checked in six fractions. In these conditions the agreement between the in vivo dosimetry and stated doses at the isocenter point were within 3%. Comparing the 480 dose values obtained in this work with those obtained for 30 patients tested with a similar method, which made use of a small ion‐chamber positioned on the EPIDs to obtain the transmitted signal, a similar agreement was observed. The method here proposed is very practical and can be applied in every treatment fraction, supplying useful information about eventual patient dose variations due to the incorrect application of the quality assurance program based on the check of patient setup, machine setting, and calculations.
Step‐and‐shoot data acquisition and reconstruction for cardiac x‐ray computed tomography
Authors: Hsieh Jiang , Londt John , Vass Melissa , Li Jay , Tang Xiangyang , Okerlund Darin
Published: November 2006

Coronary artery imaging with x‐ray computed tomography (CT) is one of the most recent advancements in CT clinical applications. Although existing “state‐of‐the‐art” clinical protocols today utilize helical data acquisition, it suffers from the lack of ability to handle irregular heart rate and relatively high x‐ray dose to patients. In this paper, we propose a step‐and‐shoot data acquisition protocol that significantly overcomes these shortcomings. The key to the proposed protocol is the large volume coverageenabled by the cone beam CT scanner, which allows the coverage of the entire heart in 3 to 4 steps. In addition, we propose a gated complementary reconstruction algorithm that overcomes the longitudinal truncation problem resulting from the cone beam geometry. Computer simulations, phantom experiments, and clinical studies were conducted to validate our approach.
Suitability of new anode materials in mammography: Dose and subject contrast considerations using Monte Carlo simulation
Authors: Delis H. , Spyrou G. , Costaridou L. , Tzanakos G. , Panayiotakis G.
Published: November 2006

Mammography is the technique with the highest sensitivity and specificity, for the early detection of nonpalpable lesions associated with breast cancer. As screening mammography refers to asymptomatic women, the task of optimization between the image quality and the radiation dose is critical. A way toward optimization could be the introduction of new anode materials. A method for producing the x‐ray spectra of different anode/filter combinations is proposed. The performance of several mammographic spectra, produced by both existing and theoretical anode materials, is evaluated, with respect to their dose and subject contrast characteristics, using a Monte Carlo simulation.

The mammographic performance is evaluated utilizing a properly designed mathematical phantom with embedded inhomogeneities, irradiated with different spectra, based on combinations of conventional and new (Ru, Ag) anode materials, with several filters (Mo, Rh, Ru, Ag, Nb, Al). An earlier developed and validated Monte Carlo model, for deriving both image and dose characteristics in mammography, was utilized and overall performance results were derived in terms of subject contrast to dose ratio and squared subject contrast to dose ratio. Results demonstrate that soft spectra, mainly produced from Mo, Rh, and Ru anodes and filtered with ‐edge filters, provide increased subject contrast for inhomogeneities of both small size, simulating microcalcifications and low density, simulating masses. The harder spectra (W and Ag anode) come short in the discrimination task but demonstrate improved performance when considering the dose delivered to the breast tissue. As far as the overall performance is concerned, new theoretical spectra demonstrate a noticeable good performance that is similar, and in some cases better compared to commonly used systems, stressing the possibility of introducing new materials in mammographic practice as a possible contribution to its optimization task. In the overall optimization task in terms of subject contrast to dose ratio, tube voltage was found to have a minor effect, while with respect to the filter material, a lesion specific performance was noticed, with Al filtered spectra showing improved characteristics in case of the inhomogeneities simulating microcalcifications, while softer ‐edge filtered spectra are more suitable for the discrimination of inhomogeneities simulating masses.
Real-Time Quantitative PCR (QPCR) and Reverse Transcription-QPCR for Detection and Enumeration of Total Yeasts in Wine
Authors: Hierro Núria , Esteve-Zarzoso Braulio , González Ángel , Mas Albert , Guillamón Jose M.
Published: November 2006

Real-time PCR, or quantitative PCR (QPCR), has been developed to rapidly detect and quantify the total number of yeasts in wine without culturing. Universal yeast primers were designed from the variable D1/D2 domains of the 26S rRNA gene. These primers showed good specificity with all the wine yeasts tested, and they did not amplify the most representative wine species of acetic acid bacteria and lactic acid bacteria. Numerous standard curves were constructed with different strains and species grown in yeast extract-peptone-dextrose medium or incubated in wine. The small standard errors with these replicas proved that the assay is reproducible and highly robust. This technique was validated with artificially contaminated and natural wine samples. We also performed a reverse transcription-QPCR (RT-QPCR) assay from rRNA for total viable yeast quantification. This technique had a low detection limit and was more accurate than QPCR because the dead cells were not quantified. As far as we know, this is the first time that RT-QPCR has been performed to quantify viable yeasts from rRNA. RT-QPCR is a rapid and accurate technique for enumerating yeasts during industrial wine fermentation and controlling the risk of wine spoilage.
Capsular Polysaccharide Phase Variation in
Vibrio vulnificus
Authors: Hilton Tamara , Rosche Tom , Froelich Brett , Smith Benjamin , Oliver James
Published: November 2006

Commonly found in raw oysters,
Vibrio vulnificus
poses a serious health threat to immunocompromised individuals and those with serum iron overload, with a fatality rate of approximately 50%. An essential virulence factor is its capsular polysaccharide (CPS), which is responsible for a significant increase in virulence compared to nonencapsulated strains. However, this bacterium is known to vary the amount of CPS expressed on the cell surface, converting from an opaque (Op) colony phenotype to a translucent (Tr) colony phenotype. In this study, the consistency of CPS conversion was determined for four strains of
V. vulnificus
. Environmental conditions including variations in aeration, temperature, incubation time, oxidative stress, and media (heart infusion or modified maintenance medium agar) were investigated to determine their influence on CPS conversion. All conditions, with the exception of variations in media and oxidative stress, significantly affected the conversion of the population, with high ranges of CPS expression found even within cells from a single colony. The global quorum-sensing regulators RpoS and AI-2 were also examined. While RpoS was found to significantly mediate phenotypic conversion, quorum sensing was not. Finally, 12 strains that comprise the recently found clinical (C) and environmental (E) genotypes of
V. vulnificus
were examined to determine their rates of population conversion. C-genotype strains, which are most often associated with infection, had a significantly lower rate of population conversion from Op to Tr phenotypes than did E-genotype strains (ca. 38% versus ca. 14%, respectively). Biofilm capabilities of these strains, however, were not correlated with increased population conversion.
Phylogenetic Analysis of Buggy Creek Virus: Evidence for Multiple Clades in the Western Great Plains, United States of America
Authors: Pfeffer Martin , Foster Jerome E. , Edwards Eric A. , Brown Mary Bomberger , Komar Nicholas , Brown Charles R.
Published: November 2006

We present the first detailed phylogenetic analysis of Buggy Creek virus (BCRV), a poorly known alphavirus with transmission cycles involving a cimicid swallow bug (
Oeciacus vicarius
) vector and cliff swallows (
Petrochelidon pyrrhonota
) and house sparrows (
Passer domesticus
) as the principal avian hosts. Nucleotide sequences of a 2,075-bp viral envelope glycoprotein-coding region, covering the entire PE2 gene, were determined for 33 BCRV isolates taken from swallow bugs at cliff swallow colonies in Nebraska and Colorado in the summer of 2001 and were compared with the corresponding region of BCRV isolates collected from Oklahoma in the 1980s. We also analyzed isolates of the closely related Fort Morgan virus (FMV) collected from Colorado in the 1970s. Phylogenetic analysis indicated that BCRV falls into the western equine encephalomyelitis complex of alphaviruses, in agreement with antigenic results and a previous alphavirus phylogeny based on the E1 coding region. We found four distinct BCRV/FMV clades, one each unique to Nebraska, Colorado, and Oklahoma and one containing isolates from both Nebraska and Colorado. BCRV isolates within the two clades from Nebraska showed 5.7 to 6.2% nucleotide divergence and 0.7 to 1.9% amino acid divergence, and within these clades, we found multiple subclades. Nebraska subclades tended to be confined to one or a few cliff swallow colonies that were close to each other in space, although in some cases, near-identical isolates were detected at sites up to 123 km apart. Viral gene flow occurs when cliff swallows move (bugs) between colony sites, and the genetic structure of BCRV may reflect the limited dispersal abilities of its insect vector.
Inactivation of Adhesion and Invasion of Food-Borne
Listeria monocytogenes
by Bacteriocin-Producing
Bifidobacterium
Strains of Human Origin
Authors: Moroni Olivier , Kheadr Ehab , Boutin Yvan , Lacroix Christophe , Fliss Ismaïl
Published: November 2006

Three bacteriocin-producing bifidobacterial isolates from newborns were identified as
Bifidobacterium thermacidophilum
(two strains) and
B. thermophilum
(one strain). This study was undertaken to evaluate the ability of these strains to compete with food-borne
Listeria monocytogenes
for adhesion and invasion sites on Caco-2 and HT-29 cells. The bifidobacteria adhered at levels ranging from 4% to 10% of the CFU added, but none of the bifidobacteria were able to invade cells. The abilities of
Listeria
to adhere to and to invade cells varied widely depending on the strain tested. Three groups of
Listeria
were identified based on invasiveness: weakly invasive, moderately invasive, and highly invasive strains. One strain from each group was tested in competition with bifidobacteria.
B. thermacidophilum
RBL70 was the most effective in blocking invasion of
Listeria
, and the decreases in invasion ranged from 38% to 90%. For all three bifidobacterial strains, contact between the cell monolayer and the bifidobacteria for 1 h before exposure to
Listeria
increased the degree of inhibition. Finally, visualization of competition for adhesion sites on cells by fluorescent in situ hybridization suggested that the two bacteria tended to adhere in close proximity.
Occurrence and Antibiotic Sensitivity of
Listeria monocytogenes
Strains Isolated from Oysters, Fish, and Estuarine Water
Authors: Rodas-Suárez O. R. , Flores-Pedroche J. F. , Betancourt-Rule J. M. , Quiñones-Ramírez E. I. , Vázquez-Salinas C.
Published: November 2006

We analyzed the presence of
Listeria
spp. in oyster, fish, and seawater samples and tested isolates for antibiotic sensitivity.
Listeria monocytogenes
was found in 4.5% of fish samples and 8.3% of seawater samples and was not recovered from oysters. Multiresistant environmental strains were found, representing a potential threat to human health.
Minireplicon from pBtoxis of
Bacillus thuringiensis
subsp.
israelensis
Authors: Tang Mujin , Bideshi Dennis K. , Park Hyun-Woo , Federici Brian A.
Published: November 2006

A 2.2-kb fragment containing a replicon from pBtoxis, the large plasmid that encodes the insecticidal endotoxins of
Bacillus thuringiensis
subsp.
israelensis
, was identified, cloned, and sequenced. This fragment contains
cis
elements, including iterons, found in replication origins of other large plasmids and suggests that pBtoxis replicates by a type A theta mechanism. Two genes, pBt156 and pBt157, encoding proteins of 54.4 kDa and 11.8 kDa, respectively, were present in an operon within this minireplicon, and each was shown by deletion analysis to be essential for replication. The deduced amino acid sequences of the 54.4-kDa and 11.8-kDa proteins showed no substantial homology with known replication (Rep) proteins. However, the 54.4-kDa protein contained a conserved FtsZ domain, and the 11.8 kDa protein contained a helix-turn-helix motif. As FtsZ proteins have known functions in bacterial cell division and the helix-turn-helix motif is present in Rep proteins, it is likely that these proteins function in plasmid replication and partitioning. The minireplicon had a copy number of two or three per chromosome equivalent in
B. thuringiensis
subsp.
israelensis
but did not replicate in
B. cereus
,
B. megaterium
, or
B. subtilis
. A plasmid constructed to synthesize large quantities of the Cry11A and Cyt1A endotoxins demonstrated that this minireplicon can be used to engineer vectors for
cry
and
cyt
gene expression.
c
-Type Cytochromes in
Pelobacter carbinolicus
Authors: Haveman Shelley A. , Holmes Dawn E. , Ding Yan-Huai R. , Ward Joy E. , DiDonato Raymond J. , Lovley Derek R.
Published: November 2006

Previous studies failed to detect
c
-type cytochromes in
Pelobacter
species despite the fact that other close relatives in the
Geobacteraceae
, such as
Geobacter
and
Desulfuromonas
species, have abundant
c-
type cytochromes. Analysis of the recently completed genome sequence of
Pelobacter carbinolicus
revealed 14 open reading frames that could encode
c
-type cytochromes. Transcripts for all but one of these open reading frames were detected in acetoin-fermenting and/or Fe(III)-reducing cells. Three putative
c
-type cytochrome genes were expressed specifically during Fe(III) reduction, suggesting that the encoded proteins may participate in electron transfer to Fe(III). One of these proteins was a periplasmic triheme cytochrome with a high level of similarity to PpcA, which has a role in Fe(III) reduction in
Geobacter sulfurreducens
. Genes for heme biosynthesis and system II cytochrome
c
biogenesis were identified in the genome and shown to be expressed. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis gels of protein extracted from acetoin-fermenting
P. carbinolicus
cells contained three heme-staining bands which were confirmed by mass spectrometry to be among the 14 predicted
c
-type cytochromes. The number of cytochrome genes, the predicted amount of heme
c
per protein, and the ratio of heme-stained protein to total protein were much smaller in
P. carbinolicus
than in
G. sulfurreducens
. Furthermore, many of the
c
-type cytochromes that genetic studies have indicated are required for optimal Fe(III) reduction in
G. sulfurreducens
were not present in the
P. carbinolicus
genome. These results suggest that further evaluation of the functions of
c
-type cytochromes in the
Geobacteraceae
is warranted.
Genetic Differences between Blight-Causing
Erwinia
Species with Differing Host Specificities, Identified by Suppression Subtractive Hybridization
Authors: Triplett Lindsay R. , Zhao Youfu , Sundin George W.
Published: November 2006

PCR-based subtractive hybridization was used to isolate sequences from
Erwinia amylovora
strain Ea110, which is pathogenic on apples and pears, that were not present in three closely related strains with differing host specificities:
E. amylovora
MR1, which is pathogenic only on
Rubus
spp.;
Erwinia pyrifoliae
Ep1/96, the causal agent of shoot blight of Asian pears; and
Erwinia
sp. strain Ejp556, the causal agent of bacterial shoot blight of pear in Japan. In total, six subtractive libraries were constructed and analyzed. Recovered sequences included type III secretion components, hypothetical membrane proteins, and ATP-binding proteins. In addition, we identified an Ea110-specific sequence with homology to a type III secretion apparatus component of the insect endosymbiont
Sodalis glossinidius
, as well as an Ep1/96-specific sequence with homology to the
Yersinia pestis
effector protein tyrosine phosphatase YopH.
Role ofptsP,orfT, andsssRecombinase Genes in Root Colonization byPseudomonas fluorescensQ8r1-96
Authors: Mavrodi Olga V. , Mavrodi Dmitri V. , Weller David M. , Thomashow Linda S.
Published: November 2006

Pseudomonas fluorescensQ8r1-96 produces 2,4-diacetylphloroglucinol (2,4-DAPG), a polyketide antibiotic that suppresses a wide variety of soilborne fungal pathogens, includingGaeumannomyces graminisvar.tritici, which causes take-all disease of wheat. Strain Q8r1-96 is representative of the D-genotype of 2,4-DAPG producers, which are exceptional because of their ability to aggressively colonize and maintain large populations on the roots of host plants, including wheat, pea, and sugar beet. In this study, three genes, ansssrecombinase gene,ptsP, andorfT, which are important in the interaction ofPseudomonasspp. with various hosts, were investigated to determine their contributions to the unusual colonization properties of strain Q8r1-96. Thesssrecombinase andptsPgenes influence global processes, including phenotypic plasticity and organic nitrogen utilization, respectively. TheorfTgene contributes to the pathogenicity ofPseudomonas aeruginosain plants and animals and is conserved among saprophytic rhizosphere pseudomonads, but its function is unknown. Clones containing these genes were identified in a Q8r1-96 genomic library, sequenced, and used to construct gene replacement mutants of Q8r1-96. Mutants were characterized to determine their 2,4-DAPG production, motility, fluorescence, colony morphology, exoprotease and hydrogen cyanide (HCN) production, carbon and nitrogen utilization, and ability to colonize the rhizosphere of wheat grown in natural soil. TheptsPmutant was impaired in wheat root colonization, whereas mutants with mutations in thesssrecombinase gene andorfTwere not. However, all three mutants were less competitive than wild-typeP. fluorescensQ8r1-96 in the wheat rhizosphere when they were introduced into the soil by paired inoculation with the parental strain.
Quantitative Detection of
Corynebacterium casei
in Cheese by Real-Time PCR
Authors: Monnet Christophe , Correia Karine , Sarthou Anne-Sophie , Irlinger Françoise
Published: November 2006

The flora on the surface of smear-ripened cheeses is composed of numerous species of bacteria and yeasts that contribute to the production of the desired organoleptic properties. Due to the absence of selective media, it is very difficult to quantify cheese surface bacteria, and, consequently, the ecology of the cheese surface microflora has not been extensively investigated. We developed a SYBR green I real-time PCR method to quantify
Corynebacterium casei
, a major species of smear-ripened cheeses, using primers designed to target the 16S rRNA gene. It was possible to recover
C. casei
genomic DNA from the cheese matrix with nearly the same yield that
C. casei
genomic DNA is recovered from cells recovered by centrifugation from liquid cultures. Quantification was linear over a range from 10
5
to 10
10
CFU per g of cheese. The specificity of the assay was demonstrated with DNA from species related to
C. casei
and from other bacteria and yeasts belonging to the cheese flora. Nine commercial cheeses were analyzed by real-time PCR, and six of them were found to contain more than 10
5
CFU equivalents of
C. casei
per g. In two of them, the proportion of
C. casei
in the total bacterial flora was nearly 40%. The presence of
C. casei
in these samples was further confirmed by single-strand conformation polymorphism analysis and by a combined approach consisting of plate counting and 16S rRNA gene sequencing. We concluded that SYBR green I real-time PCR may be used as a reliable species-specific method for quantification of bacteria from the surface of cheeses.
Identification of Specific Gene Sequences Conserved in Contemporary Epidemic Strains ofSalmonella enterica
Authors: Kang Min-Su , Besser Thomas E. , Hancock Dale D. , Porwollik Steffen , McClelland Michael , Call Douglas R.
Published: November 2006

Genetic elements specific to recent and contemporary epidemic strains ofSalmonella entericawere identified using comparative genomic analysis. Two epidemic multidrug-resistant (MDR) strains, MDRSalmonella entericaserovar Typhimurium definitive phage type 104 (DT104) and cephalosporin-resistant MDRSalmonella entericaserovar Newport, and an epidemic pansusceptible strain,Salmonellaserovar Typhimurium DT160, were subjected toSalmonellagene microarray and suppression subtractive hybridization analyses. Their genome contents were compared with those of coexisting sporadic strains matched by serotype, geographic and temporal distribution, and host species origin. These paired comparisons revealed that epidemic strains ofS. entericahad specific genes and gene regions that were shared by isolates of the same subtype. Most of these gene sequences are related to mobile genetic elements, including phages, plasmids, and plasmid-like and transposable elements, and some genes may encode proteins conferring growth or survival advantages. The emergence of epidemic MDR strains may therefore be associated with the presence of fitness-associated genetic factors in addition to their antimicrobial resistance genes.
Temporal and Spatial Dispersal of
Cladobotryum
Conidia in the Controlled Environment of a Mushroom Growing Room
Authors: Adie Bruce , Grogan Helen , Archer Simon , Mills Peter
Published: November 2006

Cladobotryum
spp. are responsible for cobweb disease of mushrooms. In two commercial and one experimental mushroom-growing room,
Cladobotryum
conidia were released into the air in direct response to physical disturbance of disease colonies during either crop watering or treatment by covering with salt to 10 mm. Conidia were detected using a Burkard spore trap or agar-based trap plates. A maximum concentration of ∼25,000 conidia m
−3
was recorded in a small (75-m
3
) experimental growing room in the hour following the salting of 16 cobweb patches (0.55 m
2
). Concentrations of 100 and 40 conidia m
−3
were recorded in the two larger commercial growing rooms in the hour following the salting of 18 and 11 patches of cobweb (diameter, approximately 50 to 200 mm), respectively. In controlled experiments, disturbed conidia were dispersed rapidly throughout a small growing room, with 91 to 97% of conidia settling out within 15 min. Eighty-five percent of conidia settled out within a 0.5-m radius when air-conditioning fans were switched off, consistent with airborne spore dispersal. Alternative methods for treating diseased areas to minimize conidial release and distribution were investigated and included covering disease colonies with damp paper tissue prior to salt application (tissue salting) and holding a dust extractor above disease colonies during salt application. Both methods resulted in no detectable airborne conidia, but the tissue paper salting technique was more convenient. Prevention of airborne conidial release and distribution is essential to avoid mushroom spotting symptoms, secondary colonies, and early crop termination.
Simultaneous Biodetoxification of S, N, and O Pollutants by Engineering of a Carbazole-Degrading Gene Cassette in a Recombinant Biocatalyst
Authors: Yu Bo , Ma Cuiqing , Zhou Wenjuan , Zhu Shanshan , Wang Ying , Qu Jingyao , Li Fuli , Xu Ping
Published: November 2006

The gene cassette encoding enzymes responsible for degrading carbazole to anthranilic acid was introduced into a dibenzothiophene degrader. The resultant strain,
Rhodococcus erythropolis
XPDN, could simultaneously transform the model pollutants dibenzothiophene, carbazole, and dibenzofuran to nontoxic metabolites and may have an application potential for bioremediation.
An Integrated Approach to Functional Genomics: Construction of a Novel Reporter Gene Fusion Library forSinorhizobium meliloti
Authors: Cowie Alison , Cheng Jiujun , Sibley Christopher D. , Fong Ying , Zaheer Rahat , Patten Cheryl L. , Morton Richard M. , Golding G. Brian , Finan Turlough M.
Published: November 2006

As a means of investigating gene function, we developed a robust transcription fusion reporter vector to measure gene expression in bacteria. The vector, pTH1522, was used to construct a random insert library for theSinorhizobium melilotigenome. pTH1522 replicates inEscherichia coliand can be transferred to, but cannot replicate in,S. meliloti. Homologous recombination of the DNA fragments cloned in pTH1522 into theS. melilotigenome generates transcriptional fusions to either the reporter genesgfp+andlacZorgusAandrfp, depending on the orientation of the cloned fragment. Over 12,000 fusion junctions in 6,298 clones were identified by DNA sequence analysis, and the plasmid clones were recombined intoS. meliloti. Reporter enzyme activities following growth of these recombinants in complex medium (LBmc) and in minimal medium with glucose or succinate as the sole carbon source allowed the identification of genes highly expressed under one or more growth condition and those expressed at very low to background levels. In addition to generating reporter gene fusions, the vector allows Flp recombinase-directed deletion formation and gene disruption, depending on the nature of the cloned fragment. We report the identification of genes essential for growth on complex medium as deduced from an inability to recover recombinants from pTH1522 clones that carried fragments internal to gene or operon transcripts. A database containing all the gene expression activities together with a web interface showing the precise locations of reporter fusion junctions has been constructed (www.sinorhizobium.org).
The Surfactant Tween 80 Enhances Biodesulfurization
Authors: Feng Jinhui , Zeng Yiyong , Ma Cuiqing , Cai Xiaofeng , Zhang Quan , Tong Mingyou , Yu Bo , Xu Ping
Published: November 2006

In biocatalytic conversions, substrates and products may display inhibitory or toxic effects on the biocatalyst.
Rhodococcus erythropolis
1awq could further remove sulfur from hydrodesulfurized diesel oil, and the biodesulfurization was enhanced by the surfactant Tween 80. Tween 80 was shown to decrease the product concentration associated with the cells, reducing product inhibition.
Interspecific Transfer of Bacterial Endosymbionts between Tsetse Fly Species: Infection Establishment and Effect on Host Fitness
Authors: Weiss Brian L. , Mouchotte Rosa , Rio Rita V. M. , Wu Yi-neng , Wu Zheyang , Heddi Abdelaziz , Aksoy Serap
Published: November 2006

Tsetse flies (
Glossina
spp.) can harbor up to three distinct species of endosymbiotic bacteria that exhibit unique modes of transmission and evolutionary histories with their host. Two mutualist enterics,
Wigglesworthia
and
Sodalis
, are transmitted maternally to tsetse flies' intrauterine larvae. The third symbiont, from the genus
Wolbachia
, parasitizes developing oocytes. In this study, we determined that
Sodalis
isolates from several tsetse fly species are virtually identical based on a phylogenetic analysis of their
ftsZ
gene sequences. Furthermore, restriction fragment-length polymorphism analysis revealed little variation in the genomes of
Sodalis
isolates from tsetse fly species within different subgenera (
Glossina fuscipes fuscipes
and
Glossina morsitans morsitans
). We also examined the impact on host fitness of transinfecting
G. fuscipes fuscipes
and
G. morsitans morsitans
flies with reciprocal
Sodalis
strains. Tsetse flies cleared of their native
Sodalis
symbionts were successfully repopulated with the
Sodalis
species isolated from a different tsetse fly species. These transinfected flies effectively transmitted the novel symbionts to their offspring and experienced no detrimental fitness effects compared to their wild-type counterparts, as measured by longevity and fecundity. Quantitative PCR analysis revealed that transinfected flies maintained their
Sodalis
populations at densities comparable to those in flies harboring native symbionts. Our ability to transinfect tsetse flies is indicative of
Sodalis
' recent evolutionary history with its tsetse fly host and demonstrates that this procedure may be used as a means of streamlining future paratransgenesis experiments.
Role of Quorum Sensing and Antimicrobial Component Production by
Serratia plymuthica
in Formation of Biofilms, Including Mixed Biofilms with
Escherichia coli
Authors: Moons Pieter , Van Houdt Rob , Aertsen Abram , Vanoirbeek Kristof , Engelborghs Yves , Michiels Chris W.
Published: November 2006

We have previously characterized the
N
-acyl-
l
-homoserine lactone-based quorum-sensing system of the biofilm isolate
Serratia plymuthica
RVH1. Here we investigated the role of quorum sensing and of quorum-sensing-dependent production of an antimicrobial compound (AC) on biofilm formation by RVH1 and on the cocultivation of RVH1 and
Escherichia coli
in planktonic cultures or in biofilms. Biofilm formation of
S. plymuthica
was not affected by the knockout of
splI
or
splR
, the
S. plymuthica
homologs of the
luxI
or
luxR
quorum-sensing gene, respectively, or by the knockout of AC production.
E. coli
grew well in mixed broth culture with RVH1 until the latter reached 8.5 to 9.5 log CFU/ml, after which the
E. coli
colony counts steeply declined. In comparison, only a very small decline occurred in cocultures with the
S. plymuthica
AC-deficient and
splI
mutants. Complementation with exogenous
N
-hexanoyl-
l
-homoserine lactone rescued the wild-type phenotype of the
splI
mutant. The
splR
knockout mutant also induced a steep decline of
E. coli
, consistent with its proposed function as a repressor of quorum-sensing-regulated genes. The numbers of
E. coli
in 3-day-old mixed biofilms followed a similar pattern, being higher with
S. plymuthica
deficient in SplI or AC production than with wild-type
S. plymuthica
, the
splR
mutant, or the
splI
mutant in the presence of
N
-hexanoyl-
l
-homoserine lactone. Confocal laser scanning microscopic analysis of mixed biofilms established with strains producing different fluorescent proteins showed that
E. coli
microcolonies were less developed in the presence of RVH1 than in the presence of the AC-deficient mutant.
Sensitivity of an Immunomagnetic-Separation-Based Test for DetectingEscherichia coliO26 in Bovine Feces
Authors: Hall L. M. , Evans J. , Smith A. W. , Pearce M. C. , Knight H. I. , Foster G. , Low J. C. , Gunn G. J.
Published: November 2006

The sensitivity of a test for cattle sheddingEscherichia coliserogroup O26 was estimated using several fecal pats artificially inoculated at a range of concentrations with differentE. coliO26 strains. The test involves the enrichment of fecal microflora in buffered peptone water, the selective concentration ofE. coliO26 using antibody-coated immunomagnetic-separation beads, the identification ofE. colicolonies on Chromocult tryptone bile X-glucuronide agar, and confirmation of the serogroup withE. coliserogroup O26-specific antisera using slide agglutination. The effective dose ofE. coliO26 for an 80% test sensitivity (ED80) was 1.0 × 104CFU g−1feces (95% confidence interval, 4.7 × 103to 2.4 × 104). Differences in test sensitivity between differentE. coliO26 strains and fecal pats were also observed. Individual estimates of ED80for each strain and fecal pat combination ranged from 4.2 × 102to 4.8 × 105CFU g−1. These results suggest that the test is useful for identifying individuals shedding a large number ofE. coliO26 organisms or, if an appropriate number of individuals in a herd are sampled, for identifying affected herds. The study also provides a benchmark estimate of sensitivity that can be used to compare alternative tests forE. coliO26 and a methodological approach that can be applied to tests for other pathogenic members of theEnterobacteriaceaeand other sample types.
Reverse Transcription-PCR-Enzyme-Linked Immunosorbent Assay for Rapid Detection and Differentiation of Alphavirus Infections
Authors: Wang Eryu , Paessler Slobodan , Aguilar Patricia V. , Carrara Anne-Sophie , Ni Haolin , Greene Ivorlyne P. , Weaver Scott C.
Published: November 2006

Due to the lack of a rapid, simple, and inexpensive assay for detecting alphavirus infections, we combined a reverse transcription-PCR with an enzyme-linked immunosorbent assay (RT-PCR-ELISA) to identify human pathogenic alphaviruses that are endemic in the New World. By combining the sensitivity of PCR, the detection simplicity of ELISA, and the specificities of DNA probes, this method rapidly detected and differentiated closely related species and subtypes of several medically important alphaviruses. After an amplification using RT-PCR with primers targeting conserved sequences in the nonstructural protein 1 gene, sequence-specific, biotin-labeled probes targeted against Venezuelan, eastern, and western equine encephalitis or Mayaro virus genes were used for the detection of amplicons using ELISA. The assay is simple, fast, and easy to perform in an ordinary diagnostic laboratory or clinical setting. Nucleic acid derived from cell cultures infected with several alphaviruses, clinical specimens, and mosquito pools as well as frozen and paraffin-embedded animal tissues were detected and identified within 6 to 7 h in a sensitive and specific manner.
Variable-Number Tandem Repeats That Are Useful in Genotyping Isolates of
Salmonella enterica
subsp.
enterica
Serovars Typhimurium and Newport
Authors: Witonski D. , Stefanova R. , Ranganathan A. , Schutze G. E. , Eisenach K. D. , Cave M. D.
Published: November 2006

The genome of
Salmonella enterica
subsp.
enterica
serovar Typhimurium strain LT2 was analyzed for direct repeats, and 54 sequences containing variable-number tandem repeat loci were identified. Ten primer pairs that anneal upstream and downstream of each selected locus were designed and used to amplify PCR targets in isolates of
S. enterica
serovars Typhimurium and Newport. Four of the 10 loci did not show polymorphism in the length of products. Six loci were selected for analysis. Isolates of
S. enterica
serovars Typhimurium and Newport that were related to specific outbreaks and showed identical pulsed-field gel electrophoresis patterns were indistinguishable by the length of the six variable-number tandem repeats. Isolates that differed in their pulsed-field gel electrophoresis patterns showed polymorphism in variable-number tandem repeat profiles. Length of the products was confirmed by DNA sequence analysis. Only 2 of the 10 loci contained exact integers of the direct repeat. Eight loci contained partial copies. The partial copies were maintained at the ends of the variable-number tandem repeat loci in all isolates. In spite of having partial copies that were maintained in all isolates, the number of direct repeats at a locus was polymorphic. Six variable-number tandem repeat loci were useful in distinguishing isolates of
S. enterica
serovars Typhimurium and Newport that had different pulsed-field gel electrophoresis patterns and in identifying outbreak-associated cases that shared a common pulsed-field gel pattern.
Limitations of DNA Sequencing for Diagnosis of a Mixed Infection by Two Fungi,Phaeoacremonium venezuelenseand aPlectophomellasp., in a Transplant Recipient
Authors: Guarro Josep , Silvestre Agenor Messias , Verkley Gerard , Cano Josep , Gompertz Olga Fischman , Gené Josepa , Ogawa Marília Marufuji , Tomimori-Yamashita Jane , Teixeira Solange Pistori , de Almeida Fernando Augusto
Published: November 2006

We describe a rare case of a subcutaneous infection by bothPhaeoacremonium venezuelenseandPlectophomellasp. in a Brazilian male. Sequencing of a β-tubulin gene fragment allowed us to confirm the identification of the former. However, a similar procedure of sequencing rRNA gene fragments was not useful for the identification of the latter fungus.
Evidence for Indirect Nosocomial Transmission of
Neisseria meningitidis
Resulting in Two Cases of Invasive Meningococcal Disease
Authors: Elias Johannes ,   Health Office in the Rural District Office Wartburgkreis, Claus Heike , Frosch Matthias , Vogel Ulrich
Published: November 2006

Nosocomial transmission of
Neisseria meningitidis
has only rarely been reported. Here, we present a significant spatiotemporal association of two cases of invasive meningococcal disease identified by retrospective cluster analysis with the program SaTScan. The most likely epidemiological link was simultaneous hospitalization, resulting in indirect nosocomial transmission.