bluuebunny/crossref_metadata_2025 huggingface dataset:
The species‐area relationship in the hoverfly (Diptera, Syrphidae) communities of forest fragments in southern France
Authors: Ouin Annie , Sarthou Jean‐Pierre , Bouyjou Bernard , Deconchat Marc , Lacombe Jean‐Paul , Monteil Claude
Published: December 2005

The effect of forest fragmentation was studied in hoverfly communities of 54 isolated forests (0.14–171 ha) in south west France. The positive relationship between species richness and wood patch area was investigated by testing the three hypotheses usually put forward to explain it: 1) the sampling effect hypothesis, 2) the patch heterogeneity hypothesis, 3) the hypothesis of equilibrium between distance from other patch (colonisation) and surface area of the patch (extinction). The syrphid species were divided into 3 ecological groups, based on larval biology as summarized in the “Syrph the Net” database: non forest species, facultative forest species and forest species. A total of 3317 adults belonging to 100 species, were captured in the 86 Malaise traps. Eight species were non forest (N=16), 65 facultative forest (N=2803) and 27 forest species (N=498).

Comparison of the slopes of the species‐area curves for species richness and species density per forest patch showed a strong sampling effect in the species‐area relationship. Wood patch heterogeneity increased with wood patch area and positively influenced hoverflies richness. Less isolated wood patches presented high richness of forest species and low richness of non forest species. Only forest species richness seemed to respond to the equilibrium between surface area and isolation. Depending on which hypothesis explained best the species‐area relationship, management recommendations to mitigate fragmentation effects were formulated at various spatial scales and for different stakeholders.
Expandable and rigid endorectal coils for prostate MRI: Impact on prostate distortion and rigid image registration
Authors: Kim Yongbok , Hsu I‐Chow J. , Pouliot Jean , Noworolski Susan Moyher , Vigneron Daniel B. , Kurhanewicz John
Published: December 2005

Endorectal coils (ERCs) are used for acquiring high spatial resolution magnetic resonance (MR) images of the human prostate. The goal of this study is to determine the impact of an expandable versus a rigid ERC on changes in the location and deformation of the prostate gland and subsequently on registering prostate images acquired with and without an ERC. Sagittal and axial weighted MR images were acquired from 25 patients receiving a combined MR imaging/MR spectroscopic imaging staging exam for prostate cancer. Within the same exam, images were acquired using an external pelvic phased array coil both alone and in combination with either an expandable ERC (MedRad, Pittsburgh, PA) or a rigid ERC (USA Instruments, Aurora, OH). Rotations, translations and deformations caused by the ERC were measured and compared. The ability to register images acquired with and without the ERC using a manual rigid‐body registration was assessed using a similarity index (SI). Both ERCs caused the prostate to tilt anteriorly with an average tilt of ( and , , for expandable and rigid ERC, respectively). However, the expandable coil caused a significantly larger distortion of the prostate as compared to the rigid coil; compressing the prostate in the anterior/posterior direction by vs (14.5% vs 4.8%) , and widening the prostate in the right/left direction by vs (8.3% vs 3.4%) . Additionally, the ability to manually align prostate images acquired with and without ERC was significantly better for the rigid coil ( vs , for the rigid and expandable coils, respectively). In conclusion, the manual rigid‐body alignment of prostate MR images acquired with and without the ERC can be improved through the use of a rigid ERC.
Dosimetric characteristics of a new unshielded silicon diode and its application in clinical photon and electron beams
Authors: Griessbach Irmgard , Lapp Markus , Bohsung Jörg , Gademann Günther , Harder Dietrich
Published: December 2005

Shielded ‐silicon diodes, frequently applied in general photon‐beam dosimetry, show certain imperfections when applied in the small photon fields occurring in stereotactic or intensity modulated radiotherapy (IMRT), in electron beams and in the buildup region of photon beam dose distributions. Using as a study object the shielded ‐silicon diode PTW 60008, well known for its reliable performance in general photon dosimetry, we have identified these imperfections as effects of electron scattering at the metallic parts of the shielding. In order to overcome these difficulties a new, unshielded diode PTW 60012 has been designed and manufactured by PTW Freiburg. By comparison with reference detectors, such as thimble and plane‐parallel ionization chambers and a diamond detector, we could show the absence of these imperfections. An excellent performance of the new unshielded diode for the special dosimetric tasks in small photon fields, electron beams and build‐up regions of photon beams has been observed. The new diode also has an improved angular response. However, due to its over‐response to low‐energy scattered photons, its recommended range of use does not include output factor measurements in large photon fields, although this effect can be compensated by a thin auxiliary lead shield.
The effects of the imaging system on the validity limits of the ray‐optical approach to phase contrast imaging
Authors: Peterzol A. , Olivo A. , Rigon L. , Pani S. , Dreossi D.
Published: December 2005

A theoretical analysis of the x‐ray phase contrast imaging and its validation via synchrotron radiation imaging is here presented. Two different mathematical models have been followed: the simpler ray‐optical approach and the more rigorous Fresnel‐Kirchoff diffraction theory. Subsequently, the conditions upon which the x‐ray optical approximation can be used to describe the image formation mechanism have been analyzed, taking into account also the effects due to the finite source size and detector resolution. It is possible to demonstrate that the ray‐optics results can also be obtained by opportunely developing the diffraction formalism only with some restrictions on the spatial frequencies present in the final image, without any limitation on the maximum phase shift. The conditions allowing the use of the simplified ray‐optical approach to describe the phase contrast images have been here defined and their validation has been proved by means of computer simulations and phantom experiments.
On using an adaptive neural network to predict lung tumor motion during respiration for radiotherapy applications
Authors: Isaksson Marcus , Jalden Joakim , Murphy Martin J.
Published: December 2005

In this study we address the problem of predicting the position of a moving lung tumor during respiration on the basis of external breathing signals—a technique used for beam gating, tracking, and other dynamic motion management techniques in radiation therapy. We demonstrate the use of neural network filters to correlate tumor position with external surrogate markers while simultaneously predicting the motion ahead in time, for situations in which neither the breathing pattern nor the correlation between moving anatomical elements is constant in time. One pancreatic cancer patient and two lung cancer patients with mid/upper lobe tumors were fluoroscopically imaged to observe tumor motion synchronously with the movement of external chest markers during free breathing. The external marker position was provided as input to a feed‐forward neural network that correlated the marker and tumor movement to predict the tumor position up to in advance. The predicted tumor position was compared to its observed position to establish the accuracy with which the filter could dynamically track tumor motion under nonstationary conditions. These results were compared to simplified linear versions of the filter. The two lung cancer patients exhibited complex respiratory behavior in which the correlation between surrogate marker and tumor position changed with each cycle of breathing. By automatically and continuously adjusting its parameters to the observations, the neural network achieved better tracking accuracy than the fixed and adaptive linear filters. Variability and instability in human respiration complicate the task of predicting tumor position from surrogate breathing signals. Our results show that adaptive signal‐processing filters can provide more accurate tumor position estimates than simpler stationary filters when presented with nonstationary breathing motion.
Performance of Media for Recovering Stressed Cells of
Enterobacter sakazakii
as Determined Using Spiral Plating and Ecometric Techniques
Authors: Gurtler J. B. , Beuchat L. R.
Published: December 2005

A study was done to determine the performance of differential, selective media for supporting resuscitation and colony development by stressed cells of
Enterobacter sakazakii
. Cells of four strains of
E. sakazakii
isolated from powdered infant formula were exposed to five stress conditions: heat (55°C for 5 min), freezing (−20°C for 24 h, thawed, frozen again at −20°C for 2 h, thawed), acidic pH (3.54), alkaline pH (11.25), and desiccation in powdered infant formula (water activity, 0.25; 21°C for 31 days). Control and stressed cells were spiral plated on tryptic soy agar supplemented with 0.1% pyruvate (TSAP, a nonselective control medium); Leuschner, Baird, Donald, and Cox (LBDC) agar (a differential, nonselective medium); Oh and Kang agar (OK); fecal coliform agar (FCA); Druggan-Forsythe-Iversen (DFI) medium; violet red bile glucose (VRBG) agar; and
Enterobacteriaceae
enrichment (EE) agar. With the exception of desiccation-stressed cells, suspensions of stressed cells were also plated on these media and on R&F
Enterobacter sakazakii
chromogenic plating (RF) medium using the ecometric technique. The order of performance of media for recovering control and heat-, freeze-, acid-, and alkaline-stressed cells by spiral plating was TSAP > LBDC > FCA > OK, VRBG > DFI > EE; the general order for recovering desiccated cells was TSAP, LBDC, FCA, OK > DFI, VRBG, EE. Using the ecometric technique, the general order of growth indices of stressed cells was TSAP, LBDC > FCA > RF, VRBG, OK > DFI, EE. The results indicate that differential, selective media vary greatly in their abilities to support resuscitation and colony formation by stressed cells of
E. sakazakii
. The orders of performance of media for recovering stressed cells were similar using spiral plating and ecometric techniques, but results from spiral plating should be considered more conclusive.
Genomic Comparison of Plant Pathogenic and Nonpathogenic
Serratia marcescens
Strains by Suppressive Subtractive Hybridization
Authors: Zhang Q. , Melcher U. , Zhou L. , Najar F. Z. , Roe B. A. , Fletcher J.
Published: December 2005

Cucurbit yellow vine disease (CYVD) is caused by disease-associated
Serratia marcescens
strains that have phenotypes significantly different from those of nonphytopathogenic strains. To identify the genetic differences responsible for pathogenicity-related phenotypes, we used a suppressive subtractive hybridization (SSH) strategy.
S. marcescens
strain Z01-A, isolated from CYVD-affected zucchini, was used as the tester, whereas rice endophytic
S. marcescens
strain R02-A (IRBG 502) was used as the driver. SSH revealed 48 sequences, ranging from 200 to 700 bp, that were present in Z01-A but absent in R02-A. Sequence analysis showed that a large proportion of these sequences resembled genes involved in synthesis of surface structures. By construction of a fosmid library, followed by colony hybridization, selection, and DNA sequencing, a phage gene cluster and a genome island containing a fimbrial-gene cluster were identified. Arrayed dot hybridization showed that the conservation of subtracted sequences among CYVD pathogenic and nonpathogenic
S. marcescens
strains varied. Thirty-four sequences were present only in pathogenic strains. Primers were designed based on one Z01-A-specific sequence, A79, and used in a multiplex PCR to discriminate between
S. marcescens
strains causing CYVD and those from other ecological niches.
Genetic Similarity of Flag Shoot and Ascospore Subpopulations of
Erysiphe necator
in Italy
Authors: Cortesi Paolo , Mazzoleni Anna , Pizzatti Cristina , Milgroom Michael G.
Published: December 2005

The overwintering mode of the grape powdery mildew fungus,
Erysiphe necator
(syn.
Uncinula necator
), as mycelium in dormant buds (resulting in symptoms known as flag shoots) or as ascospores in cleistothecia, affects the temporal dynamics of epidemics early in the growing season. We tested whether distinct genetic groups (I and III) identified previously in
E. necator
correlate to overwintering modes in two vineyards in Tuscany, Italy, to determine whether diagnostic genetic markers could be used to predict overwintering. Samples from one vineyard were collected from flag shoots; the other vineyard, 60 km away, had no flag shoots, and mildew colonies were assumed to be derived from ascospores. Genetic markers putatively diagnostic for groups I and III showed that both types were common in the flag shoot subpopulation. Both genetic types were found in the ascospore population, although group III was dominant. We did not find strong genetic differentiation between the two subpopulations based on inter-simple sequence repeat markers. Although there was significant (
P
< 0.001) genetic differentiation between these subpopulations in 1997 and when 1997 and 1998 subpopulations were pooled (θ = 0.214 and 0.150, respectively), no differentiation was evident between vineyards in 1998 (θ = 0.138,
P
= 0.872). Moreover, we did not observe distinct lineages corresponding to overwintering modes, as observed in previous studies. We could not determine if differentiation resulted from biological differences or restricted gene flow between the two vineyards. Our samples were taken from both subpopulations early in the epidemic, while previous studies confounded overwintering mode and sampling time. These results do not support a strong correlation between overwintering and genetic groups, highlighting the need to base population biology studies on sound biological and epidemiological knowledge.
Cofactor Dependence in Furan Reduction by
Saccharomyces cerevisiae
in Fermentation of Acid-Hydrolyzed Lignocellulose
Authors: Nilsson Anneli , Gorwa-Grauslund Marie F. , Hahn-Hägerdal Bärbel , Lidén Gunnar
Published: December 2005

A decreased fermentation rate due to inhibition is a significant problem for economic conversion of acid-pretreated lignocellulose hydrolysates to ethanol, since the inhibition gives rise to a requirement for separate detoxification steps. Together with acetic acid, the sugar degradation products furfural and 5-hydroxymethyl furfural are the inhibiting compounds found at the highest concentrations in hydrolysates. These aldehydes have been shown to affect both the specific growth rate and the rate of fermentation by yeast. Two strains of
Saccharomyces cerevisiae
with different abilities to ferment inhibiting hydrolysates were evaluated in fermentations of a dilute acid hydrolysate from spruce, and the reducing activities for furfural and 5-hydroxymethyl furfural were determined. Crude cell extracts of a hydrolysate-tolerant strain (TMB3000) converted both furfural and 5-hydroxymethyl furfural to the corresponding alcohol at a rate that was severalfold higher than the rate observed for cell extracts of a less tolerant strain (CBS 8066), thereby confirming that there is a correlation between the fermentation rate in a lignocellulosic hydrolysate and the bioconversion capacity of a strain. The in vitro NADH-dependent furfural reduction capacity of TMB3000 was three times higher than that of CBS 8066 (1,200 mU/mg protein and 370 mU/mg protein, respectively) in fed-batch experiments. Furthermore, the inhibitor-tolerant strain TMB3000 displayed a previously unknown NADH-dependent reducing activity for 5-hydroxymethyl furfural (400 mU/mg protein during fed-batch fermentation of hydrolysates). No corresponding activity was found in strain CBS 8066 (<2 mU/mg). The ability to reduce 5-hydroxymethyl furfural is an important characteristic for the development of yeast strains with increased tolerance to lignocellulosic hydrolysates.
Signature-Tagged Transposon Mutagenesis Studies Demonstrate the Dynamic Nature of Cecal Colonization of 2-Week-Old Chickens by
Campylobacter jejuni
Authors: Grant Andrew J. , Coward Christopher , Jones Michael A. , Woodall Claire A. , Barrow Paul A. , Maskell Duncan J.
Published: December 2005

We have constructed plasmids to be used for in vitro signature-tagged mutagenesis (STM) of
Campylobacter jejuni
and used these to generate STM libraries in three different strains. Statistical analysis of the transposon insertion sites in the
C. jejuni
NCTC 11168 chromosome and the plasmids of strain 81-176 indicated that their distribution was not uniform. Visual inspection of the distribution suggested that deviation from uniformity was not due to preferential integration of the transposon into a limited number of hot spots but rather that there was a bias towards insertions around the origin. We screened pools of mutants from the STM libraries for their ability to colonize the ceca of 2-week-old chickens harboring a standardized gut flora. We observed high-frequency random loss of colonization proficient mutants. When cohoused birds were individually inoculated with different tagged mutants, random loss of colonization-proficient mutants was similarly observed, as was extensive bird-to-bird transmission of mutants. This indicates that the nature of campylobacter colonization in chickens is complex and dynamic, and we hypothesize that bottlenecks in the colonization process and between-bird transmission account for these observations.
Distribution of Typical Freshwater Bacterial Groups Is Associated with pH, Temperature, and Lake Water Retention Time
Authors: Lindström Eva S. , Kamst-Van Agterveld Miranda P. , Zwart Gabriel
Published: December 2005

The distribution of 15 typical freshwater bacterial groups in 15 diverse lakes in northern Europe was investigated using reverse line blot hybridization. Statistical evaluation of the data in relation to the characteristics of the lakes showed that pH, temperature, and the theoretical hydrological retention time of the lakes were most strongly related to variations in the distribution of bacterial taxa. This suggests that pH and temperature are steering factors in the selection of taxa and supports the notion that communities in lakes with short water turnover times are influenced by the input of bacterial cells from the drainage areas. Within the beta subdivision of the
Proteobacteria
(
Betaproteobacteria
), as well as within the divisions
Actinobacteria
and
Verrucomicrobia
, different subgroups were associated differently with environmental variables.
Production and Characterization of Antibodies against Each of the Three Subunits of the
Bacillus cereus
Nonhemolytic Enterotoxin Complex
Authors: Dietrich Richard , Moravek Maximilian , Bürk Christine , Granum Per Einar , Märtlbauer Erwin
Published: December 2005

The nonhemolytic enterotoxin (Nhe) is one of the two three-component enterotoxins which are responsible for diarrheal food poisoning syndrome caused by
Bacillus cereus
. To facilitate the detection of this toxin, consisting of the subunits NheA, NheB, and NheC, a complete set of high-affinity antibodies against each of the three components was established and characterized. A rabbit antiserum specific for the C-terminal part (15 amino acids) of NheC was produced using a respective synthetic peptide coupled to a protein carrier for immunization. Using purified
B. cereus
exoprotein preparations as immunogens, one monoclonal antibody against NheA and several antibodies against NheB were obtained. No cross-reactivity with other proteins produced by different strains of
B. cereus
was observed. Antibodies against the NheB component were able to neutralize the cytotoxic activity (up to 98%) of Nhe. Based on indirect enzyme immunoassays, the antibodies developed in this study were successfully used in the characterization of the enterotoxic activity of several
B. cereus
strains. For the first time, it could be shown that strains carrying the
nhe
genes usually express the complete set of the three components, including NheC. However, the amount of toxin produced varies considerably between the different strains.
Engineering of Solvent-TolerantPseudomonas putidaS12 for Bioproduction of Phenol from Glucose
Authors: Wierckx Nick J. P. , Ballerstedt Hendrik , de Bont Jan A. M. , Wery Jan
Published: December 2005

Efficient bioconversion of glucose to phenol via the central metabolite tyrosine was achieved in the solvent-tolerant strainPseudomonas putidaS12. Thetplgene fromPantoea agglomerans, encoding tyrosine phenol lyase, was introduced intoP. putidaS12 to enable phenol production. Tyrosine availability was a bottleneck for efficient production. The production host was optimized by overexpressing thearoF-1gene, which codes for the first enzyme in the tyrosine biosynthetic pathway, and by random mutagenesis procedures involving selection with the toxic antimetabolitesm-fluoro-dl-phenylalanine andm-fluoro-l-tyrosine. High-throughput screening of analogue-resistant mutants obtained in this way yielded aP. putidaS12 derivative capable of producing 1.5 mM phenol in a shake flask culture with a yield of 6.7% (mol/mol). In a fed-batch process, the productivity was limited by accumulation of 5 mM phenol in the medium. This toxicity was overcome by use of octanol as an extractant for phenol in a biphasic medium-octanol system. This approach resulted in accumulation of 58 mM phenol in the octanol phase, and there was a twofold increase in the overall production compared to a single-phase fed batch.
Mineralization of the Cyclic Nitramine Explosive Hexahydro-1,3,5-Trinitro-1,3,5-Triazine by
Gordonia
and
Williamsia
spp
Authors: Thompson Karen T. , Crocker Fiona H. , Fredrickson Herbert L.
Published: December 2005

Hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) is a cyclic nitroamine explosive that is a major component in many military high-explosive formulations. In this study, two aerobic bacteria that are capable of using RDX as the sole source of carbon and nitrogen to support their growth were isolated from surface soil. These bacterial strains were identified by their fatty acid profiles and 16S ribosomal gene sequences as
Williamsia
sp. KTR4 and
Gordonia
sp. KTR9. The physiology of each strain was characterized with respect to the rates of RDX degradation and [U-
14
C]RDX mineralization when RDX was supplied as a sole carbon and nitrogen source in the presence and absence of competing carbon and nitrogen sources. Strains KTR4 and KTR9 degraded 180 μM RDX within 72 h when RDX served as the only added carbon and nitrogen source while growing to total protein concentrations of 18.6 and 16.5 μg/ml, respectively. Mineralization of [U-
14
C]RDX to
14
CO
2
was 30% by strain KTR4 and 27% by KTR9 when RDX was the only added source of carbon and nitrogen. The addition of (NH
4
)
2
SO
4
greatly inhibited KTR9's degradation of RDX but had little effect on that of KTR4. These are the first two pure bacterial cultures isolated that are able to use RDX as a sole carbon and nitrogen source. These two genera possess different physiologies with respect to RDX mineralization, and each can serve as a useful microbiological model for the study of RDX biodegradation with regard to physiology, biochemistry, and genetics.
Functional Analysis of Putative Adhesion Factors in
Lactobacillus acidophilus
NCFM
Authors: Buck B. Logan , Altermann Eric , Svingerud Tina , Klaenhammer Todd R.
Published: December 2005

Lactobacilli are major inhabitants of the normal microflora of the gastrointestinal tract, and some select species have been used extensively as probiotic cultures. One potentially important property of these organisms is their ability to interact with epithelial cells in the intestinal tract, which may promote retention and host-bacterial communication. However, the mechanisms by which they attach to intestinal epithelial cells are unknown. The objective of this study was to investigate cell surface proteins in
Lactobacillus acidophilus
that may promote attachment to intestinal tissues. Using genome sequence data, predicted open reading frames were searched against known protein and protein motif databases to identify four proteins potentially involved in adhesion to epithelial cells. Homologous recombination was used to construct isogenic mutations in genes encoding a mucin-binding protein, a fibronectin-binding protein, a surface layer protein, and two streptococcal R28 homologs. The abilities of the mutants to adhere to intestinal epithelial cells were then evaluated in vitro. Each strain was screened on Caco-2 cells, which differentiate and express markers characteristic of normal small-intestine cells. A significant decrease in adhesion was observed in the fibronectin-binding protein mutant (76%) and the mucin-binding protein mutant (65%). A surface layer protein mutant also showed reduction in adhesion ability (84%), but the effect of this mutation is likely due to the loss of multiple surface proteins that may be embedded in the S-layer. This study demonstrated that multiple cell surface proteins in
L. acidophilus
NCFM can individually contribute to the organism's ability to attach to intestinal cells in vitro.
In Vitro Determination of Prebiotic Properties of Oligosaccharides Derived from an Orange Juice Manufacturing By-Product Stream
Authors: Manderson K. , Pinart M. , Tuohy K. M. , Grace W. E. , Hotchkiss A. T. , Widmer W. , Yadhav M. P. , Gibson G. R. , Rastall R. A.
Published: December 2005

Fermentation properties of oligosaccharides derived from orange peel pectin were assessed in mixed fecal bacterial culture. The orange peel oligosaccharide fraction contained glucose in addition to rhamnogalacturonan and xylogalacturonan pectic oligosaccharides. Twenty-four-hour, temperature- and pH-controlled, stirred anaerobic fecal batch cultures were used to determine the effects that oligosaccharides derived from orange products had on the composition of the fecal microbiota. The effects were measured through fluorescent in situ hybridization to determine changes in bacterial populations, fermentation end products were analyzed by high-performance liquid chromatography to assess short-chain fatty acid concentrations, and subsequently, a prebiotic index (PI) was determined. Pectic oligosaccharides (POS) were able to increase the bifidobacterial and
Eubacterium rectale
numbers, albeit resulting in a lower prebiotic index than that from fructo-oligosaccharide metabolism. Orange albedo maintained the growth of most bacterial populations and gave a PI similar to that of soluble starch. Fermentation of POS resulted in an increase in the
Eubacterium rectale
numbers and concomitantly increased butyrate production. In conclusion, this study has shown that POS can have a beneficial effect on the fecal microflora; however, a classical prebiotic effect was not found. An increase in the
Eubacterium rectale
population was found, and butyrate levels increased, which is of potential benefit to the host.
Ecological Behavior ofLactobacillus reuteri100-23 Is Affected by Mutation of theluxSGene
Authors: Tannock Gerald W. , Ghazally Salina , Walter Jens , Loach Diane , Brooks Heather , Cook Gregory , Surette Michael , Simmers Cameron , Bremer Phil , Dal Bello Fabio , Hertel Christian
Published: December 2005

TheluxSgene ofLactobacillus reuteri100-23C was amplified by PCR, cloned, and then sequenced. To define a physiological and ecological role for theluxSgene inL. reuteri100-23C, aluxSmutant was constructed by insertional mutagenesis. TheluxSmutant did not produce autoinducers AI-2 or AI-3. Complementation of theluxSmutation by a plasmid construct containingluxSrestored AI-2 and AI-3 synthesis. In vitro experiments revealed that neither the growth rate, nor the cell yield, nor cell survival in the stationary phase were compromised in theluxSmutant relative to the wild type and complemented mutant. The ATP content of exponentially growing cells of theluxSmutant was, however, 65% of that of wild-type cells. Biofilms formed by theluxSmutant on plastic surfaces in a bioreactor were thicker than those formed by the wild type. Biofilm thickness was not restored to wild-type values by the addition of purified AI-2 to the culture medium. In vivo experiments, conducted with ex-Lactobacillus-free mice, showed that biofilms formed by the mutant strain on the epithelial surface of the forestomach were approximately twice as thick as those formed by the wild type. The ecological performance of theluxSmutant, when in competition withL. reuteristrain 100-93 in the mouse cecum, was reduced compared to that of axylAmutant of 100-23C. These results demonstrate that LuxS influences important ecological attributes ofL. reuteri100-23C, the consequences of which are niche specific.
Phospholipid Furan Fatty Acids and Ubiquinone-8: Lipid Biomarkers That May Protect
Dehalococcoides
Strains from Free Radicals
Authors: White David C. , Geyer Roland , Peacock Aaron D. , Hedrick David B. , Koenigsberg Stephen S. , Sung Youlboong , He Jianzhong , Löffler Frank E.
Published: December 2005

Dehalococcoides
species have a highly restricted lifestyle and are only known to derive energy from reductive dehalogenation reactions. The lipid fraction of two
Dehalococcoides
isolates, strains BAV1 and FL2, and a tetrachloroethene-to-ethene-dechlorinating
Dehalococcoides
-containing consortium were analyzed for neutral lipids and phospholipid fatty acids. Unusual phospholipid modifications, including the replacement of unsaturated fatty acids with furan fatty acids, were detected in both
Dehalococcoides
isolates and the mixed culture. The following three furan fatty acids are reported as present in bacterial phospholipids for the first time: 9-(5-pentyl-2-furyl)-nonanoate (Fu18:2ω6), 9-(5-butyl-2-furyl)-nonanoate (Fu17:2ω5), and 8-(5-pentyl-2-furyl)-octanoate (Fu17:2ω6). The neutral lipids of the
Dehalococcoides
cultures contained unusually large amounts of benzoquinones (i.e., ubiquinones [UQ]), which is unusual for anaerobes. In particular, the UQ-8 content of
Dehalococcoides
was 5- to 20-fold greater than that generated in aerobically grown
Escherichia coli
cultures relative to the phospholipid fatty acid content. Naphthoquinone isoprenologues (MK), which are often found in anaerobically grown bacteria and archaea, were also detected.
Dehalococcoides
shows a difference in isoprenologue pattern between UQ-8 and MK-5 that is atypical of other bacteria capable of producing both quinone types. The difference in UQ-8 and MK-5 isoprenologue patterns strongly suggests a special function for UQ in
Dehalococcoides
, and
Dehalococcoides
may utilize structural modifications in its lipid armamentarium to protect against free radicals that are generated in the process of reductive dechlorination.
Genetic Variability of the Heme Uptake System among Different Strains of the Fish Pathogen
Vibrio anguillarum
: Identification of a New Heme Receptor
Authors: Mouriño Susana , Rodríguez-Ares Isabel , Osorio Carlos R. , Lemos Manuel L.
Published: December 2005

The ability to utilize heme compounds as iron sources was investigated in
Vibrio anguillarum
strains belonging to serotypes O1 to O10. All strains, regardless of their serotype or isolation origin could utilize hemin and hemoglobin as sole iron sources. Similarly, all of the isolates could bind hemin and Congo red, and this binding was mediated by cell envelope proteins. PCR and Southern hybridization were used to assay the occurrence of heme transport genes
huvABCD
, which have been previously described in serotype O1. Of 23 strains studied, two serotype O3 isolates proved negative for all
huvABCD
genes, whereas nine strains included in serotypes O2, O3, O4, O6, O7, and O10 tested negative for the outer membrane heme receptor gene
huvA
. A gene coding for a novel outer membrane heme receptor was cloned and characterized in a
V. anguillarum
serotype O3 strain lacking
huvA
. The new heme receptor, named HuvS, showed significant similarity to other outer membrane heme receptors described in
Vibrionaceae
, but little homology (39%) to HuvA. This heme receptor was present in 9 out of 11 of the
V. anguillarum
strains that tested negative for HuvA. Furthermore, complementation experiments demonstrated that HuvS could substitute for the HuvA function in
Escherichia coli
and
V. anguillarum
mutants. The
huvS
and
huvA
sequences alignment, as well as the analysis of their respective upstream and downstream DNA sequences, suggest that horizontal transfer and recombination might be responsible for generating this genetic diversity.
Twin-Arginine Translocation of Active Human Tissue Plasminogen Activator in
Escherichia coli
Authors: Kim Jae-Young , Fogarty Elizabeth A. , Lu Franklin J. , Zhu Hui , Wheelock Geoffrey D. , Henderson Lee A. , DeLisa Matthew P.
Published: December 2005

When eukaryotic proteins with multiple disulfide bonds are expressed at high levels in
Escherichia coli
, the efficiency of thiol oxidation and isomerization is typically not sufficient to yield soluble products with native structures. Even when such proteins are secreted into the oxidizing periplasm or expressed in the cytoplasm of cells carrying mutations in the major intracellular disulfide bond reduction systems (e.g.,
trxB gor
mutants), correct folding can be problematic unless a folding modulator is simultaneously coexpressed. In the present study we explored whether the bacterial twin-arginine translocation (Tat) pathway could serve as an alternative expression system for obtaining appreciable levels of recombinant proteins which exhibit complex patterns of disulfide bond formation, such as full-length human tissue plasminogen activator (tPA) (17 disulfides) and a truncated but enzymatically active version of tPA containing nine disulfides (vtPA). Remarkably, targeting of both tPA and vtPA to the Tat pathway resulted in active protein in the periplasmic space. We show here that export by the Tat translocator is dependent upon oxidative protein folding in the cytoplasm of
trxB gor
cells prior to transport. Whereas previous efforts to produce high levels of active tPA or vtPA in
E. coli
required coexpression of the disulfide bond isomerase DsbC, we observed that Tat-targeted vtPA and tPA reach a native conformation without thiol-disulfide oxidoreductase coexpression. These results demonstrate that the Tat system may have inherent and unexpected benefits compared with existing expression strategies, making it a viable alternative for biotechnology applications that hinge on protein expression and secretion.
Characterization of Microbial Communities Found in the Human Vagina by Analysis of Terminal Restriction Fragment Length Polymorphisms of 16S rRNA Genes
Authors: Coolen Marco J. L. , Post Eduard , Davis Catherine C. , Forney Larry J.
Published: December 2005

To define and monitor the structure of microbial communities found in the human vagina, a cultivation-independent approach based on analyses of terminal restriction fragment length polymorphisms (T-RFLP) of 16S rRNA genes was developed and validated. Sixteen bacterial strains commonly found in the human vagina were used to construct model communities that were subsequently used to develop efficient means for the isolation of genomic DNA and an optimal strategy for T-RFLP analyses. The various genera in the model community could best be resolved by digesting amplicons made using bacterial primers 8f and 926r with HaeIII; fewer strains could be resolved using other primer-enzyme combinations, and no combination successfully distinguished certain species of the same genus. To demonstrate the utility of the approach, samples from five women that had been collected over a 2-month period were analyzed. Differences and similarities among the vaginal microbial communities of the women were readily apparent. The T-RFLP data suggest that the communities of three women were dominated by a single phylotype, most likely species of
Lactobacillus
. In contrast, the communities of two other women included numerically abundant populations that differed from
Lactobacillus
strains whose 16S rRNA genes had been previously determined. The T-RFLP profiles of samples from all the women were largely invariant over time, indicating that the kinds and abundances of the numerically dominant populations were relatively stable throughout two menstrual cycles. These findings show that T-RFLP of 16S rRNA genes can be used to compare vaginal microbial communities and gain information about the numerically dominant populations that are present.
Community Analysis of a Mercury Hot Spring Supports Occurrence of Domain-Specific Forms of Mercuric Reductase
Authors: Simbahan Jessica , Kurth Elizabeth , Schelert James , Dillman Amanda , Moriyama Etsuko , Jovanovich Stevan , Blum Paul
Published: December 2005

Mercury is a redox-active heavy metal that reacts with active thiols and depletes cellular antioxidants. Active resistance to the mercuric ion is a widely distributed trait among bacteria and results from the action of mercuric reductase (MerA). Protein phylogenetic analysis of MerA in bacteria indicated the occurrence of a second distinctive form of MerA among the archaea, which lacked an N-terminal metal recruitment domain and a C-terminal active tyrosine. To assess the distribution of the forms of MerA in an interacting community comprising members of both prokaryotic domains, studies were conducted at a naturally occurring mercury-rich geothermal environment. Geochemical analyses of Coso Hot Springs indicated that mercury ore (cinnabar) was present at concentrations of parts per thousand. Under high-temperature and acid conditions, cinnabar may be oxidized to the toxic form Hg
2+
, necessitating mercury resistance in resident prokaryotes. Culture-independent analysis combined with culture-based methods indicated the presence of thermophilic crenarchaeal and gram-positive bacterial taxa. Fluorescence in situ hybridization analysis provided quantitative data for community composition. DNA sequence analysis of archaeal and bacterial
merA
sequences derived from cultured pool isolates and from community DNA supported the hypothesis that both forms of MerA were present. Competition experiments were performed to assess the role of archaeal
merA
in biological fitness. An essential role for this protein was evident during growth in a mercury-contaminated environment. Despite environmental selection for mercury resistance and the proximity of community members, MerA retains the two distinct prokaryotic forms and avoids genetic homogenization.
FlhA InfluencesBacillus thuringiensisPlcR-Regulated Gene Transcription, Protein Production, and Virulence
Authors: Bouillaut Laurent , Ramarao Nalini , Buisson Christophe , Gilois Nathalie , Gohar Michel , Lereclus Didier , Nielsen-LeRoux Christina
Published: December 2005

Bacillus thuringiensisandBacillus cereusare closely related.B. thuringiensisis well known for its entomopathogenic properties, principally due to the synthesis of plasmid-encoded crystal toxins.B. cereusappears to be an emerging opportunistic human pathogen.B. thuringiensisandB. cereusproduce many putative virulence factors which are positively controlled by the pleiotropic transcriptional regulator PlcR. The inactivation ofplcRdecreases but does not abolish virulence, indicating that additional factors like flagella may contribute to pathogenicity. Therefore, we further analyzed a mutant (B. thuringiensis407 Cry−ΔflhA) previously described as being defective in flagellar apparatus assembly and in motility as well as in the production of hemolysin BL and phospholipases. A large picture of secreted proteins was obtained by two-dimensional electrophoresis analysis, which revealed that flagellar proteins are not secreted and that production of several virulence-associated factors is reduced in theflhAmutant. Moreover, we quantified the effect of FlhA onplcAandhblCgene transcription. The results show that theflhAmutation results in a significant reduction ofplcAandhblCtranscription. These results indicate that the transcription of several PlcR-regulated virulence factors is coordinated with the flagellar apparatus. Consistently, theflhAmutant also shows a strong decrease in cytotoxicity towards HeLa cells and in virulence againstGalleria mellonellalarvae following oral and intrahemocoelic inoculation. The decrease in virulence may be due to both a lack of flagella and a lower production of secreted factors. Hence, FlhA appears to be an essential virulence factor with a pleiotropic role.
Improvement of Catalytic Properties of
Escherichia coli
Penicillin G Acylase Immobilized on Glyoxyl Agarose by Addition of a Six-Amino-Acid Tag
Authors: Scaramozzino Francesca , Estruch Ilona , Rossolillo Paola , Terreni Marco , Albertini Alessandra M.
Published: December 2005

A tag of three lysines alternating with three glycines was added to the C-terminal end of the β chain of penicillin G acylase (PGA). This modification improved the immobilization efficiency of PGA on glyoxyl agarose and the catalytic properties of the PGA derivative, although it impaired the posttranslational steps of overexpressed protein maturation.
Legionella
Confirmation Using Real-Time PCR and SYTO9 Is an Alternative to Current Methodology
Authors: Giglio Steven , Monis Paul T. , Saint Christopher P.
Published: December 2005

The currently accepted culture techniques for the detection of
Legionella
spp. in water samples (AS/NZS 3896:1998 and ISO 11731 standard methods) are slow and laborious, requiring from 7 to 14 days for a result. We describe a fully validated rapid confirmation technique that uses real-time PCR incorporating the intercalating dye SYTO9 for the direct identification of primary cultures, significantly decreasing turnaround time and allowing faster remedial action to be taken by the industry.
Differential Real-Time PCR Assay for Enumeration of Lactic Acid Bacteria in Wine
Authors: Neeley Ezekiel T. , Phister Trevor G. , Mills David A.
Published: December 2005

Oenococcus oeni
is often employed to perform the malolactic fermentation in wine production, while nonoenococcal lactic acid bacteria often contribute to wine spoilage. Two real-time PCR assays were developed to enumerate the total, and nonoenococcal, lactic acid bacterial populations in wine. Used together, these assays can assess the spoilage risk of juice or wine from lactic acid bacteria.
Rapid and Simple Method for Detecting the Toxin B Gene of
Clostridium difficile
in Stool Specimens by Loop-Mediated Isothermal Amplification
Authors: Kato Haru , Yokoyama Toshiyuki , Kato Hideaki , Arakawa Yoshichika
Published: December 2005

We applied the loop-mediated isothermal amplification (LAMP) assay to the detection of the toxin B gene (
tcdB
) of
Clostridium difficile
for identification of toxin B (TcdB)-positive
C. difficile
strains and detection of
tcdB
in stool specimens.
tcdB
was detected in all toxin A (TcdA)-positive, TcdB-positive (A
+
B
+
) and TcdA-negative, TcdB-positive (A
−
B
+
)
C. difficile
strains but not from TcdA-negative, TcdB-negative strains. Of the 74 stool specimens examined, A
+
B
+
or A
−
B
+
C. difficile
was recovered from 39 specimens, of which 38 specimens were LAMP positive and one was negative. Amplification was obtained in 10 specimens that were culture negative, indicating that LAMP is highly sensitive. The LAMP assay was applied to detection of
tcdB
in DNA extracted by a simple boiling method from 47 of those 74 specimens, which were cultured overnight in cooked-meat medium (CMM). Twenty-two of 24 culture-positive specimens were positive for LAMP on DNA from the culture in CMM. Four specimens were culture negative but positive by LAMP on DNA from CMM cultures. The LAMP assay is a reliable tool for identification of TcdB-positive
C. difficile
as well as for direct detection of
tcdB
in stool specimens with high sensitivity. Detection of
tcdB
by LAMP from overnight cultures in CMM could be an alternative method of diagnostic testing at clinical laboratories without special apparatus.
Association between Cellular Human Immunodeficiency Virus DNA Level and Immunological Parameters in Patients with Undetectable Plasma Viremia Level during Highly Active Antiretroviral Therapy
Authors: Sarmati Loredana , Parisi Saverio Giuseppe , Nicastri Emanuele , d'Ettorre Gabriella , Palmisano Lucia , Andreotti Mauro , Andreoni Carolina , Giuliano Marina , Gatti Francesca , Boldrin Caterina , Palù Giorgio , Vullo Vincenzo , Vella Stefano , Andreoni Massimo
Published: December 2005

The association between human immunodeficiency virus (HIV) DNA load and immunologic parameters was investigated in 163 HIV-infected patients with undetectable plasma viremia during highly active antiretroviral therapy (HAART). Patients with HIV DNA below the 25th percentile (133 copies/10
6
peripheral blood mononuclear cells) had higher pre-HAART (
P
= 0.001) and current (
P
= 0.005) CD4 counts and a prolonged duration of treatment (
P
= 0.001). At adjusted analysis, prolonged duration of treatment was independently associated with lower (
P
= 0.006) and undetectable (
P
< 0.001) HIV DNA values.
Life-Threatening Invasive
Helcococcus kunzii
Infections in Intravenous-Drug Users and
ermA
-Mediated Erythromycin Resistance
Authors: Woo Patrick C. Y. , Tse Herman , Wong Samson S. Y. , Tse Cindy W. S. , Fung Ami M. Y. , Tam Dorothy M. W. , Lau Susanna K. P. , Yuen Kwok-yung
Published: December 2005

We report the first two cases of life-threatening invasive
Helcococcus kunzii
infection, with primary bacteremia and empyema thoracis, respectively. Gram smears of both
H. kunzii
isolates showed a mixture of gram-positive and gram-negative cocci. The isolate from the first patient, resistant to erythromycin and clindamycin, possessed an
ermA
gene.
When narratives matter: men, sport, and spinal cord injury: Table 1
Authors: Sparkes A C , Smith B
Published: December 2005

Experiencing a spinal cord injury (SCI) and becoming disabled through sport is a major disruptive life event that instigates a multiplicity of difficult and complex issues that the person has to deal with. One of these problems is how to restory a life and construct new body/self relationships and identities over time. To explore this process, we focus on the life stories of a small group of men (n = 14) who have suffered SCI and become disabled through playing rugby football. We illustrate the ways in which certain metaphors, notions of time, and kinds of hope, congregate and coalesce within three specific narrative types and how these operate to shape the individual experiences of these men following SCI. The implications of this dynamic process for the storied body/self and identity construction are highlighted throughout.
Self and narrative in schizophrenia: time to author a new story
Authors: Roe D , Davidson L
Published: December 2005

The prevailing, clinical view of schizophrenia, as reflected in the psychiatric literature, suggests both that people with schizophrenia have lost their sense of self and that they have a diminished capacity to create coherent narratives about their own lives. Drawing on our empirical research in the growing area of recovery, we describe not only the disruptions and discontinuities introduced by the illness and its social and personal consequences, but also the person’s efforts to overcome these, to reconstruct a sense of self, to regain agency and to create a coherent life narrative. We suggest in closing that, rather than simply being a byproduct of recovery, these processes of re-authoring one’s life story are actually integral components of the recovery process itself.