bluuebunny/crossref_metadata_2025 huggingface dataset:
Simulation of Soft Tissue Failure Using the Material Point Method
Authors: Ionescu Irina , Guilkey James E. , Berzins Martin , Kirby Robert M. , Weiss Jeffrey A.
Published: December 2006

Understanding the factors that control the extent of tissue damage as a result of material failure in soft tissues may provide means to improve diagnosis and treatment of soft tissue injuries. The objective of this research was to develop and test a computational framework for the study of the failure of anisotropic soft tissues subjected to finite deformation. An anisotropic constitutive model incorporating strain-based failure criteria was implemented in an existing computational solid mechanics software based on the material point method (MPM), a quasi-meshless particle method for simulations in computational mechanics. The constitutive model and the strain-based failure formulations were tested using simulations of simple shear and tensile mechanical tests. The model was then applied to investigate a scenario of a penetrating injury: a low-speed projectile was released through a myocardial material slab. Sensitivity studies were performed to establish the necessary grid resolution and time-step size. Results of the simple shear and tensile test simulations demonstrated the correct implementation of the constitutive model and the influence of both fiber family and matrix failure on predictions of overall tissue failure. The slab penetration simulations produced physically realistic wound tracts, exhibiting diameter increase from entrance to exit. Simulations examining the effect of bullet initial velocity showed that the anisotropy influenced the shape and size of the exit wound more at lower velocities. Furthermore, the size and taper of the wound cavity was smaller for the higher bullet velocity. It was concluded that these effects were due to the amount of momentum transfer. The results demonstrate the feasibility of using MPM and the associated failure model for large-scale numerical simulations of soft tissue failure.
Empirical Relationship Between Lengthening an Anterior Cruciate Ligament Graft and Increases in Knee Anterior Laxity: A Human Cadaveric Study
Authors: Grover Dustin , Thompson Dustin , Hull M. L. , Howell S. M.
Published: December 2006

Lengthening of an anterior cruciate ligament (ACL) graft construct can occur as a result of lengthening at the sites of tibial and/or femoral fixation and manifests as an increase in anterior laxity. Although lengthening at the site of fixation has been measured for a variety of fixation devices, it is difficult to place these results in a clinical context because the mathematical relationship between lengthening of an ACL graft construct and anterior laxity is unknown. The purpose of our study was to determine empirically this relationship. Ten cadaveric knees were reconstructed with a double-looped tendon graft. With the knee in 25° of flexion, the position of the proximal end of the graft inside the femoral tunnel was adjusted by moving the femoral fixation device until the anterior laxity at an applied anterior force of 134N matched that of the intact knee. In random order, the graft construct was lengthened 1, 2, 3, 4, and 5mm by moving the femoral fixation device distally along the femoral tunnel and anterior laxity was measured. The increase in the length of the graft construct was related to the increase in anterior laxity by a simple linear regression model. Lengthening the graft construct from 1 to 5mm caused an equal increase in anterior laxity (slope=1.0mm∕mm, r2=0.800, p<0.0001). Because an anterior laxity increase of 3mm or greater in a reconstructed knee is considered unstable clinically and because many fixation devices in widespread use clinically allow 3mm or greater of lengthening in in vitro tests, our empirical relationship indicates that lengthening at the site of fixation probably is an important cause of knee instability following ACL reconstructive surgery. Our empirical relation also indicates that an important criterion in the design of future fixation devices is that lengthening at the sites of fixation in in vitro tests should be limited to less than 3mm.
Computational Analysis of Blood Flow in an Integrated Model of the Left Ventricle and the Aorta
Authors: Nakamura Masanori , Wada Shigeo , Yamaguchi Takami
Published: December 2006

To study the effects of intraventricular flow dynamics on the aortic flow, we created an integrated model of the left ventricle and aorta and conducted a computer simulation of diastolic and systolic blood flow within this model. The results demonstrated that the velocity profile at the aortic annulus changed dynamically, and was influenced by the intraventricular flow dynamics. The profile was almost flat in early systole but became nonuniform as systole progressed, and was skewed toward the posterior side in midsystole and toward the anterior side in later systole. At a distance from the aortic annulus, a different velocity profile was induced by the twisting and torsion of the aorta. In the ascending aorta, the fastest flow was initially located in the posteromedial sector, and it moved to the posterior section along the circumference as systole progressed. The nonuniformity of the aortic inflow gave rise to a complex wall shear stress (WSS) distribution in the aorta. A comparison of the WSS distribution obtained in this integrated analysis with that obtained in flow calculations using an isolated aorta model with Poiseuille and flat inlet conditions showed that intraventricular flow affected the WSS distribution in the ascending aorta. These results address the importance of an integrated analysis of flow in the left ventricle and aorta.
Inhibition of
Plasmodium falciparum
Choline Kinase by Hexadecyltrimethylammonium Bromide: a Possible Antimalarial Mechanism
Authors: Choubey Vinay , Maity Pallab , Guha Mithu , Kumar Sanjay , Srivastava Kumkum , Puri Sunil Kumar , Bandyopadhyay Uday
Published: December 2006

Choline kinase is the first enzyme in the Kennedy pathway (CDP-choline pathway) for the biosynthesis of the most essential phospholipid, phosphatidylcholine, in
Plasmodium falciparum
. In addition, choline kinase also plays a pivotal role in trapping essential polar head group choline inside the malaria parasite. Recently,
Plasmodium falciparum
choline kinase (PfCK) has been cloned, overexpressed, and purified. However, the function of this enzyme in parasite growth and survival has not been evaluated owing to the lack of a suitable inhibitor. Purified recombinant PfCK enabled us to identify an inhibitor of PfCK, hexadecyltrimethylammonium bromide (HDTAB), which has a very close structural resemblance to hexadecylphosphocholine (miltefosin), the well-known antiproliferative and antileishmanial drug. HDTAB inhibited PfCK in a dose-dependent manner and offered very potent antimalarial activity in vitro against
Plasmodium falciparum
. Moreover, HDTAB exhibited profound antimalarial activity in vivo against the rodent malaria parasite
Plasmodium yoelii
(N-67 strain). Interestingly, parasites at the trophozoite and schizont stages were found to be particularly sensitive to HDTAB. The stage-specific antimalarial effect of HDTAB correlated well with the expression pattern of PfCK in
P. falciparum
, which was observed by reverse transcription-PCR and immunofluorescence microscopy. Furthermore, the antimalarial activity of HDTAB paralleled the decrease in phosphatidylcholine content, which was found to correlate with the decreased phosphocholine generation. These results suggest that inhibition of choline kinase by HDTAB leads to decreased phosphocholine, which in turn causes a decrease in phosphatidylcholine biosynthesis, resulting in death of the parasite.
Emergence and Dissemination of
Enterobacteriaceae
Isolates Producing CTX-M-1-Like Enzymes in Spain Are Associated with IncFII (CTX-M-15) and Broad-Host-Range (CTX-M-1, -3, and -32) Plasmids
Authors: Novais Ângela , Cantón Rafael , Moreira Raquel , Peixe Luísa , Baquero Fernando , Coque Teresa M.
Published: December 2006

The spread of CTX-M-1-like enzymes in Spain is associated with particular plasmids of broad-host-range IncN (
bla
CTX-M-32
,
bla
CTX-M-1
), IncL/M (
bla
CTX-M-1
), and IncA/C
2
(
bla
CTX-M-3
) or narrow-host-range IncFII (
bla
CTX-M-15
). The identical genetic surroundings of
bla
CTX-M-32
and
bla
CTX-M-1
and their locations on related 40-kb IncN plasmids indicate the in vivo evolution of this element.
Concentration-Dependent Effects of Caspofungin on the Metabolic Activity of
Aspergillus
Species
Authors: Antachopoulos Charalampos , Meletiadis Joseph , Sein Tin , Roilides Emmanuel , Walsh Thomas J.
Published: December 2006

The minimum effective concentration (MEC) used to assess the in vitro antifungal activity of caspofungin against
Aspergillus
spp. is a qualitative endpoint requiring microscopic examination of hyphae. We therefore developed a tool for the quantitative assessment of caspofungin activity against
Aspergillus
spp. at clinically applicable concentrations. Susceptibility to caspofungin (0.008 to 8 μg/ml) was studied for 9
A. fumigatus
, 8
A. flavus
, and 12
A. terreus
isolates based on the Clinical and Laboratory Standards Institute M38-A protocol. After 48 h of incubation, the MEC was defined microscopically, and metabolic activity assessed with a modified XTT assay, using 100 μg of the tetrazolium salt XTT/ml and 6.25 μM menadione. A significant reduction in metabolic activity was demonstrated at the MEC (0.25 to 0.5 μg/ml) for all
Aspergillus
spp. and was more pronounced for
A. flavus
(median metabolic activity, 25% of control) compared to
A. fumigatus
and
A. terreus
(median metabolism, 42 and 53%, respectively), allowing determination of MEC with the XTT assay (93 to 100% agreement with microscopic MEC). Fungal metabolism tended to reach the lowest levels (median, 17 to 38% of control) one to two dilutions higher than the MEC, at the minimum metabolic activity concentration (MMC). For 5 of 9
A. fumigatus
isolates, 6 of 12
A. terreus
isolates, and 1 of 8
A. flavus
isolates, a paradoxical increase in metabolism was observed at concentrations greater than the MMC. Sigmoid (
E
max
) or bell-shaped models described accurately (median
R
2
= 0.97) the concentration-dependent metabolic changes in the absence or presence, respectively, of paradoxical response. Assessment of metabolic activity may provide useful quantitative endpoints for in vitro studies of caspofungin against
Aspergillus
spp.
Comparative Pharmacokinetics of Voriconazole Administered Orally as either Crushed or Whole Tablets
Authors: Dodds Ashley E. S. , Zaas A. K. , Fang A. F. , Damle B. , Perfect J. R.
Published: December 2006

Voriconazole is a triazole antifungal agent used to treat serious, invasive fungal infections including aspergillosis and candidemia. Limitations with existing formulations of voriconazole including restricted utility in patients with renal dysfunction (intravenous preparation) and the unavailability of an oral suspension in some countries make the administration of crushed tablets desirable in many clinical scenarios. However, concerns that this approach may alter the systemic absorption of voriconazole exist. Therefore, an open-label, randomized, two-way crossover comparative pharmacokinetic (PK) study using healthy volunteers was performed to compare these methods of tablet administration. In a random sequence, subjects received voriconazole tablets either crushed or whole. The voriconazole dose was 400 mg every 12 h for 1 day orally followed by 200 mg every 12 h orally for 5.5 days. Study periods were separated by 7 days. PK parameters were determined by the noncompartmental method. An equivalence approach with no-effect boundaries of 80 to 125% was used to assess bioequivalence. Twenty healthy subjects (10 males; aged 20 to 43 years) were enrolled in and completed the study. The adjusted mean areas under the plasma concentration-time curve from 0 to τ, where τ equals 12 h, for the crushed and whole tablet groups were 9,793 and 11,164 ng · h/ml, respectively (ratio, 87.72; 90% confidence interval [CI], 80.97, 95.04). The ratio of the maximum concentration of drug in serum for the crushed tablet versus whole tablet arms was 94.94 (90% CI, 86.51, 104.22). The only difference noted between groups was a slightly faster time to maximum concentration of drug in serum when subjects received crushed tablets, 0.5 h versus 1.5 h (90% CI, −0.75, −0.25). Treatment-related adverse events occurred in 12 subjects receiving whole tablets and 9 subjects receiving crushed tablets; all were mild. The administration of crushed voriconazole tablets is bioequivalent to whole-tablet administration.
Deletion of the
Trypanosoma brucei
Superoxide Dismutase Gene
sodb1
Increases Sensitivity to Nifurtimox and Benznidazole
Authors: Prathalingham S. Radhika , Wilkinson Shane R. , Horn David , Kelly John M.
Published: December 2006

It has been more than 25 years since it was first reported that nifurtimox and benznidazole promote superoxide production in trypanosomes. However, there has been no direct evidence of an association between the drug-induced free radicals and trypanocidal activity. Here, we identify a superoxide dismutase required to protect
Trypanosoma brucei
from drug-generated superoxide.
Aerobic Removal of Technetium by a Marine
Halomonas
Strain
Authors: Fujimoto Ken , Morita Takami
Published: December 2006

A novel strain of
Halomonas
(Tc-202), which has the capability of removing Tc(VII) from solid- and aqueous-phase material aerobically, was isolated from the marine environment. Tc-202 removed 55% of the total
99
Tc in solutions at 15°C by reducing Tc(VII) to Tc(V), but other
Halomonas
strains did not.
Identification of a Putative Operon Involved in Fructooligosaccharide Utilization by
Lactobacillus paracasei
Authors: Goh Yong Jun , Zhang Chaomei , Benson Andrew K. , Schlegel Vicki , Lee Jong-Hwa , Hutkins Robert W.
Published: December 2006

The growth and activity of some
Lactobacillus
and
Bifidobacterium
strains are stimulated by the presence of nondigestible fructooligosaccharides (FOS), which are selectively fermented by specific intestinal bacteria. Consumption of FOS, therefore, enriches for those bacteria that possess metabolic pathways necessary for FOS metabolism. In this study, a DNA microarray consisting of 7,680 random genomic library fragments of
Lactobacillus paracasei
1195 was used to examine genes involved in the utilization of FOS in this organism. Differential expression profiles between cells grown on FOS and those grown on glucose provided a basis for identifying genes specifically induced by FOS. Several of the FOS-induced genes shared sequence identity with genes encoding β-fructosidases and components of phosphoenolpyruvate-dependent phosphotransferase systems (PTS). These genes were organized in a putative operon, designated the
fos
operon, that may play an essential role in FOS utilization. The complete 7,631-bp nucleotide sequence of the putative
fos
operon was determined and consists of
fosABCDXE
genes, which encode a putative fructose/mannose PTS (FosABCDX) and a β-fructosidase precursor (FosE). The latter contains an N-terminal signal peptide sequence and cell wall sorting signals at the C-terminal region, suggesting its localization at the cell wall. Inactivation of the
fosE
gene led to impaired growth on FOS and other β-fructose-linked carbohydrates. Transcriptional analysis by reverse transcriptase PCR suggested that
fosABCDXE
was cotranscribed as a single mRNA during growth on FOS. Expression array analysis revealed that when glucose was added to FOS-grown cells, transcription of the FOS-induced genes was repressed, indicating that FOS metabolism is subject to catabolite regulation.
Diversity of Ammonia-Oxidizing Archaea and Bacteria in the Sediments of a Hypernutrified Subtropical Estuary: Bahía del Tóbari, Mexico
Authors: Beman J. Michael , Francis Christopher A.
Published: December 2006

Nitrification within estuarine sediments plays an important role in the nitrogen cycle, both at the global scale and in individual estuaries. Although bacteria were once thought to be solely responsible for catalyzing the first and rate-limiting step of this process, several recent studies have suggested that mesophilicCrenarchaeotaare capable of performing ammonia oxidation. Here we examine the diversity (richness and community composition) of ammonia-oxidizing archaea (AOA) and bacteria (AOB) within sediments of Bahía del Tóbari, a hypernutrified estuary receiving substantial amounts of ammonium in agricultural runoff. Using PCR primers designed to specifically target the archaeal ammonia monooxygenase α-subunit (amoA) gene, we found AOA to be present at five sampling sites within this estuary and at two sampling time points (January and October 2004). In contrast, the bacterialamoAgene was PCR amplifiable from only 40% of samples. BacterialamoAlibraries were dominated by a few widely distributedNitrosomonas-like sequence types, whereas AOA diversity showed significant variation in both richness and community composition. AOA communities nevertheless exhibited consistent spatial structuring, with two distinct end member assemblages recovered from the interior and the mouths of the estuary and a mixed assemblage from an intermediate site. These findings represent the first detailed examination of archaealamoAdiversity in estuarine sediments and demonstrate that diverse communities ofCrenarchaeotacapable of ammonia oxidation are present within estuaries, where they may be actively involved in nitrification.
Quantification and Stability of Human Adenoviruses and Polyomavirus JCPyV in Wastewater Matrices
Authors: Bofill-Mas Silvia , Albinana-Gimenez Nestor , Clemente-Casares Pilar , Hundesa Ayalkibet , Rodriguez-Manzano Jesus , Allard Annika , Calvo Miquel , Girones Rosina
Published: December 2006

Human adenoviruses (HAdV) and human polyomavirus JCPyV have been previously proposed as indicators of fecal viral contamination in the environment. Different wastewater matrices have been analyzed by applying real-time quantitative PCR procedures for the presence, quantity, and stability of a wide diversity of excreted HAdV and JCPyV. High quantities of HAdV and JCPyV were detected in sewage, effluent wastewater, sludge, and biosolid samples. Both viruses showed high stability in urban sewage. These results confirm the suitability of both viruses as indicators of human fecal viral pollution.
Culture Conditions Determine the Balance between Two Different Exopolysaccharides Produced by
Lactobacillus pentosus
LPS26
Authors: Sánchez Jorge-Ignacio , Martínez Beatriz , Guillén Rafael , Jiménez-Díaz Rufino , Rodríguez Ana
Published: December 2006

Lactobacillus pentosus
LPS26, isolated from a natural fermentation of green olives, produces a capsular polymer constituted of two exopolysaccharides (EPS): EPS A, a high-molecular-weight (high-
M
w
) polysaccharide (1.9 × 10
6
Da) composed of glucose and rhamnose (3:1), and EPS B, a low-
M
w
polysaccharide (3.3 × 10
4
Da) composed of glucose and mannose (3:1). Fermentation experiments in a chemically semidefined medium with different carbon sources (glucose, fructose, mannitol, and lactose) showed that all of them except fructose supported EPS A production rather than EPS B production. The influence of temperature and pH was further analyzed. As the temperature dropped, increased synthesis of both EPS was detected. The control of pH especially enhanced EPS B production. With regard to this, the maximum total EPS production (514 mg liter
−1
) was achieved at a suboptimal growth temperature (20°C) and pH 6.0. Continuous cultures showed that EPS A, synthesized mainly at low dilution rates, is clearly dependent on the growth rate, whereas EPS B synthesis was hardly affected. EPS production was also detected in supplemented skimmed milk, but no increase on the viscosity of the fermented milk was recorded. This could be linked to the high proportion of the low-
M
w
polysaccharide produced in these conditions in contrast to that observed in culture media. Overall, the present study shows that culture conditions have a clear impact on the type and concentration of EPS produced by strain LPS26, and consequently, these conditions should be carefully selected for optimization and application studies. Finally, it should be noted that this is, to our knowledge, the first report on EPS production by
L. pentosus
.
Identification of Human and Animal Adenoviruses and Polyomaviruses for Determination of Sources of Fecal Contamination in the Environment
Authors: Hundesa Ayalkibet , Maluquer de Motes Carlos , Bofill-Mas Silvia , Albinana-Gimenez Nestor , Girones Rosina
Published: December 2006

The
Adenoviridae
and
Polyomaviridae
families comprise a wide diversity of viruses which may be excreted for long periods in feces or urine. In this study, a preliminary analysis of the prevalence in the environment and the potential usefulness as source-tracking tools of human and animal adenoviruses and polyomaviruses has been developed. Molecular assays based on PCR specifically targeting human adenoviruses (HAdV), porcine adenoviruses (PAdV), bovine adenoviruses (BAdV), and bovine polyomaviruses (BPyV) were applied to environmental samples including urban sewage, slaughterhouse, and river water samples. PAdV and BPyV were detected in a very high percentage of samples potentially affected by either porcine or bovine fecal contamination, respectively. However, BAdV were detected in only one sample, showing a lower prevalence than BPyV in the wastewater samples analyzed. The 22 slaughterhouse samples with fecal contamination of animal origin showed negative results for the presence of HAdV. The river water samples analyzed were positive for the presence of both human and animal adenoviruses and polyomaviruses, indicating the existence of diverse sources of contamination. The identities of the viruses detected were confirmed by analyses of the amplified sequences. All BPyV isolates showed a 97% similarity in nucleotide sequences. This is the first time that PAdV5, BAdV6, and BPyV have been reported to occur in environmental samples. Human and porcine adenoviruses and human and bovine polyomaviruses are proposed as tools for evaluating the presence of viral contamination and for tracking the origin of fecal/urine contamination in environmental samples.
Inactivation of Poliovirus 1 and F-Specific RNA Phages and Degradation of Their Genomes by UV Irradiation at 254 Nanometers
Authors: Simonet Julien , Gantzer Christophe
Published: December 2006

Several models (animal caliciviruses, poliovirus 1 [PV1], and F-specific RNA bacteriophages) are usually used to predict inactivation of nonculturable viruses. For the same UV fluence, viral inactivation observed in the literature varies from 0 to 5 logs according to the models and the methods (infectivity versus molecular biology). The lack of knowledge concerning the mechanisms of inactivation due to UV prevents us from selecting the best model. In this context, determining if viral genome degradation may explain the loss of infectivity under UV radiation becomes essential. Thus, four virus models (PV1 and three F-specific RNA phages: MS2, GA, and Qβ) were exposed to UV radiation from 0 to 150 mJ · cm
−2
. PV1 is the least-resistant virus, while MS2 and GA phages are the most resistant, with phage Qβ having an intermediate sensitivity; respectively, 6-log, 2.3-log, 2.5-log, and 4-log decreases for 50 mJ · cm
−2
. In parallel, analysis of RNA degradation demonstrated that this phenomenon depends on the fragment size for PV1 as well as for MS2. Long fragments (above 2,000 bases) for PV1 and MS2 fell rapidly to the background level (>1.3-log decrease) for 20 mJ · cm
−2
and 60 mJ · cm
− 2
, respectively. Nevertheless, the size of the viral RNA is not the only factor affecting UV-induced RNA degradation, since viral RNA was more rapidly degraded in PV1 than in the MS2 phage with a similar size. Finally, extrapolation of inactivation and UV-induced RNA degradation kinetics highlights that genome degradation could fully explain UV-induced viral inactivation.
Multilocus Sequence Typing Supports the Hypothesis that Cow- and Human-AssociatedSalmonellaIsolates Represent Distinct and Overlapping Populations
Authors: Alcaine S. D. , Soyer Y. , Warnick L. D. , Su W.-L. , Sukhnanand S. , Richards J. , Fortes E. D. , McDonough P. , Root T. P. , Dumas N. B. , Gröhn Y. , Wiedmann M.
Published: December 2006

A collection of 179 human and 156 bovine clinicalSalmonellaisolates obtained from across New York state over the course of 1 year was characterized using serotyping and a multilocus sequence typing (MLST) scheme based on the sequencing of three genes (fimA,manB, andmdh). The 335 isolates were differentiated into 52 serotypes and 72 sequence types (STs). Analyses of bovine isolates collected on different farms over time indicated that specific subtypes can persist over time on a given farm; in particular, a number of farms showed evidence for the persistence of a specificSalmonella entericaserotype Newport sequence type. Serotypes and STs were not randomly distributed among human and bovine isolates, and selected serotypes and STs were associated exclusively with either human or bovine sources. A number of common STs were geographically widespread. For example, ST6, which includes isolates representing serotype Typhimurium as well as the emerging serotype 4,5,12:i:-, was found among human and bovine isolates in a number of counties in New York state. Phylogenetic analyses supported the possibility that serotype 4,5,12:i:- is closely related toSalmonellaserotype Typhimurium.Salmonellaserotype Newport was found to represent two distinct evolutionary lineages that differ in their frequencies among human and bovine isolates. A number ofSalmonellaisolates carried two copies ofmanB(33 isolates) or showed small deletion events infimA(nine isolates); these duplication and deletion events may provide mechanisms for the rapid diversification ofSalmonellasurface molecules. We conclude that the combined use of an economical three-gene MLST scheme and serotyping can provide considerable new insights into the evolution and transmission ofSalmonella.
Disruption of
N
-Αcyl Homoserine Lactone-Mediated Cell Signaling and Iron Acquisition in Epiphytic Bacteria by Leaf Surface Compounds
Authors: Karamanoli Katerina , Lindow Steven E.
Published: December 2006

Since
N
-acyl homoserine lactones (AHLs) are key mediators of cell density-dependent regulation of traits involved in virulence and epiphytic fitness in gram-negative bacteria such as
Pseudomonas syringae
, a variety of plant species were examined to determine their production of leaf surface compounds that could interact with these signaling systems. Leaf washings of 17 of 52 plant species tested stimulated or inhibited AHL-dependent traits in at least one of the bacterial reporter strains used. The active compounds from most plants could be distinguished from known AHLs due to different patterns of mobility during C
8
and C
18
reverse-phase thin-layer chromatography (TLC) and normal-phase TLC compared to the patterns for authentic bacterial AHLs. All plant extracts were also tested to determine their abilities to sequester iron and trigger bacterial siderophore synthesis on a medium containing abundant iron. Leaf washings from 16 of the 52 plant species, as well as tannic acid solutions, stimulated pyoverdine synthesis in
P. syringae
in a high-iron medium. These preparations also inhibited the growth of a
P. syringae
mutant unable to produce pyoverdine siderophores but not the growth of the wild-type bacterium. The stimulation of siderophore production and the growth inhibition by plant extracts and purified tannins were both reversed by addition of ferric chloride to culture media, indicating that iron was made unavailable by the compounds released onto the leaf surface.
A 1,1,1-Trichloroethane-Degrading Anaerobic Mixed Microbial Culture Enhances Biotransformation of Mixtures of Chlorinated Ethenes and Ethanes
Authors: Grostern Ariel , Edwards Elizabeth A.
Published: December 2006

1,1,1-Trichloroethane (1,1,1-TCA) is a common groundwater pollutant as a result of improper disposal and accidental spills. It is often found as a cocontaminant with trichloroethene (TCE) and inhibits some TCE-degrading microorganisms. 1,1,1-TCA removal is therefore required for effective bioremediation of sites contaminated with mixed chlorinated organics. This study characterized MS, a 1,1,1-TCA-degrading, anaerobic, mixed microbial culture derived from a 1,1,1-TCA-contaminated site in the northeastern United States. MS reductively dechlorinated 1,1,1-TCA to 1,1-dichloroethane (1,1-DCA) and then to monochloroethane (CA) but not further. Cloning of bacterial 16S rRNA genes revealed among other organisms the presence of aDehalobactersp. and aDesulfovibriosp., which are both phylogenetically related to known dehalorespiring strains. Monitoring of these populations with species-specific quantitative PCR during degradation of 1,1,1-TCA and 1,1-DCA showed thatDehalobacterproliferated during dechlorination.Dehalobactergrowth was dechlorination dependent, whereasDesulfovibriogrowth was dechlorination independent. Experiments were also performed to test whether MS could enhance TCE degradation in the presence of inhibiting levels of 1,1,1-TCA. Dechlorination ofcis-dichloroethene (cDCE) and vinyl chloride (VC) in KB-1, a chloroethene-degrading culture used for bioaugmentation, was inhibited with 1,1,1-TCA present. When KB-1 and MS were coinoculated, degradation of cDCE and VC to ethene proceeded as soon as the 1,1,1-TCA was dechlorinated to 1,1-DCA by MS. This demonstrated the potential application of the MS and KB-1 cultures for cobioaugmentation of sites cocontaminated with 1,1,1-TCA and TCE.
Study of Biochemical Pathways and Enzymes Involved in Pyrene Degradation by
Mycobacterium
sp. Strain KMS
Authors: Liang Yanna , Gardner Dale R. , Miller Charles D. , Chen Dong , Anderson Anne J. , Weimer Bart C. , Sims Ronald C.
Published: December 2006

Pyrene degradation is known in bacteria. In this study,
Mycobacterium
sp. strain KMS was used to study the metabolites produced during, and enzymes involved in, pyrene degradation. Several key metabolites, including pyrene-4,5-dione,
cis
-4,5-pyrene-dihydrodiol, phenanthrene-4,5-dicarboxylic acid, and 4-phenanthroic acid, were identified during pyrene degradation. Pyrene-4,5-dione, which accumulates as an end product in some gram-negative bacterial cultures, was further utilized and degraded by
Mycobacterium
sp. strain KMS. Enzymes involved in pyrene degradation by
Mycobacterium
sp. strain KMS were studied, using 2-D gel electrophoresis. The first protein in the catabolic pathway, aromatic-ring-hydroxylating dioxygenase, which oxidizes pyrene to
cis
-4,5-pyrene-dihydrodiol, was induced with the addition of pyrene and pyrene-4,5-dione to the cultures. The subcomponents of dioxygenase, including the alpha and beta subunits, 4Fe-4S ferredoxin, and the Rieske (2Fe-2S) region, were all induced. Other proteins responsible for further pyrene degradation, such as dihydrodiol dehydrogenase, oxidoreductase, and epoxide hydrolase, were also found to be significantly induced by the presence of pyrene and pyrene-4,5-dione. Several nonpathway-related proteins, including sterol-binding protein and cytochrome P450, were induced. A pyrene degradation pathway for
Mycobacterium
sp. strain KMS was proposed and confirmed by proteomic study by identifying almost all the enzymes required during the initial steps of pyrene degradation.
Cross-Feeding betweenBifidobacterium longumBB536 and Acetate-Converting, Butyrate-Producing Colon Bacteria during Growth on Oligofructose
Authors: Falony Gwen , Vlachou Angeliki , Verbrugghe Kristof , Vuyst Luc De
Published: December 2006

In vitro coculture fermentations ofBifidobacterium longumBB536 and two acetate-converting, butyrate-producing colon bacteria,Anaerostipes caccaeDSM 14662 andRoseburia intestinalisDSM 14610, with oligofructose as the sole energy source, were performed to study interspecies interactions. Two clearly distinct types of cross-feeding were identified.A. caccaeDSM 14662 was not able to degrade oligofructose but could grow on the fructose released byB. longumBB536 during oligofructose breakdown.R. intestinalisDSM 14610 could degrade oligofructose, but only after acetate was added to the medium. Detailed kinetic analyses of oligofructose breakdown by the last strain revealed simultaneous degradation of the different chain length fractions, in contrast with the preferential degradation of shorter fractions byB. longumBB536. In a coculture of both strains, initial oligofructose degradation and acetate production byB. longumBB536 took place, which in turn also allowed oligofructose breakdown byR. intestinalisDSM 14610. These and similar cross-feeding mechanisms could play a role in the colon ecosystem and contribute to the combined bifidogenic/butyrogenic effect observed after addition of inulin-type fructans to the diet.
Bacterial Community Structure in the Hyperarid Core of the Atacama Desert, Chile
Authors: Drees Kevin P. , Neilson Julia W. , Betancourt Julio L. , Quade Jay , Henderson David A. , Pryor Barry M. , Maier Raina M.
Published: December 2006

Soils from the hyperarid Atacama Desert of northern Chile were sampled along an east-west elevational transect (23.75 to 24.70°S) through the driest sector to compare the relative structure of bacterial communities. Analysis of denaturing gradient gel electrophoresis (DGGE) profiles from each of the samples revealed that microbial communities from the extreme hyperarid core of the desert clustered separately from all of the remaining communities. Bands sequenced from DGGE profiles of two samples taken at a 22-month interval from this core region revealed the presence of similar populations dominated by bacteria from the
Gemmatimonadetes
and
Planctomycetes
phyla.
Detection of Human-Derived Fecal Pollution in Environmental Waters by Use of a PCR-Based Human Polyomavirus Assay
Authors: McQuaig Shannon M. , Scott Troy M. , Harwood Valerie J. , Farrah Samuel R. , Lukasik Jerzy O.
Published: December 2006

Regulatory agencies mandate the use of fecal coliforms,
Escherichia coli
or
Enterococcus
spp., as microbial indicators of recreational water quality. These indicators of fecal pollution do not identify the specific sources of pollution and at times underestimate health risks associated with recreational water use. This study proposes the use of human polyomaviruses (HPyVs), which are widespread among human populations, as indicators of human fecal pollution. A method was developed to concentrate and extract HPyV DNA from environmental water samples and then to amplify it by nested PCR. HPyVs were detected in as little as 1 μl of sewage and were not amplified from dairy cow or pig wastes. Environmental water samples were screened for the presence of HPyVs and two additional markers of human fecal pollution: the
Enterococcus faecium esp
gene and the 16S rRNA gene of human-associated
Bacteroides
. The presence of human-specific indicators of fecal pollution was compared to fecal coliform and
Enterococcus
concentrations. HPyVs were detected in 19 of 20 (95%) samples containing the
E. faecium esp
gene and
Bacteroides
human markers. Weak or no correlation was observed between the presence/absence of human-associated indicators and counts of indicator bacteria. The sensitivity, specificity, and correlation with other human-associated markers suggest that the HPyV assay could be a useful predictor of human fecal pollution in environmental waters and an important component of the microbial-source-tracking “toolbox.”
Fingerprinting of
Campylobacter jejuni
by Using Resolution-Optimized Binary Gene Targets Derived from Comparative Genome Hybridization Studies
Authors: Price Erin P. , Huygens Flavia , Giffard Philip M.
Published: December 2006

The aim of this investigation was to exploit the vast comparative data generated by comparative genome hybridization (CGH) studies of
Campylobacter jejuni
in developing a genotyping method. We examined genes in
C. jejuni
that exhibit binary status (present or absent between strains) within known plasticity regions, in order to identify a minimal subset of gene targets that provide high-resolution genetic fingerprints. Using CGH data from three studies as input, binary gene sets were identified with “Minimum SNPs” software. “Minimum SNPs” selects for the minimum number of targets required to obtain a predefined resolution, based on Simpson's index of diversity (
D
). After implementation of stringent criteria for gene presence/absence, eight binary genes were found that provided 100% resolution (
D
= 1) of 20
C. jejuni
strains. A real-time PCR assay was developed and tested on 181
C. jejuni
and
Campylobacter coli
isolates, a subset of which have previously been characterized by multilocus sequence typing,
flaA
short variable region sequencing, and pulsed-field gel electrophoresis. In addition to the binary gene real-time PCR assay, we refined the seven-member single nucleotide polymorphism (SNP) real-time PCR assay previously described for
C. jejuni
and
C. coli
. By normalizing the SNP assay with the respective
C. jejuni
and
C. coli
ubiquitous genes,
mapA
and
ceuE
, the polymorphisms at each SNP could be determined without separate reactions for every polymorphism. We have developed and refined a rapid, highly discriminatory genotyping method for
C. jejuni
and
C. coli
that uses generic technology and is amenable to high-throughput analyses.
Identification of NovelCryptosporidiumGenotypes from Avian Hosts
Authors: Ng Josephine , Pavlasek Ivan , Ryan Una
Published: December 2006

A total of 430 avian-derived fecal specimens were randomly collected from selected Western Australian commercial aviaries, poultry farms, hatcheries, wildlife parks, and the Perth Zoo and screened for the presence ofCryptosporidiumby PCR. Of these, 27Cryptosporidium-positive isolates were detected, characterized, and compared with 11 avian-derived isolates from the Czech Republic at the 18S rRNA and actin gene loci. Sequence and phylogenetic analysis identified four genetically distinct genotypes, avian genotypes I to IV, from various avian hosts. In addition, the host range forCryptosporidium galliwas extended.Cryptosporidium murisandCryptosporidium andersoniwere also identified in a tawny frogmouth and a quail-crested wood partridge, respectively.
Engineering ofDeinococcus radioduransR1 for Bioprecipitation of Uranium from Dilute Nuclear Waste
Authors: Appukuttan Deepti , Rao Amara Sambasiva , Apte Shree Kumar
Published: December 2006

Genetic engineering of radiation-resistant organisms to recover radionuclides/heavy metals from radioactive wastes is an attractive proposition. We have constructed aDeinococcus radioduransstrain harboringphoN, a gene encoding a nonspecific acid phosphatase, obtained from a local isolate ofSalmonella entericaserovar Typhi. The recombinant strain expressed an ∼27-kDa active PhoN protein and efficiently precipitated over 90% of the uranium from a 0.8 mM uranyl nitrate solution in 6 h. The engineered strain retained uranium bioprecipitation ability even after exposure to 6 kGy of60Co gamma rays. The PhoN-expressingD. radioduransoffers an effective and eco-friendly in situ approach to biorecovery of uranium from dilute nuclear waste.
A Yeast Platform for the Production of Single-Chain Antibody-Green Fluorescent Protein Fusions
Authors: Huang Dagang , Shusta Eric V.
Published: December 2006

Fusion proteins comprised of a binding domain and green fluorescent protein (GFP) have the potential to act as one-step binding reagents. In this study, eight single-chain antibodies (scFv) and one single-chain T-cell receptor (scTCR) were secreted as fusions to GFP using aSaccharomyces cerevisiaeexpression system. Fusion protein secretion levels ranged over 3 orders of magnitude, from 4 μg/liter to 4 mg/liter, and correlated well with the secretion levels of the unfused scFv/scTCR. Three fusion types with various linker lengths and fusion orientations were tested for each scFv/scTCR. Although the fusion protein secretion levels were not significantly affected by the nature of the fusion construct, the properties of the fusion protein were clearly influenced. The fluorescence yield per fusion molecule was increased by separating the scFv/scTCR and GFP with an extended (GGGGS)3linker, and fusions with scFv/scTCR at the carboxy-terminus were more resistant to degradation. By evaluating leader sequence processing and using GFP fluorescence to track intracellular processing, it was determined that the majority of fusion protein synthesized by the yeast was not secreted and in most cases was accumulating in an immature, although active, endoplasmic-reticulum (ER)-processed form. This contrasted with unfused scFv, which accumulated in both immature ER-processed and mature post-Golgi forms. The results indicated that yeast can be used as an effective host for the secretion of scFv/scTCR-GFP fusion proteins and that as a result of intracellular secretory bottlenecks, there is considerable yeast secretory capacity remaining to be exploited.
Longitudinal Emergence and Distribution of
Escherichia coli
O157 Genotypes in a Beef Feedlot
Authors: Sanderson Michael W. , Sargeant Jan M. , Shi Xiarong , Nagaraja T. G. , Zurek Ludek , Alam M. J.
Published: December 2006

The purpose of this study was to describe the prevalence and longitudinal distribution of
Escherichia coli
O157 in feedlot cattle and the feedlot environment. Pen floors, water tanks, other cattle in the feedlot, feed, and bird feces were sampled for 2 weeks prior to entry of the study cattle. Twelve pens of study cattle were sampled twice weekly. At each sample time cattle feces, water from tanks in each pen, bunk feed, feed components, bird feces, and houseflies were collected. Bunk feed samples were collected before and after cattle had access to the feed. Overall, 28% of cattle fecal samples, 3.9% of bird fecal samples, 25% of water samples, 3.4% of housefly samples, 1.25% of bunk feed before calf access, and 3.25% of bunk feed samples after cattle had access to the feed were positive for
E. coli
O157. Genetic analysis of
E. coli
O157 isolates was done using pulsed-field gel electrophoresis (PFGE). PFGE types identified in sampling of the feedlot prior to calf entry were different than the majority of types identified following calf entry. A single strain type predominated in the samples collected after entry of the cattle. It was first identified 5 days after entry of the first pen of cattle and was subsequently identified in all pens. Data support that the incoming cattle introduced a new strain that became the predominant strain in the feedlot.
Expression of the Immunity Protein of Plantaricin 423, Produced by
Lactobacillus plantarum
423, and Analysis of the Plasmid Encoding the Bacteriocin
Authors: Van Reenen C. A. , Van Zyl W. H. , Dicks L. M. T.
Published: December 2006

Plantaricin 423 is a class IIa bacteriocin produced by
Lactobacillus plantarum
isolated from sorghum beer. It has been previously determined that plantaricin 423 is encoded by a plasmid designated pPLA4, which is now completely sequenced. The plantaricin 423 operon shares high sequence similarity with the operons of coagulin, pediocin PA-1, and pediocin AcH, with small differences in the DNA sequence encoding the mature bacteriocin peptide and the immunity protein. Apart from the bacteriocin operon, no significant sequence similarity could be detected between the DNA or translated sequence of pPLA4 and the available DNA or translated sequences of the plasmids encoding pediocin AcH, pediocin PA-1, and coagulin, possibly indicating a different origin. In addition to the bacteriocin operon, sequence analysis of pPLA4 revealed the presence of two open reading frames (ORFs). ORF1 encodes a putative mobilization (Mob) protein that is homologous to the pMV158 superfamily of mobilization proteins. Highest sequence similarity occurred between this protein and the Mob protein of
L. plantarum
NCDO 1088. ORF2 encodes a putative replication protein that revealed low sequence similarity to replication proteins of plasmids pLME300 from
Lactobacillus fermentum
and pYIT356 from
Lactobacillus casei
. The immunity protein of plantaricin 423 contains 109 amino acids. Although plantaricin 423 shares high sequence similarity with the pediocin PA-1 operon, no cross-reactivity was recorded between the immunity proteins of plantaricin 423 and pediocin PA-1.
Survival of
Campylobacter
spp. in Darkling Beetles (
Alphitobius diaperinus
) and Their Larvae in Australia
Authors: Templeton Jillian M. , De Jong Amanda J. , Blackall P. J. , Miflin Jeanette K.
Published: December 2006

Campylobacter
infection is the most frequently reported notifiable food-borne disease in humans in Australia. Our studies investigated the persistence of
Campylobacter
spp. in or on darkling beetles (
Alphitobius diaperinus
) and their larvae. Our results in analyses with chickens confirm that, unless very short turnaround times are used (<72 h), beetles colonized in one production cycle (i.e., one batch of chickens) are most unlikely to still be colonized during the next cycle of chickens.
Can
Anopheles gambiae
Be Infected with
Wolbachia pipientis
? Insights from an In Vitro System
Authors: Rasgon Jason L. , Ren Xiaoxia , Petridis Michael
Published: December 2006

Wolbachia pipientis
are maternally inherited endosymbionts associated with cytoplasmic incompatibility, a potential mechanism to drive transgenic traits into
Anopheles
populations for malaria control.
W. pipientis
infections are common in many mosquito genera but have never been observed in any
Anopheles
species, leading to the hypothesis that
Anopheles
mosquitoes are incapable of harboring infection. We used an in vitro system to evaluate the ability of
Anopheles gambiae
cells to harbor diverse
W. pipientis
infections. We successfully established
W. pipientis
infections (strains
w
Ri and
w
AlbB) in the immunocompetent
Anopheles gambiae
cell line Sua5B. Infection was confirmed by PCR, antibiotic curing, DNA sequencing, and direct observation using fluorescence in situ hybridization. The infections were maintained at high passage rates for >30 passages. Our results indicate that there is no intrinsic genetic block to
W. pipientis
infection in
A. gambiae
cells, suggesting that establishment of in vivo
W. pipientis
infections in
Anopheles
mosquitoes may be feasible.
Mercury Methylation by Dissimilatory Iron-Reducing Bacteria
Authors: Kerin E. J. , Gilmour C. C. , Roden E. , Suzuki M. T. , Coates J. D. , Mason R. P.
Published: December 2006

The Hg-methylating ability of dissimilatory iron-reducing bacteria in the genera
Geobacter
,
Desulfuromonas
, and
Shewanella
was examined. All of the
Geobacter
and
Desulfuromonas
strains tested methylated mercury while reducing Fe(III), nitrate, or fumarate. In contrast, none of the
Shewanella
strains produced methylmercury at higher levels than abiotic controls under similar culture conditions.
Geobacter
and
Desulfuromonas
are closely related to known Hg-methylating sulfate-reducing bacteria within the
Deltaproteobacteria.