bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

ABSTRACT

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

ABSTRACTA 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

ABSTRACT

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

ABSTRACT1,1,1-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

ABSTRACT

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

ABSTRACTIn 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

ABSTRACT

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

ABSTRACT

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

ABSTRACT

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

ABSTRACTA 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

ABSTRACTGenetic 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

ABSTRACTFusion 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

ABSTRACT

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

ABSTRACT

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

ABSTRACT

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.