bluuebunny/crossref_metadata_2025_split huggingface dataset:
Longitudinal Study of the Molecular Epidemiology of
Campylobacter jejuni
in Cattle on Dairy Farms
Authors: Kwan Patrick S. L. , Birtles Andrew , Bolton Frederick J. , French Nigel P. , Robinson Susan E. , Newbold Lynne S. , Upton Mathew , Fox Andrew J. 
Published: April 2008

ABSTRACT

Multilocus sequence typing (MLST), an accurate and phylogenetically robust characterization method for population studies of
Campylobacter
, was applied to
Campylobacter jejuni
isolates (
n
= 297) from the fecal samples of cattle from five dairy farms in Cheshire, United Kingdom, collected throughout 2003. The population dynamics of the
C. jejuni
strains, as identified by the occurrence of sequence types and clonal complexes, demonstrated variations within and between cattle populations over time. Three clonal lineages have emerged to predominate among the cattle isolates, namely, the ST-61 complex (24.2%), ST-21 complex (23.6%), and ST-42 complex (20.5%). This provided further evidence that the ST-61 clonal complex may present a cattle-adapted
C. jejuni
genotype. In addition, the ST-42 clonal complex may also represent an important cattle-associated genotype. Strong geographical associations for these genotypes were also found among the farms. This is the first longitudinal study and the largest study to date for
C. jejuni
involving cattle populations using MLST for accurate strain characterization. This study shows the important associations between cattle and
C. jejuni
clonal complexes ST-61, ST-21, and ST-42, and it suggests that cattle and/or dairy products are likely to be a source of the human
Campylobacter
gastroenteritis caused by such genotypes. The reported findings have significant implications for the design of effective intervention strategies for disease control and prevention.
Effect of Exposure to UV-C Irradiation and Monochloramine on Adenovirus Serotype 2 Early Protein Expression and DNA Replication
Authors: Sirikanchana Kwanrawee , Shisler Joanna L. , Mariñas Benito J. 
Published: April 2008

ABSTRACT
The mechanisms of adenovirus serotype 2 inactivation with either UV light (with a narrow emission spectrum centered at 254 nm) or monochloramine were investigated by assessing the potential inhibition of two key steps of the adenovirus life cycle, namely, E1A protein synthesis and viral genomic replication. E1A early protein synthesis was assayed by using immunoblotting, while the replication of viral DNA was analyzed by using slot blotting. Disinfection experiments were performed in phosphate buffer solutions at pH 8 and room temperature (UV) or 20°C (monochloramine). Experimental results revealed that normalized E1A levels at 12 h postinfection (p.i.) were statistically the same as the corresponding decrease in survival ratio for both UV and monochloramine disinfection. Normalized DNA levels at 24 h p.i. were also found to be statistically the same as the corresponding decrease in survival ratio for monochloramine disinfection. In contrast, for UV disinfection, genomic DNA levels were much lower than E1A or survival ratios, possibly as a result of a delay in DNA replication for UV-treated virions compared to that for controls. Future efforts will determine the pre-E1A synthesis step in the adenovirus life cycle affected by exposure to UV and monochloramine, with the goal of identifying the viral molecular target of these two disinfectants.
Genetic Structure and Biology of
Xylella fastidiosa
Strains Causing Disease in Citrus and Coffee in Brazil
Authors: Almeida Rodrigo P. P. , Nascimento Fernanda E. , Chau John , Prado Simone S. , Tsai Chi-Wei , Lopes Sílvio A. , Lopes Joao R. S. 
Published: April 2008

ABSTRACT

Xylella fastidiosa
is a vector-borne, plant-pathogenic bacterium that causes disease in citrus (citrus variegated chlorosis [CVC]) and coffee (coffee leaf scorch [CLS]) plants in Brazil. CVC and CLS occur sympatrically and share leafhopper vectors; thus, determining whether
X. fastidiosa
isolates can be dispersed from one crop to another and cause disease is of epidemiological importance. We sought to clarify the genetic and biological relationships between CVC- and CLS-causing
X. fastidiosa
isolates. We used cross-inoculation bioassays and microsatellite and multilocus sequence typing (MLST) approaches to determine the host range and genetic structure of 26 CVC and 20 CLS isolates collected from different regions in Brazil. Our results show that citrus and coffee
X. fastidiosa
isolates are biologically distinct. Cross-inoculation tests showed that isolates causing CVC and CLS in the field were able to colonize citrus and coffee plants, respectively, but not the other host, indicating biological isolation between the strains. The microsatellite analysis separated most
X. fastidiosa
populations tested on the basis of the host plant from which they were isolated. However, recombination among isolates was detected and a lack of congruency among phylogenetic trees was observed for the loci used in the MLST scheme. Altogether, our study indicates that CVC and CLS are caused by two biologically distinct strains of
X. fastidiosa
that have diverged but are genetically homogenized by frequent recombination.
Associations between Antimicrobial Resistance Genes in Fecal Generic
Escherichia coli
Isolates from Cow-Calf Herds in Western Canada
Authors: Gow Sheryl P. , Waldner Cheryl L. , Harel Josee , Boerlin Patrick 
Published: April 2008

ABSTRACT

The objective of this study was to examine associations among the genetic determinants of antimicrobial resistance (AMR) in 207 fecal generic
Escherichia coli
isolates obtained from 77 cow-calf herds in western Canada. Twenty-three resistance genes corresponding to six different antimicrobial families were assessed using DNA hybridization and PCR. The most common resistance genes in the study sample (207 isolates) were
sul2
(48.3%),
tet
(B) (45.4%), and
ant(3
″
)-Ia
(
aadA1
) (19.3%). Several statistically significant associations between the examined resistance genes were detected. The strongest associations observed were those between genes for resistance to chloramphenicol (
catI
) and trimethoprim (
dhfrI
) (odds ratio [OR] = 214;
P
= 0.0001), sulfonamide (
sul1
) and chloramphenicol (
catI
) (OR = 96.9;
P
= 0.0001), streptomycin [
ant(3
″
)-Ia
(
aadA1
)] and trimethoprim (
dhfrI
) (OR = 96.2;
P
= 0.0001), sulfonamide (
sul1
) and streptomycin [
ant(3
″
)-Ia
(
aadA1
)] (OR = 79.3;
P
= 0.0001), and tetracycline [
tet
(B)] and sulfonamides (
sul2
) (OR = 25.7;
P
= 0.0001). At least one of the resistance genes corresponding to each nonaminoglycoside family of antimicrobials examined in this study was associated with the two aminoglycoside resistance genes
ant(3
″
)-Ia
(
aadA1
) and
aph(3
′)-
Ia
. The multiple, strong associations between genes and the diverse nature of the associations described in this study demonstrate the complexity of resistance gene selection in cow-calf herds and should be considered in the planning of AMR control practices for cow-calf operations.
Influence of Environmental Stress on Distributions of Times to First Division in
Escherichia coli
Populations, as Determined by Digital-Image Analysis of Individual Cells
Authors: Niven Gordon W. , Morton Jennifer S. , Fuks Tamara , Mackey Bernard M. 
Published: April 2008

ABSTRACT

The distributions of times to first cell division were determined for populations of
Escherichia coli
stationary-phase cells inoculated onto agar media. This was accomplished by using automated analysis of digital images of individual cells growing on agar and calculation of the “box area ratio.” Using approximately 300 cells per experiment, the mean time to first division and standard deviation for cells grown in liquid medium at 37°C and inoculated on agar and incubated at 20°C were determined as 3.0 h and 0.7 h, respectively. Distributions were observed to tail toward the higher values, but no definitive model distribution was identified. Both preinoculation stress by heating cultures at 50°C and postinoculation stress by growth in the presence of higher concentrations of NaCl increased mean times to first division. Both stresses also resulted in an increase in the spread of the distributions that was proportional to the mean division time, the coefficient of variation being constant at approximately 0.2 in all cases. The “relative division time,” which is the time to first division for individual cells expressed in terms of the cell size doubling time, was used as measure of the “work to be done” to prepare for cell division. Relative division times were greater for heat-stressed cells than for those growing under osmotic stress.
Anaerobic and Aerobic Degradation of Cyanophycin by the Denitrifying Bacterium
Pseudomonas alcaligenes
Strain DIP1 and Role of Three Other Coisolates in a Mixed Bacterial Consortium
Authors: Sallam Ahmed , Steinbüchel Alexander 
Published: April 2008

ABSTRACT

Four bacterial strains were isolated from a cyanophycin granule polypeptide (CGP)-degrading anaerobic consortium, identified by 16S rRNA gene sequencing, and assigned to species of the genera
Pseudomonas
,
Enterococcus
,
Clostridium
, and
Paenibacillus
. The consortium member responsible for CGP degradation was assigned as
Pseudomonas alcaligenes
strain DIP1. The growth of and CGP degradation by strain DIP1 under anaerobic conditions were enhanced but not dependent on the presence of nitrate as an electron acceptor. CGP was hydrolyzed to its constituting β-Asp-Arg dipeptides, which were then completely utilized within 25 and 4 days under anaerobic and aerobic conditions, respectively. The end products of CGP degradation by strain DIP1 were alanine, succinate, and ornithine as determined by high-performance liquid chromatography analysis. The facultative anaerobic
Enterococcus casseliflavus
strain ELS3 and the strictly anaerobic
Clostridium sulfidogenes
strain SGB2 were coisolates and utilized the β-linked isodipeptides from the common pool available to the mixed consortium, while the fourth isolate,
Paenibacillus odorifer
strain PNF4, did not play a direct role in the biodegradation of CGP. Several syntrophic interactions affecting CGP degradation, such as substrate utilization, the reduction of electron acceptors, and aeration, were elucidated. This study demonstrates the first investigation of CGP degradation under both anaerobic and aerobic conditions by one bacterial strain, with regard to the physiological role of other bacteria in a mixed consortium.
Chitin Hydrolysis by
Listeria
spp., Including
L. monocytogenes
Authors: Leisner J. J. , Larsen M. H. , Jørgensen R. L. , Brøndsted L. , Thomsen L. E. , Ingmer H. 
Published: April 2008

ABSTRACT

Listeria
spp., including the food-borne pathogen
Listeria monocytogenes
, are ubiquitous microorganisms in the environment and thus are difficult to exclude from food processing plants. The factors that contribute to their multiplication and survival in nature are not well understood, but the ability to catabolize various carbohydrates is likely to be very important. One major source of carbon and nitrogen in nature is chitin, an insoluble linear β-1,4-linked polymer of
N
-acetylglucosamine (GlcNAc). Chitin is found in cell walls of fungi and certain algae, in the cuticles of arthropods, and in shells and radulae of molluscs. In the present study, we demonstrated that
L. monocytogenes
and other
Listeria
spp. are able to hydrolyze α-chitin. The chitinolytic activity is repressed by the presence of glucose in the medium, suggesting that chitinolytic activity is subjected to catabolite repression. Activity is also regulated by temperature and is higher at 30°C than at 37°C. In
L. monocytogenes
EGD, chitin hydrolysis depends on genes encoding two chitinases, lmo0105 (
chiB
) and lmo1883 (
chiA
), but not on a gene encoding a putative chitin binding protein (lmo2467). The
chiB
and
chiA
genes are phylogenetically related to various well-characterized chitinases. The potential biological implications of chitinolytic activity of
Listeria
are discussed.
Minimal
Escherichia coli
Cell for the Most Efficient Production of Ethanol from Hexoses and Pentoses
Authors: Trinh Cong T. , Unrean Pornkamol , Srienc Friedrich 
Published: April 2008

ABSTRACT

To obtain an efficient ethanologenic
Escherichia coli
strain, we reduced the functional space of the central metabolic network, with eight gene knockout mutations, from over 15,000 pathway possibilities to 6 pathway options that support cell function. The remaining pathways, identified by elementary mode analysis, consist of four pathways with non-growth-associated conversion of pentoses and hexoses into ethanol at theoretical yields and two pathways with tight coupling of anaerobic cell growth with ethanol formation at high yields. Elimination of three additional genes resulted in a strain that selectively grows only on pentoses, even in the presence of glucose, with a high ethanol yield. We showed that the ethanol yields of strains with minimized metabolic functionality closely matched the theoretical predictions. Remarkably, catabolite repression was completely absent during anaerobic growth, resulting in the simultaneous utilization of pentoses and hexoses for ethanol production.
The Cyclic AMP-Dependent Catabolite Repression System of
Serratia marcescens
Mediates Biofilm Formation through Regulation of Type 1 Fimbriae
Authors: Kalivoda Eric J. , Stella Nicholas A. , O'Dee Dawn M. , Nau Gerard J. , Shanks Robert M. Q. 
Published: April 2008

ABSTRACT

The mechanisms by which environmental carbon sources regulate biofilm formation are poorly understood. This study investigates the roles of glucose and the catabolite repression system in
Serratia marcescens
biofilm formation. The abilities of this opportunistic pathogen to proliferate in a wide range of environments, to cause disease, and to resist antimicrobials are linked to its ability to form biofilms. We observed that growth of
S. marcescens
in glucose-rich medium strongly stimulated biofilm formation, which contrasts with previous studies showing that biofilm formation is inhibited by glucose in
Escherichia coli
and other enteric bacteria. Glucose uptake is known to inversely mediate intracellular cyclic AMP (cAMP) synthesis through regulation of adenylate cyclase (
cyaA
) activity, which in turn controls fundamental processes such as motility, carbon utilization and storage, pathogenesis, and cell division in many bacteria. Here, we demonstrate that mutation of catabolite repression genes that regulate cAMP levels (
crr
and
cyaA
) or the ability to respond to cAMP (
crp
) confers a large increase in biofilm formation. Suppressor analysis revealed that phenotypes of a cAMP receptor protein (
crp
) mutant require the
fimABCD
operon, which is responsible for type 1 fimbria production. Consistently,
fimA
transcription and fimbria production were determined to be upregulated in a
cyaA
mutant background by using quantitative real-time reverse transcription-PCR and transmission electron microscopy analysis. The regulatory pathway by which environmental carbon sources influence cAMP concentrations to alter production of type 1 fimbrial adhesins establishes a novel mechanism by which bacteria control biofilm development.
Development and Experimental Validation of a Predictive Threshold Cycle Equation for Quantification of Virulence and Marker Genes by High-Throughput Nanoliter-Volume PCR on the OpenArray Platform
Authors: Stedtfeld Robert D. , Baushke Samuel W. , Tourlousse Dieter M. , Miller Sarah M. , Stedtfeld Tiffany M. , Gulari Erdogan , Tiedje James M. , Hashsham Syed A. 
Published: April 2008

ABSTRACT

Development of quantitative PCR (QPCR) assays typically requires extensive screening within and across a given species to ensure specific detection and lucid identification among various pathogenic and nonpathogenic strains and to generate standard curves. To minimize screening requirements, multiple virulence and marker genes (VMGs) were targeted simultaneously to enhance reliability, and a predictive threshold cycle (

C
T

) equation was developed to calculate the number of starting copies based on an experimental

C
T

. The empirical equation was developed with Sybr green detection in nanoliter-volume QPCR chambers (OpenArray) and tested with 220 previously unvalidated primer pairs targeting 200 VMGs from 30 pathogens. A high correlation (
R
2
= 0.816) was observed between the predicted and experimental

C
T

s based on the organism's genome size, guanine and cytosine (GC) content, amplicon length, and stability of the primer's 3′ end. The performance of the predictive

C
T

equation was tested using 36 validation samples consisting of pathogenic organisms spiked into genomic DNA extracted from three environmental waters. In addition, the primer success rate was dependent on the GC content of the target organisms and primer sequences. Targeting multiple assays per organism and using the predictive

C
T

equation are expected to reduce the extent of the validation necessary when developing QPCR arrays for a large number of pathogens or other targets.
Competing Isogenic
Campylobacter
Strains Exhibit Variable Population Structures In Vivo
Authors: Coward Chris , van Diemen Pauline M. , Conlan Andrew J. K. , Gog Julia R. , Stevens Mark P. , Jones Michael A. , Maskell Duncan J. 
Published: April 2008

ABSTRACT

Consumption of poultry contaminated with
Campylobacter jejuni
is a risk factor for human gastrointestinal disease. The rational development of control strategies for
Campylobacter
within chickens requires an understanding of the colonization process at the molecular and population levels, both within and between hosts. Experiments employing competing strains of
Campylobacter
have been used to investigate colonization. Implicit in these studies is the assumption that the behavior of competing strains is reproducible between experiments. Variability in the recovery of mutants from the chicken gastrointestinal tract during signature-tagged mutagenesis studies demonstrated that this is not always the case. To further investigate this phenomenon in the absence of confounding factors due to phenotypic differences between mutants, we constructed individually identifiable
w
ild-type
i
sogenic
t
agged
s
trains (WITS) that have indistinguishable phenotypes in pure culture. By using mixtures of WITS, it is possible to monitor the relative amounts of subpopulations of essentially wild-type bacteria. Using a 2-week-old chicken model of colonization, we observed unpredictable variations in population structure both within and between experiments, even in the simplest case of two competing strains. This variation occurred both when birds were simultaneously infected with two WITS and when birds inoculated with different WITS were cohoused. We present evidence for founder effects during initial colonization with subsequent bird-to-bird transmission. We suggest that these and phenotypic variation contribute to the observed variability. These factors render simple models of colonization which do not take them into account inappropriate for
Campylobacter
and impact the planning and interpretation of competition experiments using this organism.
Rapid Screening of Quorum-Sensing Signal
N
-Acyl Homoserine Lactones by an In Vitro Cell-Free Assay
Authors: Kawaguchi Tomohiro , Chen Yung Pin , Norman R. Sean , Decho Alan W. 
Published: April 2008

ABSTRACT

A simple, sensitive, and rapid cell-free assay system was developed for detection of
N
-acyl homoserine lactone (AHL) autoinducers involved in bacterial quorum sensing (QS). The present approach improves upon previous whole-cell biosensor-based approaches in its utilization of a cell-free assay approach to conduct bioassays. The cell-free assay was derived from the AHL biosensor bacterium
Agrobacterium tumefaciens
NTL4(pCF218)(pCF372), allowing the expression of β-galactosidase upon addition of exogenous AHLs. We have shown that β-galactosidase expression is possible in cell-free solution [lysate from
Agrobacterium tumefaciens
NTL4(pCF218)(pCF372) culture]. Assay detection limits with the use of chromogenic substrate X-Gal (5-bromo-4-chloro-3-indolyl-β-
d
-galactopyranoside) ranged from approximately 100 nM to 300 nM depending on the specific AHL. Replacement (of X-Gal) with the luminescent substrate Beta-Glo increased sensitivity to AHLs by 10-fold. A major advantage of the cell-free assay system is elimination of time-consuming steps for biosensor cell culture conditioning, which are required prior to whole-cell bioassays. This significantly reduced assay times from greater than 24 h to less than 3 h, while maintaining high sensitivity. Assay lysate may be prepared in bulk and stored (−80°C) over 6 months for future use. Finally, the present protocol may be adapted for use with other biosensor strains and be used in high-throughput AHL screening of bacteria or metagenomic libraries.
Construction of a Reporter Vector System for In Vivo Analysis of Promoter Activity in
Propionibacterium freudenreichii
Authors: Faye Therese , Åsebø Anita , Salehian Zhian , Langsrud Thor , Nes Ingolf F. , Brede Dag Anders 
Published: April 2008

ABSTRACT

A β-galactosidase reporter system for the analysis of promoter elements in
Propionibacterium freudenreichii
was designed. The pTD210 in vivo reporter vector was constructed using a promoterless
lacZ
gene from
Bifidobacterium longum
cloned into the pAMT1 plasmid. The utility of the pTD210 reporter vector was demonstrated by an investigation of six predicted promoters in
P. freudenreichii
. The system produced accurate and reproducible measurements that facilitated both promoter identification and the quantification of promoter activities.
Characterization of a Bacterial Community in an Abandoned Semiarid Lead-Zinc Mine Tailing Site
Authors: Mendez Monica O. , Neilson Julia W. , Maier Raina M. 
Published: April 2008

ABSTRACT
Bacterial diversity in mine tailing microbial communities has not been thoroughly investigated despite the correlations that have been observed between the relative microbial diversity and the success of revegetation efforts at tailing sites. This study employed phylogenetic analyses of 16S rRNA genes to compare the bacterial communities present in highly disturbed, extremely (pH 2.7) and moderately (pH 5.7) acidic lead-zinc mine tailing samples from a semiarid environment with those from a vegetated off-site (OS) control sample (pH 8). Phylotype richness in these communities decreased from 42 in the OS control to 24 in the moderately acidic samples and 8 in the extremely acidic tailing samples. The clones in the extremely acidic tailing sample were most closely related to acidophiles, none of which were detected in the OS control sample. The comparison generated by this study between the bacteria present in extremely acidic tailing and that in moderately acidic tailing communities with those in an OS control soil provides a reference point from which to evaluate the successful restoration of mine tailing disposal sites by phytostabilization.
Biphenyl Dioxygenase from an Arctic Isolate Is Not Cold Adapted
Authors: Master Emma R. , Agar Nathalie Y. R. , Gómez-Gil Leticia , Powlowski Justin B. , Mohn William W. , Eltis Lindsay D. 
Published: April 2008

ABSTRACT

Biphenyl dioxygenase from the psychrotolerant bacterium
Pseudomonas
sp. strain Cam-1 (BPDO
Cam-1
) was purified and found to have an apparent

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for biphenyl of 1.1 ± 0.1 s
−1
(mean ± standard deviation) at 4°C. In contrast, BPDO
LB400
from the mesophile
Burkholderia xenovorans
LB400 had no detectable activity at this temperature. At 57°C, the half-life of the BPDO
Cam-1
oxygenase was less than half that of the BPDO
LB400
oxygenase. Nevertheless, BPDO
Cam-1
appears to be a typical
Pseudomonas pseudoalcaligenes
KF707-type dioxygenase.