bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcription Analysis of Genes Encoding Homologues of Reductive Dehalogenases in “
Dehalococcoides
” sp. Strain CBDB1 by Using Terminal Restriction Fragment Length Polymorphism and Quantitative PCR
Authors: Wagner Anke , Adrian Lorenz , Kleinsteuber Sabine , Andreesen Jan R. , Lechner Ute 
Published: February 2009

ABSTRACT

The transcription of reductive dehalogenase homologous (
rdh
) genes of “
Dehalococcoides
” sp. strain CBDB1 was investigated during the growth and reductive dechlorination of 1,2,3- and 1,2,4-trichlorobenzene (TCB). A method was developed to monitor the expression of all 32
rdhA
genes present in the genome based on reverse transcription-PCR amplification with 13 degenerate primer pairs and terminal restriction fragment length polymorphism (t-RFLP) analysis. With this approach, the upregulation of the transcription of 29
rdhA
genes was indicated in response to 1,2,3- and 1,2,4-TCB added after a substrate depletion period of 72 h. The transcription of the remaining three
rdhA
genes additionally was detected using specific primers. While most
rdhA
genes were upregulated similarly in cultures after induction with 1,2,3-TCB or 1,2,4-TCB, three
rdhA
genes responded differentially to 1,2,3- and 1,2,4-TCB, as revealed by the comparison of t-RFLP profiles. The enhanced transcription of cbdbA1453 and cbdbA187 was observed in the presence of 1,2,3-TCB, while the transcription of cbdbA1624 was strongly induced by 1,2,4-TCB. Comparison of t-RFLP profiles obtained from cDNA and genomic DNA indicated a particularly high induction of the transcription of
cbrA
(=cbdbA84) by both TCBs. As indicated by reverse transcription-quantitative PCR, the transcription of these plus two other
rdhA
genes (cbdbA1588 and cbdbA1618) increased within 48 to 72 h by one or two orders of magnitude. Subsequently, transcript levels slowly decreased and approached initial transcript levels several days after complete dehalogenation. Finally,
cbrA
was transcribed to a level of 22 transcripts per
cbrA
gene, suggesting that
cbrA
mRNA could be an appropriate biomarker for the investigation of the natural dechlorination potential at chlorobenzene-contaminated sites.
Inactivation of Bacterial Pathogens following Exposure to Light from a 405-Nanometer Light-Emitting Diode Array
Authors: Maclean Michelle , MacGregor Scott J. , Anderson John G. , Woolsey Gerry 
Published: February 2009

ABSTRACT

This study demonstrates the susceptibility of a variety of medically important bacteria to inactivation by 405-nm light from an array of light-emitting diodes (LEDs), without the application of exogenous photosensitizer molecules. Selected bacterial pathogens, all commonly associated with hospital-acquired infections, were exposed to the 405-nm LED array, and the results show that both gram-positive and gram-negative species were successfully inactivated, with the general trend showing gram-positive species to be more susceptible than gram-negative bacteria. Detailed investigation of the bactericidal effect of the blue-light treatment on
Staphylococcus aureus
suspensions, for a range of different population densities, demonstrated that 405-nm LED array illumination can cause complete inactivation at high population densities: inactivation levels corresponding to a 9-log
10
reduction were achieved. The results, which show the inactivation of a wide range of medically important bacteria including methicillin-resistant
Staphylococcus aureus
, demonstrate that, with further development, narrow-spectrum 405-nm visible-light illumination from an LED source has the potential to provide a novel decontamination method with a wide range of potential applications.
Detection of
Campylobacter
Bacteria in Air Samples for Continuous Real-Time Monitoring of
Campylobacter
Colonization in Broiler Flocks
Authors: Olsen Katja N. , Lund Marianne , Skov Julia , Christensen Laurids S. , Hoorfar Jeffrey 
Published: February 2009

ABSTRACT

Improved monitoring tools are important for the control of
Campylobacter
bacteria in broiler production. In this study, we compare the sensitivities of detection of
Campylobacter
by PCR with feces, dust, and air samples during the lifetimes of broilers in two poultry houses and conclude that the sensitivity of detection of
Campylobacter
in air is comparable to that in other sample materials. Profiling of airborne particles in six poultry houses revealed that the aerodynamic conditions were dependent on the age of the chickens and very comparable among different poultry houses, with low proportions of particles in the 0.5- to 2-μm-diameter range and high proportions in the 2- to 5-μm-diameter range.
Campylobacter
could also be detected by PCR in air samples collected at the hanging stage during the slaughter process but not at the other stages tested at the slaughterhouse. The exploitation of airborne dust in poultry houses as a sample material for the detection of
Campylobacter
and other pathogens provides an intriguing possibility, in conjunction with new detection technologies, for allowing continuous or semicontinuous monitoring of colonization status.
Prediction of a Required Log Reduction with Probability for
Enterobacter sakazakii
during High-Pressure Processing, Using a Survival/Death Interface Model
Authors: Koseki Shige , Matsubara Maki , Yamamoto Kazutaka 
Published: February 2009

ABSTRACT

A probabilistic model for predicting
Enterobacter sakazakii
inactivation in trypticase soy broth (TSB) and infant formula (IF) by high-pressure processing was developed. The modeling procedure is based on a previous model (S. Koseki and K. Yamamoto, Int. J. Food Microbiol. 116:136-143, 2007) that describes the probability of death of bacteria. The model developed in this study consists of a total of 300 combinations of pressure (400, 450, 500, 550, or 600 MPa), pressure-holding time (1, 3, 5, 10, or 20 min), temperature (25 or 40°C), inoculum level (3, 5, or 7 log
10
CFU/ml), and medium (TSB or IF), with each combination tested in triplicate. For each replicate response of
E. sakazakii
, survival and death were scored with values of 0 and 1, respectively. Data were fitted to a logistic regression model in which the medium was treated as a dummy variable. The model predicted that the required pressure-holding times at 500 MPa for a 5-log reduction in IF with 90% achievement probability were 26.3 and 7.9 min at 25 and 40°C, respectively. The probabilities of achieving 5-log reductions in TSB and IF by treatment with 400 MPa at 25°C for 10 min were 92 and 3%, respectively. The model enabled the identification of a minimum processing condition for a required log reduction, regardless of the underlying inactivation kinetics pattern. Simultaneously, the probability of an inactivation effect under the predicted processing condition was also provided by taking into account the environmental factors mentioned above.
Three Genomes from the PhylumAcidobacteriaProvide Insight into the Lifestyles of These Microorganisms in Soils
Authors: Ward Naomi L. , Challacombe Jean F. , Janssen Peter H. , Henrissat Bernard , Coutinho Pedro M. , Wu Martin , Xie Gary , Haft Daniel H. , Sait Michelle , Badger Jonathan , Barabote Ravi D. , Bradley Brent , Brettin Thomas S. , Brinkac Lauren M. , Bruce David , Creasy Todd , Daugherty Sean C. , Davidsen Tanja M. , DeBoy Robert T. , Detter J. Chris , Dodson Robert J. , Durkin A. Scott , Ganapathy Anuradha , Gwinn-Giglio Michelle , Han Cliff S. , Khouri Hoda , Kiss Hajnalka , Kothari Sagar P. , Madupu Ramana , Nelson Karen E. , Nelson William C. , Paulsen Ian , Penn Kevin , Ren Qinghu , Rosovitz M. J. , Selengut Jeremy D. , Shrivastava Susmita , Sullivan Steven A. , Tapia Roxanne , Thompson L. Sue , Watkins Kisha L. , Yang Qi , Yu Chunhui , Zafar Nikhat , Zhou Liwei , Kuske Cheryl R. 
Published: February 2009

ABSTRACTThe complete genomes of three strains from the phylumAcidobacteriawere compared. Phylogenetic analysis placed them as a unique phylum. They share genomic traits with members of theProteobacteria, theCyanobacteria, and the Fungi. The three strains appear to be versatile heterotrophs. Genomic and culture traits indicate the use of carbon sources that span simple sugars to more complex substrates such as hemicellulose, cellulose, and chitin. The genomes encode low-specificity major facilitator superfamily transporters and high-affinity ABC transporters for sugars, suggesting that they are best suited to low-nutrient conditions. They appear capable of nitrate and nitrite reduction but not N2fixation or denitrification. The genomes contained numerous genes that encode siderophore receptors, but no evidence of siderophore production was found, suggesting that they may obtain iron via interaction with other microorganisms. The presence of cellulose synthesis genes and a large class of novel high-molecular-weight excreted proteins suggests potential traits for desiccation resistance, biofilm formation, and/or contribution to soil structure. Polyketide synthase and macrolide glycosylation genes suggest the production of novel antimicrobial compounds. Genes that encode a variety of novel proteins were also identified. The abundance of acidobacteria in soils worldwide and the breadth of potential carbon use by the sequenced strains suggest significant and previously unrecognized contributions to the terrestrial carbon cycle. Combining our genomic evidence with available culture traits, we postulate that cells of these isolates are long-lived, divide slowly, exhibit slow metabolic rates under low-nutrient conditions, and are well equipped to tolerate fluctuations in soil hydration.
Quantitative Community Fingerprinting Methods for Estimating the Abundance of Operational Taxonomic Units in Natural Microbial Communities
Authors: Ramette Alban 
Published: February 2009

ABSTRACT
Molecular fingerprinting techniques offer great promise for analyzing changes in microbial community structure, especially when dealing with large number of samples. However, a serious limitation has been the lack of quantification offered by such techniques since the relative abundances of the identified operational taxonomic units (OTUs) in the original samples are not measured. A quantitative fingerprinting approach designated “qfingerprinting” is proposed here. This method involves serial dilutions of the sample of interest and further systematic fingerprinting of all dilution series. Using the ultimate dilutions for which OTU are still PCR amplifiable and taking into account peak size inaccuracy and peak reproducibility, the relative abundance of each OTU is then simultaneously determined over a scale spanning several orders of magnitude. The approach was illustrated by using a quantitative version of automated ribosomal intergenic spacer analysis (ARISA), here called qARISA. After validating the concept with a synthetic mixture of known DNA targets, qfingerprinting was applied to well-studied marine sediment samples to examine specific changes in OTU abundance associated with sediment depth. The new strategy represents a major advance for the detailed quantitative description of specific OTUs within complex communities. Further ecological applications of the new strategy are also proposed.
Insights into the Diversity of Eukaryotes in Acid Mine Drainage Biofilm Communities
Authors: Baker Brett J. , Tyson Gene W. , Goosherst Lindsey , Banfield Jillian F. 
Published: February 2009

ABSTRACT

Microscopic eukaryotes are known to have important ecosystem functions, but their diversity in most environments remains vastly unexplored. Here we analyzed an 18S rRNA gene library from a subsurface iron- and sulfur-oxidizing microbial community growing in highly acidic (pH < 0.9) runoff within the Richmond Mine at Iron Mountain (northern California). Phylogenetic analysis revealed that the majority (68%) of the sequences belonged to fungi. Protists falling into the deeply branching lineage named the acidophilic protist clade (APC) and the class
Heterolobosea
were also present. The APC group represents kingdom-level novelty, with <76% sequence similarity to 18S rRNA gene sequences of organisms from other environments. Fluorescently labeled oligonucleotide rRNA probes were designed to target each of these groups in biofilm samples, enabling abundance and morphological characterization. Results revealed that the populations vary significantly with the habitat and no group is ubiquitous. Surprisingly, many of the eukaryotic lineages (with the exception of the APC) are closely related to neutrophiles, suggesting that they recently adapted to this extreme environment. Molecular analyses presented here confirm that the number of eukaryotic species associated with the acid mine drainage (AMD) communities is low. This finding is consistent with previous results showing a limited diversity of archaea, bacteria, and viruses in AMD environments and suggests that the environmental pressures and interplay between the members of these communities limit species diversity at all trophic levels.
Prevalence and Characterization of Salmonellae in Commercial Ground Beef in the United States
Authors: Bosilevac Joseph M. , Guerini Michael N. , Kalchayanand Norasak , Koohmaraie Mohammad 
Published: February 2009

ABSTRACT

Commercially produced ground beef samples (
n
= 4,136) were collected from seven regions of the United States over a 24-month period (July 2005 to June 2007) and analyzed for the presence of
Salmonella enterica
by using methods that concurrently provided total prevalence and enumerable levels. The overall prevalence of
Salmonella
strains was 4.2%. Enumeration showed that 94.2% were present at levels below 2 CFU/g. Regional monthly prevalences of
Salmonella
strains varied from 1.8% to 6.5% but were not statistically different (
P
> 0.05). All
Salmonella
isolates were serotyped and their antibiotic susceptibilities determined and analyzed by pulsed-field gel electrophoresis (PFGE). The most common serotypes identified were
Salmonella enterica
serotypes Montevideo, Anatum, Muenster, and Mbandaka, with these accounting for one-half of the isolates obtained. The prevalence of multidrug-resistant (MDR)
Salmonella
was determined to be 0.6%. The most common MDR serotypes were
Salmonella enterica
serotypes Dublin, Reading, and Typhimurium. MDR strains had resistance to between 2 and 10 antibiotics. There were no regional differences in prevalence of MDR
Salmonella
. PFGE analysis revealed that indistinguishable XbaI and AvrII restriction digest patterns (RDPs) could be observed in isolates of the same serotype found in different regions and months of sampling. The RDPs of 19
Salmonella
strains were compared to RDPs in the PulseNet USA database. Thirteen were indistinguishable from existing patterns, and the number of records for each ranged from 1 to 478. These data show that
Salmonella
prevalence in commercial ground beef is low and suggest that attempts to identify sources contributing to
Salmonella
in ground beef by serotype, antibiogram, and PFGE cannot be made without additional documented evidence.
Molecular Fingerprinting by PCR-Denaturing Gradient Gel Electrophoresis Reveals Differences in the Levels of Microbial Diversity for Musty-Earthy Tainted Corks
Authors: Prat Chantal , Ruiz-Rueda Olaya , Trias Rosalia , Anticó Enriqueta , Capone Dimitra , Sefton Mark , Bañeras Lluís 
Published: February 2009

ABSTRACT

The microbial community structure of cork with marked musty-earthy aromas was analyzed using denaturing gradient gel electrophoresis of amplified ribosomal DNA. Cork stoppers and discs were used for DNA extraction and were analyzed by using selective primers for bacteria and fungi. Stoppers clearly differed from discs harboring a different fungal community. Moreover, musty-earthy samples of both types were shown to have a specific microbiota. The fungi
Penicillium glabrum
and
Neurospora
spp. were present in all samples and were assumed to make only a small contribution to off-odor development. In contrast,
Penicillium islandicum
and
Penicillium variabile
were found almost exclusively in 2,4,6-trichloroanisole (TCA) tainted discs. Conversely,
Rhodotorula minuta
and
Rhodotorula sloofiae
were most common in cork stoppers, where only small amounts of TCA were detected. Alpha- and gammaproteobacteria were the most commonly found bacteria in either control or tainted cork stoppers. Specific
Pseudomonas
and
Actinobacteria
were detected in stoppers with low amounts of TCA and 2-methoxy-3,5-dimethylpyrazine. These results are discussed in terms of biological degradation of taint compounds by specific microorganisms. Reliable and straightforward microbial identification methods based on a molecular approach provided useful data to determine and evaluate the risk of taint formation in cork.
One-Step Production of Immobilized α-Amylase in Recombinant
Escherichia coli
Authors: Rasiah Indira A. , Rehm Bernd H. A. 
Published: February 2009

ABSTRACT

Industrial enzymes are often immobilized via chemical cross-linking onto solid supports to enhance stability and facilitate repeated use in bioreactors. For starch-degrading enzymes, immobilization usually places constraints on enzymatic conversion due to the limited diffusion of the macromolecular substrate through available supports. This study describes the one-step immobilization of a highly thermostable α-amylase (BLA) from
Bacillus licheniformis
and its functional display on the surface of polyester beads inside engineered
Escherichia coli
. An optimized BLA variant (Termamyl) was N-terminally fused to the polyester granule-forming enzyme PhaC of
Cupriavidus necator
. The fusion protein lacking the signal sequence mediated formation of stable polyester beads exhibiting α-amylase activity. The α-amylase beads were assessed with respect to α-amylase activity, which was demonstrated qualitatively and quantitatively. The immobilized α-amylase showed Michaelis-Menten enzyme kinetics exerting a
V
max
of about 506 mU/mg of bead protein with a

K
m

of about 5 μM, consistent with that of free α-amylase. The stability of the enzyme at 85°C and the capacity for repeated usage in a starch liquefaction process were also demonstrated. In addition, structural integrity and functionality of the beads at extremes of pH and temperature, demonstrating their suitability for industrial use, were confirmed by electron microscopy and protein/enzyme analysis. This study proposes a novel, cost-effective method for the production of immobilized α-amylase in a single step by using the polyester granules forming protein PhaC as a fusion partner in engineered
E. coli
.
Interplay between Two RND Systems Mediating Antimicrobial Resistance inBrucella suis
Authors: Martin Fernando A. , Posadas Diana M. , Carrica Mariela C. , Cravero Silvio L. , O'Callaghan David , Zorreguieta Angeles 
Published: February 2009

ABSTRACTThe RND-type efflux pumps are responsible for the multidrug resistance phenotype observed in many clinically relevant species. Also, RND pumps have been implicated in physiological processes, with roles in the virulence mechanisms of several pathogenic bacteria. We have previously shown that the BepC outer membrane factor ofBrucella suisis involved in the efflux of diverse drugs, probably as part of a tripartite complex with an inner membrane translocase. In the present work, we characterize two membrane fusion protein-RND translocases ofB. suisencoded by thebepDEandbepFGloci. MIC assays showed that theB. suisΔbepEmutant was more sensitive to deoxycholate (DOC), ethidium bromide, and crystal violet. Furthermore, multicopybepDEincreased resistance to DOC and crystal violet and also to other drugs, including ampicillin, norfloxacin, ciprofloxacin, tetracycline, and doxycycline. In contrast to the ΔbepEmutant, the resistance profile ofB. suisremained unaltered when the other RND gene (bepG) was deleted. However, the ΔbepEΔbepGdouble mutant showed a more severe phenotype than the ΔbepEmutant, indicating that BepFG also contributes to drug resistance. An open reading frame (bepR) coding for a putative regulatory protein of the TetR family was found upstream of thebepDElocus. BepR strongly repressed the activity of thebepDEpromoter, but DOC released the repression mediated by BepR. A clear induction of thebepFGpromoter activity was observed only in the BepDE-defective mutant, indicating a regulatory interplay between the two RND efflux pumps. Although only the BepFG-defective mutant showed a moderate attenuation in model cells, the activities of bothbepDEandbepFGpromoters were induced in the intracellular environment of HeLa cells. Our results show thatB. suisharbors two functional RND efflux pumps that may contribute to virulence.
TheMycobacterium tuberculosisGroEL1 Chaperone Is a Substrate of Ser/Thr Protein Kinases
Authors: Canova Marc J. , Kremer Laurent , Molle Virginie 
Published: February 2009

ABSTRACTWe demonstrate thatMycobacterium tuberculosisGroEL1 is phosphorylated by PknF at two positions, Thr25 and Thr54. Unexpectedly,Mycobacterium smegmatisGroEL1 is not a substrate of its cognate PknF. This study shows that the phosphorylation profiles of conserved proteins are species dependent and provide insights that may explain the numerous biological functions of these important proteins.
Whole-Genome-Based Phylogeny and Divergence of the Genus
Brucella
Authors: Foster Jeffrey T. , Beckstrom-Sternberg Stephen M. , Pearson Talima , Beckstrom-Sternberg James S. , Chain Patrick S. G. , Roberto Francisco F. , Hnath Jonathan , Brettin Tom , Keim Paul 
Published: February 2009

ABSTRACT

Brucellae are worldwide bacterial pathogens of livestock and wildlife, but phylogenetic reconstructions have been challenging due to limited genetic diversity. We assessed the taxonomic and evolutionary relationships of five
Brucella
species—
Brucella abortus
,
B. melitensis
,
B. suis
,
B. canis
, and
B. ovis
—using whole-genome comparisons. We developed a phylogeny using single nucleotide polymorphisms (SNPs) from 13 genomes and rooted the tree using the closely related soil bacterium and opportunistic human pathogen,
Ochrobactrum anthropi
. Whole-genome sequencing and a SNP-based approach provided the requisite level of genetic detail to resolve species in the highly conserved brucellae. Comparisons among the
Brucella
genomes revealed 20,154 orthologous SNPs that were shared in all genomes. Rooting with
Ochrobactrum anthropi
reveals that the
B. ovis
lineage is basal to the rest of the
Brucella
lineage. We found that
B. suis
is a highly divergent clade with extensive intraspecific genetic diversity. Furthermore,
B. suis
was determined to be paraphyletic in our analyses, only forming a monophyletic clade when the
B. canis
genome was included. Using a molecular clock with these data suggests that most
Brucella
species diverged from their common
B. ovis
ancestor in the past 86,000 to 296,000 years, which precedes the domestication of their livestock hosts. Detailed knowledge of the
Brucella
phylogeny will lead to an improved understanding of the ecology, evolutionary history, and host relationships for this genus and can be used for determining appropriate genotyping approaches for rapid detection and diagnostic assays for molecular epidemiological and clinical studies.