bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phosphate Transporter Genes as Reliable Gene Markers for the Identification and Discrimination of Arbuscular Mycorrhizal Fungi in the Genus
Glomus
Authors: Sokolski Serge , Dalpé Yolande , Piché Yves 
Published: December 2010

ABSTRACT

An inorganic phosphate transporter gene sequence (852-bp section) allowed discrimination between 10
Glomus
fungal species represented by 25 strains. It was particularly valuable in differentiating between morphologically similar species with nucleotide and amino acid sequence differences higher than 3%. This gene is proposed as a reliable barcode for the
Glomeromycetes
.
Plasmid-Mediated Quinolone Resistance in
Pseudomonas putida
Isolates from Imported Shrimp
Authors: Tran Quynh T. , Nawaz Mohamed S. , Deck Joanna , Nguyen Kiet T. , Cerniglia Carl E. 
Published: December 2010

ABSTRACT

Fourteen quinolone-resistant
Pseudomonas putida
isolates were recovered from imported frozen shrimp sold in the United States. Two isolates harbored plasmids with
qnrA
and
qnrB
genes. PCR and DNA sequencing of quinolone resistance-determining regions identified novel substitutions in GyrA (His139→Glu and Thr128→Ala) and GyrB (Thr442→Asn, Gly470→Ala, and Ile487→Pro) and previously reported substitutions in GyrB (Asp489→Glu) and ParC (Thr105→Pro).
Identification and Characterization of Novel and Potent Transcription Promoters of
Francisella tularensis
Authors: Zaide Galia , Grosfeld Haim , Ehrlich Sharon , Zvi Anat , Cohen Ofer , Shafferman Avigdor 
Published: December 2010

ABSTRACT

Two alternative promoter trap libraries, based on the green fluorescence protein (
gfp
) reporter and on the chloramphenicol acetyltransferase (
cat
) cassette, were constructed for isolation of potent
Francisella tularensis
promoters. Of the 26,000
F. tularensis
strain LVS
gfp
library clones, only 3 exhibited visible fluorescence following UV illumination and all appeared to carry the bacterioferritin promoter (
Pbfr
). Out of a total of 2,000 chloramphenicol-resistant LVS clones isolated from the
cat
promoter library, we arbitrarily selected 40 for further analysis. Over 80% of these clones carry unique
F. tularensis
DNA sequences which appear to drive a wide range of protein expression, as determined by specific chloramphenicol acetyltransferase (CAT) Western dot blot and enzymatic assays. The DNA sequence information for the 33 unique and novel
F. tularensis
promoters reported here, along with the results of
in silico
and primer extension analyses, suggest that
F. tularensis
possesses classical
Escherichia coli
σ
70
-related promoter motifs. These motifs include the −10 (TATAAT) and −35 [TTGA(C/T)A] domains and an AT-rich region upstream from −35, reminiscent of but distinct from the
E. coli
upstream region that is termed the UP element. The most efficient promoter identified (
Pbfr
) appears to be about 10 times more potent than the
F. tularensis groEL
promoter and is probably among the strongest promoters in
F. tularensis
. The battery of promoters identified in this work will be useful, among other things, for genetic manipulation in the background of
F. tularensis
intended to gain better understanding of the mechanisms involved in pathogenesis and virulence, as well as for vaccine development studies.
Viability of
Bacillus licheniformis
and
Bacillus thuringiensis
Spores as a Model for Predicting the Fate of
Bacillus anthracis
Spores during Composting of Dead Livestock
Authors: Reuter Tim , Alexander Trevor W. , McAllister Tim A. 
Published: December 2010

ABSTRACT

Safe disposal of dead livestock and contaminated manure is essential for the effective control of infectious disease outbreaks. Composting has been shown to be an effective method of disposal, but no information exists on its ability to contain diseases caused by spore-forming bacteria, such as
Bacillus anthracis
. Duplicate composters (east and west), each containing 16 dead cattle, were constructed (final capacity, 85,000 kg). Spores (10
7
CFU/g manure) of
Bacillus licheniformis
and
Bacillus thuringiensis
were mixed with autoclaved feedlot manure and placed in either sterile vials or porous nylon bags. Compost temperatures in the west composter were slightly higher than in the east composter. Viable
B. thuringiensis
spores were reduced to ≤10
2
CFU in all samples after 112 days but were isolated from bags (west composter) at ≤10
2
and at 10
5
CFU (east composter) after 230 days. In contrast,
B. licheniformis
was at ≤10
2
CFU in vials (west composter) after 112 days but remained at 10
6
CFU after 230 days (east composter). Similarly,
B. licheniformis
in bags was not detected after 230 days in the west composter but remained at 10
7
CFU in the east composter. Our study suggests that spore viability was reduced in the west composter by exposure to compost and elevated temperatures over time. Different temperature profiles may explain why spores remained viable in the east structure but were largely rendered nonviable in the west structure. Under practical conditions, variation in composting microclimates may preclude the complete inactivation of
Bacillus
spores, including those of
B. anthracis
, during composting. However, composting may still have merit as a method of biocontainment, reducing and diluting the transfer of infectious spores into the environment.
Inactivation of a Human Norovirus Surrogate by High-Pressure Processing: Effectiveness, Mechanism, and Potential Application in the Fresh Produce Industry
Authors: Lou Fangfei , Neetoo Hudaa , Chen Haiqiang , Li Jianrong 
Published: December 2010

ABSTRACT
Fresh produce is often a high-risk food for norovirus contamination because it can become contaminated at both preharvest and postharvest stages and it undergoes minimal or no processing. Currently, there is no effective method to eliminate the viruses from fresh produce. This study systematically investigated the effectiveness of high-pressure processing (HPP) on inactivating murine norovirus (MNV-1), a surrogate for human norovirus, in aqueous medium and fresh produce. We demonstrated that MNV-1 was effectively inactivated by HPP. More than a 5-log-PFU/g reduction was achieved in all tested fresh produce when it was pressurized at 400 MPa for 2 min at 4°C. We found that pressure, pH, temperature, and food matrix affected the virus survival in foods. MNV-1 was more effectively inactivated at 4°C than at 20°C in both medium and fresh produce. MNV-1 was also more sensitive to HPP at neutral pH than at acidic pH. We further demonstrated that disruption of viral capsid structure, but not degradation of viral genomic RNA, is the primary mechanism of virus inactivation by HPP. However, HPP does not degrade viral capsid protein, and the pressurized capsid protein was still antigenic. Overall, HPP had a variable effect on the sensorial quality of fresh produce, depending on the pressure level and type of product. Taken together, HPP effectively inactivated a human norovirus surrogate in fresh produce with a minimal impact on food quality and thus can provide a novel intervention for processing fruits intended for frozen storage and related products such as purees, sauces, and juices.
Quantitative PCR Coupled with Melt Curve Analysis for Detection of SelectedPseudo-nitzschiaspp. (Bacillariophyceae) from the Northwestern Mediterranean Sea
Authors: Andree Karl B. , Fernández-Tejedor Margarita , Elandaloussi Laurence M. , Quijano-Scheggia Sonia , Sampedro Nagore , Garcés Esther , Camp Jordi , Diogène Jorge 
Published: December 2010

ABSTRACTThe frequency and intensity ofPseudo-nitzschiaspp. blooms along the coast of Catalonia have been increasing over the past 20 years. As species from this genus that are documented as toxigenic have been found in local waters, with both toxic and nontoxic species cooccurring in the same bloom, there is a need to develop management tools for discriminating the difference. Currently, differentiation of toxic and nontoxic species requires time-consuming electron microscopy to distinguish taxonomic features that would allow identification as to species, and cryptic species can still remain misidentified. In this study, cells ofPseudo-nitzschiafrom clonal cultures isolated from seawater were characterized to their species identity using scanning electron microscopy, and subsamples of each culture were used to create an internal transcribed spacer 1 (ITS-1), 5.8S, and ITS-2 ribosomal DNA database for development of species-specific quantitative PCR (qPCR) assays. Once developed, these qPCR assays were applied to field samples collected over a 2-year period in Alfaques Bay in the northwestern Mediterranean Sea to evaluate the possibility of a comprehensive surveillance for allPseudo-nitzschiaspp. using molecular methods to supplement optical microscopy, which can discern taxonomy only to the genus level within this taxon. TotalPseudo-nitzschiacell density was determined by optical microscopy from water samples collected weekly and compared to results obtained from the sum of eightPseudo-nitzschiaspecies-specific qPCR assays using duplicate samples. Species-specific qPCR followed by melt curve analysis allowed differentiation of amplicons and identification of false positives, and results correlated well with the totalPseudo-nitzschiacell counts from optical microscopy.
Analyses of both the
alkB
Gene Transcriptional Start Site and
alkB
Promoter-Inducing Properties of
Rhodococcus
sp. Strain BCP1 Grown on
n
-Alkanes
Authors: Cappelletti M. , Fedi S. , Frascari D. , Ohtake H. , Turner R. J. , Zannoni D. 
Published: December 2010

ABSTRACT

Rhodococcus
sp. strain BCP1, known for its capacity to grow on short-chain
n
-alkanes (C
2
to C
7
) and to cometabolize chlorinated solvents, was found to also utilize medium- and long-chain
n
-alkanes (C
12
to C
24
) as energy and carbon sources. To examine this feature in detail, a chromosomal region which includes the
alkB
gene cluster encoding a non-heme di-iron monooxygenase (
alkB
), two rubredoxins, and one rubredoxin reductase was cloned from the BCP1 genome. Furthermore, the activity of the
alkB
gene promoter (P

alkB

) was examined in the presence of gaseous, liquid, and solid
n
-alkanes along with intermediates of the putative
n
-alkane degradation pathway. A recombinant plasmid, pTP
alkB
LacZ, was constructed by inserting the
lacZ
gene downstream of P

alkB

, and it was used to transform
Rhodococcus
sp. strain BCP1. Measurements of β-galactosidase activity showed that P

alkB

is induced by C
6
to C
22
n
-alkanes. Conversely, C
2
to C
5
and >C
22
n
-alkanes and alkenes, such as hexene, were not inducers of
alkB
expression. The effects on P

alkB

expression induced by alternative carbon sources along with putative products of
n
-hexane metabolism were also evaluated. This report highlights the great versatility of
Rhodococcus
sp. strain BCP1 and defines for the first time the
alkB
gene transcriptional start site and the
alkB
promoter-inducing capacities for substrates different from
n
-alkanes in a
Rhodococcus
strain.
Efficient Homofermentative
l
-(+)-Lactic Acid Production from Xylose by a Novel Lactic Acid Bacterium,
Enterococcus mundtii
QU 25
Authors: Abdel-Rahman Mohamed Ali , Tashiro Yukihiro , Zendo Takeshi , Hanada Katsuhiro , Shibata Keisuke , Sonomoto Kenji 
Published: December 2010

ABSTRACT

Enterococcus mundtii
QU 25, a newly isolated lactic acid bacterium, efficiently metabolized xylose into
l
-lactate. In batch fermentations, the strain produced 964 mM
l
-(+)-lactate from 691 mM xylose, with a yield of 1.41 mol/mol xylose consumed and an extremely high optical purity of ≥99.9% without acetate production.
Role of the Cell Wall Microenvironment in Expression of a Heterologous SpaP-S1 Fusion Protein by
Streptococcus gordonii
Authors: Davis Elisabeth , Kennedy Dustin , Halperin Scott A. , Lee Song F. 
Published: December 2010

ABSTRACT

The charge density in the cell wall microenvironment of Gram-positive bacteria is believed to influence the expression of heterologous proteins. To test this, the expression of a SpaP-S1 fusion protein, consisting of the surface protein SpaP of
St
r
eptococcus mutans
and a pertussis toxin S1 fragment, was studied in the live vaccine candidate bacterium
Streptococcus gordonii
. Results showed that the parent strain PM14 expressed very low levels of SpaP-S1. By comparison, the
dlt
mutant strain, which has a mutation in the
dlt
operon preventing
d
-alanylation of the cell wall lipoteichoic acids, and another mutant strain, OB219(pPM14), which lacks the LPXTG major surface proteins SspA and SspB, expressed more SpaP-S1 than the parent. Both the
dlt
mutant and the OB219(pPM14) strain had a more negatively charged cell surface than PM14, suggesting that the negative charged cell wall played a role in the increase in SpaP-S1 production. Accordingly, the addition of Ca
2+
, Mg
2+
, and K
+
, presumably increasing the positive charge of the cell wall, led to a reduction in SpaP-S1 production, while the addition of bicarbonate resulted in an increase in SpaP-S1 production. The level of SpaP-S1 production could be correlated with the level of PrsA, a peptidyl-prolyl
cis/trans
isomerase, in the cells. PrsA expression appears to be regulated by the cell envelope stress two-component regulatory system LiaSR. The results collectively indicate that the charge density of the cell wall microenvironment can modulate heterologous SpaP-S1 protein expression in
S. gordonii
and that this modulation is mediated by the level of PrsA, whose expression is regulated by the LiaSR two-component regulatory system.
Development of an Aerosol Surface Inoculation Method for
Bacillus
Spores
Authors: Lee Sang Don , Ryan Shawn P. , Snyder Emily Gibb 
Published: December 2010

ABSTRACT

A method was developed to deposit
Bacillus subtilis
spores via aerosolization onto various surface materials for biological agent decontamination and detection studies. This new method uses an apparatus coupled with a metered dose inhaler to reproducibly deposit spores onto various surfaces. A metered dose inhaler was loaded with
Bacillus subtilis
spores, a surrogate for
Bacillus anthracis
. Five different material surfaces (aluminum, galvanized steel, wood, carpet, and painted wallboard paper) were tested using this spore deposition method. This aerosolization method deposited spores at a concentration of more than 10
7
CFU per coupon (18-mm diameter) with less than a 50% coefficient of variation, showing that the aerosolization method developed in this study can deposit reproducible numbers of spores onto various surface coupons. Scanning electron microscopy was used to probe the spore deposition patterns on test coupons. The deposition patterns observed following aerosol impaction were compared to those of liquid inoculation. A physical difference in the spore deposition patterns was observed to result from the two different methods. The spore deposition method developed in this study will help prepare spore coupons via aerosolization fast and reproducibly for bench top decontamination and detection studies.
Specific Real-Time PCR for Simultaneous Detection and Identification of
Legionella pneumophila
Serogroup 1 in Water and Clinical Samples
Authors: Mérault N. , Rusniok C. , Jarraud S. , Gomez-Valero L. , Cazalet C. , Marin M. , Brachet E. , Aegerter P. , Gaillard J. L. , Etienne J. , Herrmann J. L. , Lawrence C. , Buchrieser C. 
Published: December 2010

ABSTRACT

Legionella pneumophila
, a bacterium that replicates within aquatic amoebae and persists in the environment as a free-living microbe, is the causative agent of Legionnaires' disease. Among the many
Legionella
species described,
L. pneumophila
is associated with 90% of human disease, and within the 15 serogroups (Sg),
L. pneumophila
Sg1 causes more than 84% of Legionnaires' disease worldwide. Thus, rapid and specific identification of
L. pneumophila
Sg1 is of the utmost importance for evaluation of the contamination of collective water systems and the risk posed. Previously we had shown that about 20 kb of the 33-kb locus carrying the genes coding for the proteins involved in lipopolysaccharide biosynthesis (LPS gene cluster) by
L. pneumophila
was highly specific for Sg1 strains and that three genes (
lpp0831
,
wzm
, and
wzt
) may serve as genetic markers. Here we report the sequencing and comparative analyses of this specific region of the LPS gene cluster in
L. pneumophila
Sg6, -10, -12, -13, and -14. Indeed, the
wzm
and
wzt
genes were present only in the Sg1 LPS gene cluster, which showed a very specific gene content with respect to the other five serogroups investigated. Based on this observation, we designed primers and developed a classical and a real-time PCR method for the detection and simultaneous identification of
L. pneumophila
Sg1 in clinical and environmental isolates. Evaluation of the selected primers with 454
Legionella
and 38 non-
Legionella
strains demonstrated 100% specificity. Sensitivity, specificity, and predictive values were further evaluated with 209 DNA extracts from water samples of hospital water supply systems and with 96 respiratory specimens. The results showed that the newly developed quantitative Sg1-specific PCR method is a highly specific and efficient tool for the surveillance and rapid detection of high-risk
L. pneumophila
Sg1 in water and clinical samples.
Real-Time Solvent Tolerance Analysis ofPseudomonassp. Strain VLB120ΔC Catalytic Biofilms
Authors: Halan Babu , Schmid Andreas , Buehler Katja 
Published: December 2010

ABSTRACTBiofilms are ubiquitous surface-associated microbial communities embedded in an extracellular polymeric (EPS) matrix, which gives the biofilm structural integrity and strength. It is often reported that biofilm-grown cells exhibit enhanced tolerance toward adverse environmental stress conditions, and thus there has been a growing interest in recent years to use biofilms for biotechnological applications. We present a time- and locus-resolved, noninvasive, quantitative approach to study biofilm development and its response to the toxic solvent styrene.Pseudomonassp. strain VLB120ΔC-BT-gfp1 was grown in modified flow-cell reactors and exposed to the solvent styrene. Biofilm-grown cells displayed stable catalytic activity, producing (S)-styrene oxide continuously during the experimental period. The pillar-like structure and growth rate of the biofilm was not influenced by the presence of the solvent. However, the cells experience severe membrane damage during styrene treatment, although they obviously are able to adapt to the solvent, as the amount of permeabilized cells decreased from 75 to 80% down to 40% in 48 h. Concomitantly, the fraction of concanavalin A (ConA)-stainable EPS increased, substantiating the assumption that those polysaccharides play a major role in structural integrity and enhanced biofilm tolerance toward toxic environments. Compared to control experiments with planktonic grown cells, thePseudomonasbiofilm adapted much better to toxic concentrations of styrene, as nearly 65% of biofilm cells were not permeabilized (viable), compared to only 7% in analogous planktonic cultures. These findings underline the robustness of biofilms under stress conditions and its potential for fine chemical syntheses.
Lag Phase of
Salmonella enterica
under Osmotic Stress Conditions
Authors: Zhou K. , George S. M. , Métris A. , Li P. L. , Baranyi J. 
Published: December 2010

ABSTRACT

Salmonella enterica
serovar Typhimurium was grown at salt concentrations ranging from 0.5 to 7.5% in minimal medium with and without added osmoprotectant and in a rich medium. In minimal medium, the cells showed an initial decline period, and consequently the definition of the lag time of the resultant log count curve was revised. The model of Baranyi and Roberts (Int. J. Food Microbiol. 23:277-294, 1994) was modified to take into account the initial decline period, based on the assumption that the log count curve of the total population was the sum of a dying and a surviving-then-growing subpopulation. The lag time was defined as the lag of the surviving subpopulation. It was modeled by means of a parameter quantifying the biochemical work the surviving cells carry out during this phase, the “work to be done.” The logarithms of the maximum specific growth rates as a function of the water activity in the three media differed only by additive constants, which gave a theoretical basis for bias factors characterizing the relationships between different media. Models for the lag and the “work to be done” as a function of the water activity showed similar properties, but in rich medium above 5% salt concentrations, the data showed a maximum for this work. An accurate description of the lag time is important to avoid food wastage, which is an issue of increasing significance in the food industry, while maintaining food safety standards.
Metallic Copper as an Antimicrobial Surface
Authors: Grass Gregor , Rensing Christopher , Solioz Marc 
Published: December 2010

ABSTRACT
Bacteria, yeasts, and viruses are rapidly killed on metallic copper surfaces, and the term “contact killing” has been coined for this process. While the phenomenon was already known in ancient times, it is currently receiving renewed attention. This is due to the potential use of copper as an antibacterial material in health care settings. Contact killing was observed to take place at a rate of at least 7 to 8 logs per hour, and no live microorganisms were generally recovered from copper surfaces after prolonged incubation. The antimicrobial activity of copper and copper alloys is now well established, and copper has recently been registered at the U.S. Environmental Protection Agency as the first solid antimicrobial material. In several clinical studies, copper has been evaluated for use on touch surfaces, such as door handles, bathroom fixtures, or bed rails, in attempts to curb nosocomial infections. In connection to these new applications of copper, it is important to understand the mechanism of contact killing since it may bear on central issues, such as the possibility of the emergence and spread of resistant organisms, cleaning procedures, and questions of material and object engineering. Recent work has shed light on mechanistic aspects of contact killing. These findings will be reviewed here and juxtaposed with the toxicity mechanisms of ionic copper. The merit of copper as a hygienic material in hospitals and related settings will also be discussed.
Genomewide Expression Profile Analysis of the Candida glabrata Pdr1 Regulon
Authors: Caudle Kelly E. , Barker Katherine S. , Wiederhold Nathan P. , Xu Lijing , Homayouni Ramin , Rogers P. David 
Published: December 2010

ABSTRACT

The ABC transporters
Candida glabrata
Cdr1 (CgCdr1), CgPdh1, and CgSnq2 are known to mediate azole resistance in the pathogenic fungus
C. glabrata
. Activating mutations in
CgPDR1
, a zinc cluster transcription factor, result in constitutive upregulation of these ABC transporter genes but to various degrees. We examined the genomewide gene expression profiles of two matched azole-susceptible and -resistant
C. glabrata
clinical isolate pairs. Of the differentially expressed genes identified in the gene expression profiles for these two matched pairs, there were 28 genes commonly upregulated with
CgCDR1
in both isolate sets including
YOR1
,
LCB5
,
RTA1
,
POG1
,
HFD1
, and several members of the
FLO
gene family of flocculation genes. We then sequenced
CgPDR1
from each susceptible and resistant isolate and found two novel activating mutations that conferred increased resistance when they were expressed in a common background strain in which
CgPDR1
had been disrupted. Microarray analysis comparing these reengineered strains to their respective parent strains identified a set of commonly differentially expressed genes, including
CgCDR1
,
YOR1
, and
YIM1
, as well as genes uniquely regulated by specific mutations. Our results demonstrate that while CgPdr1 activates a broad repertoire of genes, specific activating mutations result in the activation of discrete subsets of this repertoire.