bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization of Ozone Disinfection of Murine Norovirus
Authors: Lim Mi Young , Kim Ju-Mi , Lee Jung Eun , Ko GwangPyo 
Published: December 2009

ABSTRACT
Despite the importance of human noroviruses (NoVs) in public health, little information concerning the effectiveness of ozone against NoVs is available. We determined the efficacy of ozone disinfection using murine norovirus (MNV) as a surrogate of human NoV. MNV in ozone demand-free buffer was exposed to a predetermined dose of ozone at two different pHs and temperatures. The virus remaining in the solution was analyzed by plaque assay, real-time TaqMan reverse transcriptase PCR (RT-PCR) (short template), and long-template conventional RT-PCR. Under all conditions, more than 99% of the MNV was inactivated by ozone at 1 mg/liter within 2 min. Both RT-PCR assays significantly underestimated the inactivation of MNV, compared with that measured by plaque assay. Our results indicate that NoV may be more resistant to ozone than has been previously reported. Nevertheless, proper ozone disinfection practices can be used to easily control its transmission in water.
NoxE NADH Oxidase and the Electron Transport Chain Are Responsible for the Ability of
Lactococcus lactis
To Decrease the Redox Potential of Milk
Authors: Tachon Sybille , Brandsma Johannes Bernhard , Yvon Mireille 
Published: December 2009

ABSTRACT

The redox potential plays a major role in the microbial and sensorial quality of fermented dairy products. The redox potential of milk (around 400 mV) is mainly due to the presence of oxygen and many other oxidizing compounds.
Lactococcus lactis
has a strong ability to decrease the redox potential of milk to a negative value (−220 mV), but the molecular mechanisms of milk reduction have never been addressed. In this study, we investigated the impact of inactivation of genes encoding NADH oxidases (
noxE
and
ahpF
) and components of the electron transport chain (ETC) (
menC
and
noxAB
) on the ability of
L. lactis
to decrease the redox potential of ultrahigh-temperature (UHT) skim milk during growth under aerobic and anaerobic conditions. Our results revealed that elimination of oxygen is required for milk reduction and that NoxE is mainly responsible for the rapid removal of oxygen from milk before the exponential growth phase. The ETC also contributes slightly to oxygen consumption, especially during the stationary growth phase. We also demonstrated that the ETC is responsible for the decrease in the milk redox potential from 300 mV to −220 mV when the oxygen concentration reaches zero or under anaerobic conditions. This suggests that the ETC is responsible for the reduction of oxidizing compounds other than oxygen. Moreover, we found great diversity in the reducing activities of natural
L. lactis
strains originating from the dairy environment. This diversity allows selection of specific strains that can be used to modulate the redox potential of fermented dairy products to optimize their microbial and sensorial qualities.
Effects of Carbon Dioxide on Growth of ProteolyticClostridium botulinum, Its Ability To Produce Neurotoxin, and Its Transcriptome
Authors: Artin Ingrid , Mason David R. , Pin Carmen , Schelin Jenny , Peck Michael W. , Holst Elisabet , Rådström Peter , Carter Andrew T. 
Published: December 2009

ABSTRACTThe antimicrobial gas carbon dioxide is frequently used in modified atmosphere packaging. In the present study, the effects of CO2(10 to 70%, vol/vol) on gene expression (measured using quantitative reverse transcription-PCR and a whole-genome DNA microarray) and neurotoxin formation (measured using an enzyme-linked immunosorbent assay [ELISA]) by proteolyticClostridium botulinumtype A1 strain ATCC 3502 were studied during the growth cycle. Interestingly, in marked contrast to the situation with nonproteolyticC. botulinumtypes B and E, CO2had little effect on any of these parameters. At all CO2concentrations, relative expression of neurotoxin cluster genes peaked in the transition between exponential and stationary phases, with evidence of a second rise in expression in late stationary phase. Microarray analysis enabled identification of coding sequences whose expression profiles matched those of the neurotoxin cluster. Further research is needed to determine whether these are connected to neurotoxin formation or are merely growth phase associated.
Methanotrophic Communities in Brazilian Ferralsols from Naturally Forested, Afforested, and Agricultural Sites
Authors: Dörr Nicole , Glaser Bruno , Kolb Steffen 
Published: December 2009

ABSTRACT
Conversion of forests to farmland permanently lowers atmospheric methane consumption due to unresolved reasons. Alphaproteobacterial methanotrophs were predominant in forested soils and gammaproteobacterial species were predominant in farmland soils of subtropical ferralsols in Brazil. The capability of atmospheric methane consumption was obliterated in farmland soils, suggesting a shift from oligotrophic to copiotrophic species.
Distribution and Diversity of
Escherichia coli
Populations in the South Nation River Drainage Basin, Eastern Ontario, Canada
Authors: Lyautey Emilie , Lu Zexun , Lapen David R. , Wilkes Graham , Scott Andrew , Berkers Tanya , Edge Thomas A. , Topp Edward 
Published: December 2009

ABSTRACT

We investigated the prevalence and diversity of
Escherichia coli
strains isolated from surface waters from multiple watersheds within the South Nation River basin in eastern Ontario, Canada. The basin is composed of mixed but primarily agricultural land uses. From March 2004 to November 2007, a total of 2,004 surface water samples were collected from 24 sampling sites.
E. coli
densities ranged from undetectable to 1.64 × 10
5
CFU 100 ml
−1
and were correlated with stream order and proximity to livestock production systems. The diversity of 21,307
E. coli
isolates was characterized using repetitive extragenic palindromic PCR (rep-PCR), allowing for the identification of as many as 7,325 distinct genotypes, without capturing all of the diversity. The community was temporally and spatially dominated by a few dominant genotypes (clusters of more than 500 isolates) and several genotypes of intermediary abundance (clustering between 10 and 499 isolates). Simpson diversity indices, assessed on a normalized number of isolates per sample, ranged from 0.050 to 0.668. Simpson indices could be statistically discriminated on the basis of year and stream order, but land use, discharge, weather, and water physical-chemical properties were not statistically important discriminators. The detection of
Campylobacter
species was associated with statistically lower Simpson indices (greater diversity;
P
< 0.05). Waterborne
E. coli
isolates from genotypes of dominant and intermediary abundance were clustered with isolates obtained from fecal samples collected in the study area over the same period, and 90% of the isolates tested proved to share genotypes with fecal isolates. Overall, our data indicated that the densities and distribution of
E. coli
in these mixed-use watersheds were linked to stream order and livestock-based land uses. Waterborne
E. coli
populations that were distinct from fecal isolates were detected and, on this basis, were possibly naturalized
E. coli
strains.
Genes Involved in Long-Chain Alkene Biosynthesis in
Micrococcus luteus
Authors: Beller Harry R. , Goh Ee-Been , Keasling Jay D. 
Published: December 2009

ABSTRACT

Aliphatic hydrocarbons are highly appealing targets for advanced cellulosic biofuels, as they are already predominant components of petroleum-based gasoline and diesel fuels. We have studied alkene biosynthesis in
Micrococcus luteus
ATCC 4698, a close relative of
Sarcina lutea
(now
Kocuria rhizophila
), which 4 decades ago was reported to biosynthesize
iso
- and
anteiso
-branched, long-chain alkenes. The underlying biochemistry and genetics of alkene biosynthesis were not elucidated in those studies. We show here that heterologous expression of a three-gene cluster from
M
.
luteus
(Mlut_13230-13250) in a fatty acid-overproducing
Escherichia coli
strain resulted in production of long-chain alkenes, predominantly 27:3 and 29:3 (no. carbon atoms: no. C＝C bonds). Heterologous expression of Mlut_13230 (
oleA
) alone produced no long-chain alkenes but unsaturated aliphatic monoketones, predominantly 27:2, and
in vitro
studies with the purified Mlut_13230 protein and tetradecanoyl-coenzyme A (CoA) produced the same C
27
monoketone. Gas chromatography-time of flight mass spectrometry confirmed the elemental composition of all detected long-chain alkenes and monoketones (putative intermediates of alkene biosynthesis). Negative controls demonstrated that the
M
.
luteus
genes were responsible for production of these metabolites. Studies with wild-type
M
.
luteus
showed that the transcript copy number of Mlut_13230-13250 and the concentrations of 29:1 alkene isomers (the dominant alkenes produced by this strain) generally corresponded with bacterial population over time. We propose a metabolic pathway for alkene biosynthesis starting with acyl-CoA (or-ACP [acyl carrier protein]) thioesters and involving decarboxylative Claisen condensation as a key step, which we believe is catalyzed by OleA. Such activity is consistent with our data and with the homology (including the conserved Cys-His-Asn catalytic triad) of Mlut_13230 (OleA) to FabH (β-ketoacyl-ACP synthase III), which catalyzes decarboxylative Claisen condensation during fatty acid biosynthesis.
Long-Term Persistence and Leaching ofEscherichia coliin Temperate Maritime Soils
Authors: Brennan Fiona P. , O'Flaherty Vincent , Kramers Gaelene , Grant Jim , Richards Karl G. 
Published: December 2009

ABSTRACTEnteropathogen contamination of groundwater, including potable water sources, is a global concern. The spreading on land of animal slurries and manures, which can contain a broad range of pathogenic microorganisms, is considered a major contributor to this contamination. Some of the pathogenic microorganisms applied to soil have been observed to leach through the soil into groundwater, which poses a risk to public health. There is a critical need, therefore, for characterization of pathogen movement through the vadose zone for assessment of the risk to groundwater quality due to agricultural activities. A lysimeter experiment was performed to investigate the effect of soil type and condition on the fate and transport of potential bacterial pathogens, usingEscherichia colias a marker, in four Irish soils (n= 9). Cattle slurry (34 tonnes per ha) was spread on intact soil monoliths (depth, 1 m; diameter, 0.6 m) in the spring and summer. No effect of treatment or the initial soil moisture on theE. colithat leached from the soil was observed. Leaching ofE. coliwas observed predominantly from one soil type (average, 1.11 ± 0.77 CFU ml−1), a poorly drained Luvic Stagnosol, under natural rainfall conditions, and preferential flow was an important transport mechanism.E. coliwas found to have persisted in control soils for more than 9 years, indicating that autochthonousE. colipopulations are capable of becoming naturalized in the low-temperature environments of temperate maritime soils and that they can move through soil. This may compromise the use ofE. colias an indicator of fecal pollution of waters in these regions.
Biogenic Silver for Disinfection of Water Contaminated with Viruses
Authors: De Gusseme Bart , Sintubin Liesje , Baert Leen , Thibo Ellen , Hennebel Tom , Vermeulen Griet , Uyttendaele Mieke , Verstraete Willy , Boon Nico 
Published: December 2009

ABSTRACT

The presence of enteric viruses in drinking water is a potential health risk. Growing interest has arisen in nanometals for water disinfection, in particular the use of silver-based nanotechnology. In this study,
Lactobacillus fermentum
served as a reducing agent and bacterial carrier matrix for zerovalent silver nanoparticles, referred to as biogenic Ag
0
. The antiviral action of biogenic Ag
0
was examined in water spiked with an
Enterobacter aerogenes
-infecting bacteriophage (UZ1). Addition of 5.4 mg liter
−1
biogenic Ag
0
caused a 4.0-log decrease of the phage after 1 h, whereas the use of chemically produced silver nanoparticles (
n
Ag
0
) showed no inactivation within the same time frame. A control experiment with 5.4 mg liter
−1
ionic Ag
+
resulted in a similar inactivation after 5 h only. The antiviral properties of biogenic Ag
0
were also demonstrated on the murine norovirus 1 (MNV-1), a model organism for human noroviruses. Biogenic Ag
0
was applied to an electropositive cartridge filter (NanoCeram) to evaluate its capacity for continuous disinfection. Addition of 31.25 mg biogenic Ag
0
m
−2
on the filter (135 mg biogenic Ag
0
kg
−1
filter medium) caused a 3.8-log decline of the virus. In contrast, only a 1.5-log decrease could be obtained with the original filter. This is the first report to demonstrate the antiviral efficacy of extracellular biogenic Ag
0
and its promising opportunities for continuous water disinfection.
Identification of a Secreted Lipolytic Esterase in
Propionibacterium freudenreichii
, a Ripening Process Bacterium Involved in Emmental Cheese Lipolysis
Authors: Dherbécourt J. , Falentin H. , Jardin J. , Maillard M.-B. , Baglinière F. , Barloy-Hubler F. , Thierry A. 
Published: December 2009

ABSTRACT

Lipolysis plays an important role in the formation of cheese flavor. In Emmental cheese, the main part of lipolysis has been associated with the presence of
Propionibacterium freudenreichii
, a species used as a ripening culture. Our aim was to identify the most probable lipolytic esterase(s) involved in cheese lipolysis by
P. freudenreichii
. Since cheese lipolysis mainly occurs during
P. freudenreichii
growth, we hypothesized that
P. freudenreichii
possesses secreted lipolytic esterase(s). For 12 putative esterase genes previously identified from the genome of
P. freudenreichii
CIRM1, the level of expression was quantified by real-time reverse transcriptase (RT)-PCR, and the subcellular localization of esterases was predicted
in silico
. The esterase activity in extracellular and intracellular extracts of
P. freudenreichii
was characterized by zymography, and the extracellular esterases were identified by mass spectrometry. Finally, the best candidate was overexpressed in the same strain. All of the 12 genes encoding putative esterases were expressed. Esterase PF#279 was predicted to be secreted in the medium, PF#774 to be surface exposed, and the 10 remaining putative esterases to be intracellular. Zymography revealed that esterase activities in culture supernatant differed from the ones detected in intracellular extracts. PF#279 was identified as the sole esterase present in culture supernatant. Transformed
P. freudenreichii
CIRM1 clones overexpressing PF#279 showed 5 to 8 times more lipolytic activity on milk fat than the wild-type strain. Combining
in silico
, biochemical, and genetic approaches, we showed that PF#279 is the sole secreted esterase in
P. freudenreichii
and is active on milk fat. Therefore, it is likely a key component in cheese lipolysis by
P. freudenreichii
.
Identification of a Two-Component Regulatory Pathway Essential for Mn(II) Oxidation in
Pseudomonas putida
GB-1
Authors: Geszvain Kati , Tebo Bradley M. 
Published: December 2009

ABSTRACT

Bacterial manganese(II) oxidation has a profound impact on the biogeochemical cycling of Mn and the availability of the trace metals adsorbed to the surfaces of solid Mn(III, IV) oxides. The Mn(II) oxidase enzyme was tentatively identified in
Pseudomonas putida
GB-1 via transposon mutagenesis: the mutant strain GB-1-007, which fails to oxidize Mn(II), harbors a transposon insertion in the gene
cumA
.
cumA
encodes a putative multicopper oxidase (MCO), a class of enzymes implicated in Mn(II) oxidation in other bacterial species. However, we show here that an in-frame deletion of
cumA
did not affect Mn(II) oxidation. Through complementation analysis of the oxidation defect in GB-1-007 with a cosmid library and subsequent sequencing of candidate genes we show the causative mutation to be a frameshift within the
mnxS1
gene that encodes a putative sensor histidine kinase. The frameshift mutation results in a truncated protein lacking the kinase domain. Multicopy expression of
mnxS1
restored Mn(II) oxidation to GB-1-007 and in-frame deletion of
mnxS1
resulted in a loss of oxidation in the wild-type strain. These results clearly demonstrated that the oxidation defect of GB-1-007 is due to disruption of
mnxS1
, not
cumA
::Tn
5
, and that CumA is not the Mn(II) oxidase.
mnxS1
is located upstream of a second sensor histidine kinase gene,
mnxS2
, and a response regulator gene,
mnxR
. In-frame deletions of each of these genes also led to the loss of Mn(II) oxidation. Therefore, we conclude that the MnxS1/MnxS2/MnxR two-component regulatory pathway is essential for Mn(II) oxidation in
P. putida
GB-1.
Involvement of a Novel ABC Transporter and Monoalkyl Phthalate Ester Hydrolase in Phthalate Ester Catabolism by
Rhodococcus jostii
RHA1
Authors: Hara Hirofumi , Stewart Gordon R. , Mohn William W. 
Published: December 2009

ABSTRACT

Phthalate esters (PEs) are important environmental pollutants. While the biodegradation of the parent compound, phthalate (PTH), is well characterized, the biodegradation of PEs is not well understood. In particular, prior to this study, genes involved in the uptake and hydrolysis of these compounds were not conclusively identified. We found that
Rhodococcus jostii
RHA1 could grow on a variety of monoalkyl PEs, including methyl, butyl, hexyl, and 2-ethylhexyl PTHs. Strain RHA1 could not grow on most dialkyl PEs, but suspensions of cells grown on PTH transformed dimethyl, diethyl, dipropyl, dibutyl, dihexyl and di-(2-ethylhexyl) PTHs. The major products of these dialkyl PEs were PTH and the corresponding monoalkyl PEs, and minor products resulted from the shortening of the alkyl side chains. RHA1 exhibited an inducible, ATP-dependent uptake system for PTH with a

K
m

of 22 μM. The deletion and complementation of the
patB
gene demonstrated that the ATP-binding cassette (ABC) transporter encoded by
patDABC
is required for the uptake of PTH and monoalkyl PEs by RHA1. The hydrolase encoded by
patE
of RHA1 was expressed in
Escherichia coli
. PatE specifically hydrolyzed monoalkyl PEs to PTH but did not transform dialkyl PEs or other aromatic esters. This investigation of RHA1 elucidates key processes that are consistent with the environmental fate of PEs.
Yeast Cell Adhesion Molecules Have Functional Amyloid-Forming Sequences
Authors: Ramsook Caleen B. , Tan Cho , Garcia Melissa C. , Fung Raymond , Soybelman Gregory , Henry Ryan , Litewka Anna , O'Meally Shanique , Otoo Henry N. , Khalaf Roy A. , Dranginis Anne M. , Gaur Nand K. , Klotz Stephen A. , Rauceo Jason M. , Jue Chong K. , Lipke Peter N. 
Published: December 2009

ABSTRACT

The occurrence of highly conserved amyloid-forming sequences in
Candida albicans
Als proteins (H. N. Otoo et al., Eukaryot. Cell
7:
776–782, 2008) led us to search for similar sequences in other adhesins from
C. albicans
and
Saccharomyces cerevisiae
. The β-aggregation predictor TANGO found highly β-aggregation-prone sequences in almost all yeast adhesins. These sequences had an unusual amino acid composition: 77% of their residues were β-branched aliphatic amino acids Ile, Thr, and Val, which is more than 4-fold greater than their prevalence in the
S. cerevisiae
proteome. High β-aggregation potential peptides from
S. cerevisiae
Flo1p and
C. albicans
Eap1p rapidly formed insoluble amyloids, as determined by Congo red absorbance, thioflavin T fluorescence, and fiber morphology. As examples of the amyloid-forming ability of the native proteins, soluble glycosylphosphatidylinositol (GPI)-less fragments of
C. albicans
Als5p and
S. cerevisiae
Muc1p also formed amyloids within a few days under native conditions at nM concentrations. There was also evidence of amyloid formation
in vivo
: the surfaces of cells expressing wall-bound Als1p, Als5p, Muc1p, or Flo1p were birefringent and bound the fluorescent amyloid-reporting dye thioflavin T. Both of these properties increased upon aggregation of the cells. In addition, amyloid binding dyes strongly inhibited aggregation and flocculation. The results imply that amyloid formation is an intrinsic property of yeast cell adhesion proteins from many gene families and that amyloid formation is an important component of cellular aggregation mediated by these proteins.
RNA Polymerase I Transcription Silences Noncoding RNAs at the Ribosomal DNA Locus in Saccharomyces cerevisiae
Authors: Cesarini Elisa , Mariotti Francesca Romana , Cioci Francesco , Camilloni Giorgio 
Published: December 2009

ABSTRACT

In
Saccharomyces cerevisiae
the repeated units of the ribosomal locus, transcribed by RNA polymerase I (Pol I), are interrupted by nontranscribed spacers (NTSs). These NTS regions are transcribed by RNA polymerase III to synthesize 5S RNA and by RNA polymerase II (Pol II) to synthesize, at low levels, noncoding RNAs (ncRNAs). While transcription of both RNA polymerase I and III is highly characterized, at the ribosomal DNA (rDNA) locus only a few studies have been performed on Pol II, whose repression correlates with the
SIR2
-dependent silencing. The involvement of both chromatin organization and Pol I transcription has been proposed, and peculiar chromatin structures might justify “ribosomal” Pol II silencing. Reporter genes inserted within the rDNA units have been employed for these studies. We studied, in the natural context, yeast mutants differing in Pol I transcription in order to find whether correlations exist between Pol I transcription and Pol II ncRNA production. Here, we demonstrate that silencing at the rDNA locus represses ncRNAs with a strength inversely proportional to Pol I transcription. Moreover, localized regions of histone hyperacetylation appear in cryptic promoter elements when Pol II is active and in the coding region when Pol I is functional; in addition, DNA topoisomerase I site-specific activity follows RNA polymerase I transcription. The repression of ncRNAs at the rDNA locus, in response to RNA polymerase I transcription, could represent a physiological circuit control whose mechanism involves modification of histone acetylation.