bluuebunny/crossref_metadata_2025_split huggingface dataset:
Criteria for Selection of Surrogates Used To Study the Fate and Control of Pathogens in the Environment
Authors: Sinclair Ryan G. , Rose Joan B. , Hashsham Syed A. , Gerba Charles P. , Haas Charles N. 
Published: January 2012

ABSTRACT
This article defines the term surrogate as an organism, particle, or substance used to study the fate of a pathogen in a specific environment. Pathogenic organisms, nonpathogenic organisms, and innocuous particles have been used as surrogates for a variety of purposes, including studies on survival and transport as well as for method development and as “indicators” of certain conditions. This article develops a qualitative surrogate attribute prioritization process and allows investigators to select a surrogate by systematically detailing the experimental process and prioritizing attributes. The results are described through the use of case studies of various laboratories that have used this process. This article also discusses the history of surrogate and microbial indicator use and outlines the method by which surrogates can be used when conducting a quantitative microbial risk assessment. The ultimate goal of selecting a sufficiently representative surrogate is to improve public health through a health-based risk assessment framework. Under- or overestimating the resistance, inactivation, or movement may negatively impact risk assessments that, in turn, will impact health assessments and estimated safety levels. Reducing uncertainty in a risk assessment is one of the objectives of using surrogates and the ultimate motive for any experiment investigating potential exposure of a pathogen.
The Composition of Camembert Cheese-Ripening Cultures Modulates both Mycelial Growth and Appearance
Authors: Lessard Marie-Hélène , Bélanger Gaétan , St-Gelais Daniel , Labrie Steve 
Published: January 2012

ABSTRACT

The fungal microbiota of bloomy-rind cheeses, such as Camembert, forms a complex ecosystem that has not been well studied, and its monitoring during the ripening period remains a challenge. One limitation of enumerating yeasts and molds on traditional agar media is that hyphae are multicellular structures, and colonies on a petri dish rarely develop from single cells. In addition, fungi tend to rapidly invade agar surfaces, covering small yeast colonies and resulting in an underestimation of their number. In this study, we developed a real-time quantitative PCR (qPCR) method using TaqMan probes to quantify a mixed fungal community containing the most common dairy yeasts and molds:
Penicillium camemberti
,
Geotrichum candidum
,
Debaryomyces hansenii
, and
Kluyveromyces lactis
on soft-cheese model curds (SCMC). The qPCR method was optimized and validated on pure cultures and used to evaluate the growth dynamics of a ripening culture containing
P. camemberti
,
G. candidum
, and
K. lactis
on the surface of the SCMC during a 31-day ripening period. The results showed that
P. camemberti
and
G. candidum
quickly dominated the ecosystem, while
K. lactis
remained less abundant. When added to this ecosystem,
D. hansenii
completely inhibited the growth of
K. lactis
in addition to reducing the growth of the other fungi. This result was confirmed by the decrease in the mycelium biomass on SCMC. This study compares culture-dependent and qPCR methods to successfully quantify complex fungal microbiota on a model curd simulating Camembert-type cheese.
Generation of a Monoclonal Antibody against Mycoplasma spp. following Accidental Contamination during Production of a Monoclonal Antibody against Lawsonia intracellularis
Authors: Hwang Jeong-Min , Lee Ji-Hye , Yeh Jung-Yong 
Published: January 2012

ABSTRACT

This report describes
Mycoplasma
contamination of
Lawsonia intracellularis
cultures that led to the unintended acquisition of a monoclonal antibody against
Mycoplasma
spp. during the attempted generation of a monoclonal antibody against
L. intracellularis
.
Swimming Behavior of Selected Species of Archaea
Authors: Herzog Bastian , Wirth Reinhard 
Published: January 2012

ABSTRACT

The swimming behavior of
Bacteria
has been studied extensively, at least for some species like
Escherichia coli
. In contrast, almost no data have been published for
Archaea
on this topic. In a systematic study we asked how the archaeal model organisms
Halobacterium salinarum
,
Methanococcus voltae
,
Methanococcus maripaludis
,
Methanocaldococcus jannaschii
,
Methanocaldococcus villosus
,
Pyrococcus furiosus
, and
Sulfolobus acidocaldarius
swim and which swimming behavior they exhibit. The two
Euryarchaeota M. jannaschii
and
M. villosus
were found to be, by far, the fastest organisms reported up to now, if speed is measured in bodies per second (bps). Their swimming speeds, at close to 400 and 500 bps, are much higher than the speed of the bacterium
E. coli
or of a very fast animal, like the cheetah, each with a speed of ca. 20 bps. In addition, we observed that two different swimming modes are used by some
Archaea
. They either swim very rapidly, in a more or less straight line, or they exhibit a slower kind of zigzag swimming behavior if cells are in close proximity to the surface of the glass capillary used for observation. We argue that such a “relocate-and-seek” behavior enables the organisms to stay in their natural habitat.
Short-Read Sequencing for Genomic Analysis of the Brown Rot Fungus Fibroporia radiculosa
Authors: Tang Juliet D. , Perkins Andy D. , Sonstegard Tad S. , Schroeder Steven G. , Burgess Shane C. , Diehl Susan V. 
Published: January 2012

ABSTRACT

The feasibility of short-read sequencing for genomic analysis was demonstrated for
Fibroporia radiculosa
, a copper-tolerant fungus that causes brown rot decay of wood. The effect of read quality on genomic assembly was assessed by filtering Illumina GAIIx reads from a single run of a paired-end library (75-nucleotide read length and 300-bp fragment size) at three different stringency levels and then assembling each data set with Velvet. A simple approach was devised to determine which filter stringency was “best.” Venn diagrams identified the regions containing reads that were used in an assembly but were of a low-enough quality to be removed by a filter. By plotting base quality histograms of reads in this region, we judged whether a filter was too stringent or not stringent enough. Our best assembly had a genome size of 33.6 Mb, an N50 of 65.8 kb for a
k
-mer of 51, and a maximum contig length of 347 kb. Using GeneMark, 9,262 genes were predicted. TargetP and SignalP analyses showed that among the 1,213 genes with secreted products, 986 had motifs for signal peptides and 227 had motifs for signal anchors. Blast2GO analysis provided functional annotation for 5,407 genes. We identified 29 genes with putative roles in copper tolerance and 73 genes for lignocellulose degradation. A search for homologs of these 102 genes showed that
F. radiculosa
exhibited more similarity to
Postia placenta
than
Serpula lacrymans
. Notable differences were found, however, and their involvements in copper tolerance and wood decay are discussed.
The 60-Kilodalton Protein Encoded by
orf2
in the
cry19A
Operon of Bacillus thuringiensis subsp. jegathesan Functions Like a C-Terminal Crystallization Domain
Authors: Barboza-Corona J. Eleazar , Park Hyun-Woo , Bideshi Dennis K. , Federici Brian A. 
Published: January 2012

ABSTRACT

The
cry19A
operon of
Bacillus thuringiensis
subsp.
jegathesan
encodes two proteins, mosquitocidal Cry19A (ORF1; 75 kDa) and an ORF2 (60 kDa) of unknown function. Expression of the
cry19A
operon in an acrystalliferous strain of
B. thuringiensis
(4Q7) yielded one small crystal per cell, whereas no crystals were produced when
cry19A
or
orf2
was expressed alone. To determine the function of the ORF2 protein, different combinations of Cry19A, ORF2, and the N- or C-terminal half of Cry1C were synthesized in strain 4Q7. Stable crystalline inclusions of these fusion proteins similar in shape to those in the strain harboring the wild-type operon were observed in sporulating cells. Comparative analysis showed that ORF2 shares considerable amino acid sequence identity with the C-terminal region of large Cry proteins. Together, these results suggest that ORF2 assists in synthesis and crystallization of Cry19A by functioning like the C-terminal domain characteristic of Cry protein in the 130-kDa mass range. In addition, to determine whether overexpression of the
cry19A
operon stabilized its shape and increased Cry19A yield, it was expressed under the control of the strong chimeric
cyt1A
-p/STAB-SD promoter. Interestingly, in contrast to the expression seen with the native promoter, overexpression of the operon yielded uniform bipyramidal crystals that were 4-fold larger on average than the wild-type crystal. In bioassays using the 4th instar larvae of
Culex quinquefasciatus
, the strain producing the larger Cry19A crystal showed moderate larvicidal activity that was 4-fold (95% lethal concentration [LC
95
] = 1.9 μg/ml) more toxic than the activity produced in the strain harboring the wild-type operon (LC
95
= 8.2 μg/ml).
Wide Variation in Antibiotic Resistance Proteins Identified by Functional Metagenomic Screening of a Soil DNA Library
Authors: McGarvey Kelly M. , Queitsch Konstantin , Fields Stanley 
Published: January 2012

ABSTRACT

Most genes for antibiotic resistance present in soil microbes remain unexplored because most environmental microbes cannot be cultured. Only recently has the identification of these genes become feasible through the use of culture-independent methods. We screened a soil metagenomic DNA library in an
Escherichia coli
host for genes that can confer resistance to kanamycin, gentamicin, rifampin, trimethoprim, chloramphenicol, or tetracycline. The screen revealed 41 genes that encode novel protein variants of eight protein families, including aminoglycoside acetyltransferases, rifampin ADP-ribosyltransferases, dihydrofolate reductases, and transporters. Several proteins of the same protein family deviate considerably from each other yet confer comparable resistance. For example, five dihydrofolate reductases sharing at most 44% amino acid sequence identity in pairwise comparisons were equivalent in conferring trimethoprim resistance. We identified variants of aminoglycoside acetyltransferases and transporters that differ in the specificity of the drugs for which they confer resistance. We also found wide variation in protein structure. Two forms of rifampin ADP-ribosyltransferases, one twice the size of the other, were similarly effective at conferring rifampin resistance, although the short form was expressed at a much lower level. Functional metagenomic screening provides insight into the large variability in antibiotic resistance protein sequences, revealing divergent variants that preserve protein function.
Candida zemplinina Can Reduce Acetic Acid Produced by Saccharomyces cerevisiae in Sweet Wine Fermentations
Authors: Rantsiou Kalliopi , Dolci Paola , Giacosa Simone , Torchio Fabrizio , Tofalo Rosanna , Torriani Sandra , Suzzi Giovanna , Rolle Luca , Cocolin Luca 
Published: January 2012

ABSTRACTIn this study we investigated the possibility of usingCandida zemplinina, as a partner ofSaccharomyces cerevisiae, in mixed fermentations of must with a high sugar content, in order to reduce its acetic acid production. Thirty-fiveC. zemplininastrains, which were isolated from different geographic regions, were molecularly characterized, and their fermentation performances were determined. Five genetically different strains were selected for mixed fermentations withS. cerevisiae. Two types of inoculation were carried out: coinoculation and sequential inoculation. A balance between the two species was generally observed for the first 6 days, after which the levels ofC. zemplininastarted to decrease. Relevant differences were observed concerning the consumption of sugars, the ethanol and glycerol content, and acetic acid production, depending on which strain was used and which type of inoculation was performed. Sequential inoculation led to the reduction of about half of the acetic acid content compared to the pureS. cerevisiaefermentation, but the ethanol and glycerol amounts were also low. A coinoculation with selected combinations ofS. cerevisiaeandC. zemplininaresulted in a decrease of ∼0.3 g of acetic acid/liter, while maintaining high ethanol and glycerol levels. This study demonstrates that mixedS. cerevisiaeandC. zemplininafermentation could be applied in sweet wine fermentation to reduce the production of acetic acid, connected to theS. cerevisiaeosmotic stress response.
Phenotypic Switching in Pseudomonas brassicacearum Involves GacS- and GacA-Dependent Rsm Small RNAs
Authors: Lalaouna David , Fochesato Sylvain , Sanchez Lisa , Schmitt-Kopplin Philippe , Haas Dieter , Heulin Thierry , Achouak Wafa 
Published: January 2012

ABSTRACT

The plant-beneficial bacterium
Pseudomonas brassicacearum
forms phenotypic variants
in vitro
as well as
in planta
during root colonization under natural conditions. Transcriptome analysis of typical phenotypic variants using microarrays containing coding as well as noncoding DNA fragments showed differential expression of several genes relevant to secondary metabolism and of the small RNA (sRNA) genes
rsmX
,
rsmY
, and
rsmZ
. Naturally occurring mutations in the
gacS-gacA
system accounted for phenotypic switching, which was characterized by downregulation of antifungal secondary metabolites (2,4-diacetylphloroglucinol and cyanide), indoleacetate, exoenzymes (lipase and protease), and three different
N
-acyl-homoserine lactone molecules. Moreover, in addition to abrogating these biocontrol traits,
gacS
and
gacA
mutations resulted in reduced expression of the type VI secretion machinery, alginate biosynthesis, and biofilm formation. In a
gacA
mutant, the expression of
rsmX
was completely abolished, unlike that of
rsmY
and
rsmZ
. Overexpression of any of the three sRNAs in the
gacA
mutant overruled the pleiotropic changes and restored the wild-type phenotypes, suggesting functional redundancy of these sRNAs. In conclusion, our data show that phenotypic switching in
P. brassicacearum
results from mutations in the
gacS-gacA
system.
Use of High Hydrostatic Pressure To Inactivate Escherichia coli O157:H7 and Salmonella enterica Internalized within and Adhered to Preharvest Contaminated Green Onions
Authors: Neetoo Hudaa , Lu Yingjian , Wu Changqing , Chen Haiqiang 
Published: January 2012

ABSTRACT

Green onions grown in soil and hydroponic medium contaminated with
Escherichia coli
O157:H7 and
Salmonella
were found to take up the pathogens in their roots, bulbs, stems, and leaves. Pressure treatment at 400 to 500 MPa for 2 min at 20 to 40°C eliminated both pathogens that were internalized within green onions during plant growth.
Biochemical and Mutational Analyses of a Multidomain Cellulase/Mannanase from Caldicellulosiruptor bescii
Authors: Su Xiaoyun , Mackie Roderick I. , Cann Isaac K. O. 
Published: January 2012

ABSTRACT

Thermophilic cellulases and hemicellulases are of significant interest to the biofuel industry due to their perceived advantages over their mesophilic counterparts. We describe here biochemical and mutational analyses of
Caldicellulosiruptor bescii
Cel9B/Man5A (CbCel9B/Man5A), a highly thermophilic enzyme. As one of the highly secreted proteins of
C. bescii
, the enzyme is likely to be critical to nutrient acquisition by the bacterium. CbCel9B/Man5A is a modular protein composed of three carbohydrate-binding modules flanked at the N terminus and the C terminus by a glycoside hydrolase family 9 (GH9) module and a GH5 module, respectively. Based on truncational analysis of the polypeptide, the cellulase and mannanase activities within CbCel9B/Man5A were assigned to the N- and C-terminal modules, respectively. CbCel9B/Man5A and its truncational mutants, in general, exhibited a pH optimum of ∼5.5 and a temperature optimum of 85°C. However, at this temperature, thermostability was very low. After 24 h of incubation at 75°C, the wild-type protein maintained 43% activity, whereas a truncated mutant, TM1, maintained 75% activity. The catalytic efficiency with phosphoric acid swollen cellulose as a substrate for the wild-type protein was 7.2 s
−1
ml/mg, and deleting the GH5 module led to a mutant (TM1) with a 2-fold increase in this kinetic parameter. Deletion of the GH9 module also increased the apparent
k
cat
of the truncated mutant TM5 on several mannan-based substrates; however, a concomitant increase in the

K
m

led to a decrease in the catalytic efficiencies on all substrates. These observations lead us to postulate that the two catalytic activities are coupled in the polypeptide.
Identification of the Herboxidiene Biosynthetic Gene Cluster in Streptomyces chromofuscus ATCC 49982
Authors: Shao Lei , Zi Jiachen , Zeng Jia , Zhan Jixun 
Published: January 2012

ABSTRACT

The 53-kb biosynthetic gene cluster for the novel anticholesterol natural product herboxidiene was identified in
Streptomyces chromofuscus
ATCC 49982 by genome sequencing and gene inactivation. In addition to herboxidiene, a biosynthetic intermediate, 18-deoxy-herboxidiene, was also isolated from the fermentation broth of
S. chromofuscus
ATCC 49982 as a minor metabolite.
Association of Pandemic Vibrio parahaemolyticus O3:K6 Present in the Coastal Environment of Northwest Mexico with Cases of Recurrent Diarrhea between 2004 and 2010
Authors: Velazquez-Roman Jorge , León-Sicairos Nidia , Flores-Villaseñor Héctor , Villafaña-Rauda Santiago , Canizalez-Roman Adrian 
Published: January 2012

ABSTRACT

In 2004, more than 1,230 cases of gastroenteritis due to pandemic O3:K6 strains of
Vibrio parahaemolyticus
were reported in southern Sinaloa, a state in Northwestern Mexico. Recurrent sporadic cases arose from 2004 to 2010, spreading from the south to the north. In the present study,
Vibrio parahaemolyticus
was detected in both environmental samples and clinical cases along the Pacific coast of Sinaloa during 2004 to 2010. An evaluation was made of the serotypes, distribution of virulence genes, and presence of pandemic O3:K6 strains. A total of 144 strains were isolated from environmental samples (from sediment, seawater, and shrimp), and 154 clinical strains were isolated. A total of 10 O serogroups and 30 serovars were identified in the strains. Environmental strains (
n
= 144) belonged to 10 O serogroups and 28 serovars, while clinical strains (
n
= 154) belonged to 8 O serogroups and 14 serovars. Ten serovars were shared by both environmental and clinical strains. Among 144 environmental isolates, 4.1% (6/144) belonged to the pandemic clone, with 83.3% containing the
orf8
gene and with O3:K6 accounting for 67%. On the other hand, pathogenic strains (
tdh
and/or
trh
) accounted for 52% (75/144) of the environmental isolates. Interestingly, among 154 clinical isolates, 80.5% (124/154) were pandemic strains, with O3:K6 (
tdh
,
toxRS
new
, and
orf8
) representing the predominant serovar (99.2%, 123/124). Overall, our results indicate that in spite of a high serodiversity and prevalence of pathogenic
Vibrio parahaemolyticus
in the environment, the pandemic strain O3:K6 caused >79% of reported cases between 2004 and 2010 in Sinaloa, Mexico.
Conserved Mechanisms of Mycobacterium marinum Pathogenesis within the Environmental Amoeba Acanthamoeba castellanii
Authors: Kennedy George M. , Morisaki J. Hiroshi , DiGiuseppe Champion Patricia A. 
Published: January 2012

ABSTRACT

Mycobacterium marinum
is a waterborne mycobacterial pathogen. Due to their common niche, protozoa likely represent natural hosts for
M. marinum
. We demonstrate that the ESX-1 secretion system is required for
M. marinum
pathogenesis and that
M. marinum
utilizes actin-based motility in amoebae. Therefore, at least two virulence pathways used by
M. marinum
in macrophages are conserved during
M. marinum
infection of amoebae.
FSL J1-208, a Virulent Uncommon Phylogenetic Lineage IV Listeria monocytogenes Strain with a Small Chromosome Size and a Putative Virulence Plasmid Carrying Internalin-Like Genes
Authors: den Bakker Henk C. , Bowen Barbara M. , Rodriguez-Rivera Lorraine D. , Wiedmann Martin 
Published: January 2012

ABSTRACTThe bacterial genusListeriacontains both saprotrophic and facultative pathogenic species. A small genome size has been suggested to be associated with the loss of pathogenic potential ofL. welshimeriandL. seeligeri. In this paper we present data on the genome ofL. monocytogenesstrain FSL J1-208, a representative of phylogenetic lineage IV. Although this strain was isolated from a clinical case in a caprine host and has no decreased invasiveness in human intestinal epithelial cells, our analyses show that this strain has one of the smallestListeriachromosomes reported to date (2.78 Mb). The chromosome contains 2,772 protein-coding genes, including well-characterized virulence-associated genes, such asinlA,inlB, andinlCand the fullprfAgene cluster. The small genome size is mainly caused by the absence of prophages in the genome ofL. monocytogenesFSL J1-208, and further analyses showed that the total size of prophage-related regions is highly correlated to chromosome size in the genusListeria. L. monocytogenesFSL J1-208 carries a unique type of plasmid of approximately 80 kbp that does not carry genes annotated as being involved in resistance to antibiotics or heavy metals. The accessory genes in this plasmid belong to the internalin family, a family of virulence-associated proteins, and therefore this is the first report of a potential virulence plasmid in the genusListeria.
Contribution of Surface β-Glucan Polysaccharide to Physicochemical and Immunomodulatory Properties of Propionibacterium freudenreichii
Authors: Deutsch Stéphanie-Marie , Parayre Sandrine , Bouchoux Antoine , Guyomarc'h Fanny , Dewulf Joëlle , Dols-Lafargue Marguerite , Baglinière François , Cousin Fabien J. , Falentin Hélène , Jan Gwénaël , Foligné Benoît 
Published: January 2012

ABSTRACT

Propionibacterium freudenreichii
is a bacterial species found in Swiss-type cheeses and is also considered for its health properties. The main claimed effect is the bifidogenic property. Some strains were shown recently to display other interesting probiotic potentialities such as anti-inflammatory properties. About 30% of strains were shown to produce a surface exopolysaccharide (EPS) composed of (1→3,1→2)-β
-d-
glucan due to a single gene named
gtfF
. We hypothesized that functional properties of
P. freudenreichii
strains, including their anti-inflammatory properties, could be linked to the presence of β-glucan. To evaluate this hypothesis,
gtfF
genes of three β-glucan-producing strains were disrupted. These knockout (KO) mutants were complemented with a plasmid harboring
gtfF
(KO-C mutants). The absence of β-glucan in KO mutants was verified by immunological detection and transmission electron microscopy. We observed by atomic force microscopy that the absence of β-glucan in the KO mutant dramatically changed the cell's topography. The capacity to adhere to polystyrene surface was increased for the KO mutants compared to wild-type (WT) strains. Anti-inflammatory properties of WT strains and mutants were analyzed by stimulation of human peripheral blood mononuclear cells (PBMCs). A significant increase of the anti-inflammatory interleukin-10 cytokine production by PBMCs was measured in the KO mutants compared to WT strains. For one strain, the role of β-glucan in mice gut persistence was assessed, and no significant difference was observed between the WT strain and its KO mutant. Thus, β-glucan appears to partly hide the anti-inflammatory properties of
P. freudenreichii
; which is an important result for the selection of probiotic strains.