bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modeling the Growth/No-Growth Boundaries of Postprocessing
Listeria monocytogenes
Contamination on Frankfurters and Bologna Treated with Lactic Acid
Authors: Yoon Yohan , Kendall Patricia A. , Belk Keith E. , Scanga John A. , Smith Gary C. , Sofos John N. 
Published: November 2008

ABSTRACT

This study developed models to predict lactic acid concentration, dipping time, and storage temperature combinations determining growth/no-growth interfaces of
Listeria monocytogenes
at desired probabilities on bologna and frankfurters.
L
.
monocytogenes
was inoculated on bologna and frankfurters, and 75 combinations of lactic acid concentrations, dipping times, and storage temperatures were tested. Samples were stored in vacuum packages for up to 60 days, and bacterial populations were enumerated on tryptic soy agar plus 0.6% yeast extract and Palcam agar on day zero and at the end point of storage. The combinations that allowed
L
.
monocytogenes
increases of ≥1 log CFU/cm
2
were assigned the value of 1 (growth), and the combinations that had increases of <l log CFU/cm
2
were given the value of 0 (no growth). These binary growth response data were fitted to logistic regression to develop a model predicting probabilities of growth. Validation with existing data and various indices showed acceptable model performance. Thus, the models developed in this study may be useful in determining probabilities of growth and in selecting lactic acid concentrations and dipping times to control
L
.
monocytogenes
growth on bologna and frankfurters, while the procedures followed may also be used to develop models for other products, conditions, or pathogens.
Coxiella burnetii
Shedding Routes and Antibody Response after Outbreaks of Q Fever-Induced Abortion in Dairy Goat Herds
Authors: Rousset Elodie , Berri Mustapha , Durand Benoit , Dufour Philippe , Prigent Myriam , Delcroix Thibault , Touratier Anne , Rodolakis Annie 
Published: November 2008

ABSTRACT

Q fever is a zoonosis caused by
Coxiella burnetii
, a bacterium largely carried by ruminants and shed into milk, vaginal mucus, and feces. The main potential hazard to humans and animals is due to shedding of bacteria that can then persist in the environment and be aerosolized. The purpose of this study was to evaluate shedding after an outbreak of Q fever abortion in goat herds and to assess the relationship with the occurrence of abortions and antibody responses. Aborting and nonaborting goats were monitored by PCR for
C. burnetii
shedding 15 and 30 days after the abortion episodes. PCR analysis of all samples showed that 70% (
n
= 50) of the aborting and 53% (
n
= 70) of the nonaborting goats were positive.
C. burnetii
was shed into vaginal mucus, feces, and milk of 44%, 21%, and 38%, respectively, of goats that aborted and 27%, 20%, and 31%, respectively, of goats that delivered normally. Statistical comparison of these shedding results did not reveal any difference between these two groups. PCR results obtained for the vaginal and fecal routes were concordant in 81% of cases, whereas those for milk correlated with only 49% of cases with either vaginal or fecal shedding status. Serological analysis, using enzyme-linked immunosorbent assay (ELISA), indirect immunofluorescence assay (IFA), and complement fixation tests, showed that at least 24% of the seronegative goats shed bacteria. Positive vaginal and fecal shedding, unlike positive milk shedding, was observed more often in animals that were weakly positive or negative by ELISA or IFA. Two opposite shedding trends were thus apparent for the milk and vaginal-fecal routes. Moreover, this study showed that a nonnegligible proportion of seronegative animals that delivered normally could excrete
C. burnetii
.
Potential Application ofN-Carbamoyl-β-Alanine Amidohydrolase fromAgrobacterium tumefaciensC58 for β-Amino Acid Production
Authors: Martínez-Gómez Ana Isabel , Martínez-Rodríguez Sergio , Pozo-Dengra Joaquín , Tessaro Davide , Servi Stefano , Clemente-Jiménez Josefa María , Rodríguez-Vico Felipe , Las Heras-Vázquez Francisco Javier 
Published: November 2008

ABSTRACTAnN-carbamoyl-β-alanine amidohydrolase of industrial interest fromAgrobacterium tumefaciensC58 (βcarAt) has been characterized. βcarAtis most active at 30°C and pH 8.0 withN-carbamoyl-β-alanine as a substrate. The purified enzyme is completely inactivated by the metal-chelating agent 8-hydroxyquinoline-5-sulfonic acid (HQSA), and activity is restored by the addition of divalent metal ions, such as Mn2+, Ni2+, and Co2+. The native enzyme is a homodimer with a molecular mass of 90 kDa from pH 5.5 to 9.0. The enzyme has a broad substrate spectrum and hydrolyzes nonsubstitutedN-carbamoyl-α-, -β-, -γ-, and -δ-amino acids, with the greatest catalytic efficiency forN-carbamoyl-β-alanine. βcarAtalso recognizes substrate analogues substituted with sulfonic and phosphonic acid groups to produce the β-amino acids taurine and ciliatine, respectively. βcarAtis able to produce monosubstituted β2- and β3-amino acids, showing better catalytic efficiency (kcat/Km) for the production of the former. For both types of monosubstituted substrates, the enzyme hydrolyzesN-carbamoyl-β-amino acids with a short aliphatic side chain better than those with aromatic rings. These properties make βcarAtan outstanding candidate for application in the biotechnology industry.
Genotypic and Phenotypic Diversity among Induced,
stx
2
-Carrying Bacteriophages from Environmental
Escherichia coli
Strains
Authors: García-Aljaro Cristina , Muniesa Maite , Jofre Juan , Blanch Anicet R. 
Published: November 2008

ABSTRACT

Shiga toxin 2 (
stx
2
) gene-carrying bacteriophages have been shown to convert
Escherichia coli
strains to Shiga toxin-producing
Escherichia coli
(STEC). In this study, 79
E. coli
strains belonging to 35 serotypes isolated from wastewaters of both human and animal origin were examined for the presence of

stx
2

-carrying bacteriophages in their genomes. The lytic cycle of the bacteriophages was induced by mitomycin, and the bacteriophage fraction was isolated and used for morphological and genetic characterization. The induced bacteriophages showed morphological diversity, as well as restriction fragment length polymorphism variation, in the different strains belonging to different serotypes. The ability to infect new hosts was highly variable, although most of the induced phages infected
Shigella sonnei
host strain 866. In summary, in spite of carrying either the same or different
stx
2
variants and in spite of the fact that they were isolated from strains belonging to the same or different serotypes, the induced bacteriophages were highly variable. The high level of diversity and the great infectious capacity of these phages could enhance the spread of the
stx
2
gene and variants of this gene among different bacterial populations in environments to which humans may be exposed.
Evidence from Internally Transcribed Spacer Sequence Analysis of Soybean Strains that ExtantBradyrhizobiumspp. Are Likely the Products of Reticulate Evolutionary Events
Authors: van Berkum Peter , Fuhrmann Jeffry J. 
Published: November 2008

ABSTRACTThe internally transcribed spacer (ITS) sequences of several members within each of 17 soybean bradyrhizobial serogroups were determined to establish whether the regions within all members of each serogroup were identical. The rationale was to provide a sequence-based alternative to serology. The objective also was to link the extensive older literature on soybean symbiosis based on serology with ITS sequence data for more recent isolates from both soybean and other legumes nodulated by rhizobia within the genusBradyrhizobium. With the exception of serogroup 31 and 110 strains, sequence identity was established within each serogroup. Variation ranged from 0 to 23 nucleotides among serogroup 31 strains, and the regions in the type strains USDA 31 (serogroup 31) and USDA 130 (serogroup 130) were identical. Sequence identity was established among most strains within serogroup 110. The exceptions were USDA 452 and USDA 456, which had ITS sequences that were identical with those of the serotype 124 strain, USDA 124. Perhaps this would imply that USDA 452, USDA 456, and serogroup 31 strains are members of rhizobial lineages resulting from genetic exchange and homologous recombination events. This conclusion would be supported by the construction of a phylogenetic network from the ITS sequence alignment implying that the genomes of extant members of the genusBradyrhizobiumare likely the products of reticulate evolutionary events. A pairwise homoplasy index (phi or Φw) test was used to obtain further evidence for recombination. The ITS sequences of USDA 110 and USDA 124 were more divergent (53 nucleotides) than this region between the type strainBradyrhizobium japonicumUSDA 6Tand the proposed speciesBradyrhizobium yuanmingense(28 nucleotides) andBradyrhizobium liaoningense(48 nucleotides). Therefore, support for assigning discrete species boundaries among these three proposed species appears limited, considering the evidence for recombination, the narrow divergence of the ITS sequence, and their relative placement on the phylogenetic network.
In Vitro Kinetic Analysis of Fermentation of Prebiotic Inulin-Type Fructans by
Bifidobacterium
Species Reveals Four Different Phenotypes
Authors: Falony Gwen , Lazidou Katerina , Verschaeren An , Weckx Stefan , Maes Dominique , De Vuyst Luc 
Published: November 2008

ABSTRACT

Kinetic analyses of bacterial growth, carbohydrate consumption, and metabolite production of 18
Bifidobacterium
strains grown on fructose, oligofructose, or inulin were performed. A principal component analysis of the data sets, expanded with the results of a genetic screen concerning the presence of a β-fructofuranosidase gene previously encountered in
Bifidobacterium animalis
subsp.
lactis
DSM 10140
T
, revealed the existence of four clusters among the bifidobacteria tested. Strains belonging to a first cluster could not degrade oligofructose or inulin. Strains in a second cluster could degrade oligofructose, displaying a preferential breakdown mechanism, but did not grow on inulin. Fructose consumption was faster than oligofructose degradation. A third cluster was composed of strains that degraded all oligofructose fractions simultaneously and could partially break down inulin. Oligofructose degradation was substantially faster than fructose consumption. A fourth, smaller cluster consisted of strains that shared high fructose consumption and oligofructose degradation rates and were able to perform partial breakdown of inulin. For all strains, a metabolic shift toward more acetate, formate, and ethanol production, at the expense of lactate production, was observed during growth on less readily fermentable energy sources. No correlation between breakdown patterns and the presence of the β-fructofuranosidase gene could be detected. These variations indicate niche-specific adaptation of bifidobacteria and could have in vivo implications on the strain specificity of the stimulatory effect of inulin-type fructans on bifidobacteria.
Efficient Production of Optically Pure
d
-Lactic Acid from Raw Corn Starch by Using a Genetically Modified
l
-Lactate Dehydrogenase Gene-Deficient and α-Amylase-Secreting
Lactobacillus plantarum
Strain
Authors: Okano Kenji , Zhang Qiao , Shinkawa Satoru , Yoshida Shogo , Tanaka Tsutomu , Fukuda Hideki , Kondo Akihiko 
Published: November 2008

ABSTRACT

In order to achieve direct and efficient fermentation of optically pure
d
-lactic acid from raw corn starch, we constructed
l
-lactate dehydrogenase gene (
ldhL1
)-deficient
Lactobacillus plantarum
and introduced a plasmid encoding
Streptococcus bovis
148 α-amylase (AmyA). The resulting strain produced only
d
-lactic acid from glucose and successfully expressed
amyA
. With the aid of secreting AmyA, direct
d
-lactic acid fermentation from raw corn starch was accomplished. After 48 h of fermentation, 73.2 g/liter of lactic acid was produced with a high yield (0.85 g per g of consumed sugar) and an optical purity of 99.6%. Moreover, a strain replacing the
ldhL1
gene with an
amyA
-secreting expression cassette was constructed. Using this strain, direct
d
-lactic acid fermentation from raw corn starch was accomplished in the absence of selective pressure by antibiotics. This is the first report of direct
d
-lactic acid fermentation from raw starch.
Virulent Bacteriophage for Efficient Biocontrol of
Listeria monocytogenes
in Ready-To-Eat Foods
Authors: Guenther Susanne , Huwyler Dominique , Richard Simon , Loessner Martin J. 
Published: November 2008

ABSTRACT

Food-borne
Listeria monocytogenes
is a serious threat to human health, and new strategies to combat this opportunistic pathogen in foods are needed. Bacteriophages are natural enemies of bacteria and are suitable candidates for the environmentally friendly biocontrol of these pathogens. In a comprehensive set of experiments, we have evaluated the virulent, broad-host-range phages A511 and P100 for control of
L. monocytogenes
strains Scott A (serovar 4b) and WSLC 1001 (serovar 1/2a) in different ready-to-eat (RTE) foods known to frequently carry the pathogen. Food samples were spiked with bacteria (1 × 10
3
CFU/g), phage added thereafter (3 × 10
6
to 3 × 10
8
PFU/g), and samples stored at 6°C for 6 days. In liquid foods, such as chocolate milk and mozzarella cheese brine, bacterial counts rapidly dropped below the level of direct detection. On solid foods (hot dogs, sliced turkey meat, smoked salmon, seafood, sliced cabbage, and lettuce leaves), phages could reduce bacterial counts by up to 5 log units. Variation of the experimental conditions (extended storage over 13 days or storage at 20°C) yielded similar results. In general, the application of more phage particles (3 × 10
8
PFU/g) was more effective than lower doses. The added phages retained most of their infectivity during storage in foods of animal origin, whereas plant material caused inactivation by more than 1 log
10
. In conclusion, our data demonstrate that virulent broad-host-range phages, such as A511 and P100, can be very effective for specific biocontrol of
L. monocytogenes
in contamination-sensitive RTE foods.
Extensive Phylogenetic Analysis of a Soil Bacterial Community Illustrates Extreme Taxon Evenness and the Effects of Amplicon Length, Degree of Coverage, and DNA Fractionation on Classification and Ecological Parameters
Authors: Morales Sergio E. , Cosart Theodore F. , Johnson Jesse V. , Holben William E. 
Published: November 2008

ABSTRACT
To thoroughly investigate the bacterial community diversity present in a single composite sample from an agricultural soil and to examine potential biases resulting from data acquisition and analytical approaches, we examined the effects of percent G+C DNA fractionation, sequence length, and degree of coverage of bacterial diversity on several commonly used ecological parameters (species estimation, diversity indices, and evenness). We also examined variation in phylogenetic placement based on multiple commonly used approaches (ARB alignments and multiple RDP tools). The results demonstrate that this soil bacterial community is highly diverse, with 1,714 operational taxonomic units demonstrated and 3,555 estimated (based on the Chao1 richness estimation) at 97% sequence similarity using the 16S rRNA gene. The results also demonstrate a fundamental lack of dominance (i.e., a high degree of evenness), with 82% of phylotypes being encountered three times or less. The data also indicate that generally accepted cutoff values for phylum-level taxonomic classification might not be as applicable or as general as previously assumed and that such values likely vary between prokaryotic phyla or groups.
In Vivo Evolution of Butane Oxidation by Terminal Alkane Hydroxylases AlkB and CYP153A6
Authors: Koch Daniel J. , Chen Mike M. , van Beilen Jan B. , Arnold Frances H. 
Published: November 2008

ABSTRACT

Enzymes of the AlkB and CYP153 families catalyze the first step in the catabolism of medium-chain-length alkanes, selective oxidation of the alkane to the 1-alkanol, and enable their host organisms to utilize alkanes as carbon sources. Small, gaseous alkanes, however, are converted to alkanols by evolutionarily unrelated methane monooxygenases. Propane and butane can be oxidized by CYP enzymes engineered in the laboratory, but these produce predominantly the 2-alkanols. Here we report the in vivo-directed evolution of two medium-chain-length terminal alkane hydroxylases, the integral membrane di-iron enzyme AlkB from
Pseudomonas putida
GPo1 and the class II-type soluble CYP153A6 from
Mycobacterium
sp. strain HXN-1500, to enhance their activity on small alkanes. We established a
P. putida
evolution system that enables selection for terminal alkane hydroxylase activity and used it to select propane- and butane-oxidizing enzymes based on enhanced growth complementation of an adapted
P. putida
GPo12(pGEc47ΔB) strain. The resulting enzymes exhibited higher rates of 1-butanol production from butane and maintained their preference for terminal hydroxylation. This in vivo evolution system could be useful for directed evolution of enzymes that function efficiently to hydroxylate small alkanes in engineered hosts.
In Silico
Geobacter sulfurreducens
Metabolism and Its Representation in Reactive Transport Models
Authors: King E. L. , Tuncay K. , Ortoleva P. , Meile C. 
Published: November 2008

ABSTRACT

Microbial activity governs elemental cycling and the transformation of many anthropogenic substances in aqueous environments. Through the development of a dynamic cell model of the well-characterized, versatile, and abundant
Geobacter sulfurreducens
, we showed that a kinetic representation of key components of cell metabolism matched microbial growth dynamics observed in chemostat experiments under various environmental conditions and led to results similar to those from a comprehensive flux balance model. Coupling the kinetic cell model to its environment by expressing substrate uptake rates depending on intra- and extracellular substrate concentrations, two-dimensional reactive transport simulations of an aquifer were performed. They illustrated that a proper representation of growth efficiency as a function of substrate availability is a determining factor for the spatial distribution of microbial populations in a porous medium. It was shown that simplified model representations of microbial dynamics in the subsurface that only depended on extracellular conditions could be derived by properly parameterizing emerging properties of the kinetic cell model.
Autoinducer-2 Production in
Campylobacter jejuni
Contributes to Chicken Colonization
Authors: Quiñones Beatriz , Miller William G. , Bates Anna H. , Mandrell Robert E. 
Published: November 2008

ABSTRACT

Inactivation of
luxS
, encoding an AI-2 biosynthesis enzyme, in
Campylobacter jejuni
strain 81-176 significantly reduced colonization of the chick lower gastrointestinal tract, chemotaxis toward organic acids, and in vitro adherence to LMH chicken hepatoma cells. Thus, AI-2 production in
C. jejuni
contributes to host colonization and interactions with epithelial cells.
Detection of Differential Host Susceptibility to the Marine Oomycete Pathogen
Eurychasma dicksonii
by Real-Time PCR: Not All Algae Are Equal
Authors: Gachon Claire M. M. , Strittmatter Martina , Müller Dieter G. , Kleinteich Julia , Küpper Frithjof C. 
Published: November 2008

ABSTRACT

In the marine environment, a growing body of evidence points to parasites as key players in the control of population dynamics and overall ecosystem structure. However, their prevalence and impact on marine macroalgal communities remain virtually unknown. Indeed, infectious diseases of seaweeds are largely underdocumented, partly because of the expertise required to diagnose them with a microscope. Over the last few years, however, real-time quantitative PCR (qPCR) has emerged as a rapid and reliable alternative to visual symptom scoring for monitoring pathogens. Thus, we present here a qPCR assay suitable for the detection and quantification of the intracellular oomycete pathogen
Eurychasma dicksonii
in its ectocarpalean and laminarialean brown algal hosts. qPCR and microscopic observations made of laboratory-controlled cultures revealed that clonal brown algal strains exhibit different levels of resistance against
Eurychasma
, ranging from high susceptibility to complete absence of symptoms. This observation strongly argues for the existence of a genetic determinism for disease resistance in brown algae, which would have broad implications for the dynamics and genetic structure of natural populations. We also used qPCR for the rapid detection of
Eurychasma
in filamentous brown algae collected in Northern Europe and South America and found that the assay is specific, robust, and widely applicable to field samples. Hence, this study opens the perspective of combining large-scale disease monitoring in the field with laboratory-controlled experiments on the genome model seaweed
Ectocarpus siliculosus
to improve our understanding of brown algal diseases.
Helix α4 of the
Bacillus thuringiensis
Cry1Aa Toxin Plays a Critical Role in the Postbinding Steps of Pore Formation
Authors: Girard Frédéric , Vachon Vincent , Préfontaine Gabrielle , Marceau Lucie , Schwartz Jean-Louis , Masson Luke , Laprade Raynald 
Published: November 2008

ABSTRACT

Helix α4 of
Bacillus thuringiensis
Cry toxins is thought to play a critical role in the toxins' mode of action. Accordingly, single-site substitutions of many Cry1Aa helix α4 amino acid residues have previously been shown to cause substantial reductions in the protein's pore-forming activity. Changes in protein structure and formation of intermolecular disulfide bonds were investigated as possible factors responsible for the inactivity of these mutants. Incubation of each mutant with trypsin and chymotrypsin for 12 h did not reveal overt structural differences with Cry1Aa, although circular dichroism was slightly decreased in the 190- to 210-nm region for the I132C, S139C, and V150C mutants. The addition of dithiothreitol stimulated pore formation by the E128C, I132C, S139C, T142C, I145C, P146C, and V150C mutants. However, in the presence of these mutants, the membrane permeability never reached that measured for Cry1Aa, indicating that the formation of disulfide bridges could only partially explain their loss of activity. The ability of a number of inactive mutants to compete with wild-type Cry1Aa for pore formation in brush border membrane vesicles isolated from
Manduca sexta
was also investigated with an osmotic swelling assay. With the exception of the L147C mutant, all mutants tested could inhibit the formation of pores by Cry1Aa, indicating that they retained receptor binding ability. These results strongly suggest that helix α4 is involved mainly in the postbinding steps of pore formation.