bluuebunny/crossref_metadata_2025_split huggingface dataset:
Virulence and Metabolic Characteristics of Salmonella enterica Serovar Enteritidis Strains with Different
sefD
Variants in Hens
Authors: Morales Cesar A. , Guard Jean , Sanchez-Ingunza Roxana , Shah Devendra H. , Harrison Mark 
Published: June 2012

ABSTRACT

Salmonella enterica
serovar Enteritidis is one of a few
Salmonella enterica
serotypes that has SEF14 fimbriae encoded by the
sef
operon, which consists of 4 cotranscribed genes,
sefABCD
, regulated by
sefR
. A parental strain was used to construct a
sefD
mutant and its complement, and all 3 strains were compared for gene expression, metabolic properties, and virulence characteristics in hens. Transcription of
sefD
by wild type was suppressed at 42°C and absent for the mutant under conditions where the complemented mutant had 10
3
times higher transcription. Growth of the complemented mutant was restricted in comparison to that of the mutant and wild type. Hens infected with the wild type and mutant showed decreased blood calcium and egg production, but infection with the complemented mutant did not. Thus, the absence of
sefD
correlated with increased metabolic capacity and enhanced virulence of the pathogen. These results suggest that any contribution that
sefD
makes to egg contamination is either unknown or would be limited to early transmission from the environment to the host. Absence of
sefD
, either through mutation or by suppression of transcription at the body temperature of the host, may contribute to the virulence of
Salmonella enterica
by facilitating growth on a wide range of metabolites.
Differential
In Vivo
Gene Expression of Major Leptospira Proteins in Resistant or Susceptible Animal Models
Authors: Matsui Mariko , Soupé Marie-Estelle , Becam Jérôme , Goarant Cyrille 
Published: June 2012

ABSTRACT

Transcripts of
Leptospira
16S rRNA, FlaB, LigB, LipL21, LipL32, LipL36, LipL41, and OmpL37 were quantified in the blood of susceptible (hamsters) and resistant (mice) animal models of leptospirosis. We first validated adequate reference genes and then evaluated expression patterns
in vivo
compared to
in vitro
cultures. LipL32 expression was downregulated
in vivo
and differentially regulated in resistant and susceptible animals. FlaB expression was also repressed in mice but not in hamsters. In contrast, LigB and OmpL37 were upregulated
in vivo
. Thus, we demonstrated that a virulent strain of
Leptospira
differentially adapts its gene expression in the blood of infected animals.
Metagenomic Analyses of Drinking Water Receiving Different Disinfection Treatments
Authors: Gomez-Alvarez Vicente , Revetta Randy P. , Santo Domingo Jorge W. 
Published: June 2012

ABSTRACTA metagenome-based approach was used to assess the taxonomic affiliation and function potential of microbial populations in free-chlorine-treated (CHL) and monochloramine-treated (CHM) drinking water (DW). In all, 362,640 (averaging 544 bp) and 155,593 (averaging 554 bp) pyrosequencing reads were analyzed for the CHL and CHM samples, respectively. Most annotated proteins were found to be of bacterial origin, although eukaryotic, archaeal, and viral proteins were also identified. Differences in community structure and function were noted. Most notably,Legionella-like genes were more abundant in the CHL samples while mycobacterial genes were more abundant in CHM samples. Genes associated with multiple disinfectant mechanisms were identified in both communities. Moreover, sequences linked to virulence factors, such as antibiotic resistance mechanisms, were observed in both microbial communities. This study provides new insights into the genetic network and potential biological processes associated with the molecular microbial ecology of DW microbial communities.
Internalization and Dissemination of Human Norovirus and Animal Caliciviruses in Hydroponically Grown Romaine Lettuce
Authors: DiCaprio Erin , Ma Yuanmei , Purgianto Anastasia , Hughes John , Li Jianrong 
Published: June 2012

ABSTRACT

Fresh produce is a major vehicle for the transmission of human norovirus (NoV) because it is easily contaminated during both pre- and postharvest stages. However, the ecology of human NoV in fresh produce is poorly understood. In this study, we determined whether human NoV and its surrogates can be internalized via roots and disseminated to edible portions of the plant. The roots of romaine lettuce growing in hydroponic feed water were inoculated with 1 × 10
6
RNA copies/ml of a human NoV genogroup II genotype 4 (GII.4) strain or 1 × 10
6
to 2 × 10
6
PFU/ml of animal caliciviruses (Tulane virus [TV] and murine norovirus [MNV-1]), and plants were allowed to grow for 2 weeks. Leaves, shoots, and roots were homogenized, and viral titers and/or RNA copies were determined by plaque assay and/or real-time reverse transcription (RT)-PCR. For human NoV, high levels of viral-genome RNA (10
5
to 10
6
RNA copies/g) were detected in leaves, shoots, and roots at day 1 postinoculation and remained stable over the 14-day study period. For MNV-1 and TV, relatively low levels of infectious virus particles (10
1
to 10
3
PFU/g) were detected in leaves and shoots at days 1 and 2 postinoculation, but virus reached a peak titer (10
5
to 10
6
PFU/g) at day 3 or 7 postinoculation. In addition, human NoV had a rate of internalization comparable with that of TV as determined by real-time RT-PCR, whereas TV was more efficiently internalized than MNV-1 as determined by plaque assay. Taken together, these results demonstrated that human NoV and animal caliciviruses became internalized via roots and efficiently disseminated to the shoots and leaves of the lettuce.
Firing Range Soils Yield a Diverse Array of Fungal Isolates Capable of Organic Acid Production and Pb Mineral Solubilization
Authors: Sullivan Tarah S. , Gottel Neil R. , Basta Nicholas , Jardine Philip M. , Schadt Christopher W. 
Published: June 2012

ABSTRACT

Anthropogenic sources of lead contamination in soils include mining and smelting activities, effluents and wastes, agricultural pesticides, domestic garbage dumps, and shooting ranges. While Pb is typically considered relatively insoluble in the soil environment, some fungi may potentially contribute to mobilization of heavy metal cations by means of secretion of low-molecular-weight organic acids (LMWOAs). We sought to better understand the potential for metal mobilization within an indigenous fungal community at an abandoned shooting range in Oak Ridge, TN, where soil Pb contamination levels ranged from 24 to >2,700 mg Pb kg dry soil
−1
. We utilized culture-based assays to determine organic acid secretion and Pb-carbonate dissolution of a diverse collection of soil fungal isolates derived from the site and verified isolate distribution patterns within the community by 28S rRNA gene analysis of whole soils. The fungal isolates examined included both ascomycetes and basidiomycetes that excreted high levels (up to 27 mM) of a mixture of LMWOAs, including oxalic and citric acids, and several isolates demonstrated a marked ability to dissolve Pb-carbonate at high concentrations up to 10.5 g liter
−1
(18.5 mM) in laboratory assays. Fungi within the indigenous community of these highly Pb-contaminated soils are capable of LMWOA secretion at levels greater than those of well-studied model organisms, such as
Aspergillus niger
. Additionally, these organisms were found in high relative abundance (>1%) in some of the most heavily contaminated soils. Our data highlight the need to understand more about autochthonous fungal communities at Pb-contaminated sites and how they may impact Pb biogeochemistry, solubility, and bioavailability, thus consequently potentially impacting human and ecosystem health.
Biotechnological Production of Caffeic Acid by Bacterial Cytochrome P450 CYP199A2
Authors: Furuya Toshiki , Arai Yuka , Kino Kuniki 
Published: June 2012

ABSTRACT

Caffeic acid is a biologically active molecule that has various beneficial properties, including antioxidant, anticancer, and anti-inflammatory activities. In this study, we explored the catalytic potential of a bacterial cytochrome P450, CYP199A2, for the biotechnological production of caffeic acid. When the CYP199A2 enzyme was reacted with
p
-coumaric acid, it stoichiometrically produced caffeic acid. The crystal structure of CYP199A2 shows that Phe at position 185 is situated directly above, and only 6.35 Å from, the heme iron. This F185 residue was replaced with hydrophobic or hydroxylated amino acids using site-directed mutagenesis to create mutants with novel and improved catalytic properties. In whole-cell assays with the known substrate of CYP199A2, 2-naphthoic acid, only the wild-type enzyme hydroxylated 2-naphthoic acid at the C-7 and C-8 positions, whereas all of the active F185 mutants exhibited a preference for C-5 hydroxylation. Interestingly, several F185 mutants (F185V, F185L, F185I, F185G, and F185A mutants) also acquired the ability to hydroxylate cinnamic acid, which was not hydroxylated by the wild-type enzyme. These results demonstrate that F185 is an important residue that controls the regioselectivity and the substrate specificity of CYP199A2. Furthermore,
Escherichia coli
cells expressing the F185L mutant exhibited 5.5 times higher hydroxylation activity for
p
-coumaric acid than those expressing the wild-type enzyme. By using the F185L whole-cell catalyst, the production of caffeic acid reached 15 mM (2.8 g/liter), which is the highest level so far attained in biotechnological production of this compound.
Chemotaxis to Furan Compounds by Furan-Degrading Pseudomonas Strains
Authors: Nichols Nancy N. , Lunde Tristan A. , Graden Kevin C. , Hallock Kate A. , Kowalchyk Cara K. , Southern Rebecca M. , Soskin Ellen J. , Ditty Jayna L. 
Published: June 2012

ABSTRACT

Two
Pseudomonas
strains known to utilize furan derivatives were shown to respond chemotactically to furfural, 5-hydroxymethylfurfural, furfuryl alcohol, and 2-furoic acid. In addition, a LysR-family regulatory protein known to regulate furan metabolic genes was found to be involved in regulating the chemotactic response.
Enumerating Viruses in Coral Mucus
Authors: Leruste Amandine , Bouvier Thierry , Bettarel Yvan 
Published: June 2012

ABSTRACT
The distribution of viruses inhabiting the coral mucus remains undetermined, as there is no suitable standardized procedure for their separation from this organic matrix, principally owing to its viscosity and autofluorescence. Seven protocols were tested, and the most efficient separations were obtained from a chemical treatment requiring potassium citrate.
The Physiological Opportunism of Desulfitobacterium hafniense Strain TCE1 towards Organohalide Respiration with Tetrachloroethene
Authors: Duret Aurélie , Holliger Christof , Maillard Julien 
Published: June 2012

ABSTRACT

Desulfitobacterium hafniense
strain TCE1 is capable of metabolically reducing tetra- and trichloroethenes by organohalide respiration. A previous study revealed that the
pce
gene cluster responsible for this process is located on an active composite transposon, Tn-
Dha1
. In the present work, we investigated the effects on the stability of the transposon during successive subcultivations of strain TCE1 in a medium depleted of tetrachloroethene. At the physiological level, an increased fitness of the population was observed after 9 successive transfers and was correlated with a decrease in the level of production of the PceA enzyme. The latter observation was a result of the gradual loss of the
pce
genes in the population of strain TCE1 and not of a regulation mechanism, as was postulated previously for a similar phenomenon described for
Sulfurospirillum multivorans
. A detailed molecular analysis of genetic rearrangements occurring around Tn-
Dha1
showed two independent but concomitant events, namely, the transposition of the first insertion sequence, IS
Dha1
-a, and homologous recombination across identical copies of IS
Dha1
flanking the transposon. A new model is proposed for the genetic heterogeneity around Tn-
Dha1
in
D. hafniense
strain TCE1, along with some considerations for the cleavage mechanism mediated by the transposase TnpA1 encoded by IS
Dha1
.
The Tape Measure Protein of the Staphylococcus aureus Bacteriophage vB_SauS-phiIPLA35 Has an Active Muramidase Domain
Authors: Rodríguez-Rubio Lorena , Gutiérrez Dolores , Martínez Beatriz , Rodríguez Ana , Götz Friedrich , García Pilar 
Published: June 2012

ABSTRACT

Tailed double-stranded DNA (dsDNA) bacteriophages frequently harbor structural proteins displaying peptidoglycan hydrolytic activities. The tape measure protein from
Staphylococcus aureus
bacteriophage vB_SauS-phiIPLA35 has a lysozyme-like and a peptidase_M23 domain. This report shows that the lysozyme-like domain (TG1) has muramidase activity and exhibits
in vitro
lytic activity against live
S. aureus
cells, an activity that could eventually find use in the treatment of infections.
Alternative Approach To Modeling Bacterial Lag Time, Using Logistic Regression as a Function of Time, Temperature, pH, and Sodium Chloride Concentration
Authors: Koseki Shige , Nonaka Junko 
Published: June 2012

ABSTRACT

The objective of this study was to develop a probabilistic model to predict the end of lag time (λ) during the growth of
Bacillus cereus
vegetative cells as a function of temperature, pH, and salt concentration using logistic regression. The developed λ model was subsequently combined with a logistic differential equation to simulate bacterial numbers over time. To develop a novel model for λ, we determined whether bacterial growth had begun, i.e., whether λ had ended, at each time point during the growth kinetics. The growth of
B. cereus
was evaluated by optical density (OD) measurements in culture media for various pHs (5.5 ∼ 7.0) and salt concentrations (0.5 ∼ 2.0%) at static temperatures (10 ∼ 20°C). The probability of the end of λ was modeled using dichotomous judgments obtained at each OD measurement point concerning whether a significant increase had been observed. The probability of the end of λ was described as a function of time, temperature, pH, and salt concentration and showed a high goodness of fit. The λ model was validated with independent data sets of
B. cereus
growth in culture media and foods, indicating acceptable performance. Furthermore, the λ model, in combination with a logistic differential equation, enabled a simulation of the population of
B. cereus
in various foods over time at static and/or fluctuating temperatures with high accuracy. Thus, this newly developed modeling procedure enables the description of λ using observable environmental parameters without any conceptual assumptions and the simulation of bacterial numbers over time with the use of a logistic differential equation.
Evaluation of Gene Modification Strategies for the Development of Low-Alcohol-Wine Yeasts
Authors: Varela C. , Kutyna D. R. , Solomon M. R. , Black C. A. , Borneman A. , Henschke P. A. , Pretorius I. S. , Chambers P. J. 
Published: June 2012

ABSTRACTSaccharomyces cerevisiaehas evolved a highly efficient strategy for energy generation which maximizes ATP energy production from sugar. This adaptation enables efficient energy generation under anaerobic conditions and limits competition from other microorganisms by producing toxic metabolites, such as ethanol and CO2. Yeast fermentative and flavor capacity forms the biotechnological basis of a wide range of alcohol-containing beverages. Largely as a result of consumer demand for improved flavor, the alcohol content of some beverages like wine has increased. However, a global trend has recently emerged toward lowering the ethanol content of alcoholic beverages. One option for decreasing ethanol concentration is to use yeast strains able to divert some carbon away from ethanol production. In the case of wine, we have generated and evaluated a large number of gene modifications that were predicted, or known, to impact ethanol formation. Using the same yeast genetic background, 41 modifications were assessed. Enhancing glycerol production by increasing expression of the glyceraldehyde-3-phosphate dehydrogenase gene,GPD1, was the most efficient strategy to lower ethanol concentration. However, additional modifications were needed to avoid negatively affecting wine quality. Two strains carrying several stable, chromosomally integrated modifications showed significantly lower ethanol production in fermenting grape juice. Strain AWRI2531 was able to decrease ethanol concentrations from 15.6% (vol/vol) to 13.2% (vol/vol), whereas AWRI2532 lowered ethanol content from 15.6% (vol/vol) to 12% (vol/vol) in both Chardonnay and Cabernet Sauvignon juices. Both strains, however, produced high concentrations of acetaldehyde and acetoin, which negatively affect wine flavor. Further modifications of these strains allowed reduction of these metabolites.
Pyrosequencing-Derived Bacterial, Archaeal, and Fungal Diversity of Spacecraft Hardware Destined for Mars
Authors: La Duc Myron T. , Vaishampayan Parag , Nilsson Henrik R. , Torok Tamas , Venkateswaran Kasthuri 
Published: June 2012

ABSTRACT

Spacecraft hardware and assembly cleanroom surfaces (233 m
2
in total) were sampled, total genomic DNA was extracted, hypervariable regions of the 16S rRNA gene (bacteria and archaea) and ribosomal internal transcribed spacer (ITS) region (fungi) were subjected to 454 tag-encoded pyrosequencing PCR amplification, and 203,852 resulting high-quality sequences were analyzed. Bioinformatic analyses revealed correlations between operational taxonomic unit (OTU) abundance and certain sample characteristics, such as source (cleanroom floor, ground support equipment [GSE], or spacecraft hardware), cleaning regimen applied, and location about the facility or spacecraft. National Aeronautics and Space Administration (NASA) cleanroom floor and GSE surfaces gave rise to a larger number of diverse bacterial communities (619 OTU; 20 m
2
) than colocated spacecraft hardware (187 OTU; 162 m
2
). In contrast to the results of bacterial pyrosequencing, where at least some sequences were generated from each of the 31 sample sets examined, only 13 and 18 of these sample sets gave rise to archaeal and fungal sequences, respectively. As was the case for bacteria, the abundance of fungal OTU in the GSE surface samples dramatically diminished (9× less) once cleaning protocols had been applied. The presence of OTU representative of actinobacteria, deinococci, acidobacteria, firmicutes, and proteobacteria on spacecraft surfaces suggests that certain bacterial lineages persist even following rigorous quality control and cleaning practices. The majority of bacterial OTU observed as being recurrent belonged to actinobacteria and alphaproteobacteria, supporting the hypothesis that the measures of cleanliness exerted in spacecraft assembly cleanrooms (SAC) inadvertently select for the organisms which are the most fit to survive long journeys in space.
Characterization of the Two Neurospora crassa Cellobiose Dehydrogenases and Their Connection to Oxidative Cellulose Degradation
Authors: Sygmund Christoph , Kracher Daniel , Scheiblbrandner Stefan , Zahma Kawah , Felice Alfons K. G. , Harreither Wolfgang , Kittl Roman , Ludwig Roland 
Published: June 2012

ABSTRACT

The genome of
Neurospora crassa
encodes two different cellobiose dehydrogenases (CDHs) with a sequence identity of only 53%. So far, only CDH IIA, which is induced during growth on cellulose and features a C-terminal carbohydrate binding module (CBM), was detected in the secretome of
N. crassa
and preliminarily characterized. CDH IIB is not significantly upregulated during growth on cellulosic material and lacks a CBM. Since CDH IIB could not be identified in the secretome, both CDHs were recombinantly produced in
Pichia pastoris
. With the cytochrome domain-dependent one-electron acceptor cytochrome
c
, CDH IIA has a narrower and more acidic pH optimum than CDH IIB. Interestingly, the catalytic efficiencies of both CDHs for carbohydrates are rather similar, but CDH IIA exhibits 4- to 5-times-higher apparent catalytic constants (
k
cat
and

K
m

values) than CDH IIB for most tested carbohydrates. A third major difference is the 65-mV-lower redox potential of the heme
b
cofactor in the cytochrome domain of CDH IIA than CDH IIB. To study the interaction with a member of the glycoside hydrolase 61 family, the copper-dependent polysaccharide monooxygenase GH61-3 (NCU02916) from
N. crassa
was expressed in
P. pastoris
. A pH-dependent electron transfer from both CDHs via their cytochrome domains to GH61-3 was observed. The different properties of CDH IIA and CDH IIB and their effect on interactions with GH61-3 are discussed in regard to the proposed
in vivo
function of the CDH/GH61 enzyme system in oxidative cellulose hydrolysis.
MhbT Is a Specific Transporter for 3-Hydroxybenzoate Uptake by Gram-Negative Bacteria
Authors: Xu Ying , Gao Xiaoli , Wang Song-He , Liu Hong , Williams Peter A. , Zhou Ning-Yi 
Published: June 2012

ABSTRACT

Klebsiella pneumoniae
M5a1 is capable of utilizing 3-hydroxybenzoate via gentisate, and the 6.3-kb gene cluster
mhbRTDHIM
conferred the ability to grow on 3-hydroxybenzoate to
Escherichia coli
and
Pseudomonas putida
PaW340. Four of the six genes (
mhbDHIM
) encode enzymes converting 3-hydroxybenzoate to pyruvate and fumarate via gentisate. MhbR is a gene activator, and MhbT is a hypothetical protein belonging to the transporter of the aromatic acid/H
+
symporter family. Since a transporter for 3-hydrxybenzoate uptake has not been characterized to date, we investigated whether MhbT is responsible for the uptake of 3-hydroxybenzoate, its metabolic intermediate gentisate, or both. The MhbT-green fluorescent protein (GFP) fusion protein was located on the cytoplasmic membrane.
P. putida
PaW340 containing
mhbR
Δ
TDHIM
could not grow on 3-hydroxybenzoate; however, supplying
mhbT
in
trans
allowed the bacterium to grow on the substrate.
K. pneumoniae
M5a1 and
P. putida
PaW340 containing recombinant MhbT transported
14
C-labeled 3-hydroxybenzoate but not
14
C-labeled gentisate and benzoate into the cells. Site-directed mutagenesis of two conserved amino acid residues (Asp-82 and Asp-314) and a less-conserved residue (Val-311) among the members of the symporter family in the hydrophilic cytoplasmic loops resulted in the loss of 3-hydroxybenzoate uptake by
P. putida
PaW340 carrying the mutant proteins. Hence, we demonstrated that MhbT is a specific 3-hydroxybenzoate transporter.