bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bioaccumulation, Retention, and Depuration of Enteric Viruses by
Crassostrea virginica
and
Crassostrea ariakensis
Oysters
Authors: Nappier Sharon P. , Graczyk Thaddeus K. , Schwab Kellogg J. 
Published: September 2008

ABSTRACT

Crassostrea ariakensis
oysters are under review for introduction into the Chesapeake Bay. However, the human health implications of the introduction have not been fully addressed. This study evaluated rates of bioaccumulation, retention, and depuration of viruses by
Crassostrea virginica
and
C. ariakensis
when the two oyster species were maintained in separate tanks containing synthetic seawater of various salinities (8, 12, or 20 ppt). Oyster bioaccumulation tanks were seeded with 10
3
PFU/ml of hepatitis A virus (HAV), poliovirus, male-specific bacteriophage (MS2), and murine norovirus 1 (MNV-1) and 10
3
PCR units/ml of human norovirus (NoV). After 24 h, depuration commenced as oysters (
n
= 255) were placed in pathogen-free seawater under continuous filtration. Oysters (
n
= 6) were sampled weekly for 1 month from each tank. Viral RNA was recovered using a modified proteinase K, guanidine, and glassmilk method and analyzed by quantitative reverse transcription-PCR. The odds of
C. ariakensis
oysters harboring NoV, MNV-1, or HAV were statistically greater than the odds of
C. virginica
oysters harboring the same viruses (MNV-1 odds ratio [OR], 4.5;
P
= 0.01; NoV OR, 8.4;
P
< 0.001; HAV OR, 11.4;
P
< 0.001). Unlike
C. virginica, C. ariakensis
bioaccumulated and retained NoV, MNV-1, and HAV for 1 month at all salinities. Additionally, the odds of an oyster testing positive for NoV was 25.5 times greater (
P
< 0.001) when the oyster also tested positive for MNV-1. This research helps assess the threat of
C. ariakensis
as a vehicle for viral pathogens due to the consumption of raw oysters and validates the role for MNV-1 as a surrogate for NoV.
Quantitative rRNA-Targeted Solution-Based Hybridization Assay Using Peptide Nucleic Acid Molecular Beacons
Authors: Li Xu , Morgenroth Eberhard , Raskin Lutgarde 
Published: September 2008

ABSTRACTThe potential of a solution-based hybridization assay using peptide nucleic acid (PNA) molecular beacon (MB) probes to quantify 16S rRNA of specific populations in RNA extracts of environmental samples was evaluated by designing PNA MB probes for the generaDechloromonasandDechlorosoma. In a kinetic study with 16S rRNA from pure cultures, the hybridization of PNA MB to target 16S rRNA exhibited a higher final hybridization signal and a lower apparent rate constant than the hybridizations to nontarget 16S rRNAs. A concentration of 10 mM NaCl in the hybridization buffer was found to be optimal for maximizing the difference between final hybridization signals from target and nontarget 16S rRNAs. Hybridization temperatures and formamide concentrations in hybridization buffers were optimized to minimize signals from hybridizations of PNA MB to nontarget 16S rRNAs. The detection limit of the PNA MB hybridization assay was determined to be 1.6 nM of 16S rRNA. To establish proof for the application of PNA MB hybridization assays in complex systems, target 16S rRNA fromDechlorosoma suillumwas spiked at different levels to RNA isolated from an environmental (bioreactor) sample, and the PNA MB assay enabled effective quantification of theD. suillumRNA in this complex mixture. For another environmental sample, the quantitative results from the PNA MB hybridization assay were compared with those from clone libraries.
Localization and Expression of MreB in
Vibrio parahaemolyticus
under Different Stresses
Authors: Chiu Shen-Wen , Chen Shau-Yan , Wong Hin-chung 
Published: September 2008

ABSTRACT

MreB, the homolog of eukaryotic actin, may play a vital role when prokaryotes cope with stress by altering their spatial organization, including their morphology, subcellular architecture, and localization of macromolecules. This study investigates the behavior of MreB in
Vibrio parahaemolyticus
under various stresses. The behavior of MreB was probed using a yellow fluorescent protein-MreB conjugate in merodiploid strain SC9. Under normal growth conditions, MreB formed helical filaments in exponential-phase cells. The shape of starved or stationary-phase cells changed from rods to small spheroids. The cells differentiated into the viable but nonculturable (VBNC) state with small spherical cells via a “swelling-waning” process. In all cases, drastic remodeling of the MreB cytoskeleton was observed. MreB helices typically were loosened and fragmented into short filaments, arcs, and spots in bacteria under these stresses. The disintegrated MreB exhibited a strong tendency to attach to the cytoplasmic membrane. The expression of
mreB
generally declined in bacteria in the stationary phase and under starvation but was upregulated during the initial periods of cold shock and VBNC state differentiation and decreased afterwards. Our findings demonstrated the behavior of MreB in the morphological changes of
V. parahaemolyticus
under intrinsic or extrinsic stresses and may have important implications for studying the cellular stress response and aging.
Characterization of a T7-Like Lytic Bacteriophage (φSG-JL2) of
Salmonella enterica
Serovar Gallinarum Biovar Gallinarum
Authors: Kwon Hyuk-Joon , Cho Sun-Hee , Kim Tae-Eun , Won Yong-Jin , Jeong Jihye , Park Se Chang , Kim Jae-Hong , Yoo Han-Sang , Park Yong-Ho , Kim Sun-Joong 
Published: September 2008

ABSTRACT

φSG-JL2 is a newly discovered lytic bacteriophage infecting
Salmonella enterica
serovar Gallinarum biovar Gallinarum but is nonlytic to a rough vaccine strain of serovar Gallinarum biovar Gallinarum (SG-9R),
S. enterica
serovar Enteritidis,
S. enterica
serovar Typhimurium, and
S. enterica
serovar Gallinarum biovar Pullorum. The φSG-JL2 genome is 38,815 bp in length (GC content, 50.9%; 230-bp-long direct terminal repeats), and 55 putative genes may be transcribed from the same strand. Functions were assigned to 30 genes based on high amino acid similarity to known proteins. Most of the expected proteins except tail fiber (31.9%) and the overall organization of the genomes were similar to those of yersiniophage φYeO3-12. φSG-JL2 could be classified as a new T7-like virus and represents the first serovar Gallinarum biovar Gallinarum phage genome to be sequenced. On the basis of intraspecific ratios of nonsynonymous to synonymous nucleotide changes (Pi[a]/Pi[s]), gene 2 encoding the host RNA polymerase inhibitor displayed Darwinian positive selection. Pretreatment of chickens with φSG-JL2 before intratracheal challenge with wild-type serovar Gallinarum biovar Gallinarum protected most birds from fowl typhoid. Therefore, φSG-JL2 may be useful for the differentiation of serovar Gallinarum biovar Gallinarum from other
Salmonella
serotypes, prophylactic application in fowl typhoid control, and understanding of the vertical evolution of T7-like viruses.
Cellulose Degradation by Micromonosporas Recovered from Freshwater Lakes and Classification of These Actinomycetes by DNA Gyrase B Gene Sequencing
Authors: de Menezes Alexandre B. , Lockhart Robert J. , Cox Michael J. , Allison Heather E. , McCarthy Alan J. 
Published: September 2008

ABSTRACT

A number of
Micromonospora
strains isolated from the water column, sediment, and cellulose baits placed in freshwater lakes were shown to be able to degrade cellulose in lake water without any addition of nutrients. A selective isolation method was also developed to demonstrate that CFU arose from both spores and hyphae that inhabit the lake environment. Gyrase B gene sequencing performed on the isolates identified a number of new centers of variation within
Micromonospora
, but the most actively cellulolytic strains were recovered in a single cluster that equated with the type species of the genus,
M. chalcea
.
Mechanisms of Cation Exchange by
Pseudomonas aeruginosa
PAO1 and PAO1
wbpL
, a Strain with a Truncated Lipopolysaccharide
Authors: Shephard J. , McQuillan A. J. , Bremer P. J. 
Published: September 2008

ABSTRACT

The ability of bacterial cells to sequester cations is well recognized, despite the fact that the specific binding sites and mechanistic details of the process are not well understood. To address these questions, the cation-exchange behavior of
Pseudomonas aeruginosa
PAO1 cells with a truncated lipopolysaccharide (LPS) (PAO1
wbpL
) and cells further modified by growth in a magnesium-deficient medium (PAO1
wbpL
− Mg
2+
) were compared with that of wild-type
P. aeruginosa
PAO1 cells.
P. aeruginosa
PAO1 cells had a negative surface charge (zeta potential) between pH 11 and 2.2, due to carboxylate groups present in the B-band LPS. The net charge on PAO1
wbpL
cells was increasingly positive below pH 3.5, due to the influence of NH
3
+
groups in the core LPS. The zeta potentials of these cells were also measured in Na
+
, Ca
2+
, and La
3+
electrolytes. Cells in the La
3+
electrolyte had a positive zeta potential at all pH values tested. Growing
P. aeruginosa
PAO1
wbpL
in magnesium-deficient medium (PAO1
wbpL
− Mg
2+
) resulted in an increase in its zeta potential in the pH range from 3.0 to 6.5. In cation-exchange experiments carried out at neutral pH with either
P. aeruginosa
PAO1 or PAO1
wbpL
, the concentration of bound Ca
2+
was found to decrease as the pH was reduced from 7.0 to 3.5. At pH 3.5, the bound Mg
2+
concentration decreased sharply, revealing the activity of surface sites for cation exchange and their pH dependence. Infrared spectroscopy of attached biofilms suggested that carboxylate and phosphomonoester functional groups within the core LPS are involved in cation exchange.
Modeling the Variability of Single-Cell Lag Times for
Listeria innocua
Populations after Sublethal and Lethal Heat Treatments
Authors: Métris A. , George S. M. , Mackey B. M. , Baranyi J. 
Published: September 2008

ABSTRACT

Optical density measurements were used to estimate the effect of heat treatments on the single-cell lag times of
Listeria innocua
fitted to a shifted gamma distribution. The single-cell lag time was subdivided into repair time (the shift of the distribution assumed to be uniform for all cells) and adjustment time (varying randomly from cell to cell). After heat treatments in which all of the cells recovered (sublethal), the repair time and the mean and the variance of the single-cell adjustment time increased with the severity of the treatment. When the heat treatments resulted in a loss of viability (lethal), the repair time of the survivors increased with the decimal reduction of the cell numbers independently of the temperature, while the mean and variance of the single-cell adjustment times remained the same irrespective of the heat treatment. Based on these observations and modeling of the effect of time and temperature of the heat treatment, we propose that the severity of a heat treatment can be characterized by the repair time of the cells whether the heat treatment is lethal or not, an extension of the
F
value concept for sublethal heat treatments. In addition, the repair time could be interpreted as the extent or degree of injury with a multiple-hit lethality model. Another implication of these results is that the distribution of the time for cells to reach unacceptable numbers in food is not affected by the time-temperature combination resulting in a given decimal reduction.
Effects of Therapeutic Ceftiofur Administration to Dairy Cattle on
Escherichia coli
Dynamics in the Intestinal Tract
Authors: Singer Randall S. , Patterson Sheila K. , Wallace Richard L. 
Published: September 2008

ABSTRACT

The goal of this study was to follow ceftiofur-treated and untreated cattle in a normally functioning dairy to examine enteric
Escherichia coli
for changes in antibiotic resistance profiles and genetic diversity. Prior to treatment, all of the bacteria cultured from the cows were susceptible to ceftiofur. Ceftiofur-resistant
E. coli
was only isolated from treated cows during and immediately following the cessation of treatment, and the 12
bla
CMY-2
-positive isolates clustered into two genetic groups.
E. coli
bacterial counts dropped significantly in the treated animals (
P
< 0.027), reflecting a disappearance of the antibiotic-susceptible strains. The resistant bacterial population, however, did not increase in quantity within the treated cows; levels stayed low and were overtaken by a returning susceptible population. There was no difference in the genetic diversities of the
E. coli
between the treated and untreated cows prior to ceftiofur administration or after the susceptible population of
E. coli
returned in the treated cows. A cluster analysis of antibiotic susceptibility profiles resulted in six clusters, two of which were multidrug resistant and were comprised solely of isolates from the treated cows immediately following treatment. The antibiotic treatment provided a window to detect the presence of ceftiofur-resistant
E. coli
but did not appear to cause its emergence or result in its amplification. The finding of resistant isolates following antibiotic treatment is not sufficient to estimate the strength of selection pressure nor is it sufficient to demonstrate a causal link between antibiotic use and the emergence or amplification of resistance.
BioluminescentAspergillus fumigatus, a New Tool for Drug Efficiency Testing and In Vivo Monitoring of Invasive Aspergillosis
Authors: Brock Matthias , Jouvion Grégory , Droin-Bergère Sabrina , Dussurget Olivier , Nicola Marie-Anne , Ibrahim-Granet Oumaïma 
Published: September 2008

ABSTRACTAspergillus fumigatusis the main cause of invasive aspergillosis in immunocompromised patients, and only a limited number of drugs for treatment are available. A screening method for new antifungal compounds is urgently required, preferably an approach suitable for in vitro and in vivo studies. Bioluminescence imaging is a powerful tool to study the temporal and spatial resolutions of the infection and the effectiveness of antifungal drugs. Here, we describe the construction of a bioluminescentA. fumigatusstrain by fusing the promoter of the glyceraldehyde-3-phosphate dehydrogenase gene fromA. fumigatuswith the luciferase gene fromPhotinus pyralisto control the expression of the bioluminescent reporter.A. fumigatustransformed with this construct revealed high bioluminescence under all tested growth conditions. Furthermore, light emission correlated with the number of conidia used for inoculation and with the biomass formed after different incubation times. The bioluminescent strains were suitable to study the effectiveness of antifungals in vitro by several independent methods, including the determination of light emission with a microplate reader and the direct visualization of light emission with an IVIS 100 system. Moreover, when glucocorticoid-treated immunosuppressed mice were infected with a bioluminescent strain, light emission was detected from infected lungs, allowing the visualization of the progression of invasive aspergillosis. Therefore, this new bioluminescence tool is suitable to study the in vitro effectiveness of drugs and the disease development, localization, and burden of fungi within tissues and may also provide a powerful tool to study the effectiveness of antifungals in vivo.
Mechanism of Synergistic Inhibition of
Listeria monocytogenes
Growth by Lactic Acid, Monolaurin, and Nisin
Authors: Tokarskyy Oleksandr , Marshall Douglas L. 
Published: September 2008

ABSTRACT

The combined lactic acid, monolaurin, and nisin effects on time-to-detection (optical density at 600 nm) extension were greater (
P
< 0.05) than any single or paired combination effect, which demonstrates a synergistic interaction among the antimicrobials. Monolaurin exposure caused C12:0 cell membrane incorporation. Lactic acid caused increased monolaurin C12:0 membrane incorporation, while nisin had no influence. We postulate that lactic acid-enhanced monolaurin C12:0 incorporation into the cell membrane increased membrane fluidity resulting in increased nisin activity.
New Strategy for Isolating Novel Nematicidal Crystal Protein Genes from
Bacillus thuringiensis
Strain YBT-1518
Authors: Guo Suxia , Liu Mei , Peng Donghai , Ji Sisi , Wang Pengxia , Yu Ziniu , Sun Ming 
Published: September 2008

ABSTRACT

We have developed a strategy for isolating
cry
genes from
Bacillus thuringiensis
. The key steps are the construction of a DNA library in an acrystalliferous
B. thuringiensis
host strain and screening for the formation of crystal through optical microscopy observation and sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) analyses. By this method, three
cry
genes—
cry55Aa1
,
cry6Aa2
, and
cry5Ba2
—were cloned from rice-shaped crystals, producing
B. thuringiensis
YBT-1518, which consists of 54- and 45-kDa crystal proteins.
cry55Aa1
encoded a 45-kDa protein,
cry6Aa2
encoded a 54-kDa protein, and
cry5Ba2
remained cryptic in strain YBT-1518, as shown by SDS-PAGE or microscopic observation. Proteins encoded by these three genes are all toxic to the root knot nematode
Meloidogyne hapla
. The two genes
cry55Aa1
and
cry6Aa2
were found to be located on a plasmid with a rather small size of 17.7 kb, designated pBMB0228.
Accumulation of
trans
C
18:1
Fatty Acids in the Rumen after Dietary Algal Supplementation Is Associated with Changes in the
Butyrivibrio
Community
Authors: Boeckaert Charlotte , Vlaeminck Bruno , Fievez Veerle , Maignien Lois , Dijkstra Jan , Boon Nico 
Published: September 2008

ABSTRACT

Optimization of the fatty acid composition of ruminant milk and meat is desirable. Dietary supplementation of algae was previously shown to inhibit rumen biohydrogenation, resulting in an altered milk fatty acid profile. Bacteria involved in biohydrogenation belong to the
Butyrivibrio
group. This study was aimed at relating accumulation of biohydrogenation intermediates with shifts in
Butyrivibrio
spp. in the rumen of dairy cows. Therefore, an experiment was performed with three rumen-fistulated dairy cows receiving a concentrate containing algae (9.35 g/kg total dry matter [DM] intake) for 20 days. Supplementation of the diet with algae inhibited biohydrogenation of C
18:2
omega 6 (
n
-6) and C
18:3
n
-3, resulting in increased concentrations of biohydrogenation intermediates, whereas C
18:0
decreased. Addition of algae increased ruminal C
18:1
trans
fatty acid concentrations, mainly due to 6- and 20-fold increases in C
18:1
trans
11 (
t
11) and C
18:1
t
10. The number of ciliates (5.37 log copies/g rumen digesta) and the composition of the ciliate community were unaffected by dietary algae. In contrast, supplementation of the diet with algae changed the composition of the bacterial community. Primers for the
Butyrivibrio
group, including the genera
Butyrivibrio
and
Pseudobutyrivibrio
, were specifically designed. Denaturing gradient gel electrophoresis showed community changes upon addition of algae without affecting the total amount of
Butyrivibrio
bacteria (7.06 log copies/g rumen DM). Clone libraries showed that algae affected noncultivated species, which cluster taxonomically between the genera
Butyrivibrio
and
Pseudobutyrivibrio
and might play a role in biohydrogenation. In addition, 20% of the clones from a randomly selected rumen sample were related to the C
18:0
-producing branch, although the associated C
18:0
concentration decreased through supplementation of the diet with algae.
Cloning and Characterization of α-Methylacyl Coenzyme A Racemase from
Gordonia polyisoprenivorans
VH2
Authors: Arenskötter Quyen , Heller Jens , Dietz David , Arenskötter Matthias , Steinbüchel Alexander 
Published: September 2008

ABSTRACT

The
mcr
gene of
Gordonia polyisoprenivorans
VH2 is not clustered with genes required for rubber degradation. Its disruption by insertion of a kanamycin resistance cassette impaired growth on methyl-branched isoprenoids but not on linear hydrocarbons. Intact
mcr
from this bacterium or from
Nocardia farcinica
IFM 10152 complemented the mutant. Reverse transcription analysis showed similar
mcr
VH2
expression results during cultivation with poly(
cis
-1,4-isoprene) and propionate. Additional genes coding for a putative cytochrome P450 monooxygenase and a short-chain dehydrogenase/reductase involved in β-oxidation and poly(
cis
-1,4-isoprene) degradation were also characterized.
Biosynthesis of Ubiquinone Compounds with Conjugated Prenyl Side Chains
Authors: Lee Pyung Cheon , Salomon Christine , Mijts Benjamin , Schmidt-Dannert Claudia 
Published: September 2008

ABSTRACT

Enzymatic steps from two different biosynthetic pathways were combined in
Escherichia coli
, directing the synthesis of a new class of biomolecules—ubiquinones with prenyl side chains containing conjugated double bonds. This was achieved by the activity of a C
30
carotenoid desaturase, CrtN, from
Staphylococcus aureus
, which exhibited an inherent flexibility in substrate recognition compared to other carotenoid desaturases. By utilizing the known plasticity of
E. coli
's native ubiquinone biosynthesis pathway and the unusual activity of CrtN, modified ubiquinone structures with prenyl side chains containing conjugated double bonds were generated. The side chains of the new structures were confirmed to have different degrees of desaturation by mass spectrometry and nuclear magnetic resonance analysis. In vivo
14
C labeling and in vitro activity studies showed that CrtN desaturates octaprenyl diphosphates but not the ubiquinone compounds directly. Antioxidant properties of conjugated side chain ubiquinones were analyzed in an in vitro β-carotene-linoleate model system and were found to be higher than the corresponding unmodified ubiquinones. These results demonstrate that by combining pathway steps from different branches of biosynthetic networks, classes of compounds not observed in nature can be synthesized and structural motifs that are functionally important can be combined or enhanced.
Nitric Oxide Reductase Gene Expression and Nitrous Oxide Production in Nitrate-Grown
Pseudomonas mandelii
Authors: Saleh-Lakha Saleema , Shannon Kelly E. , Goyer Claudia , Trevors Jack T. , Zebarth Bernie J. , Burton David L. 
Published: September 2008

ABSTRACT

Pure cultures of
Pseudomonas mandelii
were incubated with or without nitrate, which acts as a substrate and an electron acceptor for denitrification. Nitric oxide reductase (
cnorB
) gene expression was measured using a quantitative reverse transcription-PCR, and nitrous oxide emissions were measured by gas chromatography.
P. mandelii
cells in either the presence or absence of nitrate demonstrated an increase in
cnorB
gene expression during the first 3 h of growth. The level of expression of
cnorB
in nitrate-amended cells remained high (average, 2.06 × 10
8
transcripts/μg of RNA), while in untreated cells it decreased to an average of 3.63 × 10
6
transcripts/μg of RNA from 4 to 6 h. Nitrous oxide accumulation in the headspace was detected at 2 h, and cumulative emissions continued to increase over a 24-h period to 101 μmol in nitrate-amended cells.
P. mandelii cnorB
gene expression was not detected under aerobic conditions. These results demonstrate that
P. mandelii cnorB
gene expression was induced 203-fold at 4 h when nitrate was present in the medium. Accumulations of N
2
O indicated that the cNorB enzyme was synthesized and active.
csrA
Inhibits the Formation of Biofilms by
Vibrio vulnificus
Authors: Jones Melissa K. , Warner Elizabeth B. , Oliver James D. 
Published: September 2008

ABSTRACT

PCR screening of the shellfish-borne pathogen
Vibrio vulnificus
revealed
csrA
-negative strains, and these strains formed increased biofilm compared to
csrA
-positive strains. Complementation in
trans
with
csrA
resulted in reduced biofilm formation, similar to that by
csrA
+
strains. Our results provide evidence that
csrA
inhibits biofilm formation in
V. vulnificus
.