bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of the Essential Cellular Functions of the Two
murA
Genes of
Bacillus anthracis
Authors: Kedar G. C. , Brown-Driver Vickie , Reyes Daniel R. , Hilgers Mark T. , Stidham Mark A. , Shaw Karen Joy , Finn John , Haselbeck Robert J. 
Published: April 2008

ABSTRACT

Targeted antisense and gene replacement mutagenesis experiments demonstrate that only the
murA1
gene and not the
murA2
gene is required for the normal cellular growth of
Bacillus anthracis
. Antisense-based modulation of
murA1
gene expression hypersensitizes cells to the MurA-specific antibiotic fosfomycin despite the normally high resistance of
B. anthracis
to this drug.
Role of Recombination in the Evolution of the Model Plant Pathogen
Pseudomonas syringae
pv. tomato DC3000, a Very Atypical Tomato Strain
Authors: Yan Shuangchun , Liu Haijie , Mohr Toni J. , Jenrette Jenny , Chiodini Rossella , Zaccardelli Massimo , Setubal João C. , Vinatzer Boris A. 
Published: April 2008

ABSTRACT

Pseudomonas syringae
pv. tomato strain DC3000 (PtoDC3000) is one of the most intensively studied bacterial plant pathogens today. Here we report a thorough investigation into PtoDC3000 and close relatives isolated from
Antirrhinum majus
(snapdragon),
Apium graveolens
(celery), and
Solanaceae
and
Brassicaceae
species. Multilocus sequence typing (MLST) was used to resolve the precise phylogenetic relationship between isolates and to determine the importance of recombination in their evolution. MLST data were correlated with an analysis of the locus coding for the type III secreted (T3S) effector AvrPto1 to investigate the role of recombination in the evolution of effector repertoires. Host range tests were performed to determine if closely related isolates from different plants have different host ranges. It was found that PtoDC3000 is located in the same phylogenetic cluster as isolates from several
Brassicaceae
and
Solanaceae
species and that these isolates have a relatively wide host range that includes tomato,
Arabidopsis thaliana
, and cauliflower. All other analyzed tomato isolates from three different continents form a distinct cluster and are pathogenic only on tomato. Therefore, PtoDC3000 is a very unusual tomato isolate. Several recombination breakpoints were detected within sequenced gene fragments, and population genetic tests indicate that recombination contributed more than mutation to the variation between isolates. Moreover, recombination may play an important role in the reassortment of T3S effectors between strains. The data are finally discussed from a taxonomic standpoint, and
P. syringae
pv. tomato is proposed to be divided into two pathovars.
Anaerobic Consumers of Monosaccharides in a Moderately Acidic Fen
Authors: Hamberger Alexandra , Horn Marcus A. , Dumont Marc G. , Murrell J. Colin , Drake Harold L. 
Published: April 2008

ABSTRACT16S rRNA-based stable isotope probing identified active xylose- and glucose-fermentingBacteriaand activeArchaea, including methanogens, in anoxic slurries of material obtained from a moderately acidic, CH4-emitting fen. Xylose and glucose were converted to fatty acids, CO2, H2, and CH4under moderately acidic, anoxic conditions, indicating that the fen harbors moderately acid-tolerant xylose- and glucose-using fermenters, as well as moderately acid-tolerant methanogens. Organisms of the familiesAcidaminococcaceae,Aeromonadaceae,Clostridiaceae,Enterobacteriaceae, andPseudomonadaceaeand the orderActinomycetales, including hitherto unknown organisms, utilized xylose- or glucose-derived carbon, suggesting that highly diverse facultative aerobes and obligate anaerobes contribute to the flow of carbon in the fen under anoxic conditions. UnculturedEuryarchaeota(i.e.,MethanosarcinaceaeandMethanobacteriaceae) andCrenarchaeotaspecies were identified by 16S rRNA analysis of anoxic slurries, demonstrating that the acidic fen harbors novel methanogens andCrenarchaeotaorganisms capable of anaerobiosis. Fermentation-derived molecules are conceived to be the primary drivers of methanogenesis when electron acceptors other than CO2are absent, and the collective findings of this study indicate that fen soils harbor diverse, acid-tolerant, and novel xylose-utilizing as well as glucose-utilizing facultative aerobes and obligate anaerobes that form trophic links to novel moderately acid-tolerant methanogens.
Conversion Shift of
d
-Fructose to
d
-Psicose for Enzyme-Catalyzed Epimerization by Addition of Borate
Authors: Kim Nam-Hee , Kim Hye-Jung , Kang Dong-Il , Jeong Ki-Woong , Lee Jung-Kul , Kim Yangmee , Oh Deok-Kun 
Published: April 2008

ABSTRACT

The conversion yield of
d
-psicose from
d
-fructose by a
d
-psicose 3-epimerase from
Agrobacterium tumefaciens
increased with increasing molar ratios of borate to fructose, up to a ratio of 0.6. The formation of the psicose-borate complex was the result of the higher binding affinity of borate for psicose than for fructose. The formed psicose-borate complex did not participate in the conversion reaction, acting instead as if the product had been removed. Thus, more fructose was converted to psicose in order to restore the equilibrium. The maximum conversion yield of psicose with borate was about twofold that obtained without borate and occurred at a 0.6 molar ratio of borate to fructose. Above this ratio, the conversion yield decreased with increasing ratios, because the amount of fructose available decreased through the formation of the initial fructose-borate complex. The structures of the two sugar-borate complexes, determined by nuclear magnetic resonance spectroscopy, were α-
d
-psicofuranose
cis
-
C
-3,4 diol borate and β-
d
-fructopyranose
cis
-
C
-4,5 diol borate.
Rapid Species Identification of Cooked Poisonous Mushrooms by Using Real-Time PCR
Authors: Maeta Kazuhiko , Ochi Tomoya , Tokimoto Keisuke , Shimomura Norihiro , Maekawa Nitaro , Kawaguchi Nobuhisa , Nakaya Makoto , Kitamoto Yutaka , Aimi Tadanori 
Published: April 2008

ABSTRACT
Species-specific identification of the major cooked and fresh poisonous mushrooms in Japan was performed using a real-time PCR system. Specific fluorescence signals were detected, and no nonspecific signals were detected. Therefore, we succeeded in developing a species-specific test for the identification of poisonous mushrooms within 1.5 h.
Heterogeneous Selection in a Spatially Structured Environment Affects Fitness Tradeoffs of Plasmid Carriage in Pseudomonads
Authors: Slater Frances R. , Bruce Kenneth D. , Ellis Richard J. , Lilley Andrew K. , Turner Sarah L. 
Published: April 2008

ABSTRACT

Environmental conditions under which fitness tradeoffs of plasmid carriage are balanced to facilitate plasmid persistence remain elusive. Periodic selection for plasmid-encoded traits due to the spatial and temporal variation typical in most natural environments (such as soil particles, plant leaf and root surfaces, gut linings, and the skin) may play a role. However, quantification of selection pressures and their effects is difficult at a scale relevant to the bacterium in situ. The present work describes a novel experimental system for such fine-scale quantification, with conditions designed to mimic the mosaic of spatially variable selection pressures present in natural surface environments. The effects of uniform and spatially heterogeneous mercuric chloride (HgCl
2
) on the dynamics of a model community of plasmid-carrying, mercury-resistant (Hg
r
) and plasmid-free, mercury-sensitive (Hg
s
) pseudomonads were compared. Hg resulted in an increase in the surface area occupied by, and therefore an increase in the fitness of, Hg
r
bacteria relative to Hg
s
bacteria. Uniform and heterogeneous Hg distributions were demonstrated to result in different community structures by epifluorescence microscopy, with heterogeneous Hg producing spatially variable selection landscapes. The effects of heterogeneous Hg were only apparent at scales of a few hundred micrometers, emphasizing the importance of using appropriate analysis methods to detect effects of environmental heterogeneity on community dynamics. Heterogeneous Hg resulted in negative frequency-dependent selection for Hg
r
cells, suggesting that sporadic selection may facilitate the discontinuous distribution of plasmids through host populations in complex, structured environments.
Assessing Genetic Heterogeneity within Bacterial Species Isolated from Gastrointestinal and Environmental Samples: How Many Isolates Does It Take?
Authors: Döpfer D. , Buist W. , Soyer Y. , Munoz M. A. , Zadoks R. N. , Geue L. , Engel B. 
Published: April 2008

ABSTRACT

Strain typing of bacterial isolates is increasingly used to identify sources of infection or product contamination and to elucidate routes of transmission of pathogens or spoilage organisms. Usually, the number of bacterial isolates belonging to the same species that is analyzed per sample is determined by convention, convenience, laboratory capacity, or financial resources. Statistical considerations and knowledge of the heterogeneity of bacterial populations in various sources can be used to determine the number of isolates per sample that is actually needed to address specific research questions. We present data for intestinal
Escherichia coli
,
Listeria monocytogenes
,
Klebsiella pneumoniae
, and
Streptococcus uberis
from gastrointestinal, fecal, or soil samples characterized by ribotyping, pulsed-field gel electrophoresis, and PCR-based strain-typing methods. In contrast to previous studies, all calculations were performed with a single computer program, employing software that is freely available and with in-depth explanation of the choice and derivation of prior distributions. Also, some of the model assumptions were relaxed to allow analysis of the special case of two (groups of) strains that are observed with different probabilities. Sample size calculations, with a Bayesian method of inference, show that from 2 to 20 isolates per sample need to be characterized to detect all strains that are present in a sample with 95% certainty. Such high numbers of isolates per sample are rarely typed in real life due to financial or logistic constraints. This implies that investigators are not gaining maximal information on strain heterogeneity and that sources and transmission pathways may go undetected.
Engineering and Analysis of a
Saccharomyces cerevisiae
Strain That Uses Formaldehyde as an Auxiliary Substrate
Authors: Baerends Richard J. S. , de Hulster Erik , Geertman Jan-Maarten A. , Daran Jean-Marc , van Maris Antonius J. A. , Veenhuis Marten , van der Klei Ida J. , Pronk Jack T. 
Published: April 2008

ABSTRACT

We demonstrated that formaldehyde can be efficiently coutilized by an engineered
Saccharomyces cerevisiae
strain that expresses
Hansenula polymorpha
genes encoding formaldehyde dehydrogenase (
FLD1
) and formate dehydrogenase (
FMD
), in contrast to wild-type strains. Initial chemostat experiments showed that the engineered strain coutilized formaldehyde with glucose, but these mixed-substrate cultures failed to reach steady-state conditions and did not exhibit an increased biomass yield on glucose. Subsequent transcriptome analyses of chemostat cultures of the engineered strain, grown on glucose-formaldehyde mixtures, indicated that the presence of formaldehyde in the feed caused biotin limitations. Further transcriptome analysis demonstrated that this biotin inactivation was prevented by using separate formaldehyde and vitamin feeds. Using this approach, steady-state glucose-limited chemostat cultures were obtained that coutilized glucose and formaldehyde. Coutilization of formaldehyde under these conditions resulted in an enhanced biomass yield of the glucose-limited cultures. The biomass yield was quantitatively consistent with the use of formaldehyde as an auxiliary substrate that generates NADH and subsequently, via oxidative phosphorylation, ATP. On an electron pair basis, the biomass yield increase observed with formaldehyde was larger than that observed previously for formate, which is tentatively explained by different modes of formate and formaldehyde transport in
S. cerevisiae
.
Analysis of theActinobacillus pleuropneumoniaeArcA Regulon Identifies Fumarate Reductase as a Determinant of Virulence
Authors: Buettner Falk F. R. , Bendallah Ibrahim M. , Bosse Janine T. , Dreckmann Karla , Nash John H. E. , Langford Paul R. , Gerlach Gerald-F. 
Published: April 2008

ABSTRACTThe ability of the bacterial pathogenActinobacilluspleuropneumoniaeto grow anaerobically allows the bacterium to persist in the lung. The ArcAB two-component system is crucial for metabolic adaptation in response to anaerobic conditions, and we recently showed that anA. pleuropneumoniae arcAmutant had reduced virulence compared to the wild type (F. F. Buettner, A. Maas, and G.-F. Gerlach, Vet. Microbiol. 127:106-115, 2008). In order to understand the attenuated phenotype, we investigated the ArcA regulon ofA. pleuropneumoniaeby using a combination of transcriptome (microarray) and proteome (two-dimensional difference gel electrophoresis and subsequent mass spectrometry) analyses. We show that ArcA negatively regulates the expression of many genes, including those encoding enzymes which consume intermediates during fumarate synthesis. Simultaneously, the expression of glycerol-3-phosphate dehydrogenase, a component of the respiratory chain serving as a direct reduction equivalent for fumarate reductase, was upregulated. This result, together with the in silico analysis finding thatA. pleuropneumoniaehas no oxidative branch of the citric acid cycle, led to the hypothesis that fumarate reductase might be crucial for virulence by providing (i) energy via fumarate respiration and (ii) succinate and other essential metabolic intermediates via the reductive branch of the citric acid cycle. To test this hypothesis, an isogenicA. pleuropneumoniaefumarate reductase deletion mutant was constructed and studied by using a pig aerosol infection model. The mutant was shown to be significantly attenuated, thereby strongly supporting a crucial role for fumarate reductase in the pathogenesis ofA. pleuropneumoniaeinfection.
Inelastic performance of screw-connected cold-formed steel strap-braced walls
Authors: Al-Kharat M. , Rogers C. A. 
Published: April 2008

Cold-formed steel, screw-connected strap-braced walls (15 specimens, 2.44 m × 2.44 m each), designed following a capacity-based approach, were tested to evaluate their performance in the inelastic range of behaviour. Gross cross-section yielding of the tension braces was the specified failure mode in the design procedure. Extended tracks and additional shear anchors were installed, such that inelastic deformations would be limited to tension yielding of the braces. Walls without extended tracks were able to reach their yield level; however, damage to other frame elements occurred, thus reducing the ductility level that was attained. Cyclically loaded walls (0.5 Hz) with track extensions showed that wall performance is also dependent on the strain rate experienced by the braces. An Fu / Fy ratio greater than 1.2 is necessary to limit the possibility of brace fracture under seismic loading. Preliminary force modification factors, Rd = 2.0 and Ro = 1.3, are recommended for walls designed and detailed to achieve ductile performance.
Thermal effect on fiber reinforced polymer reinforced concrete slabs
Authors: Zaidi A. , Masmoudi R. 
Published: April 2008

The difference between the transverse coefficients of thermal expansion of fiber reinforced polymer (FRP) bars and concrete generates radial pressure at the FRP bar – concrete interface, which induces tensile stresses within the concrete under temperature increase and, eventually, failure of the concrete cover if the confining action of concrete is insufficient. This paper presents the results of an experimental study to investigate the thermal effect on the behaviour of FRP bars and concrete cover, using concrete slab specimens reinforced with glass FRP bars and subjected to thermal loading from –30 to +80 °C. The experimental results show that failure of concrete cover was produced at temperatures varying between +50 and +60 °C for slabs having a ratio of concrete cover thickness to FRP bar diameter (c/db) less than or equal to 1.4. A ratio of c/db greater than or equal to 1.6 seems to be sufficient to avoid splitting failure of concrete cover for concrete slabs subjected to high temperatures up to +80 °C. Also, the first cracks appear in concrete at the FRP bar – concrete interface at temperatures around +40 °C. Comparison between experimental and analytical results in terms of thermal loads and thermal strains is presented.
Exposure to high temperature influences the behaviour, physiology, and survival of sockeye salmon during spawning migration
Authors: Crossin G. T. , Hinch S. G. , Cooke S. J. , Welch D. W. , Patterson D. A. , Jones S. R.M. , Lotto A. G. , Leggatt R. A. , Mathes M. T. , Shrimpton J. M. , Van Der Kraak G. , Farrell A. P. 
Published: April 2008

Since 1996, some populations of Fraser River sockeye salmon ( Oncorhynchus nerka Walbaum in Artedi, 1792) have begun spawning migrations weeks earlier than normal, and most perish en route as a result. We suspect that a high midsummer river temperature is the principal cause of mortality. We intercepted 100 sockeye during normal migration near a spawning stream and measured somatic energy and aspects of plasma biochemistry. Fish were then held at either 10 or 18 °C for 24 days. Before release, fish were biopsied again and implanted with acoustic transmitters. A group of biopsied but untreated control salmon were released at the same time. Sixty-two percent (8 of 13) of control salmon and 68% (21 of 31) of 10 °C salmon reached spawning areas. The 18 °C-treated fish were half as successful (35%; 6 of 17). During the holding period, mortality was 2 times higher and levels of Parvicapsula minibicornis (Kent, Whitaker and Dawe, 1997) infection were higher in the 18 °C-treated group than in the 10 °C-treated group. The only physiological difference between treatments was a change in gill Na+,K+-ATPase activity. This drop correlated negatively with travel times for the 18 °C-treated males. Reproductive-hormone levels and stress measures did not differ between treatments but showed significant correlations with individual travel times.
Ruffed grouse brood habitat selection at multiple scales in Pennsylvania: implications for survival
Authors: Tirpak John M. , Giuliano William M. , Miller C. Allan 
Published: April 2008

Declines in ruffed grouse ( Bonasa umbellus (L., 1766)) populations in the central and southern Appalachians may be linked to low brood survival. Therefore, managing for high-quality brood habitat could improve grouse numbers. Understanding how brood habitat selection affects survival and the spatial scale at which this occurs is therefore fundamental to developing effective habitat management strategies. From 1999–2002, we monitored 38 broods for 5 weeks post hatch and estimated utilization distributions (n = 28), site-scale habitat use (n = 21), and daily survival rate (mean = 0.966, range = 0.920–0.997, and n = 19). Relative to available habitat, broods selected sites with greater herbaceous ground cover and higher small (<2.5 cm diameter at breast height, DBH) stem densities and landscapes containing higher proportions of road and young deciduous forest. Herbaceous ground cover provided arthropod prey and concealment from predators and was a primary factor driving habitat selection. High stem densities and early successional habitats provided increased security, but were only used if adequate ground cover was present. Broods strongly selected roads and experienced higher survival near edges. However, higher road densities were associated with lower survival at the landscape scale. This pattern reflects the differential scale at which grouse and their predators respond to edge.
Individual variation affects departure rate from the natal pond in an ephemeral pond-breeding anuran
Authors: Chelgren Nathan D. , Rosenberg Daniel K. , Heppell Selina S. , Gitelman Alix I. 
Published: April 2008

Frogs exhibit extreme plasticity and individual variation in growth and behavior during metamorphosis, driven by interactions of intrinsic state factors and extrinsic environmental factors. In northern red-legged frogs ( Rana aurora Baird and Girard, 1852), we studied the timing of departure from the natal pond as it relates to date and size of individuals at metamorphosis in the context of environmental uncertainty. To affect body size at metamorphosis, we manipulated food availability during the larval stage for a sample (317) of 1045 uniquely marked individuals and released them at their natal ponds as newly metamorphosed frogs. We recaptured 34% of marked frogs in pitfall traps as they departed and related the timing of their initial terrestrial movements to individual properties using a time-to-event model. Median age at first capture was 4 and 9 days postmetamorphosis at two sites. The rate of departure was positively related to body size and to date of metamorphosis. Departure rate was strongly negatively related to time elapsed since rainfall, and this effect was diminished for smaller and later metamorphosing frogs. Individual variation in metamorphic traits thus affects individuals’ responses to environmental variability, supporting a behavioral link with variation in survival associated with these same metamorphic traits.
CASE DETECTION AND DIRECT OBSERVATION THERAPY STRATEGY (DOTS) IN NIGERIA: ITS EFFECT ON TB DYNAMICS
Authors: OKUONGHAE DANIEL , AIHIE VINCENT 
Published: March 2008

This paper addresses the synergy between case detection and the implementation of DOTS in Nigeria in the control of tuberculosis using a deterministic model which incorporates many of the essential biological and epidemiological features of TB as well as DOTS surveillance and implementation parameters for Nigeria. The model differentiated between individuals who progress to the "primary" latent stage when they got infected for the first time and those who progress to the "secondary" latent class depending on whether they failed treatment or due to self-cure. The model was shown to have a locally asymptotically stable disease free equilibrium where the reproduction number was less than unity. However, it was also shown that the model is capable of exhibiting the backward bifurcation phenomenon, where the stable disease free equilibrium co-exists with a stable endemic equilibrium where the reproduction number is less than unity. We saw that increasing the case detection parameter actually reduces the backward bifurcation range. For smaller exogenous re-infection values, increasing the case detection parameter could totally eliminate the bifurcation range. Uncertainty and sensitivity analysis using the Latin hypercube sampling technique was also carried out on the parameters as well as the reproduction number and the results showed that there were three parameters that were highly influential in determining the magnitude of the reproduction number; of the three, only one, the case detection parameter, was highly influential in reducing the magnitude of the reproduction number. Results from the numerical simulation and qualitative analysis showed that DOTS expansion in Nigeria must include significant increase in case detection rates, otherwise the impressive cure rates under DOTS will pale into insignificance with the rise in the number of undetected infectious persons and the number of "secondary" latent cases. Overall, the study shows that increasing the case detection rate will not only lower the backward bifurcation range, in the presence of exogenous re-infection, but could also lower the reproduction number, reducing the severity of the TB epidemic. This is possible as far as the current impressive treatment success rates under DOTS in Nigeria is sustained.