bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluating PcGets and RETINA as Automatic Model Selection Algorithms*
Authors: Castle Jennifer L. 
Published: December 2005

AbstractThe paper describes two automatic model selection algorithms, RETINA and PcGets, briefly discussing how the algorithms work and what their performance claims are. RETINA's Matlab implementation of the code is explained, then the program is compared with PcGets on the data in Perez‐Amaral, Gallo and White (2005, Econometric Theory, Vol. 21, pp. 262–277), ‘A Comparison of Complementary Automatic Modelling Methods: RETINA and PcGets’, and Hoover and Perez (1999, Econometrics Journal, Vol. 2, pp. 167–191), ‘Data Mining Reconsidered: Encompassing and the General‐to‐specific Approach to Specification Search’. Monte Carlo simulation results assess the null and non‐null rejection frequencies of the RETINA and PcGets model selection algorithms in the presence of nonlinear functions.
Uniform Head in Horizontal and Vertical Wells
Authors: Steward David R. , Jin Wei 
Published: December 2005

AbstractThe steady‐state head within a fully penetrating well may be estimated by evaluating the Thiem equation at the radius of the well. A method is presented here to extend results from the Thiem equation to horizontal wells and to partially penetrating wells. The particular model used in this investigation is based upon the analytic element method; it accurately reproduces a boundary condition of uniform head along the cylindrical surface at the perforated face of the well. This model is exercised over a representative range of parameters including the well's length, radius, and pumping rate, and the aquifer's hydraulic conductivity and thickness. Results are presented in a set of figures and tables that compare the well's drawdown to the drawdown that would have been obtained using the Thiem solution with the same pumping rate and radius. A methodology is presented to estimate the head within a horizontal or partially penetrating well by adding a correction term to results that can be readily obtained from computer models of vertical fully penetrating wells. This approach may also be used to contrast the differences in head between horizontal and vertical wells of various lengths, radii, and placement elevations.
Regulation and Characterization of Two Nitroreductase Genes,
nprA
and
nprB
, of
Rhodobacter capsulatus
Authors: Pérez-Reinado Eva , Blasco Rafael , Castillo Francisco , Moreno-Vivián Conrado , Roldán M. Dolores 
Published: December 2005

ABSTRACT

Among photosynthetic bacteria, strains B10 and E1F1 of
Rhodobacter capsulatus
photoreduce 2,4-dinitrophenol (DNP), which is stoichiometrically converted into 2-amino-4-nitrophenol by a nitroreductase activity. The reduction of DNP is inhibited in vivo by ammonium, which probably acts at the level of the DNP transport system and/or physiological electron transport to the nitroreductase, since this enzyme is not inhibited by ammonium in vitro. Using the complete genome sequence data for strain SB1003 of
R. capsulatus
, two putative genes coding for possible nitroreductases were isolated from
R. capsulatus
B10 and disrupted. The phenotypes of these mutant strains revealed that both genes are involved in the reduction of DNP and code for two major nitroreductases, NprA and NprB. Both enzymes use NAD(P)H as the main physiological electron donor. The nitroreductase NprA is under ammonium control, whereas the nitroreductase NprB is not. In addition, the expression of the
nprB
gene seems to be constitutive, whereas
nprA
gene expression is inducible by a wide range of nitroaromatic and heterocyclic compounds, including several dinitroaromatics, nitrofuran derivatives, CB1954, 2-aminofluorene, benzo[a]pyrene, salicylic acid, and paraquat. The identification of two putative
mar
/
sox
boxes in the possible promoter region of the
nprA
gene and the induction of
nprA
gene expression by salicylic acid and 2,4-dinitrophenol suggest a role in the control of the
nprA
gene for the two-component MarRA regulatory system, which in
Escherichia coli
controls the response to some antibiotics and environmental contaminants. In addition, upregulation of the
nprA
gene by paraquat indicates that this gene is probably a member of the SoxRS regulon, which is involved in the response to stress conditions in other bacteria.
Infectious Swine Hepatitis E Virus Is Present in Pig Manure Storage Facilities on United States Farms, but Evidence of Water Contamination Is Lacking
Authors: Kasorndorkbua C. , Opriessnig T. , Huang F. F. , Guenette D. K. , Thomas P. J. , Meng X.-J. , Halbur P. G. 
Published: December 2005

ABSTRACT

Fresh feces, manure slurry (from earthen lagoons and/or concrete pits), and drinking and surface water samples were collected from 28 pig farms in the Midwestern United States. All samples were tested for hepatitis E virus (HEV) RNA by reverse transcription-PCR. Seven of 28 farms had fecal samples that contained HEV. Of 22 farms where pit samples were accessible, 15 contained HEV, and of 8 farms that had lagoons, 3 contained HEV. The highest virus titers were 10 and 10
3
genome equivalents per 60 ml of manure slurry in lagoon and pit samples, respectively. None of the water samples tested HEV positive. To determine the infectivity of the HEV found in the positive farm 19 lagoon (designated L19) or farm 12 pit (designated P12) samples, pigs were inoculated either intravenously (
n
= 3) or orally (
n
= 3) with the L19 or P12 manure slurry. Four pigs inoculated intravenously with prototype swine HEV served as positive controls. All positive-control pigs shed HEV in feces and 3 of 4 developed anti-HEV antibodies. Two pigs in the intravenously inoculated P12 group shed HEV in feces, and one of the pigs seroconverted to anti-HEV antibodies. None of the pigs in the negative-control, L19 oral, L19 intravenous, or P12 oral group shed HEV in feces. The findings indicate that HEV found in pig manure slurry was infectious when inoculated intravenously. Pit manure slurry is a potential source of HEV infection and for contamination of the environment. Contamination of drinking or surface water with HEV was not found on or near the pig farms.
Coaggregation Facilitates Interspecies Hydrogen Transfer betweenPelotomaculum thermopropionicumandMethanothermobacter thermautotrophicus
Authors: Ishii Shun'ichi , Kosaka Tomoyuki , Hori Katsutoshi , Hotta Yasuaki , Watanabe Kazuya 
Published: December 2005

ABSTRACTA thermophilic syntrophic bacterium,Pelotomaculum thermopropionicumstrain SI, was grown in a monoculture or coculture with a hydrogenotrophic methanogen,Methanothermobacter thermautotrophicusstrain ΔH. Microscopic observation revealed that cells of each organism were dispersed in a monoculture independent of the growth substrate. In a coculture, however, these organisms coaggregated to different degrees depending on the substrate; namely, a large fraction of the cells coaggregated when they were grown on propionate, but relatively few cells coaggregated when they were grown on ethanol or 1-propanol. Field emission-scanning electron microscopy revealed that flagellum-like filaments of SI cells played a role in making contact with ΔH cells. Microscopic observation of aggregates also showed that extracellular polymeric substance-like structures were present in intercellular spaces. In order to evaluate the importance of coaggregation for syntrophic propionate oxidation, allowable average distances between SI and ΔH cells for accomplishing efficient interspecies hydrogen transfer were calculated by using Fick's diffusion law. The allowable distance for syntrophic propionate oxidation was estimated to be approximately 2 μm, while the allowable distances for ethanol and propanol oxidation were 16 μm and 32 μm, respectively. Considering that the mean cell-to-cell distance in the randomly dispersed culture was approximately 30 μm (at a concentration in the mid-exponential growth phase of the coculture of 5 × 107cells ml−1), it is obvious that close physical contact of these organisms by coaggregation is indispensable for efficient syntrophic propionate oxidation.
Single-Site Oxidation, Cysteine 108 to Cysteine Sulfinic Acid, ind-Amino Acid Oxidase fromTrigonopsis variabilisand Its Structural and Functional Consequences
Authors: Slavica Anita , Dib Iskandar , Nidetzky Bernd 
Published: December 2005

ABSTRACTOne of the primary sources of enzyme instability is protein oxidative modification triggering activity loss or denaturation. We show here that the side chain of Cys108 is the main site undergoing stress-induced oxidation inTrigonopsis variabilisd-amino acid oxidase, a flavoenzyme employed industrially for the conversion of cephalosporin C. High-resolution anion-exchange chromatography was used to separate the reduced and oxidized protein forms, which constitute, in a molar ratio of about 3:1, the active biocatalyst isolated from the yeast. Comparative analysis of their tryptic peptides by electrospray tandem mass spectrometry allowed unequivocal assignment of the modification as the oxidation of Cys108 into cysteine sulfinic acid. Cys108 is likely located on a surface-exposed protein region within the flavin adenine dinucleotide (FAD) binding domain, but remote from the active center. Its oxidized side chain was remarkably stable in solution, thus enabling the relative biochemical characterization of native and modified enzyme forms. The oxidation of Cys108 causes a global conformational response that affects the protein environment of the FAD cofactor. In comparison with the native enzyme, it results in a fourfold-decreased specific activity, reflecting a catalytic efficiency for reduction of dioxygen lowered by about the same factor, and a markedly decreased propensity to aggregate under conditions of thermal denaturation. These results open up unprecedented routes for stabilization of the oxidase and underscore the possible significance of protein chemical heterogeneity for biocatalyst function and stability.
Distribution of Genes Encoding Putative Virulence Factors and Fragment Length Polymorphisms in the
vrrA
Gene among Brazilian Isolates of
Bacillus cereus
and
Bacillus thuringiensis
Authors: Zahner Viviane , Cabral Diana Aparecida , Régua-Mangia Adriana Hamond , Rabinovitch Leon , Moreau Gaétan , McIntosh Douglas 
Published: December 2005

ABSTRACT

One hundred twenty-one strains of the
Bacillus cereus
complex, of which 80 were isolated from a variety of sources in Brazil, were screened by PCR for the presence of sequences (
bceT
,
hblA
,
nheBC
,
plc
,
sph
, and
vip3A
) encoding putative virulence factors and for polymorphisms in variable-number tandem repeats (VNTR), using a variable region of the
vrrA
open reading frame as the target. Amplicons were generated from isolates of
B. cereus
and
Bacillus thuringiensis
for each of the sequences encoding factors suggested to play a role in infections of mammals. Intriguingly, the majority of these sequences were detected more frequently in
Bacillus thuringiensis
than in
B. cereus
. The
vip3A
sequence, which encodes an insecticidal toxin, was detected exclusively in
B. thuringiensis
. VNTR analysis demonstrated the presence of five different fragment length categories in both species, with two of these being widely distributed throughout both taxa. In common with data generated from previous studies examining European, Asian, or North American populations, our investigation of Brazilian isolates supports the notion that
B. cereus
and
B. thuringiensis
should be considered to represent a single species.
Impact of the Microscale Distribution of a
Pseudomonas
Strain Introduced into Soil on Potential Contacts with Indigenous Bacteria
Authors: Dechesne Arnaud , Pallud Céline , Bertolla Franck , Grundmann Geneviève L. 
Published: December 2005

ABSTRACT

Soil bioaugmentation is a promising approach in soil bioremediation and agriculture. Nevertheless, our knowledge of the fate and activity of introduced bacteria in soil and thus of their impact on the soil environment is still limited. The microscale spatial distribution of introduced bacteria has rarely been studied, although it determines the encounter probability between introduced cells and any components of the soil ecosystem and thus plays a role in the ecology of introduced bacteria. For example, conjugal gene transfer from introduced bacteria to indigenous bacteria requires cell-to-cell contact, the probability of which depends on their spatial distribution. To quantitatively characterize the microscale distribution of an introduced bacterial population and its dynamics, a
gfp
-tagged derivative of
Pseudomonas putida
KT2440 was introduced by percolation in repacked soil columns. Initially, the introduced population was less widely spread at the microscale level than two model indigenous functional communities: the 2,4-dichlorophenoxyacetic acid degraders and the nitrifiers (each at 10
6
CFU g
−1
soil). When the soil was percolated with a substrate metabolizable by
P. putida
or incubated for 1 month, the microscale distribution of introduced bacteria was modified towards a more widely dispersed distribution. The quantitative data indicate that the microscale spatial distribution of an introduced strain may strongly limit its contacts with the members of an indigenous bacterial community. This could constitute an explanation to the low number of indigenous transconjugants found most of time when a plasmid-donor strain is introduced into soil.
Stable Isotopic Studies of
n
-Alkane Metabolism by a Sulfate-Reducing Bacterial Enrichment Culture
Authors: Davidova Irene A. , Gieg Lisa M. , Nanny Mark , Kropp Kevin G. , Suflita Joseph M. 
Published: December 2005

ABSTRACT

Gas chromatography-mass spectrometry and nuclear magnetic resonance spectroscopy were used to study the metabolism of deuterated
n
-alkanes (C
6
to C
12
) and 1-
13
C-labeled
n
-hexane by a highly enriched sulfate-reducing bacterial culture. All substrates were activated via fumarate addition to form the corresponding alkylsuccinic acid derivatives as transient metabolites. Formation of
d
14
-hexylsuccinic acid in cell extracts from exogenously added, fully deuterated
n
-hexane confirmed that this reaction was the initial step in anaerobic alkane metabolism. Analysis of resting cell suspensions amended with 1-
13
C-labeled
n
-hexane confirmed that addition of the fumarate occurred at the C-2 carbon of the parent substrate. Subsequent metabolism of hexylsuccinic acid resulted in the formation of 4-methyloctanoic acid, and 3-hydroxy-4-methyloctanoic acid was tentatively identified. We also found that
13
C nuclei from 1-
13
C-labeled
n
-hexane became incorporated into the succinyl portion of the initial metabolite in a manner that indicated that
13
C-labeled fumarate was formed and recycled during alkane metabolism. Collectively, the findings obtained with a sulfate-reducing culture using isotopically labeled alkanes augment and support the previously proposed pathway (H. Wilkes, R. Rabus, T. Fischer, A. Armstroff, A. Behrends, and F. Widdel, Arch. Microbiol.
177:
235-243, 2002) for metabolism of deuterated
n
-hexane by a denitrifying bacterium.
UniFrac: a New Phylogenetic Method for Comparing Microbial Communities
Authors: Lozupone Catherine , Knight Rob 
Published: December 2005

ABSTRACTWe introduce here a new method for computing differences between microbial communities based on phylogenetic information. This method, UniFrac, measures the phylogenetic distance between sets of taxa in a phylogenetic tree as the fraction of the branch length of the tree that leads to descendants from either one environment or the other, but not both. UniFrac can be used to determine whether communities are significantly different, to compare many communities simultaneously using clustering and ordination techniques, and to measure the relative contributions of different factors, such as chemistry and geography, to similarities between samples. We demonstrate the utility of UniFrac by applying it to published 16S rRNA gene libraries from cultured isolates and environmental clones of bacteria in marine sediment, water, and ice. Our results reveal that (i) cultured isolates from ice, water, and sediment resemble each other and environmental clone sequences from sea ice, but not environmental clone sequences from sediment and water; (ii) the geographical location does not correlate strongly with bacterial community differences in ice and sediment from the Arctic and Antarctic; and (iii) bacterial communities differ between terrestrially impacted seawater (whether polar or temperate) and warm oligotrophic seawater, whereas those in individual seawater samples are not more similar to each other than to those in sediment or ice samples. These results illustrate that UniFrac provides a new way of characterizing microbial communities, using the wealth of environmental rRNA sequences, and allows quantitative insight into the factors that underlie the distribution of lineages among environments.
Contingency Locus in
ctsR
of
Listeria monocytogenes
Scott A: a Strategy for Occurrence of Abundant Piezotolerant Isolates within Clonal Populations
Authors: Karatzas Kimon A. G. , Valdramidis Vasileios P. , Wells-Bennik Marjon H. J. 
Published: December 2005

ABSTRACT

In a recent study we demonstrated that a high-hydrostatic-pressure-tolerant isolate of
Listeria monocytogenes
lacks a codon in the class 3 heat shock regulator gene
ctsR
. This mutation in the region that encodes four consecutive glycines was directly responsible for the observed piezotolerance, increased stress resistance, and reduced virulence. The aim of the present study was to determine whether mutations in
ctsR
are frequently associated with piezotolerance in
L. monocytogenes
. Wild-type cultures of
L. monocytogenes
were therefore exposed to 350 MPa for 20 min, and the piezotolerance of individual surviving isolates was assessed. This rendered 33 isolates with a stable piezotolerant phenotype from a total of 84 survivors. Stable piezotolerant mutants were estimated to be present in the initial wild-type population at frequencies of >10
−5
. Subsequent sequencing of the
ctsR
gene of all stable piezotolerant isolates revealed that two-thirds of the strains (i.e.,
n
= 21) had mutations in this gene. The majority of the mutations (16 of 21 strains) consisted of a triplet deletion in the glycine-encoding region of
ctsR
, identical to what was found in our previous study. Interestingly, 2 of 21 mutants contained a codon insertion in this repeat region. The remaining three stable piezotolerant strains showed a 19-bp insertion in the glycine repeat region, a 16-bp insertion downstream of the glycine repeat area (both leading to frameshifts and a truncated
ctsR
), and an in-frame 114-bp deletion encoding a drastically shortened carboxy terminus of CtsR. In four instances it was not possible to generate a PCR product. A piezotolerant phenotype could not be linked to mutations in
ctsR
in 8 of 33 isolates, indicating that other thus-far-unknown mechanisms also lead to stable piezotolerance. The present study highlights the importance of
ctsR
in piezotolerance and stress tolerance of
L. monocytogenes
, and it demonstrates that short-sequence repeat regions contribute significantly to the occurrence of a piezotolerant and stress-tolerant subpopulation within
L. monocytogenes
cultures, thus playing an important role in survival.
Adaptive Responses to Oxygen Stress in Obligatory Anaerobes
Clostridium acetobutylicum
and
Clostridium aminovalericum
Authors: Kawasaki Shinji , Watamura Yusuke , Ono Masaki , Watanabe Toshihiro , Takeda Kouji , Niimura Youichi 
Published: December 2005

ABSTRACT

Clostridium acetobutylicum
and
Clostridium aminovalericum
, both obligatory anaerobes, grow normally after growth conditions are changed from anoxic to microoxic, where the cells consume oxygen proficiently. In
C. aminovalericum
, a gene encoding a previously characterized H
2
O-forming NADH oxidase, designated
noxA
, was cloned and sequenced. The expression of
noxA
was strongly upregulated within 10 min after the growth conditions were altered to a microoxic state, indicating that
C. aminovalericum
NoxA is involved in oxygen metabolism. In
C. acetobutylicum
, genes suggested to be involved in oxygen metabolism and genes for reactive oxygen species (ROS) scavenging were chosen from the genome database. Although no clear orthologue of
C. aminovalericum
NoxA was found, Northern blot analysis identified many O
2
-responsive genes (e.g., a gene cluster [
CAC2448
to
CAC2452
] encoding an NADH rubredoxin oxidoreductase-A-type flavoprotein-desulfoferrodoxin homologue-MerR family-like protein-flavodoxin, an operon [
CAC1547
to
CAC1549
] encoding a thioredoxin-thioredoxin reductase-glutathione peroxidase-like protein, an operon [
CAC1570
and
CAC1571
] encoding two glutathione peroxidase-like proteins, and genes encoding thiol peroxidase, bacterioferritin comigratory proteins, and superoxide dismutase) whose expression was quickly and synchronously upregulated within 10 min after flushing with 5% O
2.
The corresponding enzyme activities, such as NAD(P)H-dependent peroxide (H
2
O
2
and alkyl hydroperoxides) reductase, were highly induced, indicating that microoxic growth of
C. acetobutylicum
is associated with the expression of a number of genes for oxygen metabolism and ROS scavenging.
Inhibition ofHelicobacter pyloriand Associated Urease by Oregano and Cranberry Phytochemical Synergies
Authors: Lin Y. T. , Kwon Y. I. , Labbe R. G. , Shetty K. 
Published: December 2005

ABSTRACTUlcer-associated dyspepsia is caused by infection withHelicobacter pylori. H. pyloriis linked to a majority of peptic ulcers. Antibiotic treatment does not always inhibit or killH. pyloriwith potential for antibiotic resistance. The objective of this study was to determine the potential for using phenolic phytochemical extracts to inhibitH. pyloriin a laboratory medium. Our approach involved the development of a specific phenolic profile with optimization of different ratios of extract mixtures from oregano and cranberry. Subsequently, antimicrobial activity and antimicrobial-linked urease inhibition ability were evaluated. The results indicated that the antimicrobial activity was greater in extract mixtures than in individual extracts of each species. The results also indicate that the synergistic contribution of oregano and cranberry phenolics may be more important for inhibition than any species-specific phenolic concentration. Further, based on plate assay, the likely mode of action may be through urease inhibition and disruption of energy production by inhibition of proline dehydrogenase at the plasma membrane.
Heterologous Leaky Production of Transglutaminase in
Lactococcus lactis
Significantly Enhances the Growth Performance of the Host
Authors: Fu Rui-Yan , Chen Jian , Li Yin 
Published: December 2005

ABSTRACT

This study describes a novel strategy to improve the growth performance of
Lactococcus lactis
by heterologous production of food-grade transglutaminase. The
mtg
gene from
Streptoverticillium mobaraense
that encodes the transglutaminase mature protein was cloned into a nisin-inducible expression vector and transformed into
L. lactis
subsp.
cremoris
NZ9000. The leaky expression of the
mtg
gene from the
nisA
promoter resulted in ammonia formation and carbon flux redistribution at the pyruvate branch. As a consequence, medium acidification was lessened and energy utilization was improved. This led to significantly higher biomass production under aerobic conditions and particularly under non-pH-controlled conditions (up to a 12-fold increase). The results presented here provide a novel way to enhance the growth yield of
L. lactis
, which is an important step for the purposes of producing proteins of commercial interest using
L. lactis
as a host.