bluuebunny/crossref_metadata_2025_split huggingface dataset:
Construction of Chimeric Catechol 2,3-Dioxygenase Exhibiting Improved Activity against the Suicide Inhibitor 4-Methylcatechol
Authors: Okuta Akiko , Ohnishi Kouhei , Harayama Shigeaki 
Published: March 2004

ABSTRACT

Catechol 2,3-dioxygenase (C23O; EC 1.3.11.2), exemplified by XylE and NahH, catalyzes the ring cleavage of catechol and some substituted catechols. C23O is inactivated at an appreciable rate during the ring cleavage of 4-methylcatechol due to the oxidation of the Fe(II) cofactor to Fe(III). In this study, a C23O exhibiting improved activity against 4-methylcatechol was isolated. To isolate this C23O, diverse C23O gene sequences were PCR amplified from DNA which had been isolated from mixed cultures of phenol-degrading bacteria and subcloned in the middle of a known C23O gene sequence (
xylE
or
nahH
) to construct a library of chimeric C23O genes. These chimeric C23O genes were then introduced into
Pseudomonas putida
possessing some of the toluene catabolic genes (
xylXYZLGFJQKJI
). When a C23O gene (e.g.,
xylE
) is introduced into this strain, the transformants cannot generally grow on
p
-toluate because 4-methylcatechol, a metabolite of
p
-toluate, is a substrate as well as a suicide inhibitor of C23O. However, a transformant of this strain capable of growing on
p
-toluate was isolated, and a chimeric C23O (named NY8) in this transformant was characterized. The rate of enzyme inactivation by 4-methylcatechol was lower in NY8 than in XylE. Furthermore, the rate of the reactivation of inactive C23O in a solution containing Fe(II) and ascorbic acid was higher in NY8 than in XylE. These properties of NY8 might allow the efficient metabolism of 4-methylcatechol and thus allow host cells to grow on
p
-toluate.
Spatial Heterogeneity of Crenarchaeal Assemblages within Mesophilic Soil Ecosystems as Revealed by PCR-Single-Stranded Conformation Polymorphism Profiling
Authors: Sliwinski Marek K. , Goodman Robert M. 
Published: March 2004

ABSTRACT

Microbial ecologists have discovered novel rRNA genes (rDNA) in mesophilic soil habitats worldwide, including sequences that affiliate phylogenetically within the division
Crenarchaeota
(domain
Archaea
). To characterize the spatial distribution of crenarchaeal assemblages in mesophilic soil habitats, we profiled amplified crenarchaeal 16S rDNA sequences from diverse soil ecosystems by using PCR-single-stranded-conformation polymorphism (PCR-SSCP) analysis. PCR-SSCP profiles provide a measure of relative microbial diversity in terms of richness (number of different phylotypes as estimated from the number of unique PCR-SSCP peaks) and evenness (abundance of each phylotype as estimated from the relative area under a peak). Crenarchaeal assemblages inhabiting prairie, forest, turf, and agricultural soils were characterized at six sampling locations in southern and central Wisconsin. Phylotype richness was found to be more stable than evenness among triplicate samples collected within 30 cm at each sampling location. Transformation of the PCR-SSCP data by principal-component analysis, followed by statistical testing (analysis of variance [
P
< 0.0001] and least-significant-difference analysis [α = 0.5]), supported the conclusion that each location exhibited a unique profile. To further characterize the spatial distribution of crenarchaeal assemblages at one location, additional soil samples (a total of 30) were collected from agricultural field plots at the Hancock Agricultural Research Station. PCR-SSCP revealed a patchy spatial distribution of crenarchaeal assemblages within and between these plots. This mosaic of crenarchaeal assemblages was characterized by differences in phylotype evenness that could not be correlated with horizontal distance (15 to 30 m) or with depth (0 to 20 cm below the surface). Crenarchaeal 16S rDNA clone libraries were produced and screened for unique SSCP peaks. Clones representing the dominant phylotypes at each location were identified, sequenced, and found to group phylogenetically with sequences in crenarchaeal clade C1b.
Comparison of Crenarchaeal Consortia Inhabiting the Rhizosphere of Diverse Terrestrial Plants with Those in Bulk Soil in Native Environments
Authors: Sliwinski Marek K. , Goodman Robert M. 
Published: March 2004

ABSTRACT

To explore whether the crenarchaeal consortium found in the rhizosphere is distinct from the assemblage of crenarchaeotes inhabiting bulk soil, PCR-single-stranded-conformation polymorphism (PCR-SSCP) profiles were generated for 76 plant samples collected from native environments. Divergent terrestrial plant groups including bryophytes (mosses), lycopods (club mosses), pteridophytes (ferns), gymnosperms (conifers), and angiosperms (seed plants) were collected for this study. Statistical analysis revealed significant differences between rhizosphere and bulk soil PCR-SSCP profiles (Hotelling paired T
2
test,
P
< 0.0001), suggesting that a distinct crenarchaeal consortium is associated with plants. In general, phylotype richness increased in the rhizosphere compared to the corresponding bulk soil, although the range of this increase was variable. Examples of a major change in rhizosphere (versus bulk soil) PCR-SSCP profiles were detected for all plant groups, suggesting that crenarchaeotes form associations with phylogenetically diverse plants in native environments. In addition, examples of minor to no detectable difference were found for all terrestrial plant groups, suggesting that crenarchaeal associations with plants are mediated by environmental conditions.
Detection of
Cryptosporidium parvum
in Soil Extracts
Authors: Walker Mark , Redelman Douglas 
Published: March 2004

ABSTRACT

Epifluorescent microscopy and flow cytometry were used in different combinations with fluorescein isothiocyanate-labeled immunoglobulins M and G3 to estimate the numbers of
Cryptosporidium parvum
oocysts in soil extracts containing 10 to 10,017 oocysts/ml. No combination had a systematic effect on accuracy or precision. Background debris may have produced overestimates at low oocyst concentrations when flow cytometry was used.
Detection of
Escherichia coli
Serogroups O26 and O113 by PCR Amplification of the
wzx
and
wzy
Genes
Authors: DebRoy Chitrita , Roberts Elisabeth , Kundrat James , Davis Michael A. , Briggs Connie E. , Fratamico Pina M. 
Published: March 2004

ABSTRACT

PCR-based assays for detecting enterohemorrhagic
Escherichia coli
serogroups O26 and O113 were developed by targeting the
wzx
(O-antigen flippase) and the
wzy
(O-antigen polymerase) genes found in the O-antigen gene cluster of each organism. The PCR assays were specific for the respective serogroups, as there was no amplification of DNA from non-O26 and non-O113
E. coli
serogroups or from other bacterial genera tested. Using the PCR assays, we were able to detect the organisms in seeded apple juice inoculated at concentration levels as low as ≤10 CFU/ml. The O26- and O113-specific PCR assays can potentially be used for typing
E. coli
O26 and O113 serogroups; these assays will offer an advantage to food and environmental microbiology laboratories in terms of identifying these non-O157 serogroups by replacing antigen-based serotyping.
Inactivation of
Vibrio parahaemolyticus
in Effluent Seawater by Alternating-Current Treatment
Authors: Park Jong-Chul , Lee Min Sub , Han Dong-Wook , Lee Dong Hee , Park Bong Joo , Lee In-Seop , Uzawa Masakazu , Aihara Maki , Takatori Kosuke 
Published: March 2004

ABSTRACT

Vibrio parahaemolyticus
, the cause of gastroenteritis in humans, was inactivated by alternating low-amperage electricity. In this study, the application of alternating low-amperage electric treatment to effluent seawater was investigated for the large-scale disinfection of seawater. This method was able to overcome the problem of chlorine generation that results from treatment with continuous direct current. In conclusion, our results showed that alternating-current treatment inactivates
V. parahaemolyticus
in effluent seawater while minimizing the generation of chlorine and that this alternating-current treatment is therefore suitable for practical industrial applications.
Potential Role of Pathogen Signaling in Multitrophic Plant-Microbe Interactions Involved in Disease Protection
Authors: Duffy Brion , Keel Christoph , Défago Geneviève 
Published: March 2004

ABSTRACT

Multitrophic interactions mediate the ability of fungal pathogens to cause plant disease and the ability of bacterial antagonists to suppress disease. Antibiotic production by antagonists, which contributes to disease suppression, is known to be modulated by abiotic and host plant environmental conditions. Here, we demonstrate that a pathogen metabolite functions as a negative signal for bacterial antibiotic biosynthesis, which can determine the relative importance of biological control mechanisms available to antagonists and which may also influence fungus-bacterium ecological interactions. We found that production of the polyketide antibiotic 2,4-diacetylphloroglucinol (DAPG) was the primary biocontrol mechanism of
Pseudomonas fluorescens
strain Q2-87 against
Fusarium oxysporum
f. sp.
radicis-lycopersici
on the tomato as determined with mutational analysis. In contrast, DAPG was not important for the less-disease-suppressive strain CHA0. This was explained by differential sensitivity of the bacteria to fusaric acid, a pathogen phyto- and mycotoxin that specifically blocked DAPG biosynthesis in strain CHA0 but not in strain Q2-87. In CHA0, hydrogen cyanide, a biocide not repressed by fusaric acid, played a more important role in disease suppression.
Reappraisal of the Regulation of Lactococcal
l
-Lactate Dehydrogenase
Authors: van Niel Ed W. J. , Palmfeldt Johan , Martin Rani , Paese Marco , Hahn-Hägerdal Bärbel 
Published: March 2004

ABSTRACT

Lactococcal lactate dehydrogenases (LDHs) are coregulated at the substrate level by at least two mechanisms: the fructose-1,6-biphosphate/phosphate ratio and the NADH/NAD ratio. Among the
Lactococcus lactis
species, there are strains that are predominantly regulated by the first mechanism (e.g., strain 65.1) or by the second mechanism (e.g., strain NCDO 2118). A more complete model of the kinetics of the regulation of lactococcal LDH is discussed.
Differential Expression of
Desulfovibrio vulgaris
Genes in Response to Cu(II) and Hg(II) Toxicity
Authors: Chang In Seop , Groh Jennifer L. , Ramsey Matthew M. , Ballard Jimmy D. , Krumholz Lee R. 
Published: March 2004

ABSTRACT

The response of
Desulfovibrio vulgaris
to Cu(II) and Hg(II) was characterized. Both metals increased the lag phase, and Cu(II) reduced cell yield at concentrations as low as 50 μM. mRNA expression was analyzed using random arbitrarily primed PCR, differential display, and quantitative PCR. Both Cu(II) and Hg(II) (50 μM) caused upregulation of mRNA expression for an ATP binding protein (ORF2004) and an ATPase (ORF856) with four- to sixfold increases for Hg(II) and 1.4- to 3-fold increases with Cu(II). These results suggest that
D. vulgaris
uses an ATP-dependent mechanism for adapting to toxic metals in the environment.
In Planta Production of Indole-3-Acetic Acid by
Colletotrichum gloeosporioides
f. sp.
aeschynomene
Authors: Maor Rudy , Haskin Sefi , Levi-Kedmi Hagit , Sharon Amir 
Published: March 2004

ABSTRACT

The plant pathogenic fungus
Colletotrichum gloeosporioides
f. sp
. aeschynomene
utilizes external tryptophan to produce indole-3-acetic acid (IAA) through the intermediate indole-3-acetamide (IAM). We studied the effects of tryptophan, IAA, and IAM on IAA biosynthesis in fungal axenic cultures and on in planta IAA production by the fungus. IAA biosynthesis was strictly dependent on external tryptophan and was enhanced by tryptophan and IAM. The fungus produced IAM and IAA in planta during the biotrophic and necrotrophic phases of infection. The amounts of IAA produced per fungal biomass were highest during the biotrophic phase. IAA production by this plant pathogen might be important during early stages of plant colonization.
Evaluation of a Real-Time PCR Kit for Detecting
Escherichia coli
O157 in Bovine Fecal Samples
Authors: Bono James L. , Keen James E. , Miller Laura C. , Fox James M. , Chitko-McKown Carol G. , Heaton Michael P. , Laegreid William W. 
Published: March 2004

ABSTRACT

A commercially available real-time, rapid PCR test was evaluated for its ability to detect
Escherichia coli
O157. Both the sensitivity and specificity of the assay were 99% for isolates in pure culture. The assay detected 1 CFU of
E. coli
O157:H7 g
−1
in artificially inoculated bovine feces following enrichment.
thyA
as a Selection Marker in Construction of Food-Grade Host-Vector and Integration Systems for
Streptococcus thermophilus
Authors: Sasaki Yasuko , Ito Yoshiyuki , Sasaki Takashi 
Published: March 2004

ABSTRACT

We constructed food-grade host-vector and integration systems for
Streptococcus thermophilus
by using a thymidylate synthase gene (
thyA
) as the selection marker. Two
thyA
genes,

thyA
St

and

thyA
Lb

, were cloned from
S. thermophilus
and
Lactobacillus delbrueckii
subsp.
bulgaricus
, respectively. Thymidine-requiring mutants of
S. thermophilus
were obtained after successive cultures in the presence of trimethoprim, and one of them, TM1-1, was used as the host. Food-grade vectors were constructed by using either

thyA
St

or

thyA
Lb

as the selection marker. Transformants of TM1-1 created by using these vectors were selected for thymidine autotrophy as efficiently as for erythromycin resistance. By using the host-vector system developed in this way, a foreign amylase gene (
amyA
) was expressed in TM1-1 and was also integrated into the chromosome by use of a temperature-sensitive integration vector constructed with

thyA
Lb

as the selection marker via a double-crossover event. The results obtained show that
thyA
is an efficient and safe selection marker for
S. thermophilus
that is suitable for food applications.
Arsenite-Oxidizing
Hydrogenobaculum
Strain Isolated from an Acid-Sulfate-Chloride Geothermal Spring in Yellowstone National Park
Authors: Donahoe-Christiansen Jessica , D'Imperio Seth , Jackson Colin R. , Inskeep William P. , McDermott Timothy R. 
Published: March 2004

ABSTRACT

An arsenite-oxidizing
Hydrogenobaculum
strain was isolated from a geothermal spring in Yellowstone National Park, Wyo., that was previously shown to contain microbial populations engaged in arsenite oxidation. The isolate was sensitive to both arsenite and arsenate and behaved as an obligate chemolithoautotroph that used H
2
as its sole energy source and had an optimum temperature of 55 to 60°C and an optimum pH of 3.0. The arsenite oxidation in this organism displayed saturation kinetics and was strongly inhibited by H
2
S.
l
-Alanine Auxotrophy of
Lactobacillus johnsonii
as Demonstrated by Physiological, Genomic, and Gene Complementation Approaches
Authors: van der Kaaij Hengameh , Desiere Frank , Mollet Beat , Germond Jacques-Edouard 
Published: March 2004

ABSTRACT

Using a chemically defined medium without
l
-alanine,
Lactobacillus johnsonii
was demonstrated to be strictly auxotrophic for that amino acid. A comparative genetic analysis showed that all known genes involved in
l
-alanine biosynthesis are absent from the genome of
L. johnsonii
. This auxotrophy was complemented by heterologous expression of the
Bacillus subtilis
l
-alanine dehydrogenase.
Nocardia
sp. Carboxylic Acid Reductase: Cloning, Expression, and Characterization of a New Aldehyde Oxidoreductase Family
Authors: He Aimin , Li Tao , Daniels Lacy , Fotheringham Ian , Rosazza John P. N. 
Published: March 2004

ABSTRACT

We have cloned, sequenced, and expressed the gene for a unique ATP- and NADPH-dependent carboxylic acid reductase (CAR) from a
Nocardia
species that reduces carboxylic acids to their corresponding aldehydes. Recombinant CAR containing an N-terminal histidine affinity tag had

K
m

values for benzoate, ATP, and NADPH that were similar to those for natural CAR, and recombinant CAR reduced benzoic, vanillic, and ferulic acids to their corresponding aldehydes.
car
is the first example of a new gene family encoding oxidoreductases with remote acyl adenylation and reductase sites.
Lessons from the Genome Sequence ofNeurospora crassa: Tracing the Path from Genomic Blueprint to Multicellular Organism
Authors: Borkovich Katherine A. , Alex Lisa A. , Yarden Oded , Freitag Michael , Turner Gloria E. , Read Nick D. , Seiler Stephan , Bell-Pedersen Deborah , Paietta John , Plesofsky Nora , Plamann Michael , Goodrich-Tanrikulu Marta , Schulte Ulrich , Mannhaupt Gertrud , Nargang Frank E. , Radford Alan , Selitrennikoff Claude , Galagan James E. , Dunlap Jay C. , Loros Jennifer J. , Catcheside David , Inoue Hirokazu , Aramayo Rodolfo , Polymenis Michael , Selker Eric U. , Sachs Matthew S. , Marzluf George A. , Paulsen Ian , Davis Rowland , Ebbole Daniel J. , Zelter Alex , Kalkman Eric R. , O'Rourke Rebecca , Bowring Frederick , Yeadon Jane , Ishii Chizu , Suzuki Keiichiro , Sakai Wataru , Pratt Robert 
Published: March 2004

SUMMARYWe present an analysis of over 1,100 of the ∼10,000 predicted proteins encoded by the genome sequence of the filamentous fungusNeurospora crassa. Seven major areas ofNeurosporagenomics and biology are covered. First, the basic features of the genome, including the automated assembly, gene calls, and global gene analyses are summarized. The second section covers components of the centromere and kinetochore complexes, chromatin assembly and modification, and transcription and translation initiation factors. The third area discusses genome defense mechanisms, including repeat induced point mutation, quelling and meiotic silencing, and DNA repair and recombination. In the fourth section, topics relevant to metabolism and transport include extracellular digestion; membrane transporters; aspects of carbon, sulfur, nitrogen, and lipid metabolism; the mitochondrion and energy metabolism; the proteasome; and protein glycosylation, secretion, and endocytosis. Environmental sensing is the focus of the fifth section with a treatment of two-component systems; GTP-binding proteins; mitogen-activated protein, p21-activated, and germinal center kinases; calcium signaling; protein phosphatases; photobiology; circadian rhythms; and heat shock and stress responses. The sixth area of analysis is growth and development; it encompasses cell wall synthesis, proteins important for hyphal polarity, cytoskeletal components, the cyclin/cyclin-dependent kinase machinery, macroconidiation, meiosis, and the sexual cycle. The seventh section covers topics relevant to animal and plant pathogenesis and human disease. The results demonstrate that a large proportion ofNeurosporagenes do not have homologues in the yeastsSaccharomyces cerevisiaeandSchizosaccharomyces pombe. The group of unshared genes includes potential new targets for antifungals as well as loci implicated in human and plant physiology and disease.
Eukaryotic MCM Proteins: Beyond Replication Initiation
Authors: Forsburg Susan L. 
Published: March 2004

SUMMARYThe minichromosome maintenance (or MCM) protein family is composed of six related proteins that are conserved in all eukaryotes. They were first identified by genetic screens in yeast and subsequently analyzed in other experimental systems using molecular and biochemical methods. Early data led to the identification of MCMs as central players in the initiation of DNA replication. More recent studies have shown that MCM proteins also function in replication elongation, probably as a DNA helicase. This is consistent with structural analysis showing that the proteins interact together in a heterohexameric ring. However, MCMs are strikingly abundant and far exceed the stoichiometry of replication origins; they are widely distributed on unreplicated chromatin. Analysis ofmcmmutant phenotypes and interactions with other factors have now implicated the MCM proteins in other chromosome transactions including damage response, transcription, and chromatin structure. These experiments indicate that the MCMs are central players in many aspects of genome stability.
Diversity of Microbial Sialic Acid Metabolism
Authors: Vimr Eric R. , Kalivoda Kathryn A. , Deszo Eric L. , Steenbergen Susan M. 
Published: March 2004

SUMMARY

Sialic acids are structurally unique nine-carbon keto sugars occupying the interface between the host and commensal or pathogenic microorganisms. An important function of host sialic acid is to regulate innate immunity, and microbes have evolved various strategies for subverting this process by decorating their surfaces with sialylated oligosaccharides that mimic those of the host. These subversive strategies include a de novo synthetic pathway and at least two truncated pathways that depend on scavenging host-derived intermediates. A fourth strategy involves modification of sialidases so that instead of transferring sialic acid to water (hydrolysis), a second active site is created for binding alternative acceptors. Sialic acids also are excellent sources of carbon, nitrogen, energy, and precursors of cell wall biosynthesis. The catabolic strategies for exploiting host sialic acids as nutritional sources are as diverse as the biosynthetic mechanisms, including examples of horizontal gene transfer and multiple transport systems. Finally, as compounds coating the surfaces of virtually every vertebrate cell, sialic acids provide information about the host environment that, at least in
Escherichia coli
, is interpreted by the global regulator encoded by
nanR
. In addition to regulating the catabolism of sialic acids through the
nan
operon, NanR controls at least two other operons of unknown function and appears to participate in the regulation of type 1 fimbrial phase variation. Sialic acid is, therefore, a host molecule to be copied (molecular mimicry), eaten (nutrition), and interpreted (cell signaling) by diverse metabolic machinery in all major groups of mammalian pathogens and commensals.
Iron Transport Systems in
Neisseria meningitidis
Authors: Perkins-Balding Donna , Ratliff-Griffin Melanie , Stojiljkovic Igor 
Published: March 2004

SUMMARY

Acquisition of iron and iron complexes has long been recognized as a major determinant in the pathogenesis of
Neisseria meningitidis
. In this review, high-affinity iron uptake systems, which allow meningococci to utilize the human host proteins transferrin, lactoferrin, hemoglobin, and haptoglobin-hemoglobin as sources of essential iron, are described. Classic features of bacterial iron transport systems, such as regulation by the iron-responsive repressor Fur and TonB-dependent transport activity, are discussed, as well as more specific features of meningococcal iron transport. Our current understanding of how
N. meningitidis
acquires iron from the human host and the vaccine potentials of various components of these iron transport systems are also reviewed.
Children, Childhoods, and Violence
Authors: Korbin Jill E. 
Published: March 2004

▪ Abstract  Anthropological literature on children and violence has been constrained by similar considerations that have limited an anthropology of childhood more generally, and by difficulties in conceptualizing children both as victims of violence and as violent themselves. A review of the anthropological literature on violence directed toward children reveals a litany of violence to which children may be subjected that includes child abuse and neglect, bullying, violent cultural rites, warfare, and structural violence stemming from poverty and inequality. Aggression in childhood has been the subject of a robust and long-standing literature that has examined socialization for or against aggressive behavior in children. An emerging literature considers children's own violent behavior from the perspective of child agency. Children's own voices and perspectives have been largely absent from the anthropological literature on childhood and violence. This review highlights several issues at the intersection of childhood and violence that demand a synthesis and reformulation in anthropology.“There is a growing consciousness of children at risk … there is also a growing sense of children themselves as the risk …”     ( Stephens 1995 , p. 13)