bluuebunny/crossref_metadata_2025_split huggingface dataset:
Resuscitation of
Salmonella enterica
Serovar Typhimurium and Enterohemorrhagic
Escherichia coli
from the Viable but Nonculturable State by Heat-Stable Enterobacterial Autoinducer
Authors: Reissbrodt R. , Rienaecker I. , Romanova J. M. , Freestone P. P. E. , Haigh R. D. , Lyte M. , Tschäpe H. , Williams P. H. 
Published: September 2002

ABSTRACT

Salmonella enterica
serovar Typhimurium and enterohemorrhagic
Escherichia coli
were stressed by prolonged incubation in water microcosms until it was no longer possible to observe colony formation when samples were plated on nonselective medium. Overnight incubation of samples in nutrient-rich broth medium supplemented with growth factors, however, allowed resuscitation of stressed and viable but nonculturable cells so that subsequent plating yielded observable colonies for significantly extended periods of time. The growth factors were (i) the trihydroxamate siderophore ferrioxamine E (for
Salmonella
only), (ii) the commercially available antioxidant Oxyrase, and (iii) the heat-stable autoinducer of growth secreted by enterobacterial species in response to norepinephrine. Analysis of water microcosms with the Bioscreen C apparatus confirmed that these supplements enhanced recovery of cells in stressed populations; enterobacterial autoinducer was the most effective, promoting resuscitation in populations that were so heavily stressed that ferrioxamine E or Oxyrase had no effect. Similar results were observed in Bioscreen analysis of bacterial populations stressed by heating. Patterns of resuscitation of
S. enterica
serovar Typhimurium
rpoS
mutants from water microcosms and heat stress were qualitatively similar, suggesting that the general stress response controlled by the σ
s
subunit of RNA polymerase plays no role in autoinducer-dependent resuscitation. Enterobacterial autoinducer also resuscitated stressed populations of
Citrobacter freundii
and
Enterobacter agglomerans
.
Anaerobic Oxidation of Arsenite in Mono Lake Water and by a Facultative, Arsenite-Oxidizing Chemoautotroph, Strain MLHE-1
Authors: Oremland Ronald S. , Hoeft Shelley E. , Santini Joanne M. , Bano Nasreen , Hollibaugh Ryan A. , Hollibaugh James T. 
Published: September 2002

ABSTRACT

Arsenite [As(III)]-enriched anoxic bottom water from Mono Lake, California, produced arsenate [As(V)] during incubation with either nitrate or nitrite. No such oxidation occurred in killed controls or in live samples incubated without added nitrate or nitrite. A small amount of biological As(III) oxidation was observed in samples amended with Fe(III) chelated with nitrolotriacetic acid, although some chemical oxidation was also evident in killed controls. A pure culture, strain MLHE-1, that was capable of growth with As(III) as its electron donor and nitrate as its electron acceptor was isolated in a defined mineral salts medium. Cells were also able to grow in nitrate-mineral salts medium by using H
2
or sulfide as their electron donor in lieu of As(III). Arsenite-grown cells demonstrated dark
14
CO
2
fixation, and PCR was used to indicate the presence of a gene encoding ribulose-1,5-biphosphate carboxylase/oxygenase. Strain MLHE-1 is a facultative chemoautotroph, able to grow with these inorganic electron donors and nitrate as its electron acceptor, but heterotrophic growth on acetate was also observed under both aerobic and anaerobic (nitrate) conditions. Phylogenetic analysis of its 16S ribosomal DNA sequence placed strain MLHE-1 within the haloalkaliphilic
Ectothiorhodospira
of the γ-
Proteobacteria
. Arsenite oxidation has never been reported for any members of this subgroup of the
Proteobacteria
.
Replacement of Trifluoroacetic Acid with HCl in the Hydrophobic Purification Steps of Pediocin PA-1: a Structural Effect
Authors: Gaussier Hélène , Morency Hélène , Lavoie Marc C. , Subirade Muriel 
Published: September 2002

ABSTRACT
Trifluoroacetic acid (TFA) is a purification contaminant associated with pediocin PA-1 that interferes with Fourier transform infrared spectroscopy structural analysis. As revealed by circular dichroism, its presence affects the structural folding of pediocin. Consequently, we propose a new pediocin PA-1 purification procedure using HCl instead of TFA in all of the hydrophobic steps. This procedural change does not affect the purification yield or the amount of pediocin PA-1 purified. Furthermore, removing HCl, as opposed to TFA, after purification is an easier procedure to carry out. In fact, the removal of TFA requires more experimentation and results in protein loss. Thus, HCl is a good alternative to TFA in pediocin PA-1 purification and can be extended to the purification of other proteins. We also show that TFA-induced structural modifications do not significantly affect the antimicrobial activity of pediocin PA-1.
Sequencing and Transcriptional Analysis of the Chlorite Dismutase Gene of
Dechloromonas agitata
and Its Use as a Metabolic Probe
Authors: Bender Kelly S. , O'Connor Susan M. , Chakraborty Romy , Coates John D. , Achenbach Laurie A. 
Published: September 2002

ABSTRACT

The dismutation of chlorite into chloride and O
2
represents a central step in the reductive pathway of perchlorate that is common to all dissimilatory perchlorate-reducing bacteria and is mediated by a single enzyme, chlorite dismutase. The chlorite dismutase gene
cld
was isolated and sequenced from the perchlorate-reducing bacterium
Dechloromonas agitata
strain CKB. Sequence analysis identified an open reading frame of 834 bp that would encode a mature protein with an N-terminal sequence identical to that of the previously purified
D. agitata
chlorite dismutase enzyme. The predicted translation product of the
D. agitata cld
gene is a protein of 277 amino acids (aa), including a leader peptide of 26 aa. Primer extension analysis identified a single transcription start site directly downstream of an AT-rich region that could represent the −10 promoter region of the
D. agitata cld
gene. Northern blot analysis indicated that the
cld
gene was transcriptionally up-regulated when
D. agitata
cells were grown in perchlorate-reducing versus aerobic conditions. Slot blot hybridizations with a
D. agitata cld
probe demonstrated the conservation of the
cld
gene among perchlorate-reducing bacteria. This study represents the first description of a functional gene associated with microbial perchlorate reduction.
Identification of a Hydratase and a Class II Aldolase Involved in Biodegradation of the Organic Solvent Tetralin
Authors: Hernáez M. J. , Floriano B. , Ríos J. J. , Santero E. 
Published: September 2002

ABSTRACT

Two new genes whose products are involved in biodegradation of the organic solvent tetralin were identified. These genes, designated
thnE
and
thnF
, are located downstream of the previously identified
thnD
gene and code for a hydratase and an aldolase, respectively. A sequence comparison of enzymes similar to ThnE showed the significant similarity of hydratases involved in biodegradation pathways to 4-oxalocrotonate decarboxylases and established four separate groups of related enzymes. Consistent with the sequence information, characterization of the reaction catalyzed by ThnE showed that it hydrated a 10-carbon dicarboxylic acid. The only reaction product detected was the enol tautomer, 2,4-dihydroxydec-2-ene-1,10-dioic acid. The aldolase ThnF showed significant similarity to aldolases involved in different catabolic pathways whose substrates are dihydroxylated dicarboxylic acids and which yield pyruvate and a semialdehyde. The reaction products of the aldol cleavage reaction catalyzed by ThnF were identified as pyruvate and the seven-carbon acid pimelic semialdehyde. ThnF and similar aldolases showed conservation of the active site residues identified by the crystal structure of 2-dehydro-3-deoxy-galactarate aldolase, a class II aldolase with a novel reaction mechanism, suggesting that these similar enzymes are class II aldolases. In contrast, ThnF did not show similarity to 4-hydroxy-2-oxovalerate aldolases of other biodegradation pathways, which are significantly larger and apparently are class I aldolases.
Prevalence and Characterization of Non-O157 Shiga Toxin-Producing
Escherichia coli
on Carcasses in Commercial Beef Cattle Processing Plants
Authors: Arthur Terrance M. , Barkocy-Gallagher Genevieve A. , Rivera-Betancourt Mildred , Koohmaraie Mohammad 
Published: September 2002

ABSTRACT

Beef carcass sponge samples collected from July to August 1999 at four large processing plants in the United States were surveyed for the presence of non-O157 Shiga toxin-producing
Escherichia coli
(STEC). Twenty-eight (93%) of 30 single-source lots surveyed included at least one sample containing non-O157 STEC. Of 334 carcasses sampled prior to evisceration, 180 (54%) were found to harbor non-O157 STEC. Non-O157 STEC isolates were also recovered from 27 (8%) of 326 carcasses sampled after the application of antimicrobial interventions. Altogether, 361 non-O157 STEC isolates, comprising 41 different O serogroups, were recovered. O serogroups that previously have been associated with human disease accounted for 178 (49%) of 361 isolates. Although 40 isolates (11%) carried a combination of virulence factor genes (enterohemorrhagic
E. coli hlyA
,
eae
, and at least one
stx
gene) frequently associated with STEC strains causing severe human disease, only 12 of these isolates also belonged to an O serogroup previously associated with human disease. Combining previously reported data on O157-positive samples (R. O. Elder, J. E. Keen, G. R. Siragusa, G. A. Barkocy-Gallagher, M. Koohmaraie, and W. W. Laegreid, Proc. Natl. Acad. Sci. USA 97:2999-3003, 2000) with these data regarding non-O157-positive samples indicated total STEC prevalences of 72 and 10% in preevisceration and postprocessing beef carcass samples, respectively, showing that the interventions used by the beef-processing industry effected a sevenfold reduction in carcass contamination by STEC.
Multiplex Fluorogenic Real-Time PCR for Detection and Quantification ofEscherichia coliO157:H7 in Dairy Wastewater Wetlands
Authors: Ibekwe A. Mark , Watt Pamela M. , Grieve Catherine M. , Sharma Vijay K. , Lyons Steven R. 
Published: September 2002

ABSTRACTSurface water and groundwater are continuously used as sources of drinking water in many metropolitan areas of the United States. The quality of water from these sources may be reduced due to increases in contaminants such asEscherichia colifrom urban and agricultural runoffs. In this study, a multiplex fluorogenic PCR assay was used to quantifyE. coliO157:H7 in soil, manure, cow and calf feces, and dairy wastewater in an artificial wetland. Primers and probes were designed to amplify and quantify the Shiga-like toxin 1 (stx1) and 2 (stx2) genes and the intimin (eae)gene ofE. coliO157:H7 in a single reaction. Primer specificity was confirmed with DNA from 33E. coliO157:H7 and related strains with and without the three genes. A direct correlation was determined between the fluorescence threshold cycle (CT) and the starting quantity ofE. coliO157:H7 DNA. A similar correlation was observed between theCTand number of CFU per milliliter used in the PCR assay. A detection limit of 7.9 × 10−5pg ofE. coliO157:H7 DNA ml−1equivalent to approximately 6.4 × 103CFU ofE. coliO157:H7 ml−1based on plate counts was determined. Quantification ofE. coliO157:H7 in soil, manure, feces, and wastewater was possible when cell numbers were ≥3.5 × 104CFU g−1.E. coliO157:H7 levels detected in wetland samples decreased by about 2 logs between wetland influents and effluents. The detection limit of the assay in soil was improved to less than 10 CFU g−1with a 16-h enrichment. These results indicate that the developed PCR assay is suitable for quantitative determination ofE. coliO157:H7 in environmental samples and represents a considerable advancement in pathogen quantification in different ecosystems.
Biotransformation of 2-Benzoxazolinone and 2-Hydroxy-1,4-Benzoxazin-3-one by Endophytic Fungi Isolated from
Aphelandra tetragona
Authors: Zikmundová M. , Drandarov K. , Bigler L. , Hesse M. , Werner C. 
Published: September 2002

ABSTRACT

The biotransformation of the phytoanticipins 2-benzoxazolinone (BOA) and 2-hydroxy-1,4-benzoxazin-3-one (HBOA) by four endophytic fungi isolated from
Aphelandra tetragona
was studied. Using high-performance liquid chromatography-mass spectrometry, several new products of acylation, oxidation, reduction, hydrolysis, and nitration were identified.
Fusarium sambucinum
detoxified BOA and HBOA to
N
-(2-hydroxyphenyl)malonamic acid.
Plectosporium tabacinum
,
Gliocladium cibotii
, and
Chaetosphaeria
sp. transformed HBOA to 2-hydroxy-
N
-(2-hydroxyphenyl)acetamide,
N
-(2-hydroxyphenyl)acetamide,
N
-(2-hydroxy-5-nitrophenyl)acetamide,
N
-(2-hydroxy-3-nitrophenyl)acetamide, 2-amino-3
H
-phenoxazin-3-one, 2-acetylamino-3
H
-phenoxazin-3-one, and 2-(
N
-hydroxy)acetylamino-3
H
-phenoxazin-3-one. BOA was not degraded by these three fungal isolates. Using 2-hydroxy-
N
-(2-hydroxyphenyl)[
13
C
2
]acetamide, it was shown that the metabolic pathway for HBOA and BOA degradation leads to
o
-aminophenol as a key intermediate.
Yeast Diversity and Persistence in Botrytis-Affected Wine Fermentations
Authors: Mills David A. , Johannsen Eric A. , Cocolin Luca 
Published: September 2002

ABSTRACTCulture-dependent and -independent methods were used to examine the yeast diversity present in botrytis-affected (“botrytized”) wine fermentations carried out at high (∼30°C) and ambient (∼20°C) temperatures. Fermentations at both temperatures possessed similar populations ofSaccharomyces,Hanseniaspora,Pichia,Metschnikowia,Kluyveromyces, andCandidaspecies. However, higher populations of non-Saccharomycesyeasts persisted in ambient-temperature fermentations, withCandidaand, to a lesser extent,Kluyveromycesspecies remaining long after the fermentation was dominated bySaccharomyces. In general, denaturing gradient gel electrophoresis profiles of yeast ribosomal DNA or rRNA amplified from the fermentation samples correlated well with the plating data. The direct molecular methods also revealed aHanseniaspora osmophilapopulation not identified in the plating analysis. rRNA analysis also indicated a large population (>106cells per ml) of a nonculturableCandidastrain in the high-temperature fermentation. Monoculture analysis of theCandidaisolate indicated an extreme fructophilic phenotype and correlated with an increased glucose/fructose ratio in fermentations containing higher populations ofCandida. Analysis of wine fermentation microbial ecology by using both culture-dependent and -independent methods reveals the complexity of yeast interactions enriched during spontaneous fermentations.
Bacillus thuringiensis
in Fecal Samples from Greenhouse Workers after Exposure to
B. thuringiensis
-Based Pesticides
Authors: Jensen Gert B. , Larsen Preben , Jacobsen Bodil L. , Madsen Bodil , Smidt Lasse , Andrup Lars 
Published: September 2002

ABSTRACT

In a study of occupational exposure to
Bacillus thuringiensis
, 20 exposed greenhouse workers were examined for
Bacillus cereus
-like bacteria in fecal samples and on biomonitoring filters. Bacteria with the following characteristics were isolated from eight individuals: intracellular crystalline inclusions characteristic of
B. thuringiensis
, genes for and production of
B. cereus
enterotoxins, and positivity for
cry11
as determined by PCR. DNA fingerprints of the fecal isolates were identical to those of strains isolated from the commercial products used. Work processes (i.e., spraying) correlated with the presence of
B. thuringiensis
in the fecal samples (10
2
to 10
3
CFU/g of feces). However, no gastrointestinal symptoms correlated with the presence of
B. thuringiensis
in the fecal samples.
Diversity of Endophytic Bacterial Populations and Their Interaction withXylella fastidiosain Citrus Plants
Authors: Araújo Welington L. , Marcon Joelma , Maccheroni Walter , van Elsas Jan Dirk , van Vuurde Jim W. L. , Azevedo João Lúcio 
Published: September 2002

ABSTRACTCitrus variegated chlorosis (CVC) is caused byXylella fastidiosa, a phytopathogenic bacterium that can infect allCitrus sinensiscultivars. The endophytic bacterial communities of healthy, resistant, and CVC-affected citrus plants were studied by using cultivation as well as cultivation-independent techniques. The endophytic communities were assessed in surface-disinfected citrus branches by plating and denaturing gradient gel electrophoresis (DGGE). Dominant isolates were characterized by fatty-acid methyl ester analysis asBacillus pumilus,Curtobacterium flaccumfaciens,Enterobacter cloacae,Methylobacteriumspp. (includingMethylobacterium extorquens,M. fujisawaense,M. mesophilicum,M. radiotolerans, andM. zatmanii),Nocardiasp.,Pantoea agglomerans, andXanthomonas campestris. We observed a relationship between CVC symptoms and the frequency of isolation of species ofMethylobacterium, the genus that we most frequently isolated from symptomatic plants. In contrast, we isolatedC. flaccumfacienssignificantly more frequently from asymptomatic plants than from those with symptoms of CVC whileP. agglomeranswas frequently isolated from tangerine (Citrus reticulata) and sweet-orange (C. sinensis) plants, irrespective of whether the plants were symptomatic or asymptomatic or showed symptoms of CVC. DGGE analysis of 16S rRNA gene fragments amplified from total plant DNA resulted in several bands that matched those from the bacterial isolates, indicating that DGGE profiles can be used to detect some endophytic bacteria of citrus plants. However, some bands had no match with any isolate, suggesting the occurrence of other, nonculturable or as yet uncultured, endophytic bacteria. A specific band with a high G+C ratio was observed only in asymptomatic plants. The higher frequency ofC. flaccumfaciensin asymptomatic plants suggests a role for this organism in the resistance of plants to CVC.
Phenotypic and Genotypic Characterization of AvianEscherichia coliO86:K61 Isolates Possessing a Gamma-Like Intimin
Authors: La Ragione R. M. , McLaren I. M. , Foster G. , Cooley W. A. , Woodward M. J. 
Published: September 2002

ABSTRACTEscherichia coliO86:K61 has long been associated with outbreaks of infantile diarrhea in humans and with diarrheal disease in many animal species. Studies in the late 1990s identifiedE. coliO86:K61 as the cause of mortality in a variety of wild birds, and in this study, 34E. coliO86:K61 isolates were examined. All of the isolates were nonmotile, but most elaborated at least two morphologically distinct surface appendages that were confirmed to be type 1 and curli fimbriae. Thirty-three isolates were positive for theeaeAgene encoding a gamma type of intimin. No phenotypic or genotypic evidence was obtained for elaboration of Shiga-like toxins, but most isolates possessed the gene coding for the cytolethal distending toxin. Five isolates were selected for adherence assays performed with tissue explants and HEp-2 cells, and four of these strains produced attaching and effacing lesions on HEp-2 cells and invaded the cells, as determined by transmission electron microscopy. Two of the five isolates were inoculated orally into 1-day-old specific-pathogen-free chicks, and both of these isolates colonized, invaded, and persisted well in this model. Neither isolate produced attaching and effacing lesions in chicks, although some pathology was evident in the alimentary tract. No deaths were recorded in inoculated chicks. These findings are discussed in light of the possibility that wild birds are potential zoonotic reservoirs of attaching and effacingE. coli.
Growth-Dependent Stable Carbon Isotope Fractionation by Basidiomycete Fungi: δ
13
C Pattern and Physiological Process
Authors: Henn Matthew R. , Gleixner Gerd , Chapela Ignacio H. 
Published: September 2002

ABSTRACT

We grew 11 basidiomycetes in axenic culture to characterize their physiological capacities to fractionate stable C isotopes. Generally, δ
13
C values of the fungal biomass were (i) enriched in
13
C relative to the growth medium, (ii) variable among the isolates, and (iii) dependent on the growth rate and growth stage of the fungi. We found a multiphasic dynamic of fractionation for
Cryptoporus volvatus
and
Marasmius androsaceus
during various growth stages. The first phase, P1, corresponded to the exponential growth stage and was characterized by an increasing enrichment in
13
C content of the fungal biomass relative to the growth medium ranging between 4.6 and 6.9‰. The second phase, P2, exhibited a continual depletion in
13
C of the fungal biomass, with the δ
13
C values of the fungal biomass asymptotically returning to the δ
13
C value of the growth medium at inoculation. The expression of the various fractionation phases was dependent on the amount of low-concentration micronutrients and growth factors added to the growth medium. The onset of P2 occurred at reduced concentrations of these elements. All of the sugars in the growth medium (sucrose, maltose, and glucose) were utilized for growth, indicating that the observed fractionation was not an artifact derived from the preferential use of
13
C-rich maltose, which was found at low concentrations in the growth medium. In this study, we establish a framework with which to explore the impact of physiological fractionations by fungal interfaces on natural distributions of stable C isotopes.
Accumulation of 2-Aminophenoxazin-3-one-7-Carboxylate during Growth of
Pseudomonas putida
TW3 on 4-Nitro-Substituted Substrates Requires 4-Hydroxylaminobenzoate Lyase (PnbB)
Authors: Hughes Michelle A. , Baggs Michael J. , al-Dulayymi Juma'a , Baird Mark S. , Williams Peter A. 
Published: September 2002

ABSTRACT

During growth of
Pseudomonas putida
strain TW3 on 4-nitrotoluene (4NT) or its metabolite 4-nitrobenzoate (4NB), the culture medium gradually becomes yellow-orange with a λ
max
of 446 nm. The compound producing this color has been isolated and identified as a new phenoxazinone, 2-aminophenoxazin-3-one-7-carboxylate (APOC). This compound is formed more rapidly and in greater quantity when 4-amino-3-hydroxybenzoate (4A3HB) is added to growing cultures of strain TW3 and is also formed nonbiologically when 4A3HB is shaken in mineral salts medium but not in distilled water. It is postulated that APOC is formed by the oxidative dimerization of 4A3HB, although 4A3HB has not been reported to be a metabolite of 4NT or a product of 4NB catabolism by strain TW3. Using the cloned
pnb
structural genes from TW3, we demonstrated that the formation of the phenoxazinone requires 4-hydroxylaminobenzoate lyase (PnbB) activity, which converts 4-hydroxylaminobenzoate (4HAB) to 3,4-dihydroxybenzoate (protocatechuate) and that 4-nitrobenzoate reductase (PnbA) activity, which causes the accumulation of 4HAB from 4NB, does not on its own result in the formation of APOC. This rules out the possibility that 4A3HB is formed abiotically from 4HAB by a Bamberger rearrangement but suggests that PnbB first acts to effect a Bamberger-like rearrangement of 4HAB to 4A3HB followed by the replacement of the 4-amino group by a hydroxyl to form protocatechuate and that the phenoxazinone is produced as a result of some misrouting of the intermediate 4A3HB from its active site.