bluuebunny/crossref_metadata_2025_split huggingface dataset:
Environmental Surveillance System To Track Wild Poliovirus Transmission
Authors: Deshpande Jagadish M. , Shetty Sushmitha J. , Siddiqui Zaeem A. 
Published: May 2003

ABSTRACT
Eradication of poliomyelitis from large metropolis cities in India has been difficult due to high population density and the presence of large urban slums. Three paralytic poliomyelitis cases were reported in Mumbai, India, in 1999 and 2000 in spite of high immunization coverage and good-quality supplementary immunization activities. We therefore established a systematic environmental surveillance study by weekly screening of sewage samples from three high-risk slum areas to detect the silent transmission of wild poliovirus. In 2001, from among the 137 sewage samples tested, wild poliovirus type 1 was isolated from 35 and wild poliovirus type 3 was isolated from 1. Acute flaccid paralysis (AFP) surveillance indicated one case of paralytic poliomyelitis from the city. Phylogenetic analysis with complete VP1 sequences revealed that the isolates from environmental samples belonged to four lineages of wild polioviruses recently isolated from poliomyelitis cases in Uttar Pradesh and not to those previously isolated from AFP cases in Mumbai. Wild poliovirus thus introduced caused one case of paralytic poliomyelitis. The virus was detected in environmental samples 3 months before. It was found that wild polioviruses introduced several times during the year circulated in Mumbai for a limited period before being eliminated. Environmental surveillance was found to be sensitive for the detection of wild poliovirus silent transmission. Nucleotide sequence analysis helped identify wild poliovirus reservoir areas.
An Improved Protocol for Quantification of Freshwater
Actinobacteria
by Fluorescence In Situ Hybridization
Authors: Sekar Raju , Pernthaler Annelie , Pernthaler Jakob , Warnecke Falk , Posch Thomas , Amann Rudolf 
Published: May 2003

ABSTRACT

We tested a previously described protocol for fluorescence in situ hybridization of marine bacterioplankton with horseradish peroxidase-labeled rRNA-targeted oligonucleotide probes and catalyzed reporter deposition (CARD-FISH) in plankton samples from different lakes. The fraction of
Bacteria
detected by CARD-FISH was significantly lower than after FISH with fluorescently monolabeled probes. In particular, the abundances of aquatic
Actinobacteria
were significantly underestimated. We thus developed a combined fixation and permeabilization protocol for CARD-FISH of freshwater samples. Enzymatic pretreatment of fixed cells was optimized for the controlled digestion of gram-positive cell walls without causing overall cell loss. Incubations with high concentrations of lysozyme (10 mg ml
−1
) followed by achromopeptidase (60 U ml
−1
) successfully permeabilized cell walls of
Actinobacteria
for subsequent CARD-FISH both in enrichment cultures and environmental samples. Between 72 and >99% (mean, 86%) of all
Bacteria
could be visualized with the improved assay in surface waters of four lakes. For freshwater samples, our method is thus superior to the CARD-FISH protocol for marine
Bacteria
(mean, 55%) and to FISH with directly fluorochrome labeled probes (mean, 67%). Actinobacterial abundances in the studied systems, as detected by the optimized protocol, ranged from 32 to >55% (mean, 45%). Our findings confirm that members of this lineage are among the numerically most important
Bacteria
of freshwater picoplankton.
Identification of an Emergent and Atypical
Pseudomonas viridiflava
Lineage Causing Bacteriosis in Plants of Agronomic Importance in a Spanish Region
Authors: González Ana J. , Rodicio M. Rosario , Mendoza M. Carmen 
Published: May 2003

ABSTRACT

Pseudomonas
strains with an atypical LOPAT profile (where LOPAT is a series of determinative tests: L, levan production; O, oxidase production; P, pectinolitic activity; A, arginine dihydrolase production; and T, tobacco hypersensibility) can be regarded as emergent pathogens in the Principality of Asturias (Spain), where they have been causing, since 1999, severe damage in at least three taxonomically unrelated orchard plants of agronomic importance: common bean (
Phaseolus vulgaris
), kiwifruit (
Actinidia deliciosa
), and lettuce (
Lactuca sativa
). These strains are mainly differentiated by production of yellowish mucoid material in hypersucrose medium, used for the levan test, and by a variable pectinolytic activity on different potato varieties. The atypical organisms were identified as
Pseudomonas viridiflava
based on their 16S rRNA sequences. Among them a certain intraspecies genetic heterogeneity was detected by randomly amplified polymorphic DNA (RAPD) typing. To differentiate between isolates of
P. viridiflava
and
Pseudomonas syringae
pathovars, a 16S ribosomal DNA restriction fragment length polymorphism method employing the restriction endonucleases
Sac
I and
Hin
fI was developed. This could be used as a means of reliable species determination after the usual phenotypical characterization, which includes the LOPAT tests.
Stable Carbon Isotope Fractionation by Sulfate-Reducing Bacteria
Authors: Londry Kathleen L. , Des Marais David J. 
Published: May 2003

ABSTRACT

Biogeochemical transformations occurring in the anoxic zones of stratified sedimentary microbial communities can profoundly influence the isotopic and organic signatures preserved in the fossil record. Accordingly, we have determined carbon isotope discrimination that is associated with both heterotrophic and lithotrophic growth of pure cultures of sulfate-reducing bacteria (SRB). For heterotrophic-growth experiments, substrate consumption was monitored to completion. Sealed vessels containing SRB cultures were harvested at different time intervals, and δ
13
C values were determined for gaseous CO
2
, organic substrates, and products such as biomass. For three of the four SRB, carbon isotope effects between the substrates, acetate or lactate and CO
2
, and the cell biomass were small, ranging from 0 to 2‰. However, for
Desulfotomaculum acetoxidans
, the carbon incorporated into biomass was isotopically heavier than the available substrates by 8 to 9‰. SRB grown lithoautotrophically consumed less than 3% of the available CO
2
and exhibited substantial discrimination (calculated as isotope fractionation factors [α]), as follows: for
Desulfobacterium autotrophicum
, α values ranged from 1.0100 to 1.0123; for
Desulfobacter hydrogenophilus
, the α value was 0.0138, and for
Desulfotomaculum acetoxidans
, the α value was 1.0310. Mixotrophic growth of
Desulfovibrio desulfuricans
on acetate and CO
2
resulted in biomass with a δ
13
C composition intermediate to that of the substrates. The extent of fractionation depended on which enzymatic pathways were used, the direction in which the pathways operated, and the growth rate, but fractionation was not dependent on the growth phase. To the extent that environmental conditions affect the availability of organic substrates (e.g., acetate) and reducing power (e.g., H
2
), ecological forces can also influence carbon isotope discrimination by SRB.
Sequence versus Structure for the Direct Detection of 16S rRNA on Planar Oligonucleotide Microarrays
Authors: Chandler Darrell P. , Newton Gregory J. , Small Jonathan A. , Daly Don S. 
Published: May 2003

ABSTRACT
A two-probe proximal chaperone detection system consisting of a species-specific capture probe for the microarray and a labeled, proximal chaperone probe for detection was recently described for direct detection of intact rRNAs from environmental samples on oligonucleotide arrays. In this study, we investigated the physical spacing and nucleotide mismatch tolerance between capture and proximal chaperone detector probes that are required to achieve species-specific 16S rRNA detection for the dissimilatory metal and sulfate reducer 16S rRNAs. Microarray specificity was deduced by analyzing signal intensities across replicate microarrays with a statistical analysis-of-variance model that accommodates well-to-well and slide-to-slide variations in microarray signal intensity. Chaperone detector probes located in immediate proximity to the capture probe resulted in detectable, nonspecific binding of nontarget rRNA, presumably due to base-stacking effects. Species-specific rRNA detection was achieved by using a 22-nt capture probe and a 15-nt detector probe separated by 10 to 14 nt along the primary sequence. Chaperone detector probes with up to three mismatched nucleotides still resulted in species-specific capture of 16S rRNAs. There was no obvious relationship between position or number of mismatches and within- or between-genus hybridization specificity. From these results, we conclude that relieving secondary structure is of principal concern for the successful capture and detection of 16S rRNAs on planar surfaces but that the sequence of the capture probe is more important than relieving secondary structure for achieving specific hybridization.
Antimicrobial Effects of Mustard Flour and Acetic Acid against
Escherichia coli
O157:H7,
Listeria monocytogenes
, and
Salmonella enterica
Serovar Typhimurium
Authors: Rhee Min-Suk , Lee Sun-Young , Dougherty Richard H. , Kang Dong-Hyun 
Published: May 2003

ABSTRACT

This study was designed to investigate the individual and combined effects of mustard flour and acetic acid in the inactivation of food-borne pathogenic bacteria stored at 5 and 22°C. Samples were prepared to achieve various concentrations by the addition of acetic acid (0, 0.5, or 1%) along with mustard flour (0, 10, or 20%) and 2% sodium chloride (fixed amount). Acid-adapted three-strain mixtures of
Escherichia coli
O157:H7,
Listeria monocytogenes
, and
Salmonella enterica
serovar Typhimurium strains (10
6
to 10
7
CFU/ml) were inoculated separately into prepared mustard samples stored at 5 and 22°C, and samples were assayed periodically. The order of bacterial resistance, assessed by the time required for the nominated populations to be reduced to undetectable levels against prepared mustards at 5°C, was
S. enterica
serovar Typhimurium (1 day) <
E. coli
O157:H7 (3 days) <
L. monocytogenes
(9 days). The food-borne pathogens tested were reduced much more rapidly at 22°C than at 5°C. There was no synergistic effect with regard to the killing of the pathogens tested with the addition of 0.5% acetic acid to the mustard flour (10 or 20%). Mustard in combination with 0.5% acetic acid had less bactericidal activity against the pathogens tested than did mustard alone. The reduction of
E. coli
O157:H7 and
L. monocytogenes
among the combined treatments on the same storage day was generally differentiated as follows: control < mustard in combination with 0.5% acetic acid < mustard alone < mustard in combination with 1% acetic acid < acetic acid alone. Our study indicates that acidic products may limit microbial growth or survival and that the addition of small amounts of acetic acid (0.5%) to mustard can retard the reduction of
E. coli
O157:H7 and
L. monocytogenes
. These antagonistic effects may be changed if mustard is used alone or in combination with >1% acetic acid.
Characterization of Two Tetrachloroethene-Reducing, Acetate-Oxidizing Anaerobic Bacteria and Their Description asDesulfuromonas michiganensissp. nov
Authors: Sung Youlboong , Ritalahti Kirsti M. , Sanford Robert A. , Urbance John W. , Flynn Shannon J. , Tiedje James M. , Löffler Frank E. 
Published: May 2003

ABSTRACTTwo tetrachlorethene (PCE)-dechlorinating populations, designated strains BB1 and BRS1, were isolated from pristine river sediment and chloroethene-contaminated aquifer material, respectively. PCE-to-cis-1,2-dichloroethene-dechlorinating activity could be transferred in defined basal salts medium with acetate as the electron donor and PCE as the electron acceptor. Taxonomic analysis based on 16S rRNA gene sequencing placed both isolates within theDesulfuromonascluster in the δ subdivision of theProteobacteria. PCE was dechlorinated at rates of at least 139 nmol min−1mg of protein−1at pH values between 7.0 and 7.5 and temperatures between 25 and 30°C. Dechlorination also occurred at 10°C. The electron donors that supported dechlorination included acetate, lactate, pyruvate, succinate, malate, and fumarate but not hydrogen, formate, ethanol, propionate, or sulfide. Growth occurred with malate or fumarate alone, whereas oxidation of the other electron donors depended strictly on the presence of fumarate, malate, ferric iron, sulfur, PCE, or TCE as an electron acceptor. Nitrate, sulfate, sulfite, thiosulfate, and other chlorinated compounds were not used as electron acceptors. Sulfite had a strong inhibitory effect on growth and dechlorination. Alternate electron acceptors (e.g., fumarate or ferric iron) did not inhibit PCE dechlorination and were consumed concomitantly. The putative fumarate, PCE, and ferric iron reductases were induced by their respective substrates and were not constitutively present. Sulfide was required for growth. Both strains tolerated high concentrations of PCE, and dechlorination occurred in the presence of free-phase PCE (dense non-aqueous-phase liquids). Repeated growth with acetate and fumarate as substrates yielded a BB1 variant that had lost the ability to dechlorinate PCE. Due to the 16S rRNA gene sequence differences with the closest relatives and the unique phenotypic characteristics, we propose that the new isolates are members of a new species,Desulfuromonas michiganensis, within theDesulfuromonascluster of theGeobacteraceae.
Enterolysin A, a Cell Wall-Degrading Bacteriocin fromEnterococcus faecalisLMG 2333
Authors: Nilsen Trine , Nes Ingolf F. , Holo Helge 
Published: May 2003

ABSTRACTA novel antimicrobial protein, designated enterolysin A, was purified from anEnterococcus faecalisLMG 2333 culture. Enterolysin A inhibits growth of selected enterococci, pediococci, lactococci, and lactobacilli. Antimicrobial activity was initially detected only on solid media, but by growing the bacteria in a fermentor under optimized production conditions (MRS broth with 4% [wt/vol] glucose, pH 6.5, and a temperature between 25 and 35°C), the bacteriocin activity was increased to 5,120 bacteriocin units ml−1. Enterolysin A production was regulated by pH, and activity was first detected in the transition between the logarithmic and stationary growth phases. Killing of sensitive bacteria by enterolysin A showed a dose-response behavior, and the bacteriocin has a bacteriolytic mode of action. Enterolysin A was purified, and the primary structure was determined by combined amino acid and DNA sequencing. This bacteriocin is translated as a 343-amino-acid preprotein with ansec-dependent signal peptide of 27 amino acids, which is followed by a sequence corresponding to the N-terminal part of the purified protein. Mature enterolysin A consists of 316 amino acids and has a calculated molecular weight of 34,501, and the theoretical pI is 9.24. The N terminus of enterolysin A is homologous to the catalytic domains of different cell wall-degrading proteins with modular structures. These include lysostaphin, ALE-1, zoocin A, and LytM, which are all endopeptidases belonging to the M37 protease family. The N-terminal part of enterolysin A is linked by a threonine-proline-rich region to a putative C-terminal recognition domain, which shows significant sequence identity to two bacteriophage lysins.
Thermophily in the
Geobacteraceae
:
Geothermobacter ehrlichii
gen. nov., sp. nov., a Novel Thermophilic Member of the
Geobacteraceae
from the “Bag City” Hydrothermal Vent
Authors: Kashefi Kazem , Holmes Dawn E. , Baross John A. , Lovley Derek R. 
Published: May 2003

ABSTRACT

Little is known about the microbiology of the “Bag City” hydrothermal vent, which is part of a new eruption site on the Juan de Fuca Ridge and which is notable for its accumulation of polysaccharide on the sediment surface. A pure culture, designated strain SS015, was recovered from a vent fluid sample from the Bag City site through serial dilution in liquid medium with malate as the electron donor and Fe(III) oxide as the electron acceptor and then isolation of single colonies on solid Fe(III) oxide medium. The cells were gram-negative rods, about 0.5 μm by 1.2 to 1.5 μm, and motile and contained
c
-type cytochromes. Analysis of the 16S ribosomal DNA (rDNA) sequence of strain SS015 placed it in the family
Geobacteraceae
in the delta subclass of the
Proteobacteria
. Unlike previously described members of the
Geobacteraceae
, which are mesophiles, strain SS015 was a thermophile and grew at temperatures of between 35 and 65°C, with an optimum temperature of 55°C. Like many previously described members of the
Geobacteraceae
, strain SS015 grew with organic acids as the electron donors and Fe(III) or nitrate as the electron acceptor, with nitrate being reduced to ammonia. Strain SS015 was unique among the
Geobacteraceae
in its ability to use sugars, starch, or amino acids as electron donors for Fe(III) reduction. Under stress conditions, strain SS015 produced copious quantities of extracellular polysaccharide, providing a model for the microbial production of the polysaccharide accumulation at the Bag City site. The 16S rDNA sequence of strain SS015 was less than 94% similar to the sequences of previously described members of the
Geobacteraceae
; this fact, coupled with its unique physiological properties, suggests that strain SS015 represents a new genus in the family
Geobacteraceae
. The name
Geothermobacter ehrlichii
gen. nov., sp. nov., is proposed (ATCC BAA-635 and DSM 15274). Although strains of
Geobacteraceae
are known to be the predominant Fe(III)-reducing microorganisms in a variety of Fe(III)-reducing environments at moderate temperatures, strain SS015 represents the first described thermophilic member of the
Geobacteraceae
and thus extends the known environmental range of this family to hydrothermal environments.
Community-Level Physiological Profiling Performed with an Oxygen-Sensitive Fluorophore in a Microtiter Plate
Authors: Garland Jay L. , Roberts Michael S. , Levine Lanfang H. , Mills Aaron L. 
Published: May 2003

ABSTRACT
Community-level physiological profiling based upon fluorometric detection of oxygen consumption was performed on hydroponic rhizosphere and salt marsh litter samples by using substrate levels as low as 50 ppm with incubation times between 5 and 24 h. The rate and extent of response were increased in samples acclimated to specific substrates and were reduced by limiting nitrogen availability in the wells.
Reductive Dehalogenation of Chlorobenzene Congeners in Cell Extracts of
Dehalococcoides
sp. Strain CBDB1
Authors: Hölscher Tina , Görisch Helmut , Adrian Lorenz 
Published: May 2003

ABSTRACT

Enzymatic reductive dehalogenation of tri-, tetra-, penta-, and hexachlorobenzenes was demonstrated in cell extracts with low protein concentration (0.5 to 1 μg of protein/ml) derived from the chlorobenzene-respiring anaerobe
Dehalococcoides
sp. strain CBDB1. 1,2,3-trichlorobenzene dehalogenase activity was associated with the membrane fraction. Light-reversible inhibition by alkyl iodides indicated the presence of a corrinoid cofactor.
Endotoxin Inactivation in Water by Using Medium-Pressure UV Lamps
Authors: Anderson W. B. , Huck P. M. , Dixon D. G. , Mayfield C. I. 
Published: May 2003

ABSTRACT

Deionized water was spiked with various concentrations of endotoxin and exposed to UV irradiation from medium-pressure UV lamps to assess endotoxin inactivation. It was found that endotoxin inactivation was proportional to the UV dose under the conditions examined. The inactivation rate was determined to be ∼0.55 endotoxin unit/ml per mJ/cm
2
of irradiation delivered.
Antimicrobial-Resistant
Campylobacter
Species from Retail Raw Meats
Authors: Ge Beilei , White David G. , McDermott Patrick F. , Girard Webb , Zhao Shaohua , Hubert Susannan , Meng Jianghong 
Published: May 2003

ABSTRACT

The antimicrobial susceptibilities of 378
Campylobacter
isolates were determined. Resistance to tetracycline was the most common (82%), followed by resistance to doxycycline (77%), erythromycin (54%), nalidixic acid (41%), and ciprofloxacin (35%).
Campylobacter coli
displayed significantly higher rates of resistance to ciprofloxacin and erythromycin than
Campylobacter jejuni
, and
Campylobacter
isolates from turkey meat showed a greater resistance than those from chicken meat.
Habitat-Specific Diversity of
Borrelia burgdorferi
Sensu Lato in Europe, Exemplified by Data from Latvia
Authors: Etti Susanne , Hails Rosie , Schäfer Stefanie M. , De Michelis Simona , Sewell Henna-Sisko , Bormane Antra , Donaghy Michael , Kurtenbach Klaus 
Published: May 2003

ABSTRACT

The distribution of
Borrelia burgdorferi
sensu lato genospecies in questing
Ixodes ricinus
ticks from ecologically distinct habitats in Latvia was analyzed. A significant variation in the frequency of the genospecies across sites was observed, pointing to the importance of the host community in the ecology of Lyme borreliosis.
Production of Native-Type
Streptoverticillium mobaraense
Transglutaminase in
Corynebacterium glutamicum
Authors: Date Masayo , Yokoyama Kei-ichi , Umezawa Yukiko , Matsui Hiroshi , Kikuchi Yoshimi 
Published: May 2003

ABSTRACT

We previously observed secretion of active-form transglutaminase in
Corynebacterium glutamicum
by coexpressing the subtilisin-like protease SAM-P45 from
Streptomyces albogriseolus
to process the prodomain. However, the N-terminal amino acid sequence of the transglutaminase differed from that of the native
Streptoverticillium mobaraense
enzyme. In the present work we have used site-directed mutagenesis to generate an optimal SAM-P45 cleavage site in the C-terminal region of the prodomain. As a result, native-type transglutaminase was secreted.
Unexpected Thermal Destruction of Dried, Glass Bead-Immobilized Microorganisms as a Function of Water Activity
Authors: Laroche C. , Gervais P. 
Published: May 2003

ABSTRACT

To help us understand the factors and mechanisms implicated in the death of microorganisms or their resistance to temperature in a low water activity environment, microorganisms were dried on the surface of glass beads before being subjected to high temperatures for a short period followed by rapid cooling. Two microorganisms were studied: the yeast
Saccharomyces cerevisiae
and the bacterium
Lactobacillus plantarum
. Experiments were carried out at 150, 200, and 250°C, with four durations of heat treatment and seven levels of initial water activity between 0.10 and 0.70. We observed an unexpected range of water activity, between 0.30 and 0.50, at which microorganisms were more resistant to the various treatments, with maximal viability at 0.35 for
L. plantarum
and 0.40 for
S. cerevisiae.
An Improved Cloning Vector for Construction of Gene Replacements in
Listeria monocytogenes
Authors: Li Guojie , Kathariou S. 
Published: May 2003

ABSTRACT

Listeria monocytogenes
is a gram-positive, facultative intracellular bacterium implicated in severe food-borne illness (listeriosis) in humans. The construction of well-defined gene replacements in the genome of
L. monocytogenes
has been instrumental to several genetic studies of the virulence and other attributes of the organism. Construction of such mutations by currently available procedures, however, tends to be labor intensive, and gene replacement mutants are sometimes difficult to recover due to lack of direct selection for the construct. In this study we describe the construction and use of plasmid vector pGF-EM, which can be conjugatively transferred from
Escherichia coli
S17-1 to
L. monocytogenes
and which provides the genetic means for direct selection of gene replacements.