bluuebunny/crossref_metadata_2025_split huggingface dataset:
Enteroviruses and Bacteriophages in Bathing Waters
Authors: Mocé-Llivina Laura , Lucena Francisco , Jofre Juan 
Published: November 2005

ABSTRACT

A new procedure for detecting and counting enteroviruses based on the VIRADEN method applied to 10 liters of seawater was examined. It improved the efficiency of detection by taking into account both the number of positive isolations and numbers found with traditional methods. It was then used to quantify viruses in bathing waters. A number of bacterial indicators and bacteriophages were also tested. Cultivable enteroviruses were detected in 55% of the samples, most of which complied with bacteriological criteria. In contrast, viral genomes were only detected in 20% of the samples by reverse transcription-PCR. Somatic coliphages outnumbered all other indicators. F-specific RNA phages were detected in only 15% of the samples, whereas phages infecting
Bacteroides thetaiotaomicron
were detected in 70% of samples. A numerical relationship between the numbers of enteroviruses and the numbers of enterococci and somatic coliphages was observed. In situ inactivation experiments showed that viruses persisted significantly longer than the bacterial indicators. Only somatic coliphages and bacteriophages infecting
Bacteroides
persisted longer than the viruses. These results explain the numbers of enteroviruses and indicators in bathing waters attending the numbers usually found in sewage in the area. Somatic coliphages show a very good potential to predict the risk of viruses being present in bathing waters.
Identification and Characterization of a Novel Biotin Biosynthesis Gene inSaccharomyces cerevisiae
Authors: Wu Hong , Ito Kiyoshi , Shimoi Hitoshi 
Published: November 2005

ABSTRACTYeastSaccharomyces cerevisiaecells generally cannot synthesize biotin, a vitamin required for many carboxylation reactions. Although sake yeasts, which are used for Japanese sake brewing, are classified asS. cerevisiae, they do not require biotin for their growth. In this study, we identified a novel open reading frame (ORF) in the genome of one strain of sake yeast that we speculated to be involved in biotin synthesis. Homologs of this gene are widely distributed in the genomes of sake yeasts. However, they are not found in many laboratory strains and strains used for wine making and beer brewing. This ORF was namedBIO6because it has 52% identity withBIO3, a biotin biosynthesis gene of a laboratory strain. Further research showed that yeasts without theBIO6gene are auxotrophic for biotin, whereas yeasts holding theBIO6gene are prototrophic for biotin. TheBIO6gene was disrupted in strain A364A, which is a laboratory strain with one copy of theBIO6gene. Although strain A364A is prototrophic for biotin, aBIO6disrupted mutant was found to be auxotrophic for biotin. TheBIO6disruptant was able to grow in biotin-deficient medium supplemented with 7-keto-8-amino-pelargonic acid (KAPA), while thebio3disruptant was not able to grow in this medium. These results suggest that Bio6p acts in an unknown step of biotin synthesis before KAPA synthesis. Furthermore, we demonstrated that expression of theBIO6gene, like that of other biotin synthesis genes, was upregulated by depletion of biotin. We conclude that theBIO6gene is a novel biotin biosynthesis gene ofS. cerevisiae.
Development of a Rapid Method for Simultaneous Recovery of Diverse Microbes in Drinking Water by Ultrafiltration with Sodium Polyphosphate and Surfactants
Authors: Hill Vincent R. , Polaczyk Amy L. , Hahn Donghyun , Narayanan Jothikumar , Cromeans Theresa L. , Roberts Jacquelin M. , Amburgey James E. 
Published: November 2005

ABSTRACT

The ability to simultaneously concentrate diverse microbes is an important consideration for sample collection methods that are used for emergency response and environmental monitoring when drinking water may be contaminated with an array of unknown microbes. This study focused on developing a concentration method using ultrafilters and different combinations of a chemical dispersant (sodium polyphosphate [NaPP]) and surfactants. Tap water samples were seeded with bacteriophage MS2,
Escherichia coli
,
Enterococcus faecalis
,
Cryptosporidium parvum
, 4.5-μm microspheres,
Salmonella enterica
serovar Typhimurium,
Bacillus globigii
endospores, and echovirus 1. Ten-liter tap water samples were concentrated to ∼250 ml in 12 to 42 min, depending on the experimental condition. Initial experiments indicated that pretreating filters with fetal bovine serum or NaPP resulted in an increase in microbe recovery. The addition of NaPP to the tap water samples resulted in significantly higher microbe and microsphere recovery efficiencies. Backflushing of the ultrafilter was found to significantly improve recovery efficiencies. The effectiveness of backflushing was improved further with the addition of Tween 80 to the backflush solution. The ultrafiltration method developed in this study, incorporating the use of NaPP pretreatment and surfactant solution backflushing, was found to recover MS2,
C. parvum
, microspheres, and several bacterial species with mean recovery efficiencies of 70 to 93%. The mean recovery efficiency for echovirus 1 (49%) was the lowest of the microbes studied for this method. This research demonstrates that ultrafiltration can be effective for recovering diverse microbes simultaneously in tap water and that chemical dispersants and surfactants can be beneficial for improving microbial recovery using this technique.
Bacterial Populations Active in Metabolism of C
1
Compounds in the Sediment of Lake Washington, a Freshwater Lake
Authors: Nercessian Olivier , Noyes Emma , Kalyuzhnaya Marina G. , Lidstrom Mary E. , Chistoserdova Ludmila 
Published: November 2005

ABSTRACT

Active
members of the bacterial community in the sediment of Lake Washington,
with special emphasis on C
1
utilizers, were identified by
employing two complementary culture-independent approaches: reverse
transcription of environmental mRNA and 16S rRNA combined with PCR
(RT-PCR) and stable-isotope probing (SIP) of DNA with the
13
C-labeled C
1
substrates methanol, methylamine,
formaldehyde, and formate. Analysis of RT-PCR-amplified fragments of
16S rRNA-encoding genes revealed that gammaproteobacterial
methanotrophs belonging to
Methylobacter
and
Methylomonas
dominate the active methylotroph population,
while only one other known methylotrophic lineage,
Methylophilaceae
, was detected via this approach. Analysis of
RT-PCR-amplified functional genes,
pmoA
and
fae
,
allowed detection of alphaproteobacterial (
Methylosinus
) and
gammaproteobacterial (
Methylobacter
,
Methylomonas
,
and
Methylomicrobium
) methanotrophs, methylotrophs of
the genus
Methylobacterium
, and yet-unidentified
proteobacteria. SIP experiments allowed detection of a broad variety of
groups actively metabolizing C
1
compounds. Comparisons
between 16S rRNA gene pools amplified from
[
13
C]DNA and from [
12
C]DNA revealed that the
proportion of
Methylophilus
-related sequences increased in the
presence of [
13
C]methanol, [
13
C]methylamine, and
[
13
C]formaldehyde;
Novosphingobium
-related
sequences were enriched in the presence of [
13
C]methanol;
Gemmatimonadaceae
-related sequences were enriched in the
presence of [
13
C]formaldehyde and [
13
C]formate;
and
Xanthomonadaceae
-related sequences were enriched in the
presence of [
13
C]formate. Analysis of
fae
genes
amplified from [
13
C]DNAs isolated from different microcosms
revealed specific shifts in populations in response to a specific
C
1
compound:
Methylosinus
sequences dominated the
[
13
C]methanol microcosm pool, and beta- and
gammaproteobacterial sequences dominated the
[
13
C]methylamine microcosm pool. The
[
13
C]formaldehyde microcosm was dominated by
betaproteobacterial sequences and by sequences of a nonaffiliated
group, while the [
13
C]formate microcosm was dominated by
alpha- and betaproteobacterial sequences. Overall, these data point
toward the presence of a diverse population of active methylotrophs in
Lake Washington sediments and toward the existence of yet-uncultivated
organisms.
Efficient Procedure for Purification of ObligateIntracellular
Wolbachia pipientis
and RepresentativeAmplification of Its Genome by Multiple-DisplacementAmplification
Authors: Mavingui Patrick , Tran Van Van , Labeyrie Estelle , Rancès Edwige , Vavre Fabrice , Simonet Pascal 
Published: November 2005

ABSTRACT

Bacteria
belonging to the genus
Wolbachia
are obligatorymicroendocytobionts that infect a variety of arthropods and a majority
of filarial nematode species, where they induce reproductive
alterations or establish a mutualistic symbiosis. Although two whole
genome sequences of
Wolbachia pipientis
, for strain wMel from
Drosophila melanogaster
and strain wBm from
Brugia
malayi
, have been fully completed and six other genome sequencing
projects are ongoing
(
http://www.genomesonline.org/index.cgi?want=Prokaryotic+Ongoin
),
genetic analyses of these bacteria are still scarce, mainly due to the
inability to cultivate them outside of eukaryotic cells. Usually, a
large amount of host tissue (a thousand individuals, or about
10 g) is required in order to purify
Wolbachia
and
extract its DNA, which is often recovered in small amounts and
contaminated by host cell DNA, thus hindering genomic studies. In this
report, we describe an efficient and reliable procedure to
representatively amplify the
Wolbachia
genome by
multiple-displacement amplification from limited infected host tissue
(0.2 g or 2 × 10
7
cells). We obtained sufficient
amounts (8 to 10 μg) of DNA of suitable quality for genomic
studies, and we demonstrated that the amplified DNA contained all of
the
Wolbachia
loci targeted. In addition, our data indicated
that the genome of strain wRi, an obligatory endosymbiont of
Drosophila simulans
, shares a similar overall architecture
with its relative strain
wMel.
Redox Fluctuation Structures Microbial Communities in a Wet Tropical Soil
Authors: Pett-Ridge J. , Firestone M. K. 
Published: November 2005

ABSTRACTFrequent high-amplitude redox fluctuation may be a strong selective force on the phylogenetic and physiological composition of soil bacterial communities and may promote metabolic plasticity or redox tolerance mechanisms. To determine effects of fluctuating oxygen regimens, we incubated tropical soils under four treatments: aerobic, anaerobic, 12-h oxic/anoxic fluctuation, and 4-day oxic/anoxic fluctuation. Changes in soil bacterial community structure and diversity were monitored with terminal restriction fragment length polymorphism (T-RFLP) fingerprints. These profiles were correlated with gross N cycling rates, and a Web-based phylogenetic assignment tool was used to infer putative community composition from multiple fragment patterns. T-RFLP ordinations indicated that bacterial communities from 4-day oxic/anoxic incubations were most similar to field communities, whereas those incubated under consistently aerobic or anaerobic regimens developed distinctly different molecular profiles. Terminal fragments found in field soils persisted either in 4-day fluctuation/aerobic conditions or in anaerobic/12-h treatments but rarely in both. Only 3 of 179 total fragments were ubiquitous in all soils. Soil bacterial communities inferred from in silico phylogenetic assignment appeared to be dominated byActinobacteria(especiallyMicrococcusandStreptomycetes), “Bacilli,” “Clostridia,” andBurkholderiaand lost significant diversity under consistently or frequently anoxic incubations. Community patterns correlated well with redox-sensitive processes such as nitrification, dissimilatory nitrate reduction to ammonium (DNRA), and denitrification but did not predict patterns of more general functions such as N mineralization and consumption. The results suggest that this soil's indigenous bacteria are highly adapted to fluctuating redox regimens and generally possess physiological tolerance mechanisms which allow them to withstand unfavorable redox periods.
Inactivation of
Bacillus
Endospores in Envelopes by Electron Beam Irradiation
Authors: Helfinstine Shannon L. , Vargas-Aburto Carlos , Uribe Roberto M. , Woolverton Christopher J. 
Published: November 2005

ABSTRACT

The anthrax incidents in the United States in the fall of 2001 led to the use of electron beam (EB) processing to sanitize the mail for the U.S. Postal Service. This method of sanitization has prompted the need to further investigate the effect of EB irradiation on the destruction of
Bacillus
endospores. In this study, endospores of an anthrax surrogate,
B. atrophaeus
, were destroyed to demonstrate the efficacy of EB treatment of such biohazard spores. EB exposures were performed to determine (i) the inactivation of varying
B. atrophaeus
spore concentrations, (ii) a D
10
value (dose required to reduce a population by 1 log
10
) for the
B. atrophaeus
spores, (iii) the effects of spore survival at the bottom of a standardized paper envelope stack, and (iv) the maximum temperature received by spores. A maximum temperature of 49.2°C was reached at a lethal dose of ∼40 kGy, which is a significantly lower temperature than that needed to kill spores by thermal effects alone. A D
10
value of 1.53 kGy was determined for the species. A surface EB dose between 25 and 32 kGy produced the appropriate killing dose of EB between 11 and 16 kGy required to inactivate 8 log
10
spores, when spore samples were placed at the bottom of a 5.5-cm stack of envelopes.
European Origin of
Bradyrhizobium
Populations Infecting Lupins and Serradella in Soils of Western Australia and South Africa
Authors: Stępkowski Tomasz , Moulin Lionel , Krzyżańska Agnieszka , McInnes Alison , Law Ian J. , Howieson John 
Published: November 2005

ABSTRACT

We applied a multilocus phylogenetic approach to elucidate the origin of serradella and lupin
Bradyrhizobium
strains that persist in soils of Western Australia and South Africa. The selected strains belonged to different randomly amplified polymorphic DNA (RAPD)-PCR clusters that were distinct from RAPD clusters of applied inoculant strains. Phylogenetic analyses were performed with nodulation genes (
nodA
,
nodZ
,
nolL
,
noeI
), housekeeping genes (
dnaK
,
recA
,
glnII
,
atpD
), and 16S-23S rRNA intergenic transcribed spacer sequences. Housekeeping gene phylogenies revealed that all serradella and
Lupinus cosentinii
isolates from Western Australia and three of five South African narrow-leaf lupin strains were intermingled with the strains of
Bradyrhizobium canariense
, forming a well supported branch on each of the trees. All
nodA
gene sequences of the lupin and serradella bradyrhizobia formed a single branch, referred to as clade II, together with the sequences of other lupin and serradella strains. Similar patterns were detected in
nodZ
and
nolL
trees. In contrast,
nodA
sequences of the strains isolated from native Australian legumes formed either a new branch called clade IV or belonged to clade I or III, whereas their nonsymbiotic genes grouped outside the
B. canariense
branch. These data suggest that the lupin and serradella strains, including the strains from uncultivated
L. cosentinii
plants, are descendants of strains that most likely were brought from Europe accidentally with lupin and serradella seeds. The observed dominance of
B. canariense
strains may be related to this species' adaptation to acid soils common in Western Australia and South Africa and, presumably, to their intrinsic ability to compete for nodulation of lupins and serradella.
Occurrence of
Mycobacterium avium
subsp.
paratuberculosis
in Untreated Water in Northern Ireland
Authors: Whan Lynne , Ball Hywel J. , Grant Irene R. , Rowe Michael T. 
Published: November 2005

ABSTRACT

Mycobacterium avium
subsp.
paratuberculosis
is the known cause of Johne's disease of both domestic and wild ruminants and has been implicated as a possible cause of Crohn's disease in humans. The organism is shed in the feces of infected animals and can survive for protracted periods in the environment and hence could be present in catchment areas receiving agricultural runoff. A limited survey was undertaken in Northern Ireland to test for
M. avium
subsp.
paratuberculosis
in untreated water entering nine water treatment works (WTWs) over a 1-year period. Three detection methods were employed, viz., immunomagnetic separation-PCR and culture on Herrold's egg yolk medium (HEYM) and BACTEC 12B medium, the latter both supplemented with mycobactins. Of the 192 untreated water samples tested, 15 (8%) tested
M. avium
subsp.
paratuberculosis
positive by one or more of the three detection methods.
M. avium
subsp.
paratuberculosis
was successfully isolated from eight untreated water samples, three by BACTEC culture and five by culture on HEYM. Although the highest incidence of
M. avium
subsp.
paratuberculosis
was found in spring, overall, there was no statistically significant difference between the seasons. No significant correlation was found between numbers of coliforms or fecal coliforms and the presence of
M. avium
subsp.
paratuberculosis
. In general, a higher incidence of
M. avium
subsp.
paratuberculosis
was found in untreated water entering those WTWs that had a high mean water pH value over the sampling period. This work indicates the need to determine the efficacy of water treatment processes to either kill or remove
M. avium
subsp.
paratuberculosis
from untreated water and the possible risks posed by contact with recreational water sources.
Transcriptional Expression of the
tceA
Gene in a
Dehalococcoides-
Containing Microbial Enrichment
Authors: Johnson David R. , Lee Patrick K. H. , Holmes Victor F. , Fortin Alexander C. , Alvarez-Cohen Lisa 
Published: November 2005

ABSTRACT

Dynamic changes in the transcriptional expression of the
tceA
gene, which encodes a trichloroethene reductive dehalogenase, were characterized in a
Dehalococcoides
-containing microbial enrichment culture. Expression was quantified by real-time PCR as the number of
tceA
transcripts per
tceA
gene. Expression of
tceA
increased 40-fold after chlorinated ethene-starved cells were exposed to trichloroethene (TCE),
cis
-dichloroethene (DCE), or 1,1-DCE but did not increase after exposure to tetrachloroethene or vinyl chloride. Surprisingly,
tceA
expression also increased 30-fold after cellular exposure to the nonmetabolic substrate
trans
-DCE, indicating that expression of
tceA
is induced by both growth-supporting and non-growth-supporting chlorinated ethenes. Additional experiments revealed that the level of
tceA
expression was independent of the concentration of chlorinated ethenes (sum concentrations of TCE and DCEs of 2.2 to 333 μM), the concentration of the electron donor hydrogen (concentrations of 12 nM to 17 μM), and the presence of alternate bacterial electron acceptors (5 mM concentrations of fumarate, sulfate, sulfite, thiosulfate, nitrate, or nitrite) but was highly dependent on incubation temperature.
Fate and Role of Ammonium Ions during Fermentation of Citric Acid by
Aspergillus niger
Authors: Papagianni Maria , Wayman Frank , Mattey Michael 
Published: November 2005

ABSTRACT

Stoichiometric modeling of the early stages of the citric acid fermentation process by
Aspergillus niger
revealed that ammonium ions combine with a carbon-containing metabolite inside the cell, in a ratio 1:1, to form a nitrogen compound which is then excreted by the mycelium. High-performance liquid chromatography analysis identified glucosamine as the product of the relationship between glucose and ammonium during the early stages of the citric acid fermentation process. Slightly acidic internal pHs, extremely low ammonium ion concentrations inside the cell, and glucosamine synthesis come into direct contradiction with the earlier theory of the ammonium pool inside the cell, regarded as responsible for inhibition of the enzyme phosphofructokinase. At later fermentation stages, when the mycelium is involved in a process of fragmentation and regrowth, the addition of ammonium sulfate leads to a series of events: the formation and secretion of glucosamine in elevated amounts, the short inhibition of citrate synthesis, growth enhancement, the utilization of glucosamine, and finally, the enhancement of citric acid production rates. Obviously, the enzymatic processes underlining the phenomena need to be reexamined. As a by-product of the citric acid fermentation, glucosamine is reported for the first time here. Suitable process manipulations of the system described in this work could lead to successful glucosamine recovery at the point of its highest yield before degradation by the fungus occurs.
Prevalence ofBorrelia burgdorferiSensu Lato Genospecies inIxodes ricinusTicks in Europe: a Metaanalysis
Authors: Rauter Carolin , Hartung Thomas 
Published: November 2005

ABSTRACTIn Europe,Borrelia burgdorferigenospecies causing Lyme borreliosis are mainly transmitted by the tickIxodes ricinus. Since its discovery,B. burgdorferihas been the subject of many epidemiological studies to determine its prevalence and the distribution of the different genospecies in ticks. In the current study we systematically reviewed the literature on epidemiological studies ofI. ricinusticks infected withB. burgdorferisensu lato. A total of 1,186 abstracts in English published from 1984 to 2003 were identified by a PubMed keyword search and from the compiled article references. A multistep filter process was used to select relevant articles; 110 articles from 24 countries contained data on the rates of infection ofI. ricinuswithBorreliain Europe (112,579 ticks), and 44 articles from 21 countries included species-specific analyses (3,273 positive ticks). These data were used to evaluate the overall rate of infection ofI. ricinuswithBorreliagenospecies, regional distributions within Europe, and changes over time, as well as the influence of different detection methods on the infection rate. While the infection rate was significantly higher in adults (18.6%) than in nymphs (10.1%), no effect of detection method, tick gender, or collection period (1986 to 1993 versus 1994 to 2002) was found. The highest rates of infection ofI. ricinuswere found in countries in central Europe.B. afzeliiandB. gariniiare the most commonBorreliaspecies, but the distribution of genospecies seems to vary in different regions in Europe. The most frequent coinfection byBorreliaspecies was found forB. gariniiandB. valaisiana.
Feedback Inhibition of Chorismate Mutase/Prephenate Dehydrogenase (TyrA) ofEscherichia coli: Generation and Characterization of Tyrosine-Insensitive Mutants
Authors: Lütke-Eversloh Tina , Stephanopoulos Gregory 
Published: November 2005

ABSTRACTIn order to get insights into the feedback regulation by tyrosine of theEscherichia colichorismate mutase/prephenate dehydrogenase (CM/PDH), which is encoded by thetyrAgene, feedback-inhibition-resistant (fbr) mutants were generated by error-prone PCR. ThetyrAfbrmutants were selected by virtue of their resistance towardm-fluoro-d,l-tyrosine, and seven representatives were characterized on the biochemical as well as on the molecular level. The PDH activities of the purified His6-tagged TyrA proteins exhibited up to 35% of the enzyme activity of TyrAWT, but tyrosine did not inhibit the mutant PDH activities. On the other hand, CM activities of the TyrAfbrmutants were similar to those of the TyrAWTprotein. Analyses of the DNA sequences of thetyrAgenes revealed thattyrAfbrcontained amino acid substitutions either at Tyr263 or at residues 354 to 357, indicating that these two sites are involved in the feedback inhibition by tyrosine.