bluuebunny/crossref_metadata_2025_split huggingface dataset:
Formation of Catechols via Removal of Acid Side Chains from Ibuprofen and Related Aromatic Acids
Authors: Murdoch Robert W. , Hay Anthony G. 
Published: October 2005

ABSTRACT

Although ibuprofen [2-(4-isobutylphenyl)-propionic acid] is one of the most widely consumed drugs in the world, little is known regarding its degradation by environmental bacteria.
Sphingomonas
sp. strain Ibu-2 was isolated from a wastewater treatment plant based on its ability to use ibuprofen as a sole carbon and energy source. A slight preference toward the
R
enantiomer was observed, though both ibuprofen enantiomers were metabolized. A yellow color, indicative of
meta
-cleavage, accumulated transiently in the culture supernatant when Ibu-2 was grown on ibuprofen. When and only when 3-flurocatechol was used to poison the
meta
-cleavage system, isobutylcatechol was identified in the culture supernatant via gas chromatography-mass spectrometry analysis. Ibuprofen-induced washed-cell suspensions also metabolized phenylacetic acid and 2-phenylpropionic acid to catechol, while 3- and 4-tolylacetic acids and 2-(4-tolyl)-propionic acid were metabolized to the corresponding methyl catechols before ring cleavage. These data suggest that, in contrast to the widely distributed coenzyme A ligase, homogentisate, or homoprotocatechuate pathway for metabolism of phenylacetic acid and similar compounds, Ibu-2 removes the acidic side chain of ibuprofen and related compounds prior to ring cleavage.
Fermentation of Fructooligosaccharides and Inulin by Bifidobacteria: a Comparative Study of Pure and Fecal Cultures
Authors: Rossi Maddalena , Corradini Claudio , Amaretti Alberto , Nicolini Marcello , Pompei Anna , Zanoni Simona , Matteuzzi Diego 
Published: October 2005

ABSTRACT

The utilization of fructooligosaccharides (FOS) and inulin by 55
Bifidobacterium
strains was investigated. Whereas FOS were fermented by most strains, only eight grew when inulin was used as the carbon source. Residual carbohydrates were analyzed by high-performance anion-exchange chromatography with pulsed amperometric detection after batch fermentation. A strain-dependent capability to degrade fructans of different lengths was observed. During batch fermentation on inulin, the short fructans disappeared first, and then the longer ones were gradually consumed. However, growth occurred through a single uninterrupted exponential phase without exhibiting polyauxic behavior in relation to the chain length. Cellular β-fructofuranosidases were found in all of the 21
Bifidobacterium
strains tested. Four strains were tested for extracellular hydrolytic activity against fructans, and only the two strains which ferment inulin showed this activity. Batch cultures inoculated with human fecal slurries confirmed the bifidogenic effect of both FOS and inulin and indicated that other intestinal microbial groups also grow on these carbon sources. We observed that bifidobacteria grew by cross-feeding on mono- and oligosaccharides produced by primary inulin intestinal degraders, as evidenced by the high hydrolytic activity of fecal supernatants. FOS and inulin greatly affected the production of short-chain fatty acids in fecal cultures; butyrate was the major fermentation product on inulin, whereas mostly acetate and lactate were produced on FOS.
Diversity of the Microeukaryotic Community in Sulfide-Rich Zodletone Spring (Oklahoma)
Authors: Luo Qingwei , Krumholz Lee R. , Najar Fares Z. , Peacock Aaron D. , Roe Bruce A. , White David C. , Elshahed Mostafa S. 
Published: October 2005

ABSTRACTThe microeukaryotic community in Zodletone Spring, a predominantly anaerobic sulfide and sulfur-rich spring, was examined using an 18S rRNA gene cloning and sequencing approach. The majority of the 288 clones sequenced from three different locations at Zodletone Spring belonged to theStramenopiles,Alveolata, andFungi, with members of the phylumCercozoa, orderDiplomonadida, and familyJakobidaerepresenting a minor fraction of the clone library. No sequences suggesting the presence of novel kingdom level diversity were detected in any of the three libraries. A large fraction of stramenopile clones encountered were monophyletic with either members of the genusCafeteria(orderBicosoecida) or members of the orderLabyrinthulida(slime nets), both of which have so far been encountered mainly in marine habitats. The majority of the observed fungal clone sequences belonged to the ascomycetous yeasts (orderSaccharomycetales), were closely related to yeast genera within theHymenobasidiomycetes(phylumBasidiomycetes), or formed a novel fungal lineage with several previously published or database-deposited clones. To determine whether the unexpected abundance of fungal sequences in Zodletone Spring clone libraries represents a general pattern in anaerobic habitats, we generated three clone libraries from three different anaerobic settings (anaerobic sewage digester, pond sediment, and hydrocarbon-exposed aquifer sediments) and partially sequenced 210 of these clones. Phylogenetic analysis indicated that clone sequences belonging to the kingdomFungirepresent a significant fraction of all three clone libraries, an observation confirmed by phospholipid fatty acid and ergosterol analysis. Overall, this work reveals an unexpected abundance ofFungiin anaerobic habitats, describes a novel, yet-uncultured group ofFungithat appears to be widespread in anaerobic habitats, and indicates that several of the previously considered marine protists could also occur in nonmarine habitats.
Genetic and Transcriptional Organization of the
clpC
Locus in
Bifidobacterium breve
UCC 2003
Authors: Ventura Marco , Fitzgerald Gerald F. , van Sinderen Douwe 
Published: October 2005

ABSTRACT

A homolog of the
clpC
ATPase gene was identified in the genome of
Bifidobacterium breve
UCC 2003. Since this gene is very well conserved among eubacteria, we employed a PCR-based approach using primers based on highly conserved regions of ClpC proteins in order to identify homologous genes in other bifidobacterial species. Analysis by slot blot, Northern blot, and primer extension experiments showed that transcription of
clpC
is induced in response to moderate heat shock regimes. Moreover, we identified in the genome sequence of
B. breve
UCC 2003 a gene, designated
clgR
, which is predicted to encode a transcriptional regulator involved in regulation of the bifidobacterial
clpC
gene. The role of this protein in the regulation of
B. breve
UCC 2003
clpC
gene expression was investigated by performing gel retardation experiments. We show that a biologically active ClgR molecule requires one or more proteinaceous coactivators to assist in the specific binding of ClgR to the
clpC
promoter region.
Speciation of
Campylobacter coli
,
C. jejuni
,
C. helveticus
,
C. lari
,
C. sputorum
, and
C. upsaliensis
by Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry
Authors: Mandrell Robert E. , Harden Leslie A. , Bates Anna , Miller William G. , Haddon William F. , Fagerquist Clifton K. 
Published: October 2005

ABSTRACT

Multiple strains of
Campylobacter coli
,
C. jejuni
,
C. helveticus
,
C. lari
,
C. sputorum
, and
C. upsaliensis
isolated from animal, clinical, or food samples have been analyzed by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). Whole bacterial cells were harvested from colonies or confluent growth on agar and transferred directly into solvent and then to a spot of dried 3-methoxy-4-hydroxycinnamic acid (matrix). Multiple ions in the 5,000- to 15,000-Da mass range were evident in spectra for each strain; one or two ions in the 9,500- to 11,000-Da range were consistently high intensity. “Species-identifying” biomarker ions (SIBIs) were evident from analyses of multiple reference strains for each of the six species, including the genome strains
C. jejuni
NCTC 11168 and
C. jejuni
RM1221. Strains grown on nine different combinations of media and atmospheres yielded SIBI masses within ±5 Da with external instrument calibration. The highest-intensity
C. jejuni
SIBIs were cytosolic proteins, including GroES, HU/HCj, and RplL. Multiple intraspecies SIBIs, corresponding probably to nonsynonymous nucleotide polymorphisms, also provided some intraspecies strain differentiation. MALDI-TOF MS analysis of 75 additional
Campylobacter
strains isolated from humans, poultry, swine, dogs, and cats revealed (i) associations of SIBI type with source, (ii) strains previously speciated incorrectly, and (iii) “strains” composed of more than one species. MALDI-TOF MS provides an accurate, sensitive, and rapid method for identification of multiple
Campylobacter
species relevant to public health and food safety.
Microbiological and Geochemical Heterogeneity in an In Situ Uranium Bioremediation Field Site
Authors: Vrionis Helen A. , Anderson Robert T. , Ortiz-Bernad Irene , O'Neill Kathleen R. , Resch Charles T. , Peacock Aaron D. , Dayvault Richard , White David C. , Long Philip E. , Lovley Derek R. 
Published: October 2005

ABSTRACT

The geochemistry and microbiology of a uranium-contaminated subsurface environment that had undergone two seasons of acetate addition to stimulate microbial U(VI) reduction was examined. There were distinct horizontal and vertical geochemical gradients that could be attributed in large part to the manner in which acetate was distributed in the aquifer, with more reduction of Fe(III) and sulfate occurring at greater depths and closer to the point of acetate injection. Clone libraries of 16S rRNA genes derived from sediments and groundwater indicated an enrichment of sulfate-reducing bacteria in the order
Desulfobacterales
in sediment and groundwater samples. These samples were collected nearest the injection gallery where microbially reducible Fe(III) oxides were highly depleted, groundwater sulfate concentrations were low, and increases in acid volatile sulfide were observed in the sediment. Further down-gradient, metal-reducing conditions were present as indicated by intermediate Fe(II)/Fe(total) ratios, lower acid volatile sulfide values, and increased abundance of 16S rRNA gene sequences belonging to the dissimilatory Fe(III)- and U(VI)-reducing family
Geobacteraceae
. Maximal Fe(III) and U(VI) reduction correlated with maximal recovery of
Geobacteraceae
16S rRNA gene sequences in both groundwater and sediment; however, the sites at which these maxima occurred were spatially separated within the aquifer. The substantial microbial and geochemical heterogeneity at this site demonstrates that attempts should be made to deliver acetate in a more uniform manner and that closely spaced sampling intervals, horizontally and vertically, in both sediment and groundwater are necessary in order to obtain a more in-depth understanding of microbial processes and the relative contribution of attached and planktonic populations to in situ uranium bioremediation.
Agreement between Theory and Measurement in Quantification of Ammonia-Oxidizing Bacteria
Authors: Coskuner Gulnur , Ballinger Stuart J. , Davenport Russell J. , Pickering Rheanne L. , Solera Rosario , Head Ian M. , Curtis Thomas P. 
Published: October 2005

ABSTRACT
Autotrophic ammonia-oxidizing bacteria (AOB) are of vital importance to wastewater treatment plants (WWTP), as well as being an intriguing group of microorganisms in their own right. To date, corroboration of quantitative measurements of AOB by fluorescence in situ hybridization (FISH) has relied on assessment of the ammonia oxidation rate per cell, relative to published values for cultured AOB. Validation of cell counts on the basis of substrate transformation rates is problematic, however, because published cell-specific ammonia oxidation rates vary by over two orders of magnitude. We present a method that uses FISH in conjunction with confocal scanning laser microscopy to quantify AOB in WWTP, where AOB are typically observed as microcolonies. The method is comparatively simple, requiring neither detailed cell counts or image analysis, and yet it can give estimates of either cell numbers or biomass. Microcolony volume and diameter were found to have a log-normal distribution. We were able to show that virtually all (>96%) of the AOB biomass occurred as microcolonies. Counts of microcolony abundance and measurement of their diameter coupled with a calibration of microcolony dimensions against cell numbers or AOB biomass were used to determine AOB cell numbers and biomass in WWTP. Cell-specific ammonia oxidation rates varied between plants by over three orders of magnitude, suggesting that cell-specific ammonia oxidation is an important process variable. Moreover, when measured AOB biomass was compared with process-based estimates of AOB biomass, the two values were in agreement.
Differentiation of
Campylobacter
Populations as Demonstrated by Flagellin Short Variable Region Sequences
Authors: Meinersmann Richard J. , Phillips Robert W. , Hiett Kelli L. , Fedorka-Cray Paula 
Published: October 2005

ABSTRACT

The DNA sequence of the
flaA
short variable region (SVR) was used to analyze a random population of
Campylobacter
isolates to investigate the weakly clonal population structure of members of the genus. The SVR sequence from 197 strains of
C. jejuni
and
C. coli
isolated from humans, bovine, swine, and chickens identified a group of 43 strains containing disparate short variable region sequences compared to the rest of the population. This group contains both
C. jejuni
and
C. coli
strains but disproportionately consisted of bovine isolates. Relative synonymous codon usage analysis of the sequences identified two groups: one group typified
C. jejuni
, and the second group was characteristic for
C. coli
and the disparate alleles were not clustered. The data show that there is significant differentiation of
Campylobacter
populations according to the source of the isolate even without considering the disparate isolates. Even though there is significant differentiation of chicken and bovine isolates, the bovine isolates did not show any difference in ability to colonize chickens. It is possible that disparate sequences were obtained through the lateral transfer of DNA from
Campylobacter
species other than
C. jejuni
and
C. coli
. It is evident that recombination within the
flaA
SVR occurs rapidly. However, the rate of migration between populations appears to limit the distribution of sequences and results in a weakly clonal population structure.
Effects of Dissolved Sulfide, pH, and Temperature on Growth and Survival of Marine Hyperthermophilic Archaea
Authors: Lloyd Karen G. , Edgcomb Virginia P. , Molyneaux Stephen J. , Böer Simone , Wirsen Carl O. , Atkins Michael S. , Teske Andreas 
Published: October 2005

ABSTRACT

The ability of metabolically diverse hyperthermophilic archaea to withstand high temperatures, low pHs, high sulfide concentrations, and the absence of carbon and energy sources was investigated. Close relatives of our study organisms,
Methanocaldococcus jannaschii
,
Archaeoglobus profundus
,
Thermococcus fumicolans
, and
Pyrococcus
sp. strain GB-D, are commonly found in hydrothermal vent chimney walls and hot sediments and possibly deeper in the subsurface, where highly dynamic hydrothermal flow patterns and steep chemical and temperature gradients provide an ever-changing mosaic of microhabitats. These organisms (with the possible exception of
Pyrococcus
strain GB-D) tolerated greater extremes of low pH, high sulfide concentration, and high temperature when actively growing and metabolizing than when starved of carbon sources and electron donors/acceptors. Therefore these organisms must be actively metabolizing in the hydrothermal vent chimneys, sediments, and subsurface in order to withstand at least 24 h of exposure to extremes of pH, sulfide, and temperature that occur in these environments.
Engineering
Candida tenuis
Xylose Reductase for Improved Utilization of NADH: Antagonistic Effects of Multiple Side Chain Replacements and Performance of Site-Directed Mutants under Simulated In Vivo Conditions
Authors: Petschacher Barbara , Nidetzky Bernd 
Published: October 2005

ABSTRACT

Six single- and multiple-site variants of
Candida tenuis
xylose reductase that were engineered to have side chain replacements in the coenzyme 2′-phosphate binding pocket were tested for NADPH versus NADH selectivity (
R
sel
) in the presence of physiological reactant concentrations. The experimental
R
sel
values agreed well with predictions from a kinetic mechanism describing mixed alternative coenzyme utilization. The Lys-274→Arg and Arg-280→His substitutions, which individually improved wild-type
R
sel
50- and 20-fold, respectively, had opposing structural effects when they were combined in a double mutant.
Effect of Bovine Manure onCryptosporidium parvumOocyst Attachment to Soil
Authors: Kuczynska Ewa , Shelton Daniel R. , Pachepsky Yakov 
Published: October 2005

ABSTRACTThe objective of this work was to assess the effect of dilute bovine manure (1.0% and 0.1%) versus that of no manure on attachment and subsequent detachment ofCryptosporidium parvumoocysts to soil. Manure enhanced the attachment of oocysts to soil particles; the maximum attachment was observed with 0.1% manure. Oocyst attachment was partially reversible; maximum detachment was observed with dilute manure. These results indicate that oocyst attachment to soil is substantially affected by bovine manure in a complex manner and should have implications for how oocysts may be transported through or over soils.
Sau-PCR, a Novel Amplification Technique for Genetic Fingerprinting of Microorganisms
Authors: Corich Viviana , Mattiazzi Alessandro , Soldati Elisa , Carraro Angela , Giacomini Alessio 
Published: October 2005

ABSTRACT
The proposed technique is based on the digestion of genomic DNA with the restriction endonuclease Sau3AI and subsequent amplification with primers whose core sequence is based on the Sau3AI recognition site. The method was tested on strains of lactic acid bacteria but could be proposed for virtually any culturable organism from which DNA can be extracted.
Reduction of Uranium(VI) Phosphate during Growth of the Thermophilic Bacterium
Thermoterrabacterium ferrireducens
Authors: Khijniak T. V. , Slobodkin A. I. , Coker V. , Renshaw J. C. , Livens F. R. , Bonch-Osmolovskaya E. A. , Birkeland N.-K. , Medvedeva-Lyalikova N. N. , Lloyd J. R. 
Published: October 2005

ABSTRACT

The thermophilic, gram-positive bacterium
Thermoterrabacterium ferrireducens
coupled organotrophic growth to the reduction of sparingly soluble U(VI) phosphate. X-ray powder diffraction and X-ray absorption spectroscopy analysis identified the electron acceptor in a defined medium as U(VI) phosphate [uramphite; (NH
4
)(UO
2
)(PO
4
) · 3H
2
O], while the U(IV)-containing precipitate formed during bacterial growth was identified as ningyoite [CaU(PO
4
)
2
· H
2
O]. This is the first report of microbial reduction of a largely insoluble U(VI) compound.
Fecal Microbiota Composition and Frailty
Authors: van Tongeren Sandra P. , Slaets Joris P. J. , Harmsen H. J. M. , Welling Gjalt W. 
Published: October 2005

ABSTRACTThe relationship between fecal microbiota composition and frailty in the elderly was studied. Fecal samples from volunteers with high frailty scores showed a significant reduction in the number of lactobacilli (26-fold). At much higher population levels, both theBacteroides/Prevotella(threefold) and theFaecalibacterium prausnitzii(fourfold) groups showed a significant reduction in percentage of total number of hybridizable bacteria in the elderly with high frailty scores. In contrast to this, the number ofEnterobacteriaceaewas significantly higher (sevenfold) in samples from very frail volunteers.
Humoral and Cellular Immunity in Children withMycoplasma pneumoniaeInfection: a 1-Year Prospective Study
Authors: Stelmach Iwona , Podsiadłowicz-Borzęcka Malgorzata , Grzelewski Tomasz , Majak Pawel , Stelmach Wlodzimierz , Jerzyńska Joanna , Popławska Marta , Dziadek Jaroslaw 
Published: October 2005

ABSTRACTTo determine whether children have persistent abnormalities in cellular and humoral immunity development after acuteMycoplasma pneumoniaeinfection, serum immunoglobulin G (IgG), IgA, IgM, and IgE levels and lymphocyte phenotypes were determined. There were no changes in the levels of IgG, IgM, IgA, or CD4+or CD19+lymphocytes that were measured inM. pneumoniae-positive patients after 3 months or after 12 months, but there were increases in these inM. pneumoniae-negative patients. Serum IgE increased inM. pneumoniae-positive patients. We have shown alterations in immunity development afterM. pneumoniaeinfection.
Headstarting in European pond turtles (Emys orbicularis): Does it work?
Authors: Mitrus Sławomir 
Published: October 2005

AbstractThe European pond turtle (Emys orbicularis) is an endangered species in Poland. From 1998 to 2000, as part of an active protection program for the species in central Poland, 123 one-year-old headstarted individuals were released into their original population. Survival rate in artificial rearing was 0.85. Annual recapture rate of the released turtles during the first year in the wild was 0.24, and during next year 0.43 or higher. For comparable groups of one-year-old turtles the annual recapture rates of wild vs. headstarted were not statistically different, but they were based on small samples. Analysis of the data based on a life table for Emydoidea blandingii and data on survival rate of E. orbicularis to age one suggests that headstarting programs can increase population size only if a large percentage of hatchlings is taken to artificial rearing. However, as we know nothing about behaviour and survivorship of older headstarted turtles, such programs still should be considered as experiments.
Optimizing Parameters in an Atmospheric General Circulation Model
Authors: Severijns C. A. , Hazeleger W. 
Published: October 2005

Abstract
An efficient method to optimize the parameter values of the subgrid parameterizations of an atmospheric general circulation model is described. The method is based on the downhill simplex minimization of a cost function computed from the difference between simulated and observed fields. It is used to find optimal values of the radiation and cloud-related parameters. The model error is reduced significantly within a limited number of iterations (about 250) of short integrations (5 yr). The method appears to be robust and finds the global minimum of the cost function. The radiation budget of the model improves considerably without violating the already well simulated general circulation. Different aspects of the general circulation, such as the Hadley and Walker cells improve, although they are not incorporated into the cost function. It is concluded that the method can be used to efficiently determine optimal parameters for general circulation models even when the model behavior has a strong nonlinear dependence on these parameters.