bluuebunny/crossref_metadata_2025_split huggingface dataset:
Carbon Isotope Fractionation during Anaerobic Degradation of Methyl
tert
-Butyl Ether under Sulfate-Reducing and Methanogenic Conditions
Authors: Somsamak Piyapawn , Richnow Hans H. , Häggblom Max M. 
Published: February 2006

ABSTRACT

Methyl
tert
-butyl ether (MTBE), an octane enhancer and a fuel oxygenate in reformulated gasoline, has received increasing public attention after it was detected as a major contaminant of water resources. Although several techniques have been developed to remediate MTBE-contaminated sites, the fate of MTBE is mainly dependent upon natural degradation processes. Compound-specific stable isotope analysis has been proposed as a tool to distinguish the loss of MTBE due to biodegradation from other physical processes. Although MTBE is highly recalcitrant, anaerobic degradation has been demonstrated under different anoxic conditions and may be an important process. To accurately assess in situ MTBE degradation through carbon isotope analysis, carbon isotope fractionation during MTBE degradation by different cultures under different electron-accepting conditions needs to be investigated. In this study, carbon isotope fractionation during MTBE degradation under sulfate-reducing and methanogenic conditions was studied in anaerobic cultures enriched from two different sediments. Significant enrichment of
13
C in residual MTBE during anaerobic biotransformation was observed under both sulfate-reducing and methanogenic conditions. The isotopic enrichment factors (ε) estimated for each enrichment were almost identical (−13.4

to −14.6

;
r
2
= 0.89 to 0.99). A ε value of −14.4

± 0.7

was obtained from regression analysis (
r
2
= 0.97,
n
= 55, 95% confidence interval), when all data from our MTBE-transforming anaerobic cultures were combined. The similar magnitude of carbon isotope fractionation in all enrichments regardless of culture or electron-accepting condition suggests that the terminal electron-accepting process may not significantly affect carbon isotope fractionation during anaerobic MTBE degradation.
Nonlinear Dependency of Intracellular Fluxes on Growth Rate in Miniaturized Continuous Cultures ofEscherichia coli
Authors: Nanchen Annik , Schicker Alexander , Sauer Uwe 
Published: February 2006

ABSTRACTA novel mini-scale chemostat system was developed for the physiological characterization of 10-ml cultures. The parallel operation of eight such mini-scale chemostats was exploited for systematic13C analysis of intracellular fluxes over a broad range of growth rates in glucose-limitedEscherichia coli. As expected, physiological variables changed monotonously with the dilution rate, allowing for the assessment of maintenance metabolism. Despite the linear dependence of total cellular carbon influx on dilution rate, the distribution of almost all major fluxes varied nonlinearly with dilution rate. Most prominent were the distinct maximum of glyoxylate shunt activity and the concomitant minimum of tricarboxylic acid cycle activity at low to intermediate dilution rates of 0.05 to 0.2 h−1. During growth on glucose, this glyoxylate shunt activity is best understood from a network perspective as the recently described phosphoenolpyruvate (PEP)-glyoxylate cycle that oxidizes PEP (or pyruvate) to CO2. At higher or extremely low dilution rates, in vivo PEP-glyoxylate cycle activity was low or absent. The step increase in pentose phosphate pathway activity at around 0.2 h−1was not related to the cellular demand for the reduction equivalent NADPH, since NADPH formation was 20 to 50% in excess of the anabolic demand at all dilution rates. The results demonstrate that mini-scale continuous cultivation enables quantitative and parallel characterization of intra- and extracellular phenotypes in steady state, thereby greatly reducing workload and costs for stable-isotope experiments.
Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry for the Discrimination of Food-Borne Microorganisms
Authors: Mazzeo Maria Fiorella , Sorrentino Alida , Gaita Marcello , Cacace Giuseppina , Di Stasio Michele , Facchiano Angelo , Comi Giuseppe , Malorni Antonio , Siciliano Rosa Anna 
Published: February 2006

ABSTRACT

A methodology based on matrix-assisted laser desorption ionization-time of flight mass spectrometry of intact bacterial cells was used for rapid discrimination of 24 bacterial species, and detailed analyses to identify
Escherichia coli
O157:H7 were carried out. Highly specific mass spectrometric profiles of pathogenic and nonpathogenic bacteria that are well-known major food contaminants were obtained, uploaded in a specific database, and made available on the Web. In order to standardize the analytical protocol, several experimental, sample preparation, and mass spectrometry parameters that can affect the reproducibility and accuracy of data were evaluated. Our results confirm the conclusion that this strategy is a powerful tool for rapid and accurate identification of bacterial species and that mass spectrometric methodologies could play an essential role in polyphasic approaches to the identification of pathogenic bacteria.
Coexistence of
Burkholderia
,
Cupriavidus
, and
Rhizobium
sp. Nodule Bacteria on two
Mimosa
spp. in Costa Rica
Authors: Barrett Craig F. , Parker Matthew A. 
Published: February 2006

ABSTRACT

rRNA gene sequencing and PCR assays indicated that 215 isolates of root nodule bacteria from two
Mimosa
species at three sites in Costa Rica belonged to the genera
Burkholderia
,
Cupriavidus
, and
Rhizobium
. This is the first report of
Cupriavidus
sp. nodule symbionts for
Mimosa
populations within their native geographic range in the neotropics.
Burkholderia
spp. predominated among samples from
Mimosa pigra
(86% of isolates), while there was a more even distribution of
Cupriavidus
,
Burkholderia
, and
Rhizobium
spp. on
Mimosa pudica
(38, 37, and 25% of isolates, respectively). All
Cupriavidus
and
Burkholderia
genotypes tested formed root nodules and fixed nitrogen on both
M. pigra
and
M. pudica
, and sequencing of rRNA genes in strains reisolated from nodules verified identity with inoculant strains. Inoculation tests further indicated that both
Cupriavidus
and
Burkholderia
spp. resulted in significantly higher plant growth and nodule nitrogenase activity (as measured by acetylene reduction assays) relative to plant performance with strains of
Rhizobium
. Given the prevalence of
Burkholderia
and
Cupriavidus
spp. on these
Mimosa
legumes and the widespread distribution of these plants both within and outside the neotropics, it is likely that both β-proteobacterial genera are more ubiquitous as root nodule symbionts than previously believed.
Characterization of the
tre
Locus and Analysis of Trehalose Cryoprotection in
Lactobacillus acidophilus
NCFM
Authors: Duong Tri , Barrangou Rodolphe , Russell W. Michael , Klaenhammer Todd R. 
Published: February 2006

ABSTRACT

Freezing and lyophilization are common methods used for preservation and storage of microorganisms during the production of concentrated starter cultures destined for industrial fermentations or product formulations. The compatible solute trehalose has been widely reported to protect bacterial, yeast and animal cells against a variety of environmental stresses, particularly freezing and dehydration. Analysis of the
Lactobacillus acidophilus
NCFM genome revealed a putative trehalose utilization locus consisting of a transcriptional regulator,
treR
; a trehalose phosphoenolpyruvate transferase system (PTS) transporter,
treB
; and a trehalose-6-phosphate hydrolase,
treC
. The objective of this study was to characterize the
tre
locus in
L. acidophilus
and determine whether or not intracellular uptake of trehalose contributes to cryoprotection. Cells subjected to repeated freezing and thawing cycles were monitored for survival in the presence of various concentrations of trehalose. At 20% trehalose a 2-log increase in survival was observed. The trehalose PTS transporter and trehalose hydrolase were disrupted by targeted plasmid insertions. The resulting mutants were unable to grow on trehalose, indicating that both trehalose transport into the cell via a PTS and hydrolysis via a trehalose-6-phosphate hydrolase were necessary for trehalose fermentation. Trehalose uptake was found to be significantly reduced in the transporter mutant but unaffected in the hydrolase mutant. Additionally, the cryoprotective effect of trehalose was reduced in these mutants, suggesting that intracellular transport and hydrolysis contribute significantly to cryoprotection.
Sequence Variation among Group III F-Specific RNA Coliphages from Water Samples and Swine Lagoons
Authors: Stewart Jill R. , Vinjé Jan , Oudejans Sjon J. G. , Scott Geoff I. , Sobsey Mark D. 
Published: February 2006

ABSTRACT
Typing of F-specific RNA (FRNA) coliphages has been proposed as a useful method for distinguishing human from animal fecal contamination in environmental samples. Group II and III FRNA coliphages are generally associated with human wastes, but several exceptions have been noted. In the present study, we have genotyped and partially sequenced group III FRNA coliphage field isolates from swine lagoons in North Carolina (NC) and South Carolina (SC), along with isolates from surface waters and municipal wastewaters. Phylogenetic analysis of a region of the 5′ end of the maturation protein gene revealed two genetically different group III FRNA subclusters with 36.6% sequence variation. The SC swine lagoon isolates were more closely related to group III prototype virus M11, whereas the isolates from a swine lagoon in NC, surface waters, and wastewaters grouped with prototype virus Q-beta. These results suggest that refining phage genotyping systems to discriminate M11-like phages from Q-beta-like phages would not necessarily provide greater discriminatory power in distinguishing human from animal sources of pollution. Within the group III subclusters, nucleotide sequence diversity ranged from 0% to 6.9% for M11-like strains and from 0% to 8.7% for Q-beta-like strains. It is demonstrated here that nucleotide sequencing of closely related FRNA strains can be used to help track sources of contamination in surface waters. A similar use of phage genomic sequence information to track fecal pollution promises more reliable results than phage typing by nucleic acid hybridization and may hold more potential for field applications.
Isolation and Characterization of a Cyanophage Infecting the Toxic Cyanobacterium
Microcystis aeruginosa
Authors: Yoshida Takashi , Takashima Yukari , Tomaru Yuji , Shirai Yoko , Takao Yoshitake , Hiroishi Shingo , Nagasaki Keizo 
Published: February 2006

ABSTRACT

We isolated a cyanophage (Ma-LMM01) that specifically infects a toxic strain of the bloom-forming cyanobacterium
Microcystis aeruginosa
. Transmission electron microscopy showed that the virion is composed of anisometric head and a tail complex consisting of a central tube and a contractile sheath with helical symmetry. The morphological features and the host specificity suggest that Ma-LMM01 is a member of the cyanomyovirus group. Using semi-one-step growth experiments, the latent period and burst size were estimated to be 6 to 12 h and 50 to 120 infectious units per cell, respectively. The size of the phage genome was estimated to be ca. 160 kbp using pulse-field gel electrophoresis; the nucleic acid was sensitive to DNase I, Bal31, and all 14 restriction enzymes tested, suggesting that it is a linear double-stranded DNA having a low level of methylation. Phylogenetic analyses based on the deduced amino acid sequences of two open reading frames coding for ribonucleotide reductase alpha- and beta-subunits showed that Ma-LMM01 forms a sister group with marine and freshwater cyanobacteria and is apparently distinct from T4-like phages. Phylogenetic analysis of the deduced amino acid sequence of the putative sheath protein showed that Ma-LMM01 does not form a monophyletic group with either the T4-like phages or prophages, suggesting that Ma-LMM01 is distinct from other T4-like phages that have been described despite morphological similarity. The host-phage system which we studied is expected to contribute to our understanding of the ecology of
Microcystis
blooms and the genetics of cyanophages, and our results suggest the phages could be used to control toxic cyanobacterial blooms.
Catabolism of 1,5-Anhydro-d-Fructose inSinorhizobium morelenseS-30.7.5: Discovery, Characterization, and Overexpression of a New 1,5-Anhydro-d-Fructose Reductase and Its Application in Sugar Analysis and Rare Sugar Synthesis
Authors: Kühn Annette , Yu Shukun , Giffhorn Friedrich 
Published: February 2006

ABSTRACTThe bacteriumSinorhizobium morelenseS-30.7.5 was isolated by a microbial screening using the sugar 1,5-anhydro-d-fructose (AF) as the sole carbon source. This strain metabolized AF by a novel pathway involving its reduction to 1,5-anhydro-d-mannitol (AM) and the further conversion of AM tod-mannose by C-1 oxygenation. Growth studies showed that the AF metabolizing capability is not confined toS. morelenseS-30.7.5 but is a more common feature among theRhizobiaceae. The AF reducing enzyme was purified and characterized as a new NADPH-dependent monomeric reductase (AFR, EC 1.1.1.-) of 35.1 kDa. It catalyzed the stereoselective reduction of AF to AM and also the conversion of a number of 2-keto aldoses (osones) to the corresponding manno-configurated aldoses. In contrast, common aldoses and ketoses, as well as nonsugar aldehydes and ketones, were not reduced. A database search using the N-terminal AFR sequence retrieved a putative 35-kDa oxidoreductase encoded by the open reading frameSmc04400localized on the chromosome ofSinorhizobium meliloti1021. Based on sequence information for this locus, theafrgene was cloned fromS. morelenseS-30.7.5 and overexpressed inEscherichia coli. In addition to the oxidoreductase ofS. meliloti1021, AFR showed high sequence similarities to putative oxidoreductases ofMesorhizobium loti,Brucella suis, andB. melitensisbut not to any oxidoreductase with known functions. AFR could be assigned to the GFO/IDH/MocA family on the basis of highly conserved common structural features. His6-tagged AFR was used to demonstrate the utility of this enzyme for AF analysis and synthesis of AM, as well as related derivatives.
Root-Associated Bacteria Contribute to Mineral Weathering and to Mineral Nutrition in Trees: a Budgeting Analysis
Authors: Calvaruso Christophe , Turpault Marie-Pierre , Frey-Klett Pascale 
Published: February 2006

ABSTRACT

The principal nutrient source for forest trees derives from the weathering of soil minerals which results from water circulation and from plant and microbial activity. The main objectives of this work were to quantify the respective effects of plant- and root-associated bacteria on mineral weathering and their consequences on tree seedling growth and nutrition. That is why we carried out two column experiments with a quartz-biotite substrate. The columns were planted with or without pine seedlings and inoculated or not with three ectomycorrhizosphere bacterial strains to quantify biotite weathering and pine growth and to determine how bacteria improve pine growth. We showed that the pine roots significantly increased biotite weathering by a factor of 1.3 for magnesium and 1.7 for potassium. We also demonstrated that the inoculation of
Burkholderia glathei
PML1(12) significantly increased biotite weathering by a factor of 1.4 for magnesium and 1.5 for potassium in comparison with the pine alone. In addition, we observed a significant positive effect of
B. glathei
PMB1(7) and PML1(12) on pine growth and on root morphology (number of lateral roots and root hairs). We demonstrated that PML1(12) improved pine growth when the seedlings were supplied with a nutrient solution which did not contain the nutrients present in the biotite. No improvement of pine growth was observed when the seedlings were supplied with all the nutrients necessary for pine growth. We therefore propose that the growth-promoting effect of
B. glathei
PML1(12) mainly resulted from the improved plant nutrition via increased mineral weathering.
RNA-Mediated Gene Silencing in Monokaryons and Dikaryons of
Schizophyllum commune
Authors: de Jong Jan F. , Deelstra Heine J. , Wösten Han A. B. , Lugones Luis G. 
Published: February 2006

ABSTRACT

Disruption of genes by homologous recombination occurs at a low frequency in the basidiomycete
Schizophyllum commune
. For instance, the
SC3
and
SC15
genes were inactivated at frequencies of 1 and 5%, respectively. As an alternative to disruption, we used gene silencing through the introduction of a hairpin construct. The
SC15
gene, which encodes an abundantly secreted structural protein, was silenced at a frequency of 80% in monokaryons of
S. commune
after introduction of a hairpin construct of the gene. Silencing also occurred in dikaryons in which one of the partners was not a silenced strain. The silencing mechanism resembles RNAi in other filamentous fungi and is a powerful tool for the functional analysis of genes expressed in monokaryons or dikaryons.
Construction and Complementation of In-Frame Deletions of the Essential
Escherichia coli
Thymidylate Kinase Gene
Authors: Chaperon David-Nicolas 
Published: February 2006

ABSTRACT

This work reports the construction of
Escherichia coli
in-frame deletion strains of
tmk
, which encodes thymidylate kinase, Tmk. The
tmk
gene is located at the third position of a putative five-gene operon at 24.9 min on the
E. coli
chromosome, which comprises the genes
pabC
,
yceG
,
tmk
,
holB
, and
ycfH
. To avoid potential polar effects on downstream genes of the operon, as well as recombination with plasmid-encoded
tmk
, the
tmk
gene was replaced by the kanamycin resistance gene
kka1
, encoding amino glycoside 3′-phosphotransferase kanamycin kinase. The kanamycin resistance gene is expressed under the control of the natural promoter(s) of the putative operon. The
E. coli tmk
gene is essential under any conditions tested. To show functional complementation in bacteria, the
E. coli tmk
gene was replaced by thymidylate kinases of bacteriophage T4 gp
1
,
E. coli tmk
,
Saccharomyces cerevisiae cdc8
, or the
Homo sapiens
homologue,
dTYMK
. Growth of these transgenic
E. coli
strains is completely dependent on thymidylate kinase activities of various origin expressed from plasmids. The substitution constructs show no polar effects on the downstream genes
holB
and
ycfH
with respect to cell viability. The presented transgenic bacteria could be of interest for testing of thymidylate kinase-specific phosphorylation of nucleoside analogues that are used in therapies against cancer and infectious diseases.
Cloning and Functional Characterization of the
styE
Gene, Involved in Styrene Transport in
Pseudomonas putida
CA-3
Authors: Mooney Aisling , O'Leary Niall D. , Dobson Alan D. W. 
Published: February 2006

ABSTRACT

A 1.5-kb region immediately downstream of the
styABCD
operon involved in styrene degradation in
Pseudomonas putida
CA-3 has been cloned. Sequence analysis revealed a 1,296-bp open reading frame, designated
styE
, and BLAST P database comparisons of the deduced StyE amino acid sequence revealed 33 to 98% identity with several membrane-associated ATPase-dependent kinase proteins involved in the active transport of aromatic hydrocarbons across bacterial membranes and also with FadL, an outer membrane protein necessary for the uptake of long-chain fatty acids in
Escherichia coli
. Transcription of
styE
is styrene dependent, and the gene is cotranscribed with the
styABCD
structural genes. StyE appears to be membrane associated, with a corresponding 45.9-kDa band being identified following sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis of membrane preparations from styrene-grown cells.
P. putida
CA-3 cells in which the
styE
gene had been interrupted were no longer capable of growth on styrene. In contrast, overexpression of
styE
in
P. putida
CA-3 resulted in a 4.2-fold increase in styrene monooxygenase activity compared with wild-type cells grown on styrene, with a concomitant 8-fold increase in
styA
mRNA transcript levels. Experiments with the classic, ATPase inhibitor vanadate revealed that growth of wild-type cells on styrene was inhibited at a concentration of 1 mM, while 1.75 mM was required to achieve a similar effect in the StyE overexpression strain. Growth of either strain on citrate was not inhibited in the presence of up to 7 mM vanadate. These findings suggest a role for StyE in the active transport of styrene in
Pseudomonas putida
CA-3 and identify styrene transport as a potentially limiting factor with respect to mRNA transcript levels and associated enzymatic activity of the styrene degradative pathway.
Genetic Modification of
Bacillus subtilis
for Production of
d
-
chiro
-Inositol, an Investigational Drug Candidate for Treatment of Type 2 Diabetes and Polycystic Ovary Syndrome
Authors: Yoshida Ken-ichi , Yamaguchi Masanori , Morinaga Tetsuro , Ikeuchi Maya , Kinehara Masaki , Ashida Hitoshi 
Published: February 2006

ABSTRACT

d
-
chiro
-Inositol (DCI) is a drug candidate for the treatment of type 2 diabetes and polycystic ovary syndrome, since it improves the efficiency with which the body uses insulin and also promotes ovulation. Here, we report genetic modification of
Bacillus subtilis
for production of DCI from
myo
-inositol (MI). The
B. subtilis iolABCDEFGHIJ
operon encodes enzymes for the multiple steps of the MI catabolic pathway. In the first and second steps, MI is converted to 2-keto-MI (2KMI) by IolG and then to 3
d
-(3,5/4)-trihydroxycyclohexane-1,2-dione by IolE. In this study, we identified
iolI
encoding inosose isomerase, which converts 2KMI to 1-keto-
d
-
chiro
-inositol (1KDCI), and found that IolG reduces 1KDCI to DCI. Inactivation of
iolE
in a mutant constitutively expressing the
iol
operon blocked the MI catabolic pathway to accumulate 2KMI, which was converted to DCI via the activity of IolI and IolG. The mutant was able to convert at least 6% of input MI in the culture medium to DCI.
Natural Transformation-Mediated Transfer of Erythromycin Resistance in
Campylobacter coli
Strains from Turkeys and Swine
Authors: Kim Joo-Sung , Carver Donna K. , Kathariou Sophia 
Published: February 2006

ABSTRACT

Erythromycin resistance in
Campylobacter coli
from meat animals is frequently encountered and could represent a substantial barrier to antibiotic treatment of human infections. Erythromycin resistance in this organism has been associated with a point mutation (A2075G) in the 23S rRNA gene. However, the mechanisms responsible for possible dissemination of erythromycin resistance in
C. coli
remain poorly understood. In this study, we investigated transformation-mediated acquisition of erythromycin resistance by genotypically diverse
C. coli
strains from turkeys and swine, with total genomic DNA from erythromycin-resistant
C. coli
of either turkey or swine origin used as a donor. Overall, transformation to erythromycin resistance was significantly more frequent in
C. coli
strains from turkeys than in swine-derived strains (
P
< 0.01). The frequency of transformation to erythromycin resistance was 10
−5
to 10
−6
for turkey-derived strains but 10
−7
or less for
C. coli
from swine. Transformants harbored the point mutation A2075G in the 23S rRNA gene, as did the erythromycin-resistant strains used as DNA donors. Erythromycin resistance was stable in transformants following serial transfers in the absence of the antibiotic, and most transformants had high MICs (>256 μg/ml), as did the
C. coli
donor strains. In contrast to the results obtained with transformation, spontaneous mutants had relatively low erythromycin MICs (32 to 64 μg/ml) and lacked the A2075G mutation in the 23S rRNA gene. These findings suggest that natural transformation has the potential to contribute to the dissemination of high-level resistance to erythromycin among
C. coli
strains colonizing meat animals.