bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bacteria of the γ-Subclass
Proteobacteria
Associated with Zooplankton in Chesapeake Bay
Authors: Heidelberg J. F. , Heidelberg K. B. , Colwell R. R. 
Published: April 2009

ABSTRACT

The seasonal abundance of γ-subclass
Proteobacteria, Vibrio-Photobacterium, Vibrio cholerae-Vibrio mimicus, Vibrio cincinnatiensis,
and
Vibrio vulnificus
in the Choptank River of Chesapeake Bay associated with zooplankton was monitored from April to December 1996. Large (>202-μm) and small (64- to 202-μm) size classes of zooplankton were collected, and the bacteria associated with each of the zooplankton size classes were enumerated by fluorescent oligonucleotide direct count. Large populations of bacteria were found to be associated with both the large and small size classes of zooplankton. Also, the species of bacteria associated with the zooplankton showed seasonal abundance, with the largest numbers occurring in the early spring and again in the summer, when zooplankton total numbers were correspondingly large. Approximately 0.01 to 40.0% of the total water column bacteria were associated with zooplankton, with the percentage of the total water column bacteria population associated with zooplankton varying by season. A taxonomically diverse group of bacteria was associated with zooplankton, and a larger proportion was found in and on zooplankton during the cooler months of the year, with selected taxa comprising a larger percent of the
Bacteria
in the summer.
V. cholerae-V. mimicus
and
V. vulnificus
comprised the bulk of the large and small zooplankton-associated
Vibrio-Photobacterium
species. In contrast,
V. cincinnatiensis
accounted for less than 0.1 to 3%. It is concluded that water column and zooplankton bacterial populations vary independently with respect to species composition since no correlation was observed between taxa occurring with highest frequency in the water column and those in association with zooplankton.
Robust Hydrocarbon Degradation and Dynamics of Bacterial Communities during Nutrient-Enhanced Oil Spill Bioremediation
Authors: Röling Wilfred F. M. , Milner Michael G. , Jones D. Martin , Lee Kenneth , Daniel Fabien , Swannell Richard J. P. , Head Ian M. 
Published: April 2009

ABSTRACT

Degradation of oil on beaches is, in general, limited by the supply of inorganic nutrients. In order to obtain a more systematic understanding of the effects of nutrient addition on oil spill bioremediation, beach sediment microcosms contaminated with oil were treated with different levels of inorganic nutrients. Oil biodegradation was assessed respirometrically and on the basis of changes in oil composition. Bacterial communities were compared by numerical analysis of denaturing gradient gel electrophoresis (DGGE) profiles of PCR-amplified 16S rRNA genes and cloning and sequencing of PCR-amplified 16S rRNA genes. Nutrient amendment over a wide range of concentrations significantly improved oil degradation, confirming that N and P limited degradation over the concentration range tested. However, the extent and rate of oil degradation were similar for all microcosms, indicating that, in this experiment, it was the addition of inorganic nutrients rather than the precise amount that was most important operationally. Very different microbial communities were selected in all of the microcosms. Similarities between DGGE profiles of replicate samples from a single microcosm were high (95% ± 5%), but similarities between DGGE profiles from replicate microcosms receiving the same level of inorganic nutrients (68% ± 5%) were not significantly higher than those between microcosms subjected to different nutrient amendments (63% ± 7%). Therefore, it is apparent that the different communities selected cannot be attributed to the level of inorganic nutrients present in different microcosms. Bioremediation treatments dramatically reduced the diversity of the bacterial community. The decrease in diversity could be accounted for by a strong selection for bacteria belonging to the alkane-degrading
Alcanivorax/Fundibacter
group. On the basis of Shannon-Weaver indices, rapid recovery of the bacterial community diversity to preoiling levels of diversity occurred. However, although the overall diversity was similar, there were considerable qualitative differences in the community structure before and after the bioremediation treatments.
Enhancing Transport ofHydrogenophagaflavaENV735 for Bioaugmentation of Aquifers Contaminated with Methyltert-Butyl Ether
Authors: Streger Sheryl H. , Vainberg Simon , Dong Hailiang , Hatzinger Paul B. 
Published: April 2009

ABSTRACTThe gasoline oxygenate methyltert-butyl ether (MTBE) has become a widespread contaminant in groundwater throughout the United States. Bioaugmentation of aquifers with MTBE-degrading cultures may be necessary to enhance degradation of the oxygenate in some locations. However, poor cell transport has sometimes limited bioaugmentation efforts in the past. The objective of this study was to evaluate the transport characteristics ofHydrogenophaga flavaENV735, a pure culture capable of growth on MTBE, and to improve movement of the strain through aquifer solids. The wild-type culture moved only a few centimeters in columns of aquifer sediment. An adhesion-deficient variant (H. flavaENV735:24) of the wild-type strain that moved more readily through sediments was obtained by sequential passage of cells through columns of sterile sediment. Hydrophobic and electrostatic interaction chromatography revealed that the wild-type strain is much more hydrophobic than the adhesion-deficient variant. Electrophoretic mobility assays and transmission electron microscopy showed that the wild-type bacterium contains two distinct subpopulations, whereas the adhesion-deficient strain has only a single, homogeneous population. Both the wild-type strain and adhesion-deficient variant degraded MTBE, and both were identified by 16S rRNA analysis as pure cultures ofH. flava. The effectiveness of surfactants for enhancing transport of the wild-type strain was also evaluated. Many of the surfactants tested were toxic to ENV735; however, one nonionic surfactant, Tween 20, enhanced cell transport in sand columns. Improving microbial transport may lead to a more effective bioaugmentation strategy for MTBE-contaminated sites where indigenous oxygenate degraders are absent.
Molecular Epidemiology of
Salmonella enterica
Serovar Typhimurium Isolates Determined by Pulsed-Field Gel Electrophoresis: Comparison of Isolates from Avian Wildlife, Domestic Animals, and the Environment in Norway
Authors: Refsum Thorbjørn , Heir Even , Kapperud Georg , Vardund Traute , Holstad Gudmund 
Published: April 2009

ABSTRACT

The molecular epidemiology of 142 isolates of
Salmonella enterica
serovar Typhimurium from avian wildlife, domestic animals, and the environment in Norway was investigated using pulsed-field gel electrophoresis (PFGE) and computerized numerical analysis of the data. The bacterial isolates comprised 79 isolates from wild-living birds, including 46 small passerines and 26 gulls, and 63 isolates of nonavian origin, including 50 domestic animals and 13 environmental samples. Thirteen main clusters were discernible at the 90% similarity level. Most of the isolates (83%) were grouped into three main clusters. These were further divided into 20 subclusters at the 95% similarity level. Isolates from passerines, gulls, and pigeons dominated within five subclusters, whereas isolates from domestic animals and the environment belonged to many different subclusters with no predominance. The results support earlier results that passerines constitute an important source of infection to humans in Norway, whereas it is suggested that gulls and pigeons, based on PFGE analysis, represent only a minor source of human serovar Typhimurium infections. Passerines, gulls, and pigeons may also constitute a source of infection of domestic animals and feed plants or vice versa. Three isolates from cattle and a grain source, of which two were multiresistant, were confirmed as serovar Typhimurium phage type DT 104. These represent the first reported phage type DT 104 isolates from other sources than humans in Norway.
Donor Substrate Regeneration for Efficient Synthesis of Globotetraose and Isoglobotetraose
Authors: Shao Jun , Zhang Jianbo , Kowal Przemyslaw , Wang Peng George 
Published: April 2009

ABSTRACTHere we describe the efficient synthesis of two oligosaccharide moieties of human glycosphingolipids, globotetraose (GalNAcβ1→3Galα1→4Galβ1→4Glc) and isoglobotetraose (GalNAcβ1→3Galα1→3Galβ1→4Glc), with in situ enzymatic regeneration of UDP-N-acetylgalactosamine (UDP-GalNAc). We demonstrate that the recombinant β-1,3-N-acetylgalactosaminyltransferase fromHaemophilus influenzaestrain Rd can transferN-acetylgalactosamine to a wide range of acceptor substrates with a terminal galactose residue. The donor substrate UDP-GalNAc can be regenerated by a six-enzyme reaction cycle consisting of phosphoglucosamine mutase, UDP-N-acetylglucosamine pyrophosphorylase, phosphate acetyltransferase, pyruvate kinase, and inorganic pyrophosphatase fromEscherichia coli, as well as UDP-N-acetylglucosamine C4 epimerase fromPlesiomonas shigelloides. All these enzymes were overexpressed inE. coliwith six-histidine tags and were purified by one-step nickel-nitrilotriacetic acid affinity chromatography. Multiple-enzyme synthesis of globotetraose or isoglobotetraose with the purified enzymes was achieved with relatively high yields.
Gbu Glycine Betaine Porter and Carnitine Uptake in Osmotically Stressed
Listeria monocytogenes
Cells
Authors: Mendum Mary Lou , Smith Linda Tombras 
Published: April 2009

ABSTRACT

The food-borne pathogen
Listeria monocytogenes
grows actively under high-salt conditions by accumulating compatible solutes such as glycine betaine and carnitine from the medium. We report here that the dominant transport system for glycine betaine uptake, the Gbu porter, may act as a secondary uptake system for carnitine, with a

K
m

of 4 mM for carnitine uptake and measurable uptake at carnitine concentrations as low as 10 μM. This porter has a

K
m

for glycine betaine uptake of about 6 μM. The dedicated carnitine porter, OpuC, has a

K
m

for carnitine uptake of 1 to 3 μM and a
V
max
of approximately 15 nmol/min/mg of protein. Mutants lacking either
opuC
or
gbu
were used to study the effects of four carnitine analogs on growth and uptake of osmolytes. In strain DP-L1044, which had OpuC and the two glycine betaine porters Gbu and BetL, triethylglycine was most effective in inhibiting growth in the presence of glycine betaine, but trigonelline was best at inhibiting growth in the presence of carnitine. Carnitine uptake through OpuC was inhibited by γ-butyrobetaine. Dimethylglycine inhibited both glycine betaine and carnitine uptake through the Gbu porter. Carnitine uptake through the Gbu porter was inhibited by triethylglycine. Glycine betaine uptake through the BetL porter was strongly inhibited by trigonelline and triethylglycine. These results suggest that it is possible to reduce the growth of
L. monocytogenes
under osmotically stressful conditions by inhibiting glycine betaine and carnitine uptake but that to do so, multiple uptake systems must be affected.
Cloning and Characterization of a Gene Cluster Involved in Cyclopentanol Metabolism in
Comamonas
sp. Strain NCIMB 9872 and Biotransformations Effected by
Escherichia coli
-Expressed Cyclopentanone 1,2-Monooxygenase
Authors: Iwaki Hiroaki , Hasegawa Yoshie , Wang Shaozhao , Kayser Margaret M. , Lau Peter C. K. 
Published: April 2009

ABSTRACT

Cyclopentanone 1,2-monooxygenase, a flavoprotein produced by
Pseudomonas
sp. strain NCIMB 9872 upon induction by cyclopentanol or cyclopentanone (M. Griffin and P. W. Trudgill, Biochem. J. 129:595-603, 1972), has been utilized as a biocatalyst in Baeyer-Villiger oxidations. To further explore this biocatalytic potential and to discover new genes, we have cloned and sequenced a 16-kb chromosomal locus of strain 9872 that is herein reclassified as belonging to the genus
Comamonas
. Sequence analysis revealed a cluster of genes and six potential open reading frames designated and grouped in at least four possible transcriptional units as (
orf11-orf10-orf9)-(cpnE-cpnD-orf6-cpnC)-(cpnR-cpnB-cpnA)-(orf3-orf4
[partial 3′ end]
)
. The
cpnABCDE
genes encode enzymes for the five-step conversion of cyclopentanol to glutaric acid catalyzed by cyclopentanol dehydrogenase, cyclopentanone 1,2-monooxygenase, a ring-opening 5-valerolactone hydrolase, 5-hydroxyvalerate dehydrogenase, and 5-oxovalerate dehydrogenase, respectively. Inactivation of
cpnB
by using a
lacZ
-Km
r
cassette resulted in a strain that was not capable of growth on cyclopentanol or cyclopentanone as a sole carbon and energy source. The presence of σ
54
-dependent regulatory elements in front of the divergently transcribed
cpnB
and
cpnC
genes supports the notion that
cpnR
is a regulatory gene of the NtrC type. Knowledge of the nucleotide sequence of the
cpn
genes was used to construct isopropyl-β-thio-
d
-galactoside-inducible clones of
Escherichia coli
cells that overproduce the five enzymes of the
cpn
pathway. The substrate specificities of CpnA and CpnB were studied in particular to evaluate the potential of these enzymes and establish the latter recombinant strain as a bioreagent for Baeyer-Villiger oxidations. Although frequently nonenantioselective, cyclopentanone 1,2-monooxygenase was found to exhibit a broader substrate range than the related cyclohexanone 1,2-monooxygenase from
Acinetobacter
sp. strain NCIMB 9871. However, in a few cases opposite enantioselectivity was observed between the two biocatalysts.
Characterization of Serracin P, a Phage-Tail-Like Bacteriocin, and Its Activity against
Erwinia amylovora
, the Fire Blight Pathogen
Authors: Jabrane Abdelhamid , Sabri Ahmed , Compère Philippe , Jacques Philippe , Vandenberghe Isabel , Van Beeumen Jozef , Thonart Philippe 
Published: April 2009

ABSTRACT

Serratia plymithicum
J7 culture supernatant displayed activity against many pathogenic strains of
Erwinia amylovora
, the causal agent of the most serious bacterial disease of apple and pear trees, fire blight, and against
Klebsiella pneumoniae, Serratia liquefaciens, Serratia marcescens,
and
Pseudomonas fluorescens.
This activity increased significantly upon induction with mitomycin C. A phage-tail-like bacteriocin, named serracin P, was purified from an induced culture supernatant of
S. plymithicum
J7. It was found to be the only compound involved in the antibacterial activity against sensitive strains. The N-terminal amino acid sequence analysis of the two major subunits (23 and 43 kDa) of serracin P revealed high homology with the Fels-2 prophage of
Salmonella enterica
, the coliphages P2 and 168, the φCTX prophage of
Pseudomonas aeruginosa,
and a prophage of
Yersinia pestis
. This strongly suggests a common ancestry for serracin P and these bacteriophages.
Function of Native OmtA In Vivo and Expression and Distribution of This Protein in Colonies of
Aspergillus parasiticus
Authors: Lee Li-Wei , Chiou Ching-Hsun , Linz John E. 
Published: April 2009

ABSTRACT

The activities of two enzymes, a 168-kDa protein and a 40-kDa protein, OmtA, purified from the filamentous fungus
Aspergillus parasiticus
were reported to convert the aflatoxin pathway intermediate sterigmatocystin to
O-
methylsterigmatocystin in vitro. Our initial goal was to determine if OmtA is necessary and sufficient to catalyze this reaction in vivo and if this reaction is necessary for aflatoxin synthesis. We generated
A. parasiticus omtA
-null mutant LW1432 and a maltose binding protein-OmtA fusion protein expressed in
Escherichia coli
. Enzyme activity analysis of OmtA fusion protein in vitro confirmed the reported catalytic function of OmtA. Feeding studies conducted with LW1432 demonstrated a critical role for OmtA, and the reaction catalyzed by this enzyme in aflatoxin synthesis in vivo. Because of a close regulatory link between aflatoxin synthesis and asexual sporulation (conidiation), we hypothesized a spatial and temporal association between OmtA expression and conidiospore development. We developed a novel time-dependent colony fractionation protocol to analyze the accumulation and distribution of OmtA in fungal colonies grown on a solid medium that supports both toxin synthesis and conidiation. OmtA-specific polyclonal antibodies were purified by affinity chromatography using an LW1432 protein extract. OmtA was not detected in 24-h-old colonies but was detected in 48-h-old colonies using Western blot analysis; the protein accumulated in all fractions of a 72-h-old colony, including cells (0 to 24 h) in which little conidiophore development was observed. OmtA in older fractions of the colony (24 to 72 h) was partly degraded. Fluorescence-based immunohistochemical analysis conducted on thin sections of paraffin-embedded fungal cells from time-fractionated fungal colonies demonstrated that OmtA is evenly distributed among different cell types and is not concentrated in conidiophores. These data suggest that OmtA is present in newly formed fungal tissue and then is proteolytically cleaved as cells in that section of the colony age.
Uptake Rates of Oxygen and Sulfide Measured with Individual
Thiomargarita namibiensis
Cells by Using Microelectrodes
Authors: Schulz Heide N. , de Beer Dirk 
Published: April 2009

ABSTRACT

Gradients of oxygen and sulfide measured towards individual cells of the large nitrate-storing sulfur bacterium
Thiomargarita namibiensis
showed that in addition to nitrate oxygen is used for oxidation of sulfide. Stable gradients around the cells were found only if acetate was added to the medium at low concentrations.
Regulation of
freA
,
acoA
,
lysF
, and
cycA
Expression by Iron Availability in
Aspergillus nidulans
Authors: Oberegger Harald , Schoeser Michelle , Zadra Ivo , Schrettl Markus , Parson Walther , Haas Hubertus 
Published: April 2009

ABSTRACT

In the filamentous fungus
Aspergillus nidulans
, iron homeostasis is regulated at the transcriptional level by the negative-acting GATA factor SREA. In this study the expression of a putative heme-containing metalloreductase-encoding gene,
freA
, was found to be upregulated by iron limitation independently of SREA, demonstrating the existence of an iron-regulatory mechanism which does not involve SREA. In contrast to
freA
, various other genes encoding proteins in need of iron-containing cofactors—
acoA
,
lysF
, and
cycA
—were downregulated in response to iron depletion. Remarkably, SREA deficiency led to increased expression of
acoA
,
lysF
, and
cycA
under iron-replete growth conditions.
Evaluation of a Novel Therapeutic Approach to Treating Severe Pneumococcal Infection Using a Mouse Model
Authors: Melnick Nikkol , Rajam Gowrisankar , Carlone George M. , Sampson Jacquelyn S. , Ades Edwin W. 
Published: April 2009

ABSTRACT

P4, a 28-amino-acid peptide, is a eukaryotic cellular activator that enhances specific in vitro opsonophagocytic killing of multiple bacterial pathogens. In a previous study, we successfully recreated this phenomenon in mice in vivo by using a two-dose regimen of P4 and pathogen-specific antibodies, which significantly reduced moribundity in mice. For the present study, we hypothesized that the inclusion of a low-dose antibiotic would make it possible to treat the infected mice with a single dose containing a mixture of P4 and a pathogen-specific antibody. A single dose consisting of P4, intravenous immunoglobulin (IVIG), and ceftriaxone effectively reduced moribundity compared to that of untreated controls (
n
= 10) by 75% (
P
< 0.05) and rescued all (10 of 10) infected animals (
P
< 0.05). If rescued animals were reinfected with
Streptococcus pneumoniae
and treated with a single dose containing P4, IVIG, and ceftriaxone, they could be rerescued. This observation of the repeated successful use of P4 combination therapy demonstrates a low risk of tolerance development. Additionally, we examined the polymorphonuclear leukocytes (PMN) derived from infected mice and observed that P4 enhanced in vitro opsonophagocytic killing (by >80% over the control level;
P
< 0.05). This finding supports our hypothesis that PMN are activated by P4 during opsonophagocytosis and the recovery of mice from pneumococcal infection. P4 peptide-based combination therapy may offer an alternative and rapid immunotherapy to treat fulminant pneumococcal infection.
Occupational exposure of UK adults to extremely low frequency magnetic fields
Authors: Mee T , Whatmough P , Broad L , Dunn C , Maslanyj M , Allen S , Muir K , McKinney P A , van Tongeren M 
Published: April 2009

Background:Occupational exposure to extremely low frequency (ELF) magnetic fields (MF) in the UK general population is poorly documented.Aims:To assess levels of occupational exposure to ELF MF in the UK and evaluate the use of a rigid job-exposure matrix (JEM) to assign exposures to subjects in the UK Adult Brain Tumour Study (UKABTS).Methods:Personal ELF MF measurements were carried out. Exposure traces were divided into occupational, travel and elsewhere periods, under differing exposure metrics. Exposure was classified by Standard Occupational Classification (2000), Standard Industrial Classification (1997), and a combined occupation-industry classification. Statistical analyses (mixed effects model) determined the contribution of occupational exposure to the 24 h cumulative exposure and the contribution of occupation and industry to total variance.Results:Data were obtained from 317 individuals, comprising UKABTS subjects (n = 192), occupational proxies for UKABTS subjects (n = 101) and “interest” readings (n = 24). 236 individuals provided occupational data covering 117 different occupations. Average exposure was significantly higher at work than at home. Elevated average occupational exposure was found for welding trades, printers, telephonists and filing and other records assistants. The discrimination of a rigid JEM based on occupation can be improved by linking the classification with industry and by the use of contextual information.Conclusions:This report substantially expands information on adult exposure to ELF MF in the UK. The accuracy of exposure assessments based solely on job codes is improved by linking with either industry code or contextual knowledge of equipment and of power lines or substations in the work environment.
Evaluation of nitrogenous media components by Plackett–Burman statistical design for β-d-fructofuranosidase production by Saccharomyces sp. strain GVT263
Authors: Venkateshwar M. , Chaitanya K. , Altaf M. D. , Hameeda B. , Ghopal Reddy M. 
Published: April 2009

β-d-Fructofuranosidase (FFase), an important enzyme of the confectionery and fructose syrup industry, is produced by several microorganisms. However, yeasts are the most used source because of their high sucrose fermentation capacity. In this work, production of FFase was carried out in submerged fermentation using a high enzyme-producing yeast strain. Plackett–Burman statistical experimental design was applied to evaluate the fermentation medium components. The effects of 10 nitrogen sources were studied in a 16-run experimental design. Beef extract, yeast extract, N-Z-amine, tryptone, meat extract, and ammonium acetate were found to have significant effects on enzyme production. Among these, yeast extract, N-Z-amine, and ammonium acetate were the most significant. A maximum FFase activity of 299.4 U/mL was obtained after a 24 h fermentation period.