bluuebunny/crossref_metadata_2025_split huggingface dataset:
Citrate Synthase Mutants of
Sinorhizobium fredii
USDA257 Form Ineffective Nodules with Aberrant Ultrastructure
Authors: Krishnan Hari B. , Kim Won-Seok , Sun-Hyung Jeong , Kim Kil Yong , Jiang Guoqiao 
Published: June 2003

ABSTRACT

The tricarboxylic acid (TCA) cycle plays an important role in generating the energy required by bacteroids to fix atmospheric nitrogen. Citrate synthase is the first enzyme that controls the entry of carbon into the TCA cycle. We cloned and determined the nucleotide sequence of the
gltA
gene that encodes citrate synthase in
Sinorhizobium fredii
USDA257, a symbiont of soybeans (
Glycine max
[L.] Merr.) and several other legumes. The deduced citrate synthase protein has a molecular weight of 48,198 and exhibits sequence similarity to citrate synthases from several bacterial species, including
Sinorhizobium meliloti
and
Rhizobium tropici
. Southern blot analysis revealed that the fast-growing
S. fredii
strains and
Rhizobium
sp. strain NGR234 contained a single copy of the gene located in the bacterial chromosome.
S. fredii
USDA257
gltA
mutant HBK-CS1, which had no detectable citrate synthase activity, had diminished nodulation capacity and produced ineffective nodules on soybean. Light and electron microscopy observations revealed that the nodules initiated by HBK-CS1 contained very few bacteroids. The infected cells contained large vacuoles and prominent starch grains. Within the vacuoles, membrane structures that appeared to be reminiscent of disintegrating bacteroids were detected. The citrate synthase mutant had altered cell surface characteristics and produced three times more exopolysaccarides than the wild type produced. A plasmid carrying the USDA257
gltA
gene, when introduced into HBK-CS1, was able to restore all of the defects mentioned above. Our results demonstrate that a functional citrate synthase gene of
S. fredii
USDA257 is essential for efficient soybean nodulation and nitrogen fixation.
Density-Dependent Sorting of Physiologically Different Cells of
Vibrio parahaemolyticus
Authors: Nishino Tomohiko , Nayak Binaya B. , Kogure Kazuhiro 
Published: June 2003

ABSTRACT

A pure bacterial culture is composed of clonal cells in different physiological states. Separation of those subpopulations is critical for further characterization and for understanding various processes in the cultured cells. We used density-dependent cell sorting with Percoll to separate subpopulations from cultures of a marine bacterium,
Vibrio parahaemolyticus
. Cells from cultures in the exponential and stationary phases were fractionated according to their buoyant density, and their culturability and ability to maintain culturability under low-temperature and low-nutrient stress (stress resistance) were determined. The buoyant density of the major portion of the cells decreased with culture age. The culturability of stationary-phase cells increased with increasing buoyant density, but that of exponential-phase cells did not. Stress resistance decreased with increasing buoyant density regardless of the growth phase. The results indicate that density-dependent cell sorting is useful for separating subpopulations of different culturabilities and stress resistances. We expect that this method will be a powerful tool for analyzing cells in various physiological states, such as the viable but nonculturable state.
A C
35
Carotenoid Biosynthetic Pathway
Authors: Umeno Daisuke , Arnold Frances H. 
Published: June 2003

ABSTRACT

Upon coexpression with
Erwinia
geranylgeranyldiphosphate (GGDP) synthase in
Escherichia coli
, C
30
carotenoid synthase CrtM from
Staphylococcus aureus
produces novel carotenoids with the asymmetrical C
35
backbone. The products of condensation of farnesyldiphosphate and GDP, C
35
structures comprise 40 to 60% of total carotenoid accumulated. Carotene desaturases and carotene cyclases from C
40
or C
30
pathways accepted and converted the C
35
substrate, thus creating a C
35
carotenoid biosynthetic pathway in
E. coli
. Directed evolution to modulate desaturase step number, together with combinatorial expression of the desaturase variants with lycopene cyclases, allowed us to produce at least 10 compounds not previously described. This result highlights the plastic and expansible nature of carotenoid pathways and illustrates how combinatorial biosynthesis coupled with directed evolution can rapidly access diverse chemical structures.
Incidence and Diversity of Microorganisms within the Walls of an Active Deep-Sea Sulfide Chimney
Authors: Schrenk Matthew O. , Kelley Deborah S. , Delaney John R. , Baross John A. 
Published: June 2003

ABSTRACT

A large, intact sulfide chimney, designated Finn, was recovered from the Mothra Vent Field on the Juan de Fuca Ridge in 1998. Finn was venting 302°C fluids on the seafloor and contained complex mineralogical zones surrounding a large open central conduit. Examination of microorganisms within these zones, followed by community analysis with oligonucleotide probes, showed that there were variations in the abundance and diversity of eubacteria and archaea from the exterior to the interior of the chimney. The microbial abundance based upon epifluorescence microscopy and quantitative fatty acid analyses varied from >10
8
cells/g of sulfide 2 to 10 cm within the chimney wall to <10
5
cells/g in interior zones. Direct microscopic observation indicated that microorganisms were attached to mineral surfaces throughout the structure. Whole-cell hybridization results revealed that there was a transition from a mixed community of eubacteria and archaea near the cool exterior of the chimney to primarily archaea near the warm interior. Archaeal diversity was examined in three zones of Finn by cloning and sequencing of the 16S rRNA gene. The majority of sequences from the exterior of the chimney were related to marine group I of the
Crenarchaeota
and uncultured
Euryarchaeota
from benthic marine environments. In contrast, clone libraries from interior regions of the chimney contained sequences closely related to methanogens,
Thermococcales
, and
Archaeoglobales
, in addition to uncultured crenarchaeal phylotypes obtained from deep subsurface sites. These observations of microbial communities within an active hydrothermal chimney provide insight into the microbial ecology within such structures and may facilitate follow-up exploration into expanding the known upper temperature limits of life.
Development and Application of an Assay for Uranyl Complexation by Fungal Metabolites, Including Siderophores
Authors: Renshaw Joanna C. , Halliday Verity , Robson Geoffrey D. , Trinci Anthony P. J. , Wiebe Marilyn G. , Livens Francis R. , Collison David , Taylor Robin J. 
Published: June 2003

ABSTRACT

An assay to detect UO
2
2+
complexation was developed based on the chrome azurol S (CAS) assay for siderophores (B. Schwyn and J. B. Neilands, Anal. Biochem. 160:47-56, 1987) and was used to investigate the ability of fungal metabolites to complex actinides. In this assay the discoloration of two dyed agars (one containing a CAS-Fe
3+
dye and the other containing a CAS-UO
2
2+
dye) caused by ligands was quantified. The assay was tested by using the siderophore desferrioxamine B (DFO), and the results showed that there was a regular, reproducible relationship between discoloration and the amount of siderophore added. The ratio of the discoloration on the CAS-UO
2
2+
agar to the discoloration on the CAS-Fe
3+
agar was independent of the amount of siderophore added. A total of 113 fungi and yeasts were isolated from three soil samples taken from the Peak District National Park. The fungi were screened for the production of UO
2
2+
chelators by using the CAS-based assay and were also tested specifically for hydroxamate siderophore production by using the hydroxamate siderophore auxotroph
Aureobacterium flavescens
JG-9. This organism is highly sensitive to the presence of hydroxamate siderophores. However, the CAS-based assay was found to be less sensitive than the
A. flavescens
JG-9 assay. No significant difference between the results for each site for the two tests was found. Three isolates were selected for further study and were identified as two
Pencillium
species and a
Mucor
species. Our results show that the new assay can be effectively used to screen fungi for the production of UO
2
2+
chelating ligands. We suggest that hydroxamate siderophores can be produced by mucoraceous fungi.
Combining Culture-Dependent and -Independent Methodologies for Estimation of Richness of Estuarine Bacterioplankton Consuming Riverine Dissolved Organic Matter
Authors: Kisand Veljo , Wikner Johan 
Published: June 2003

ABSTRACT

Three different methods for analyzing natural microbial community diversity were combined to maximize an estimate of the richness of bacterioplankton catabolizing riverine dissolved organic matter (RDOM). We also evaluated the ability of culture-dependent quantitative DNA-DNA hybridization, a 16S rRNA gene clone library, and denaturing gradient gel electrophoresis (DGGE) to detect bacterial taxa in the same sample. Forty-two different cultivatable strains were isolated from rich and poor solid media. In addition, 50 unique clones were obtained by cloning of the bacterial 16S rDNA gene amplified by PCR from the community DNA into an
Escherichia coli
vector. Twenty-three unique bands were sequenced from 12 DGGE profiles, excluding a composite fuzzy band of the
Cytophaga-Flavobacterium
group. The different methods gave similar distributions of taxa at the genus level and higher. However, the match at the species level among the methods was poor, and only one species was identified by all three methods. Consequently, all three methods identified unique subsets of bacterial species, amounting to a total richness of 97 operational taxonomic units in the experimental system. The confidence in the results was, however, dependent on the current precision of the phylogenetic determination and definition of the species. Bacterial consumers of RDOM in the studied estuary were primarily both cultivatable and uncultivable taxa of the
Cytophaga-Flavobacterium
group, a concordant result among the methods applied. Culture-independent methods also suggested several not-yet-cultivated β-proteobacteria to be RDOM consumers.
Mapping of Genomic Regions (Quantitative Trait Loci) Controlling Production and Quality in Industrial Cultures of the Edible Basidiomycete
Pleurotus ostreatus
Authors: Larraya Luis M. , Alfonso Mikel , Pisabarro Antonio G. , Ramírez Lucía 
Published: June 2003

ABSTRACT

Industrial production of the edible basidiomycete
Pleurotus ostreatus
(oyster mushroom) is based on a solid fermentation process in which a limited number of selected strains are used. Optimization of industrial mushroom production depends on improving the culture process and breeding new strains with higher yields and productivities. Traditionally, fungal breeding has been carried out by an empirical trial and error process. In this study, we used a different approach by mapping quantitative trait loci (QTLs) controlling culture production and quality within the framework of the genetic linkage map of
P. ostreatus
. Ten production traits and four quality traits were studied and mapped. The production QTLs identified explain nearly one-half of the production variation. More interestingly, a single QTL mapping to the highly polymorphic chromosome VII appears to be involved in control of all the productivity traits studied. Quality QTLs appear to be scattered across the genome and to have less effect on the variation of the corresponding traits. Moreover, some of the new hybrid strains constructed in the course of our experiments had production or quality values higher than those of the parents or other commercial strains. This approach opens the possibility of marker-assisted selection and breeding of new industrial strains of this fungus.
Characterization of the First Molluscicidal Lipopolysaccharide from
Moraxella osloensis
Authors: Tan Li , Grewal Parwinder S. 
Published: June 2003

ABSTRACT

Moraxella osloensis
is a bacterium that is mutualistically associated with
Phasmarhabditis hermaphrodita,
a nematode that has potential for the biocontrol of mollusk pests, especially the slug
Deroceras reticulatum.
We discovered that purified
M. osloensis
lipopolysaccharide (LPS) possesses a lethal toxicity to
D. reticulatum
when administered by injection but no contact or oral toxicity to this slug. The toxicity of the LPS resides in the lipid A moiety.
M. osloensis
LPS was semiquantitated at 6 × 10
7
endotoxin units per mg. The LPS is a rough-type LPS with an estimated molecular weight of 5,300. Coinjection of galactosamine with the LPS increased the LPS's toxicity to the slug two- to four-fold. The galactosamine-induced sensitization of the slug to the LPS was reversed completely by uridine.
On the Origins of Cyanuric Acid Hydrolase: Purification, Substrates, and Prevalence of AtzD from
Pseudomonas
sp. Strain ADP
Authors: Fruchey Isaac , Shapir Nir , Sadowsky Michael J. , Wackett Lawrence P. 
Published: June 2003

ABSTRACT

Cyanuric acid hydrolase (AtzD) from
Pseudomonas
sp. strain ADP was purified to homogeneity. Of 22 cyclic amides and triazine compounds tested, only cyanuric acid and
N
-methylisocyanuric acid were substrates. Other cyclic amidases were found not to hydrolyze cyanuric acid. Ten bacteria that use cyanuric acid as a sole nitrogen source for growth were found to contain either
atzD
or
trzD
, but not both genes.
Linkage of High Rates of Sulfate Reduction in Yellowstone Hot Springs to Unique Sequence Types in the Dissimilatory Sulfate Respiration Pathway
Authors: Fishbain Susan , Dillon Jesse G. , Gough Heidi L. , Stahl David A. 
Published: June 2003

ABSTRACT

Diversity, habitat range, and activities of sulfate-reducing prokaryotes within hot springs in Yellowstone National Park were characterized using endogenous activity measurements, molecular characterization, and enrichment. Five major phylogenetic groups were identified using PCR amplification of the dissimilatory sulfite reductase genes (
dsrAB
) from springs demonstrating significant sulfate reduction rates, including a warm, acidic (pH 2.5) stream and several nearly neutral hot springs with temperatures reaching 89°C. Three of these sequence groups were unrelated to named lineages, suggesting that the diversity and habitat range of sulfate-reducing prokaryotes exceeds that now represented in culture.
Behavior of Psychrotrophic Lactic Acid Bacteria Isolated from Spoiling Cooked Meat Products
Authors: Hamasaki Yoshikatsu , Ayaki Mitsuko , Fuchu Hidetaka , Sugiyama Masaaki , Morita Hidetoshi 
Published: June 2003

ABSTRACT

Three kinds of lactic acid bacteria were isolated from spoiling cooked meat products stored below 10°C. They were identified as
Leuconostoc mesenteroides
subsp.
mesenteroides
,
Lactococcus lactis
subsp.
lactis
, and
Leuconostoc citreum
. All three strains grew well in MRS broth at 10°C. In particular,
L. mesenteroides
subsp.
mesenteroides
and
L. citreum
grew even at 4°C, and their doubling times were 23.6 and 51.5 h, respectively. On the other hand, although the bacteria were initially below the detection limit (<10 CFU/g) in model cooked meat products, the bacterial counts increased to 10
8
CFU/g at 10°C after 7 to 12 days.
Microorganisms Associated with Uranium Bioremediation in a High-Salinity Subsurface Sediment
Authors: Nevin Kelly P. , Finneran Kevin T. , Lovley Derek R. 
Published: June 2003

ABSTRACT

Although stimulation of dissimilatory metal reduction to promote the reductive precipitation of uranium has been shown to successfully remove uranium from some aquifer sediments, the organisms in the family
Geobacteraceae
that have been found to be associated with metal reduction in previous studies are not known to grow at the high salinities found in some uranium-contaminated groundwaters. Studies with a highly saline uranium-contaminated aquifer sediment demonstrated that the addition of acetate could stimulate the removal of U(VI) from the groundwater. This removal was associated with an enrichment in microorganisms most closely related to
Pseudomonas
and
Desulfosporosinus
species.
Direct Detection of
Vibrio cholerae
and
ctxA
in Peruvian Coastal Water and Plankton by PCR
Authors: Lipp Erin K. , Rivera Irma N. G. , Gil Ana I. , Espeland Eric M. , Choopun Nipa , Louis Valérie R. , Russek-Cohen Estelle , Huq Anwar , Colwell Rita R. 
Published: June 2003

ABSTRACT

Seawater and plankton samples were collected over a period of 17 months from November 1998 to March 2000 along the coast of Peru. Total DNA was extracted from water and from plankton grouped by size into two fractions (64 μm to 202 μm and >202 μm). All samples were assayed for
Vibrio cholerae
,
V. cholerae
O1,
V. cholerae
O139, and
ctxA
by PCR. Of 50 samples collected and tested, 33 (66.0%) were positive for
V. cholerae
in at least one of the three fractions. Of these, 62.5% (
n
= 32) contained
V. cholerae
O1;
ctxA
was detected in 25% (
n
= 20) of the
V. cholerae
O1-positive samples. None were positive for
V. cholerae
O139. Thus, PCR was successfully employed in detecting toxigenic
V. cholerae
directly in seawater and plankton samples and provides evidence for an environmental reservoir for this pathogen in Peruvian coastal waters.
Generation of Food-Grade Lactococcal Starters Which Produce the Lantibiotics Lacticin 3147 and Lacticin 481
Authors: O'Sullivan Lisa , Ryan Maire P. , Ross R. Paul , Hill Colin 
Published: June 2003

ABSTRACT

Transconjugant lactococcal starters which produce both lantibiotics lacticin 3147 and lacticin 481 were generated via conjugation of large bacteriocin-encoding plasmids. A representative of one of the resultant strains proved more effective at killing
Lactobacillus fermentum
and inhibiting the growth of
Listeria monocytogenes
LO28H than either of the single bacteriocin-producing parental strains, demonstrating the potential of these transconjugants as protection cultures for food safety applications.
Nationwide Surveillance for
Staphylococcus aureus
with Reduced Susceptibility to Vancomycin in Korea
Authors: Kim Hong Bin , Park Wan Beom , Lee Ki Deok , Choi Young Joo , Park Sang Won , Oh Myoung-don , Kim Eui-Chong , Choe Kang Won 
Published: June 2003

ABSTRACT

Methicillin-resistant
Staphylococcus aureus
(MRSA) accounts for more than 70% of
S. aureus
isolates from tertiary hospitals in Korea. Clinical isolates of
S. aureus
were collected from eight provincial, university-affiliated hospitals during the period from June 1999 to January 2001 for nationwide surveillance. All isolates were screened for reduced susceptibility to vancomycin by using brain heart infusion agar containing 4 μg of vancomycin per milliliter. Population analysis and the determination of the MIC of vancomycin were done for the isolates which grew on the screening agar plates. Of 682 total isolates, MRSA accounted for 64% (439 of 682). Of 27 (4%) isolates that grew on the screening agar plates, none showed the heteroresistance phenotype. No strains with reduced susceptibility to vancomycin were identified.
Longitudinal Study ofSalmonella entericaSerotype Typhimurium Infection in Three Danish Farrow-to-Finish Swine Herds
Authors: Kranker Søren , Alban Lis , Boes Jaap , Dahl Jan 
Published: June 2003

ABSTRACTA longitudinal study of the infection dynamics ofSalmonella entericawas carried out with three Danish farrow-to-finish swine herds. To account for variations inSalmonellashedding over time, litters from each herd were divided into two cohorts. Each cohort consisted of 30 pigs, for a total of 180 pigs. Pigs were individually monitored by monthly bacteriologic and serologic examinations from weaning to slaughter. At weaning, individual sows were examined bacteriologically and serologically. At slaughter, cecal contents, ileocecal lymph nodes, and carcass swab samples were obtained from 131 pigs. A total of 88 pigs were found to be sheddingSalmonellaon one or more occasions. Only theSalmonellaserotype Typhimurium was detected during the study period. At weaning, no sows or piglets were found to be shedding, but a serological reaction was detected in 11 sows. The prevalence in culture peaked in the nursery and subsequently declined to undetectable levels before slaughter. The seroprevalence peaked approximately 60 days after the peak prevalence in culture.Salmonellawas detected in individual fecal samples at least once in 53% of the pigs, and 62% of the pigs were seropositive more than once. Only 3.7% of all pigs were found to be culture positive on more than one occasion. Piglets from seroreacting sows had a significantly (P= 0.0339) lower probability of shedding in the nursery. Under the assumption that shedding lasted at least 1 or 2 weeks, the average shedding time was estimated to have been 18 or 26 days. An association between serology, on-farm bacteriology, andSalmonellaprevalence in culture at slaughter was shown. Marked differences in prevalence in sera and prevalence in culture between cohorts and within herds were observed. These differences emphasize the need for caution when using point estimates in on-farm interventions and surveillance in subclinically infected swine herds.
Prevalence of Enteroaggregative
Escherichia coli
among Children with and without Diarrhea in Switzerland
Authors: Pabst Werner L. , Altwegg Martin , Kind Christian , Mirjanic Slavko , Hardegger Daniel , Nadal David 
Published: June 2003

ABSTRACT

In a prospective study between July 1999 and September 2000, stool specimens of children below the age of 16 years with (
n
= 187) and without (
n
= 137) diarrhea were tested for the presence of enterovirulent bacteria by standard culture methods and by PCR. Targets for the PCR were the plasmid pCVD432 for enteroaggregative
Escherichia coli
(EAEC), the verotoxin 1 and verotoxin 2 genes for enterohemorrhagic
E. coli
,
ipaH
for enteroinvasive
E. coli
(EIEC) and
Shigella
spp., genes coding for heat-stable and heat-labile toxins for enterotoxigenic
E. coli
(ETEC), and the
eaeA
gene for enteropathogenic
E. coli.
The following bacteria could be associated with diarrhea:
Salmonella enterica
(
P
= 0.001),
Campylobacter
spp. (
P
= 0.036), ETEC (
P
= 0.012), and EAEC (
P
= 0.006). The detection of EAEC, ETEC, and
S. enterica
was strongly associated with a history of recent travel outside of Switzerland. EAEC isolates were found in the specimens of 19 (10.2%) of 187 children with diarrhea and in those of 3 (2.2%) of 137 children without diarrhea (
P
= 0.006) and were the most frequently detected bacteria associated with diarrhea. Among the children below the age of 5 years, the specimens of 18 (11.9%) of 151 with diarrhea were positive for EAEC, while this agent was found in the specimens of 2 (2.2%) of 91 controls (
P
= 0.007). Enteropathogenic
E. coli
isolates were found in the specimens of 30 (16.4%) of the patients and in those of 15 (10.9%) of the controls, with similar frequencies in all age groups (
P
> 0.05). We conclude that EAEC bacteria are involved in a significant proportion of diarrhea cases among children. Children younger than 5 years of age are more often affected by EAEC than older children.