bluuebunny/crossref_metadata_2025_split huggingface dataset:
Specific Detection of
Leuconostoc mesenteroides
subsp.
mesenteroides
with DNA Primers Identified by Randomly Amplified Polymorphic DNA Analysis
Authors: Moschetti Giancarlo , Blaiotta Giuseppe , Villani Francesco , Coppola Salvatore 
Published: April 2009

ABSTRACT

Randomly amplified polymorphic DNA analysis using primer 239 (5′ CTGAAGCGGA 3′) was performed to characterize
Leuconostoc
sp. strains. All the strains of
Leuconostoc mesenteroides
subsp.
mesenteroides
(with the exception of two strains), two strains formerly identified as
L. gelidum
, and one strain of
Leuconostoc
showed a common band at about 1.1 kb. This DNA fragment was cloned and sequenced in order to verify its suitability for identifying
L. mesenteroides
subsp.
mesenteroides
strains.
Pulsed-Electric Field Treatment Enhances the Bactericidal Action of Nisin against
Bacillus cereus
Authors: Pol Irene E. , Mastwijk Hennie C. , Bartels Paul V. , Smid Eddy J. 
Published: April 2009

ABSTRACT

Vegetative cells of
Bacillus cereus
were subjected to low doses of nisin (0.06 μg/ml) and mild pulsed-electric field treatment (16.7 kV/cm, 50 pulses each of 2-μs duration). Combining both treatments resulted in a reduction of 1.8 log units more than the sum of the reductions obtained with the single treatments, indicating synergy.
Coaggregation between Aquatic Bacteria Is Mediated by Specific-Growth-Phase-Dependent Lectin-Saccharide Interactions
Authors: Rickard Alex H. , Leach Stephen A. , Buswell Clive M. , High Nicola J. , Handley Pauline S. 
Published: April 2009

ABSTRACT

Coaggregating strains of aquatic bacteria were identified by partial 16S rRNA gene sequencing. The coaggregation abilities of four strains of
Blastomonas natatoria
and one strain of
Micrococcus luteus
varied with culture age but were always maximum in the stationary phase of growth. Each member of a coaggregating pair carried either a heat- and protease-sensitive protein (lectin) adhesin or a saccharide receptor, as coaggregation was reversed by sugars.
Establishment of a Polychlorinated Biphenyl-Dechlorinating Microbial Consortium, Specific for Doubly Flanked Chlorines, in a Defined, Sediment-Free Medium
Authors: Wu Qingzhong , Sowers Kevin R. , May Harold D. 
Published: April 2009

ABSTRACT

Estuarine sediment from Charleston Harbor, South Carolina, was used as inoculum for the development of an anaerobic enrichment culture that specifically dechlorinates doubly flanked chlorines (i.e., chlorines bound to carbon that are flanked on both sides by other chlorine-carbon bonds) of polychlorinated biphenyls (PCBs). Dechlorination was restricted to the
para
chlorine in cultures enriched with 10 mM fumarate, 50 ppm (173 μM) 2,3,4,5-tetrachlorobiphenyl, and no sediment. Initially the rate of dechlorination decreased upon the removal of sediment from the medium. However, the dechlorinating activity was sustainable, and following sequential transfer in a defined, sediment-free estuarine medium, the activity increased to levels near that observed with sediment. The culture was nonmethanogenic, and molybdate, ampicillin, chloramphenicol, neomycin, and streptomycin inhibited dechlorination activity; bromoethanesulfonate and vancomycin did not. Addition of 17 PCB congeners indicated that the culture specifically removes double flanked chlorines, preferably in the
para
position, and does not attack
ortho
chlorines. This is the first microbial consortium shown to
para
or
meta
dechlorinate a PCB congener in a defined sediment-free medium. It is the second PCB-dechlorinating enrichment culture to be sustained in the absence of sediment, but its dechlorinating capabilities are entirely different from those of the other sediment-free PCB-dechlorinating culture, an
ortho
-dechlorinating consortium, and do not match any previously published Aroclor-dechlorinating patterns.
Sequence Analysis of the Cryptic Plasmid pMG101 from
Rhodopseudomonas palustris
and Construction of Stable Cloning Vectors
Authors: Inui Masayuki , Roh Jung Hyeob , Zahn Kenneth , Yukawa Hideaki 
Published: April 2009

ABSTRACT

A 15-kb cryptic plasmid was obtained from a natural isolate of
Rhodopseudomonas palustris
. The plasmid, designated pMG101, was able to replicate in
R. palustris
and in closely related strains of
Bradyrhizobium japonicum
and phototrophic
Bradyrhizobium
species. However, it was unable to replicate in the purple nonsulfur bacterium
Rhodobacter sphaeroides
and in
Rhizobium
species. The replication region of pMG101 was localized to a 3.0-kb
Sal
I-
Xho
I fragment, and this fragment was stably maintained in
R. palustris
for over 100 generations in the absence of selection. The complete nucleotide sequence of this fragment revealed two open reading frames (ORFs), ORF1 and ORF2. The deduced amino acid sequence of ORF1 is similar to sequences of Par proteins, which mediate plasmid stability from certain plasmids, while ORF2 was identified as a putative
rep
gene, coding for an initiator of plasmid replication, based on homology with the Rep proteins of several other plasmids. The function of these sequences was studied by deletion mapping and gene disruptions of ORF1 and ORF2. pMG101-based
Escherichia coli-R. palustris
shuttle cloning vectors pMG103 and pMG105 were constructed and were stably maintained in
R. palustris
growing under nonselective conditions. The ability of plasmid pMG101 to replicate in
R. palustris
and its close phylogenetic relatives should enable broad application of these vectors within this group of α-proteobacteria.
Distribution and Physiological Characteristics of Hyperthermophiles in the Kubiki Oil Reservoir in Niigata, Japan
Authors: Takahata Yoh , Nishijima Miyuki , Hoaki Toshihiro , Maruyama Tadashi 
Published: April 2009

ABSTRACT

The distribution of culturable hyperthermophiles was studied in relation to environmental conditions in the Kubiki oil reservoir in Japan, where the temperature was between 50 and 58°C. Dominant hyperthermophilic cocci and rods were isolated and shown to belong to the genera
Thermococcus
and
Thermotoga
, respectively, by 16S rDNA analyses. Using the most-probable-number method, we found that hyperthermophilic cocci were widely distributed in several unconnected fault blocks in the Kubiki oil reservoir. In 1996 to 1997, their populations in the production waters from oil wells were 9.2 × 10
3
to 4.6 × 10
4
cells/ml, or 10 to 42% of total cocci. On the other hand, hyperthermophilic rods were found in only one fault block of the reservoir with populations less than 10 cells/ml. Dominant
Thermococcus
and
Thermotoga
spp. grew at reservoir temperatures and utilized amino acids and sugars, respectively, as sole carbon sources. While organic carbon was plentiful in the environment, these hyperthermophiles were unable to grow in the formation water due to lack of essential nutrients. Concentrations of some organic and inorganic substances differed among fault blocks, indicating that the movement of formation water between fault blocks was restricted. This finding suggests that the supply of nutrients via fluid current is limited in this subterranean environment and that the organisms are starved in the oil reservoir. Under starved conditions at 50°C, culturable cells of
Thermococcus
sp. remained around the initial cell density for about 200 days, while those of
Thermotoga
sp. decreased exponentially to 0.01% of the initial cell density after incubation for the same period. The difference in survivability between these two hyperthermophiles seems to reflect their populations in the fault blocks. These results indicate that hyperthermophilic cocci and rods adapt to the subterranean environment of the Kubiki oil reservoir by developing an ability to survive under starved conditions.
Rapid Isolation of a Single-Chain Antibody against the Cyanobacterial Toxin Microcystin-LR by Phage Display and Its Use in the Immunoaffinity Concentration of Microcystins from Water
Authors: McElhiney Jacqui , Drever Mathew , Lawton Linda A. , Porter Andy J. 
Published: April 2009

ABSTRACTA naïve (unimmunized) human semisynthetic phage display library was employed to isolate recombinant antibody fragments against the cyanobacterial hepatotoxin microcystin-LR. Selected antibody scFv genes were cloned into a soluble expression vector and expressed inEscherichia colifor characterization against purified microcystin-LR by competition enzyme-linked immunosorbent assay (ELISA). The most sensitive single-chain antibody (scAb) isolated was capable of detecting microcystin-LR at levels below the World Health Organization limit in drinking water (1 μg liter−1) and cross-reacted with three other purified microcystin variants (microcystin-RR, -LW, and -LF) and the related cyanotoxin nodularin. Extracts of the cyanobacteriumMicrocystis aeruginosawere assayed by ELISA, and quantifications of microcystins in toxic samples showed good correlation with analysis by high-performance liquid chromatography. Immobilized scAb was also used to prepare immunoaffinity columns, which were assessed for the ability to concentrate microcystin-LR from water for subsequent analysis by high-performance liquid chromatography. Anti-microcystin-LR scAb was immobilized on columns via a hexahistidine tag, ensuring maximum exposure of antigen binding sites, and the performance of the columns was evaluated by directly applying 150 ml of distilled water spiked with 4 μg of purified microcystin-LR. The procedure was simple, and a recovery rate of 94% was achieved following elution in 1 ml of 100% methanol. Large-scale, low-cost production of anti-microcystin-LR scAb inE. coliis an exciting prospect for the development of biosensors and on-line monitoring systems for microcystins and will also facilitate a range of immunoaffinity applications for the cleanup and concentration of these toxins from environmental samples.
Diversity of
Aphanizomenon
flos-aquae
(Cyanobacterium) Populations along a Baltic Sea Salinity Gradient
Authors: Laamanen Maria J. , Forsström Laura , Sivonen Kaarina 
Published: April 2009

ABSTRACT

Colony-forming cyanobacteria of the genus
Aphanizomenon
form massive blooms in the brackish water of the Baltic Sea during the warmest summer months. There have been recent suggestions claiming that the Baltic Sea
Aphanizomenon
species may be different from
Aphanizomenon
flos-aquae
found in lakes. In this study, we examined variability in the morphology and 16S-23S rRNA internal transcribed spacer (ITS) sequences of
A
.
flos-aquae
populations along a salinity gradient from a string of lakes to a fjord-like extension of the Baltic Sea to the open Baltic Sea. Morphological differences among the populations were negligible. We found that the Baltic Sea was dominated (25 out of 27 sequences) by one ITS1-S (shorter band of ITS 1 [ITS1]) genotype, which also was found in the lakes. The lake populations of
A
.
flos-aquae
tended to be genetically more diverse than the Baltic Sea populations. Since the lake ITS1-S genotypes of
A
.
flos-aquae
are continuously introduced to the Baltic Sea via inflowing waters, it seems that only one ITS1 genotype is able to persist in the Baltic Sea populations. The results suggest that one of the ITS1-S genotypes found in the lakes is better adapted to the conditions of the Baltic Sea and that natural selection removes most of the lake genotypes from the Baltic Sea
A
.
flos-aquae
populations.
Isolation and Functional Analysis of a Gene,
tcsB
, Encoding a Transmembrane Hybrid-Type Histidine Kinase from
Aspergillus nidulans
Authors: Furukawa Kentaro , Katsuno Yasuaki , Urao Takeshi , Yabe Tomio , Yamada-Okabe Toshiko , Yamada-Okabe Hisafumi , Yamagata Youhei , Abe Keietsu , Nakajima Tasuku 
Published: April 2009

ABSTRACT

We cloned and characterized a novel
Aspergillus nidulans
histidine kinase gene,
tcsB
, encoding a membrane-type two-component signaling protein homologous to the yeast osmosensor synthetic lethal N-end rule protein 1 (
SLN1
), which transmits signals through the high-osmolarity glycerol response 1 (
HOG1
) mitogen-activated protein kinase (MAPK) cascade in yeast cells in response to environmental osmotic stimuli. From an
A. nidulans
cDNA library, we isolated a positive clone containing a 3,210-bp open reading frame that encoded a putative protein consisting of 1,070 amino acids. The predicted
tcsB
protein (TcsB) has two probable transmembrane regions in its N-terminal half and has a high degree of structural similarity to yeast Sln1p, a transmembrane hybrid-type histidine kinase. Overexpression of the
tcsB
cDNA suppressed the lethality of a temperature-sensitive osmosensing-defective
sln1-ts
yeast mutant. However,
tcsB
cDNAs in which the conserved phosphorylation site His
552
residue or the phosphorelay site Asp
989
residue had been replaced failed to complement the
sln1-ts
mutant. In addition, introduction of the
tcsB
cDNA into an
sln1
Δ
sho1
Δ yeast double mutant, which lacked two osmosensors, suppressed lethality in high-salinity media and activated the HOG1 MAPK. These results imply that TcsB functions as an osmosensor histidine kinase. We constructed an
A. nidulans
strain lacking the
tcsB
gene (
tcsB
Δ) and examined its phenotype. However, unexpectedly, the
tcsB
Δ strain did not exhibit a detectable phenotype for either hyphal development or morphology on standard or stress media. Our results suggest that
A. nidulans
has more complex and robust osmoregulatory systems than the yeast SLN1-HOG1 MAPK cascade.
Ethylene Production byBotrytis cinereaIn Vitro and in Tomatoes
Authors: Cristescu Simona M. , De Martinis Domenico , te Lintel Hekkert Sacco , Parker David H. , Harren Frans J. M. 
Published: April 2009

ABSTRACTA laser-based ethylene detector was used for on-line monitoring of ethylene released by the phytopathogenic fungusBotrytis cinereain vitro and in tomato fruit. Ethylene data were combined with the results of a cytological analysis of germination ofB. cinereaconidia and hyphal growth. We found that aminoethoxyvinylglycine and aminooxyacetic acid, which are competitive inhibitors of the 1-aminocyclopropane-1-carboxylic acid pathway, did not inhibit the ethylene emission byB. cinereaand that the fungus most likely produces ethylene via the 2-keto-4-methylthiobutyric acid pathway.B. cinereais able to produce ethylene in vitro, and the emission of ethylene follows the pattern that is associated with hyphal growth rather than the germination of conidia. Ethylene production in vitro depended on thel-methionine concentration added to the plating medium. Higher values and higher emission rates were observed when the concentration of conidia was increased. Compared with the ethylene released by the fungus, the infection-related ethylene produced by two tomato cultivars (cultivars Money Maker and Daniela) followed a similar pattern, but the levels of emission were 100-fold higher. The time evolution of enhanced ethylene production by the infected tomatoes and the cytological observations indicate that ethylene emission by the tomato-fungus system is not triggered by the ethylene produced byB. cinerea, although it is strongly synchronized with the growth rate of the fungus inside the tomato.
Anaerobic Ammonia Oxidation in the Presence of Nitrogen Oxides (NO

x

) by Two Different Lithotrophs
Authors: Schmidt Ingo , Hermelink Cristian , van de Pas-Schoonen Katinka , Strous Marc , op den Camp Huub J. , Kuenen J. Gijs , Jetten Mike S. M. 
Published: April 2009

ABSTRACT

The anaerobic ammonia-oxidizing activity of the planctomycete
Candidatus
“Brocadia anammoxidans” was not inhibited by NO concentrations up to 600 ppm and NO
2
concentrations up to 100 ppm.
B. anammoxidans
was able to convert (detoxify) NO, which might explain the high NO tolerance of this organism. In the presence of NO
2
, the specific ammonia oxidation activity of
B. anammoxidans
increased, and
Nitrosomonas
-like microorganisms recovered an NO
2
-dependent anaerobic ammonia oxidation activity. Addition of NO
2
to a mixed population of
B. anammoxidans
and
Nitrosomonas
induced simultaneous specific anaerobic ammonia oxidation activities of up to 5.5 mmol of NH
4
+
g of protein
−1
h
−1
by
B. anammoxidans
and up to 1.5 mmol of NH
4
+
g of protein
−1
h
−1
by
Nitrosomonas
. The stoichiometry of the converted N compounds (NO
2
−
/NH
3
ratio) and the microbial community structure were strongly influenced by NO
2
. The combined activity of
B. anammoxidans
and
Nitrosomonas
-like ammonia oxidizers might be of relevance in natural environments and for technical applications.
Differentiation of Closely Related
Carnobacterium
Food Isolates Based on 16S-23S Ribosomal DNA Intergenic Spacer Region Polymorphism
Authors: Kabadjova Petia , Dousset Xavier , Le Cam Virginie , Prevost Hervé 
Published: April 2009

ABSTRACT

A novel strategy for identification of
Carnobacterium
food isolates based on restriction fragment length polymorphism (RFLP) of PCR-amplified 16S-23S ribosomal intergenic spacer regions (ISRs) was developed. PCR amplification from all
Carnobacterium
strains studied always yielded three ISR amplicons, which were designated the small ISR (S-ISR), the medium ISR (M-ISR), and the large ISR (L-ISR). The lengths of these ISRs varied from one species to another.
Carnobacterium divergens
NCDO 2763
T
and
C. mobile
DSM 4849
T
generated one major S-ISR band (ca. 400 bp) and minor M-ISR and L-ISR bands (ca. 500 and ca. 600 bp, respectively). The ISRs amplified from
C. gallinarum
NCFB 2766
T
and
C. piscicola
NCDO 2762
T
were larger (S-ISR, ca. 600 bp; M-ISR, ca. 700 bp; and L-ISR, ca. 800 bp). The L-ISR contained two tDNAs coding for tRNA
Ile
and tRNA
Ala
genes. The M-ISR included one tRNA
Ala
gene, and the S-ISR did not contain a tDNA gene. The RFLP scheme devised involves estimation of variable PCR product sizes together with
Hin
fI,
Taq
I, and
Hin
dIII restriction analysis. Forty-two isolates yielded four unique band patterns that correctly resolved these isolates into four
Carnobacterium
species. This method is very suitable for rapid, low-cost identification of a wide variety of
Carnobacterium
species without sequencing.
Evaluation of the Heat Inactivation of
Escherichia coli
and
Lactobacillus plantarum
by Differential Scanning Calorimetry
Authors: Lee Jaesung , Kaletunç Gönül 
Published: April 2009

ABSTRACT

Differential scanning calorimetry (DSC) is used to evaluate the thermal stability and reversibility after heat treatment of transitions associated with various cellular components of
Escherichia coli
and
Lactobacillus plantarum
. The reversibility and the change in the thermal stability of individual transitions are evaluated by a second temperature scan after preheating in the DSC to various temperatures between 40 and 130°C. The viability of bacteria after a heat treatment between 55 and 70°C in the DSC is determined by both plate count and calorimetric data. The fractional viability values based on calorimetric and plate count data show a linear relationship. Viability loss and the irreversible change in DSC thermograms of pretreated whole cells are highly correlated between 55 and 70°C. Comparison of DSC scans for isolated ribosomes shows that the thermal stability of
E. coli
ribosomes is greater than that of
L. plantarum
ribosomes, consistent with the greater thermal tolerance of
E. coli
observed from viability loss and DSC scans of whole cells.
Characterization of the rRNA Locus of
Pfiesteria piscicida
and Development of Standard and Quantitative PCR-Based Detection Assays Targeted to the Nontranscribed Spacer
Authors: Saito Keiko , Drgon Tomás , Robledo José A. F. , Krupatkina Danara N. , Vasta Gerardo R. 
Published: April 2009

ABSTRACT

Pfiesteria piscicida
is a heterotrophic dinoflagellate widely distributed along the middle Atlantic shore of the United States and associated with fish kills in the Neuse River (North Carolina) and the Chesapeake Bay (Maryland and Virginia). We constructed a genomic DNA library from clonally cultured
P. piscicida
and characterized the nontranscribed spacer (NTS), small subunit, internal transcribed spacer 1 (ITS1), 5.8S region, ITS2, and large subunit of the rRNA gene cluster. Based on the
P. piscicida
ribosomal DNA sequence, we developed a PCR-based detection assay that targets the NTS. The assay specificity was assessed by testing clonal
P. piscicida
and
Pfiesteria shumwayae
, 35 additional dinoflagellate species, and algal prey (
Rhodomonas
sp.). Only
P. piscicida
and nine presumptive
P. piscicida
isolates tested positive. All PCR-positive products yielded identical sequences for
P. piscicida
, suggesting that the PCR-based assay is species specific. The assay can detect a single
P. piscicida
zoospore in 1 ml of water, 10 resting cysts in 1 g of sediment, or 10 fg of
P. piscicida
DNA in 1 μg of heterologous DNA. An internal standard for the PCR assay was constructed to identify potential false-negative results in testing of environmental sediment and water samples and as a competitor for the development of a quantitative competitive PCR assay format. The specificities of both qualitative and quantitative PCR assay formats were validated with >200 environmental samples, and the assays provide simple, rapid, and accurate methods for the assessment of
P. piscicida
in water and sediments.
SED1
Gene Length and Sequence Polymorphisms in Feral Strains of
Saccharomyces cerevisiae
Authors: Mannazzu Ilaria , Simonetti Emanuela , Marinangeli Paola , Guerra Emanuela , Budroni Marilena , Thangavelu Madan , Clementi Francesca 
Published: April 2009

ABSTRACT

The
SED1
gene (YDR077W), coding for the major cell wall glycoprotein of
Saccharomyces cerevisiae
stationary-phase cells, contains two blocks of tandem repeat units located within two distinct regions of the nucleotide sequence. A PCR survey of the
SED1
open reading frames (ORFs) of 186 previously uncharacterized grape must isolates of
S. cerevisiae
yielded 13 PCR profiles arising from different combinations of seven
SED1
length variants in individuals homozygous or heterozygous for the gene. Comparison of the nucleotide sequences of a group of representatives of each of the seven length variants with those of S288C and the type strain, CBS1171, unequivocally identified them as
SED1
alleles and provided evidence for the presence of two minisatellite-like sequences, variable in length, within the ORF of an
S. cerevisiae
gene. The segregation analyses of the
SED1
length variants and other genetic markers in 13 isolates representative of each PCR profile suggested that molecular mechanisms involved in minisatellite expansion and contraction may be responsible for
SED1
heterozygosities within a population of homothallic must isolates of
S. cerevisiae.
Seasonality of Chesapeake Bay Bacterioplankton Species
Authors: Heidelberg J. F. , Heidelberg K. B. , Colwell R. R. 
Published: April 2009

ABSTRACT

Bacteria,
γ-subclass of
Proteobacteria, Vibrio-Photobacterium, Vibrio vulnificus, Vibrio cholerae-Vibrio mimicus,
and
Vibrio cincinnatiensis
in water samples collected from the Choptank River in Chesapeake Bay from 15 April to 16 December 1996 were enumerated using a fluorescent oligonucleotide direct-counting (FODC) procedure. FODC results obtained using a
Bacteria
taxon-specific probe ranged from one-third the number of to the same number as that obtained by the acridine orange direct count (AODC) procedure. The abundance of individual taxa (per liter) ranged from 0.25 × 10
10
to 2.6 × 10
10
Bacteria,
0.32 × 10
8
to 3.1 × 10
8
γ-
Proteobacteria,
0.2 × 10
8
to 2.1 × 10
8
Vibrio-Photobacterium,
0.5 × 10
7
to 10 × 10
7
V. vulnificus,
0.2 × 10
6
to 6 × 10
6
V. cholerae-V. mimicus,
and 0.5 × 10
5
to 8 × 10
5
V. cincinnatiensis.
The occurrence of all taxa monitored in this study was higher in summer; however, these taxa made up a larger proportion of the
Bacteria
when the water temperature was low. Large fluctuations in species abundance as well as in percent composition of
Vibrio-Photobacterium
occurred from week to week, indicating that localized blooms of these taxa occur. The cross-Choptank River transect sample profile of
V. vulnificus
and
V. cholerae-V. mimicus
varied significantly in abundance, and trans-Choptank River transect samples revealed a patchy distribution.