bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abr1, a Transposon-Like Element in the Genome of the Cultivated MushroomAgaricus bisporus(Lange) Imbach
Authors: Sonnenberg Anton S. M. , Baars Johan J. P. , Mikosch Thomas S. P. , Schaap Peter J. , Van Griensven Leo J. L. D. 
Published: December 2019

ABSTRACTA 300-bp repetitive element was found in the genome of the white button mushroom,Agaricus bisporus, and designatedAbr1. It is present in ∼15 copies per haploid genome in the commercial strain Horst U1. Analysis of seven copies showed 89 to 97% sequence identity. The repeat has features typical of class II transposons (i.e., terminal inverted repeats, subterminal repeats, and a target site duplication of 7 bp). The latter shows a consensus sequence. When used as probe on Southern blots,Abr1identifies relatively little variation within traditional and present-day commercial strains, indicating that most strains are identical or have a common origin. In contrast to these cultivars, high variation is found among field-collected strains. Furthermore, a remarkable difference in copy numbers ofAbr1was found betweenA. bisporusisolates with a secondarily homothallic life cycle and those with a heterothallic life cycle.Abr1is a type II transposon not previously reported in basidiomycetes and appears to be useful for the identification of strains within the speciesA. bisporus.
Production of Acylated Homoserine Lactones by Psychrotrophic Members of the
Enterobacteriaceae
Isolated from Foods
Authors: Gram Lone , Christensen Allan Beck , Ravn Lars , Molin Søren , Givskov Michael 
Published: December 2019

ABSTRACT

Bacteria are able to communicate and gene regulation can be mediated through the production of acylated homoserine lactone (AHL) signal molecules. These signals play important roles in several pathogenic and symbiotic bacteria. The following study was undertaken to investigate whether AHLs are produced by bacteria found in food at temperatures and NaCl conditions commercially used for food preservation and storage. A minimum of 116 of 154 psychrotrophic
Enterobacteriaceae
strains isolated from cold-smoked salmon or vacuum-packed chilled meat produced AHLs. Analysis by thin-layer chromatography indicated that
N
-3-oxo-hexanoyl homoserine lactone was the major AHL of several of the strains isolated from cold-smoked salmon and meat. AHL-positive strains cultured at 5°C in medium supplemented with 4% NaCl produced detectable amounts of AHL(s) at cell densities of 10
6
CFU/ml. AHLs were detected in cold-smoked salmon inoculated with strains of
Enterobacteriaceae
stored at 5°C under an N
2
atmosphere when mean cell densities increased to 10
6
CFU/g and above. Similarly, AHLs were detected in uninoculated samples of commercially produced cold-smoked salmon when the level of indigenous
Enterobacteriaceae
reached 10
6
CFU/g. This level of
Enterobacteriaceae
is often found in lightly preserved foods, and AHL-mediated gene regulation may play a role in bacteria associated with food spoilage or food toxicity.
Activation Process of Dipteran-Specific Insecticidal Protein Produced by
Bacillus thuringiensis
subsp.
israelensis
Authors: Yamagiwa Masashi , Esaki Motoyuki , Otake Kanao , Inagaki Manabu , Komano Tohru , Amachi Teruo , Sakai Hiroshi 
Published: December 2019

ABSTRACT

Dipteran-specific insecticidal protein Cry4A is produced as a protoxin of 130 kDa in
Bacillus thuringiensis
subsp.
israelensis
. Here we performed the in vitro processing of Cry4A and showed that the 130-kDa protoxin of Cry4A was processed into the two protease-resistant fragments of 20 and 45 kDa through the intramolecular cleavage of a 60-kDa intermediate. The processing into these two fragments was also observed in vivo. To investigate functional properties of the two fragments, GST (glutathione
S
-transferase) fusion proteins of the 60-kDa intermediate and the 20- and 45-kDa fragments were constructed. Neither the GST–20-kDa fusion protein (GST-20) nor the GST–45-kDa fusion protein (GST-45) was actively toxic against mosquito larvae of
Culex pipiens
, whereas the GST–60-kDa intermediate fusion protein (GST-60) exhibited significant toxicity. However, when the two fusion proteins GST-20 and GST-45 coexisted, significant toxicity was observed. The coprecipitation experiment demonstrated that the two fragments associated with each other. Therefore, it is strongly suggested that the two fragments formed an active complex of apparently 60 kDa. A mutant of the 60-kDa protein which was apparently resistant to the intramolecular cleavage with the midgut extract of
C. pipiens
larvae had toxicity slightly lower than that of GST-60.
Genomic Characterization of Human and Environmental Polioviruses Isolated in Albania
Authors: Divizia Maurizio , Palombi Leonardo , Buonomo Ersilia , Donia Domenica , Ruscio Vito , Equestre Michele , Leno Luljeta , Panà Augusto , Degener Anna Marta 
Published: December 2019

ABSTRACT
Between April and December 1996, a serious outbreak of poliomyelitis occurred in Albania; almost 140 subjects were involved, and the episode presented an unusually high mortality rate (12%). During the outbreak, water samples from the Lana River in Tirana, Albania, and stool samples from two cases of paralytic poliomyelitis were collected and analyzed for the presence of polioviruses. Six polioviruses were isolated from the environmental and human samples, according to standard methods. All the samples were characterized by partial genomic sequencing of 330 bases across the 5′ untranslated region (5′-UTR) (nucleotide positions 200 to 530) and of 300 bases across the VP1 region (nucleotide positions 2474 to 2774). Comparison of these sequences with those present in data banks permitted the identification of environmental isolates Lana A and Lana B as, respectively, a Sabin-like type 2 poliovirus and an intertypic recombinant poliovirus (Sabin-like type 2/wild type 1), both bearing a G instead of an A at nucleotide position 481. The two other environmental polioviruses were similar to the isolates from the paralytic cases. They were characterized by a peculiar 5′-UTR and by a VP1 region showing 98% homology with the Albanian epidemic type 1 isolates reported by other authors. This study confirms the environmental circulation in Albania of recombinant poliovirus strains, likely sustained by a massive vaccination effort and by the presence in the environment of a type 1 poliovirus, as isolated from the Lana River in Tirana about 2 months before the first case of symptomatic acute flaccid paralysis was reported in this town.
Regiospecificity of Dioxygenation of Di- to Pentachlorobiphenyls and Their Degradation to Chlorobenzoates by the
bph
-Encoded Catabolic Pathway of
Burkholderia
sp. Strain LB400
Authors: Seeger Michael , Zielinski Marco , Timmis Kenneth N. , Hofer Bernd 
Published: December 2019

ABSTRACT

Burkholderia
sp. strain LB400 is one of the most potent aerobic polychlorobiphenyl (PCB)-degrading microorganisms that have been characterized. Its PCB-dioxygenating activity originates predominantly or exclusively from the biphenyl dioxygenase encoded by its
bph
gene cluster. Analysis of the dioxygenation products of several di- to pentachlorinated biphenyls formed by this enzyme revealed a complex dependence of the regiospecificity and the yield of dioxygenation on the substitution patterns of both the oxidized and the nonoxidized rings. No dioxygenolytic attack involving chlorinated
meta
or
para
carbons was observed. Therefore, the ability of the enzyme to hydroxylate chlorinated carbons appears to be limited to the
ortho
position. However, it is not limited to monochlorinated rings, as evidenced by dioxygenation of the 2,4-disubstituted ring at carbons 2 and 3. This site of attack is strikingly different from that of the 2,5-dichlorinated ring, which has been shown to be dihydroxylated at positions 3 and 4 (J. D. Haddock, J. R. Horton, and D. T. Gibson, J. Bacteriol. 177:20–26, 1995). These results demonstrate that a second substituent of
ortho
-chlorinated rings crucially influences the site of dioxygenation at this ring and thereby determines whether or not the initial chlorobiphenyl oxidation product is further metabolized through the
bph
-encoded pathway. The 2,4-dichlorinated ring can alternatively be attacked at carbons 5 and 6. The preferred site crucially depends on the substitution pattern of the other ring. The formation of more than a single dioxygenation product was found predominantly with congeners that contain two chlorinated rings, both of which are similarly prone to dioxygenation or one is substituted only at carbon 3.
Isolation and Characterization of
Methanomethylovorans hollandica
gen. nov., sp. nov., Isolated from Freshwater Sediment, a Methylotrophic Methanogen Able To Grow on Dimethyl Sulfide and Methanethiol
Authors: Lomans Bart P. , Maas Ronald , Luderer Rianne , Op den Camp Huub J. M. , Pol Arjan , van der Drift Chris , Vogels Godfried D. 
Published: December 2019

ABSTRACT

A newly isolated methanogen, strain DMS1
T
, is the first obligately anaerobic archaeon which was directly enriched and isolated from a freshwater sediment in defined minimal medium containing dimethyl sulfide (DMS) as the sole carbon and energy source. The use of a chemostat with a continuous DMS-containing gas stream as a method of enrichment, followed by cultivation in deep agar tubes, resulted in a pure culture. Since the only substrates utilized by strain DMS1
T
are methanol, methylamines, methanethiol (MT), and DMS, this organism is considered an obligately methylotrophic methanogen like most other DMS-degrading methanogens. Strain DMS1
T
differs from all other DMS-degrading methanogens, since it was isolated from a freshwater pond and requires NaCl concentrations (0 to 0.04 M) typical of the NaCl concentrations required by freshwater microorganisms for growth. DMS was degraded effectively only in a chemostat culture in the presence of low hydrogen sulfide and MT concentrations. Addition of MT or sulfide to the chemostat significantly decreased degradation of DMS. Transient accumulation of DMS in MT-amended cultures indicated that transfer of the first methyl group during DMS degradation is a reversible process. On the basis of its low level of homology with the most closely related methanogen,
Methanococcoides burtonii
(94.5%), its position on the phylogenetic tree, its morphology (which is different from that of members of the genera
Methanolobus
,
Methanococcoides
, and
Methanohalophilus
), and its salt tolerance and optimum (which are characteristic of freshwater bacteria), we propose that strain DMS1
T
is a representative of a novel genus. This isolate was named
Methanomethylovorans hollandica
. Analysis of DMS-amended sediment slurries with a fluorescence microscope revealed the presence of methanogens which were morphologically identical to
M. hollandica
, as described in this study. Considering its physiological properties,
M. hollandica
DMS1
T
is probably responsible for degradation of MT and DMS in freshwater sediments in situ. Due to the reversibility of the DMS conversion, methanogens like strain DMS1
T
can also be involved in the formation of DMS through methylation of MT. This phenomenon, which previously has been shown to occur in sediment slurries of freshwater origin, might affect the steady-state concentrations and, consequently, the total flux of DMS and MT in these systems.
Rapid Fluorescence Assessment of the Viability of Stressed
Lactococcus lactis
Authors: Bunthof Christine J. , van den Braak Sabina , Breeuwer Pieter , Rombouts Frank M. , Abee Tjakko 
Published: December 2019

ABSTRACT

The aim of this study was to establish the use of the fluorescent probes carboxyfluorescein (cF) and propidium iodide (PI) for rapid assessment of viability, using
Lactococcus lactis
subsp.
lactis
ML3 exposed to different stress treatments. The cF labeling indicated the reproductive capacity of mixtures of nontreated cells and cells killed at 70°C very well. However, after treatment up to 60°C the fraction of cF-labeled cells remained high, whereas the survival decreased for cells treated at above 50°C and was completely lost for those treated at 60°C. In an extended series of experiments, cell suspensions were exposed to heating, freezing, low pH, or bile salts, after which the colony counts, acidification capacity, glycolytic activity, PI exclusion, cF labeling, and cF efflux were measured and compared. The acidification capacity corresponded with the number of CFU. The glycolytic activity, which is an indicator of vitality, was more sensitive to the stress conditions than the reproduction, acidification, and fluorescence parameters. The cF labeling depended on membrane integrity, as was confirmed by PI exclusion. The fraction of cF-labeled cells was not a general indicator of reproduction or acidification, nor was PI exclusion or cF labeling capacity (the internal cF concentration). When the cells were labeled by cF, a subsequent lactose-energized efflux assay was needed for decisive viability assessment. This novel assay proved to be a good and rapid indicator of the reproduction and acidification capacities of stressed
L. lactis
and has potential for physiological research and dairy applications related to lactic acid bacteria.
High Rates of Conjugation in Bacterial Biofilms as Determined by Quantitative In Situ Analysis
Authors: Hausner Martina , Wuertz Stefan 
Published: December 2019

ABSTRACT
Quantitative in situ determination of conjugative gene transfer in defined bacterial biofilms using automated confocal laser scanning microscopy followed by three-dimensional analysis of cellular biovolumes revealed conjugation rates 1,000-fold higher than those determined by classical plating techniques. Conjugation events were not affected by nutrient concentration alone but were influenced by time and biofilm structure.
Development and Testing of a Microbiological Assay To Detect Residual Effects of Disinfectant on Hard Surfaces
Authors: Mariscal Alberto , Carnero-Varo Manuel , Gómez-Aracena Jorge , Fernández-Crehuet Joaquín 
Published: December 2019

ABSTRACT
We describe a glucuronidase bioassay for detecting residual bactericidal activity from the use of disinfectants on hard surfaces; in this assay we used formaldehyde, ethanol, isopropanol, chlorine, and a commercial preparation containing 2-bromo-2-nitro-1,3-propanediol. Chlorine and the commercial preparation showed bactericidal activity (53.5% and 98.2%, respectively) for a week after disinfection.
Identification of
Ruminococcus flavefaciens
as the Predominant Cellulolytic Bacterial Species of the Equine Cecum
Authors: Julliand Veronique , de Vaux Albane , Millet Liliane , Fonty Gerard 
Published: December 2019

ABSTRACT

Detection and quantification of cellulolytic bacteria with oligonucleotide probes showed that
Ruminococcus flavefaciens
was the predominant species in the pony and donkey cecum.
Fibrobacter succinogenes
and
Ruminococcus albus
were present at low levels. Four isolates, morphologically resembling
R. flavefaciens
, differed from ruminal strains by their carbohydrate utilization and their end products of cellobiose fermentation.
A Nisin Bioassay Based on Bioluminescence
Authors: Wahlström G. , Saris P. E. J. 
Published: December 2019

ABSTRACT

A
Lactococcus lactis
subsp.
lactis
strain that can sense the bacteriocin nisin and transduce the signal into bioluminescence was constructed. By using this strain, a bioassay based on bioluminescence was developed for quantification of nisin, for detection of nisin in milk, and for identification of nisin-producing strains. As little as 0.0125 ng of nisin per ml was detected within 3 h by this bioluminescence assay. This detection limit was lower than in previously described methods.
Polycyclic Aromatic Hydrocarbon Metabolism by White Rot Fungi and Oxidation by
Coriolopsis gallica
UAMH 8260 Laccase
Authors: Pickard Michael A. , Roman Rosa , Tinoco Raunel , Vazquez-Duhalt Rafael 
Published: December 2019

ABSTRACT

We studied the metabolism of polycyclic aromatic hydrocarbons (PAHs) by using white rot fungi previously identified as organisms that metabolize polychlorinated biphenyls. Bran flakes medium, which has been shown to support production of high levels of laccase and manganese peroxidase, was used as the growth medium. Ten fungi grown for 5 days in this medium in the presence of anthracene, pyrene, or phenanthrene, each at a concentration of 5 μg/ml could metabolize these PAHs. We studied the oxidation of 10 PAHs by using laccase purified from
Coriolopsis gallica
. The reaction mixtures contained 20 μM PAH, 15% acetonitrile in 60 mM phosphate buffer (pH 6), 1 mM 2,2′-azinobis-(3-ethylbenzthiazoline-6-sulfonate) (ABTS), and 5 U of laccase. Laccase exhibited 91% of its maximum activity in the absence of acetonitrile. The following seven PAHs were oxidized by laccase: benzo[
a
]pyrene, 9-methylanthracene, 2-methylanthracene, anthracene, biphenylene, acenaphthene, and phenanthrene. There was no clear relationship between the ionization potential of the substrate and the first-order rate constant (
k
) for substrate loss in vitro in the presence of ABTS. The effects of mediating substrates were examined further by using anthracene as the substrate. Hydroxybenzotriazole (HBT) (1 mM) supported approximately one-half the anthracene oxidation rate (
k
= 2.4 h
−1
) that ABTS (1 mM) supported (
k
= 5.2 h
−1
), but 1 mM HBT plus 1 mM ABTS increased the oxidation rate ninefold compared with the oxidation rate in the presence of ABTS, to 45 h
−1
. Laccase purified from
Pleurotus ostreatus
had an activity similar to that of
C. gallica
laccase with HBT alone, with ABTS alone, and with 1 mM HBT plus 1 mM ABTS. Mass spectra of products obtained from oxidation of anthracene and acenaphthene revealed that the dione derivatives of these compounds were present.
Spatial Heterogeneity of Bacterial Populations along an Environmental Gradient at a Shallow Submarine Hydrothermal Vent near Milos Island (Greece)
Authors: Sievert Stefan M. , Brinkhoff Thorsten , Muyzer Gerard , Ziebis Wiebke , Kuever Jan 
Published: December 2019

ABSTRACT

The spatial heterogeneity of bacterial populations at a shallow-water hydrothermal vent in the Aegean Sea close to the island of Milos (Greece) was examined at two different times by using acridine orange staining for total cell counts, cultivation-based techniques, and denaturing gradient gel electrophoresis (DGGE) analysis of PCR-amplified 16S rRNA gene fragments. Concurrent with measurements of geochemical parameters, samples were taken along a transect from the center of the vent to the surrounding area. Most-probable-number (MPN) counts of metabolically defined subpopulations generally constituted a minor fraction of the total cell counts; both counting procedures revealed the highest cell numbers in a transition zone from the strongly hydrothermally influenced sediments to normal sedimentary conditions. Total cell counts ranged from 3.2 × 10
5
cells ml
−1
in the water overlying the sediments to 6.4 × 10
8
cells g (wet weight) of sediment
−1
. MPN counts of chemolithoautotrophic sulfur-oxidizing bacteria varied between undetectable and 1.4 × 10
6
cells g
−1
. MPN counts for sulfate-reducing bacteria and dissimilatory iron-reducing bacteria ranged from 8 to 1.4 × 10
5
cells g
−1
and from undetectable to 1.4 × 10
6
cells g
−1
, respectively. DGGE revealed a trend from a diverse range of bacterial populations which were present in approximately equal abundance in the transition zone to a community dominated by few populations close to the center of the vent. Temperature was found to be an important parameter in determining this trend. However, at one sampling time this trend was not discernible, possibly due to storm-induced disturbance of the upper sediment layers.
Transduction of Enteric
Escherichia coli
Isolates with a Derivative of Shiga Toxin 2-Encoding Bacteriophage φ3538 Isolated from
Escherichia coli
O157:H7
Authors: Schmidt Herbert , Bielaszewska Martina , Karch Helge 
Published: December 2019

ABSTRACT

We investigated the ability of a detoxified derivative of a Shiga toxin 2 (Stx2)-encoding bacteriophage to infect and lysogenize enteric
Escherichia coli
strains and to develop infectious progeny from such lysogenized strains. The

stx
2

gene of the patient
E. coli
O157:H7 isolate 3538/95 was replaced by the chloramphenicol acetyltransferase (
cat
) gene from plasmid pACYC184. Phage φ3538(Δ

stx
2

::
cat
) was isolated after induction of
E. coli
O157:H7 strain 3538/95 with mitomycin. A variety of strains of enteropathogenic
E. coli
(EPEC), enteroinvasive
E. coli
(EIEC), Stx-producing
E. coli
(STEC), enterotoxigenic
E. coli
(ETEC), enteroaggregative
E. coli
(EAEC), and
E. coli
from the physiological stool microflora were infected with φ3538(Δ

stx
2

::
cat
), and plaque formation and lysogenic conversion of wild-type
E. coli
strains were investigated. With the exception of one EIEC strain, none of the
E. coli
strains supported the formation of plaques when used as indicators for φ3538(Δ

stx
2

::
cat
). However, 2 of 11 EPEC, 11 of 25 STEC, 2 of 7 EAEC, 1 of 3 EIEC, and 1 of 6
E. coli
isolates from the stool microflora of healthy individuals integrated the phage in their chromosomes and expressed resistance to chloramphenicol. Following induction with mitomycin, these lysogenic strains released infectious particles of φ3538(Δ

stx
2

::
cat
) that formed plaques on a lawn of
E. coli
laboratory strain C600. The results of our study demonstrate that φ3538(Δ

stx
2

::
cat
) was able to infect and lysogenize particular enteric strains of pathogenic and nonpathogenic
E. coli
and that the lysogens produced infectious phage progeny. Stx-encoding bacteriophages are able to spread
stx
genes among enteric
E. coli
strains.
Identification of an NADH-Cytochrome b
5
Reductase Gene from an Arachidonic Acid-Producing Fungus,
Mortierella alpina
1S-4, by Sequencing of the Encoding cDNA and Heterologous Expression in a Fungus,
Aspergillus oryzae
Authors: Sakuradani Eiji , Kobayashi Michihiko , Shimizu Sakayu 
Published: December 2019

ABSTRACT

Based on the sequence information for bovine and yeast NADH-cytochrome
b
5
reductases (CbRs), a DNA fragment was cloned from
Mortierella alpina
1S-4 after PCR amplification. This fragment was used as a probe to isolate a cDNA clone with an open reading frame encoding 298 amino acid residues which show marked sequence similarity to CbRs from other sources, such as yeast (
Saccharomyces cerevisiae
), bovine, human, and rat CbRs. These results suggested that this cDNA is a CbR gene. The results of a structural comparison of the flavin-binding β-barrel domains of CbRs from various species and that of the
M. alpina
enzyme suggested that the overall barrel-folding patterns are similar to each other and that a specific arrangement of three highly conserved amino acid residues (i.e., arginine, tyrosine, and serine) plays a role in binding with the flavin (another prosthetic group) through hydrogen bonds. The corresponding genomic gene, which was also cloned from
M. alpina
1S-4 by means of a hybridization method with the above probe, had four introns of different sizes. These introns had GT at the 5′ end and AG at the 3′ end, according to a general GT-AG rule. The expression of the full-length cDNA in a filamentous fungus,
Aspergillus oryzae
, resulted in an increase (4.7 times) in ferricyanide reduction activity involving the use of NADH as an electron donor in the microsomes. The
M. alpina
CbR was purified by solubilization of microsomes with cholic acid sodium salt, followed by DEAE-Sephacel, Mono-Q HR 5/5, and AMP-Sepharose 4B affinity column chromatographies; there was a 645-fold increase in the NADH-ferricyanide reductase specific activity. The purified CbR preferred NADH over NADPH as an electron donor. This is the first report of an analysis of this enzyme in filamentous fungi.