bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phylogenetic Analysis of an Anaerobic, Trichlorobenzene-Transforming Microbial Consortium
Authors: von Wintzingerode Friedrich , Selent Burkhard , Hegemann Werner , Göbel Ulf B. 
Published: December 2019

ABSTRACT

A culture-independent phylogenetic survey for an anaerobic trichlorobenzene-transforming microbial community was carried out. Small-subunit rRNA genes were PCR amplified from community DNA by using primers specific for
Bacteria
or
Euryarchaeota
and were subsequently cloned. Application of a new hybridization-based screening approach revealed 51 bacterial clone families, one of which was closely related to dechlorinating
Dehalobacter
species. Several clone sequences clustered to rDNA sequences obtained from a molecular study of an anaerobic aquifer contaminated with hydrocarbons and chlorinated solvents (Dojka et al., Appl. Env. Microbiol. 64:3869–3877, 1998).
Quantification of Hepatitis A Virus in Shellfish by Competitive Reverse Transcription-PCR with Coextraction of Standard RNA
Authors: Arnal Charlotte , Ferre-Aubineau Virginie , Mignotte Berangere , Imbert-Marcille Berthe Marie , Billaudel Sylviane 
Published: December 2019

ABSTRACT

To quantify hepatitis A virus (HAV) in experimentally contaminated mussels, we developed an internal standard RNA with a 7-nucleotide deletion for competitive reverse transcription (RT)-PCR. Deposited directly into the sample, this standard was used both as extraction control and as quantification tool. After coextraction and competitive RT-PCR, standard and wild-type products were detected by differential hybridization with specific probes and a DNA enzyme immunoassay. The quantifiable range with this reproducible method was 10
4
to 10
7
copies of HAV/gram or 400 to 10
6
50% tissue culture infective doses/ml.
Expression, Regulation, and Mode of Action of the AbiG Abortive Infection System of
Lactococcus lactis
subsp.
cremoris
UC653
Authors: O’Connor Lisa , Tangney Mark , Fitzgerald Gerald F. 
Published: December 2019

ABSTRACT

The abortive infection system AbiG is encoded by the lactococcal plasmid pCI750. The
abiG
locus (consisting of two genes,
abiGi
and
abiGii
) was examined by Northern blot analysis, revealing two transcripts of approximately 2.8 and 1.5 kb which were homologous to the two gene-specific probes. A transcriptional start site was mapped upstream of
abiGi
, and it appeared that the two genes were cotranscribed, resulting in the 2.8-kb transcript. The smaller transcript may be the result of independent transcription of
abiGii
within
abiGi
or of the presence of a weak terminator within
abiGii
. The locus was shown to be constitutively expressed. Evidence is presented for the possible existence of a second Abi mechanism on pCI750. Examination of phage sk1 RNA synthesis demonstrated that both the subcloned AbiG and, to a greater extent, pCI750 inhibited this process. pCI750 also severely inhibited synthesis of both early and late phage c2 transcripts, while the presence of the subclone resulted in a reduction in late transcript synthesis only.
Growth of
Listeria monocytogenes
and
Yersinia enterocolitica
on Cooked Modified-Atmosphere-Packaged Poultry in the Presence and Absence of a Naturally Occurring Microbiota
Authors: Barakat R. K. , Harris L. J. 
Published: December 2019

ABSTRACT

Cooked poultry cuts were inoculated with five-strain composite mixtures of either
Listeria monocytogenes
or
Yersinia enterocolitica
(1,000 CFU/150-g piece), packaged in 44:56 CO
2
-N
2
, and stored at 3.5, 6.5, or 10°C for up to 5 weeks. Both
L. monocytogenes
and
Y. enterocolitica
grew under all test conditions. The presence of a naturally occurring microbiota did not influence the growth of either pathogen. Addition of lactate with the shelf life extender ALTA 2341 lengthened the lag phases of
L. monocytogenes
and
Y. enterocolitica
but did not prevent their growth.
Fate of Free DNA and Transformation of the Oral Bacterium
Streptococcus gordonii
DL1 by Plasmid DNA in Human Saliva
Authors: Mercer Derry K. , Scott Karen P. , Bruce-Johnson Wendy A. , Glover L. Anne , Flint Harry J. 
Published: December 2019

ABSTRACT

Competitive PCR was used to monitor the survival of a 520-bp DNA target sequence from a recombinant plasmid, pVACMC1, after admixture of the plasmid with freshly sampled human saliva. The fraction of the target remaining amplifiable ranged from 40 to 65% after 10 min of exposure to saliva samples from five subjects and from 6 to 25% after 60 min of exposure. pVACMC1 plasmid DNA that had been exposed to degradation by fresh saliva was capable of transforming naturally competent
Streptococcus gordonii
DL1 to erythromycin resistance, although transforming activity decreased rapidly, with a half-life of approximately 50 s.
S. gordonii
DL1 transformants were obtained in the presence of filter-sterilized saliva and a 1-μg/ml final concentration of pVACMC1 DNA. Addition of filter-sterilized saliva instead of heat-inactivated horse serum to
S. gordonii
DL1 cells induced competence, although with slightly lower efficiency. These findings indicate that DNA released from bacteria or food sources within the mouth has the potential to transform naturally competent oral bacteria. However, further investigations are needed to establish whether transformation of oral bacteria can occur at significant frequencies in vivo.
A Mechanism of Resistance to Hydrogen Peroxide in
Vibrio rumoiensis
S-1
Authors: Ichise Nobutoshi , Morita Naoki , Hoshino Tamotsu , Kawasaki Kosei , Yumoto Isao , Okuyama Hidetoshi 
Published: December 2019

ABSTRACT

A possible mechanism of resistance to hydrogen peroxide (H
2
O
2
) in
Vibrio rumoiensis
, isolated from the H
2
O
2
-rich drain pool of a fish processing plant, was examined. When
V. rumoiensis
cells were inoculated into medium containing either 5 mM or no H
2
O
2
, they grew in similar manners. A spontaneous mutant strain, S-4, derived from
V. rumoiensis
and lacking catalase activity did not grow at all in the presence of 5 mM H
2
O
2
. These results suggest that catalase is inevitably involved in the resistance and survival of
V. rumoiensis
in the presence of H
2
O
2
. Catalase activity was constitutively present in
V. rumoiensis
cells grown in the absence of H
2
O
2
, and its occurrence was dependent on the age of the cells, a characteristic which is observed for the HP II-type catalase of
Escherichia coli
. The presence of the HP II-type catalase in
V. rumoiensis
cells was evidenced by partial sequencing of the gene encoding the HP II-type catalase from this organism. A notable difference between
V. rumoiensis
and
E. coli
is that catalase is accumulated at very high levels (∼2% of the total soluble proteins) in
V. rumoiensis
, in contrast to the case for
E. coli
. When
V. rumoiensis
cells which had been exposed to 5 mM H
2
O
2
were centrifuged, most intracellular proteins, including catalase, were recovered in the medium. On the other hand, when
V. rumoiensis
cells were grown on plates containing various concentrations of H
2
O
2
, individual cells had a colony-forming ability inferior to those of
E. coli
,
Bacillus subtilis
, and
Vibrio parahaemolyticus
. Thus, it is suggested that when
V. rumoiensis
cells are exposed to high concentrations of H
2
O
2
, most cells will immediately be broken by H
2
O
2
. In addition, the cells which have had little or no damage will start to grow in a medium where almost all H
2
O
2
has been decomposed by the catalase released from broken cells.
Identification of
Bacillus
Spores by Matrix-Assisted Laser Desorption Ionization–Mass Spectrometry
Authors: Hathout Yetrib , Demirev Plamen A. , Ho Yen-Peng , Bundy Jonathan L. , Ryzhov Victor , Sapp Lisa , Stutler James , Jackman Joany , Fenselau Catherine 
Published: December 2019

ABSTRACT

Unique patterns of biomarkers were reproducibly characterized by matrix-assisted laser desorption ionization (MALDI)–mass spectrometry and were used to distinguish
Bacillus
species members from one another. Discrimination at the strain level was demonstrated for
Bacillus cereus
spores. Lipophilic biomarkers were invariant in
Bacillus globigii
spores produced in three different media and in
B. globigii
spores stored for more than 30 years. The sensitivity was less than 5,000 cells deposited for analysis. Protein biomarkers were also characterized by MALDI analysis by using spores treated briefly with corona plasma discharge. Protein biomarkers were readily desorbed following this treatment. The effect of corona plasma discharge on the spores was examined.
Biodegradation of Pentachlorophenol in a Continuous Anaerobic Reactor Augmented with
Desulfitobacterium frappieri
PCP-1
Authors: Tartakovsky B. , Levesque M.-J. , Dumortier R. , Beaudet R. , Guiot S. R. 
Published: December 2019

ABSTRACT

In this work, a strain of anaerobic pentachlorophenol (PCP) degrader,
Desulfitobacterium frappieri
PCP-1, was used to augment a mixed bacterial community of an anaerobic upflow sludge bed reactor degrading PCP. To estimate the efficiency of augmentation, the population of PCP-1 in the reactor was enumerated by a competitive PCR technique. The PCP-1 strain appeared to compete well with other microorganisms of the mixed bacterial community, with its population increasing from 10
6
to 10
10
cells/g of volatile suspended solids within a period of 70 days. Proliferation of strain PCP-1 allowed for a substantial increase of the volumetric PCP load from 5 to 80 mg/liter of reaction volume/day. A PCP removal efficiency of 99% and a dechlorination efficiency of not less than 90.5% were observed throughout the experiment, with 3-Cl-phenol and phenol being observable dechlorination intermediates.
Cold Shock Proteins and Low-Temperature Response of
Streptococcus thermophilus
CNRZ302
Authors: Wouters Jeroen A. , Rombouts Frank M. , de Vos Willem M. , Kuipers Oscar P. , Abee Tjakko 
Published: December 2019

ABSTRACT

Low-temperature adaptation and cryoprotection were studied in the thermophilic lactic acid bacterium
Streptococcus thermophilus
CNRZ302.
S. thermophilus
actively adapts to freezing during a pretreatment at 20°C, resulting in an approximately 1,000-fold increased survival after four freeze-thaw cycles compared to mid-exponential-phase cells grown at an optimal temperature of 42°C. No adaptation is observed when cells are exposed to a temperature (10°C) below the minimal growth temperature of the strain (just below 15°C). By two-dimensional gel electrophoresis several 7-kDa cold-induced proteins were identified, which are the major induced proteins after a shift to 20°C. These cold shock proteins were maximally expressed at 20°C, while the induction level was low after cold shock to 10°C. To confirm the presence of
csp
genes in
S. thermophilus
, a PCR strategy was used which yielded products of different sizes. Sequence analysis revealed
csp
-like sequences that were up to 95% identical to those of
csp
genes of
S. thermophilus
ST1-1,
Streptococcus dysgalactiae
,
Streptococcus pyogenes
, and
Lactococcus lactis
. Northern blot analysis revealed a seven- to ninefold induction of
csp
mRNA after a temperature shift to 20°C, showing that this thermophilic bacterium indeed contains at least one cold-inducible
csp
gene and that its regulation takes place at the transcriptional level.
Registered Designation of Origin Areas of Fermented Food Products Defined by Microbial Phenotypes and Artificial Neural Networks
Authors: Lopes M. F. S. , Pereira C. I. , Rodrigues F. M. S. , Martins M. P. , Mimoso M. C. , Barros T. C. , Figueiredo Marques J. J. , Tenreiro R. P. , Almeida J. S. , Barreto Crespo M. T. 
Published: December 2019

ABSTRACT

Cheese produced from raw ewes’ milk and
chouriço
, a Portuguese dry fermented sausage, are still produced in a traditional way in certain regions of Portugal by relying on colonization by microbial populations associated with the raw materials, equipment, and local environments. For the purpose of describing the product origins and types of these fermented foods, metabolic phenotypes can be used as descriptors of the product as well as to determine the presence of compounds with organoleptic value. The application of artificial neural networks to the metabolic profiles of bacterial isolates was assayed and allowed the separation of products from different regions. This method could then be used for the Registered Designation of Origin certification process of food products. Therefore, besides test panel results for these traditionally produced food products, another tool for validating products for the marketplace is available to the producers. The method can be improved for the detection of counterfeit products.
Natural Diversity of
Frankia
Strains in Actinorhizal Root Nodules from Promiscuous Hosts in the Family Myricaceae
Authors: Clawson Michael L. , Benson David R. 
Published: December 2019

ABSTRACT

Actinorhizal plants invade nitrogen-poor soils because of their ability to form root nodule symbioses with N
2
-fixing actinomycetes known as
Frankia
.
Frankia
strains are difficult to isolate, so the diversity of strains inhabiting nodules in nature is not known. To address this problem, we have used the variability in bacterial 16S rRNA gene sequences amplified from root nodules as a means to estimate molecular diversity. Nodules were collected from 96 sites primarily in northeastern North America; each site contained one of three species of the family Myricaceae. Plants in this family are considered to be promiscuous hosts because several species are effectively nodulated by most isolated strains of
Frankia
in the greenhouse. We found that strain evenness varies greatly between the plant species so that estimating total strain richness of
Frankia
within myricaceous nodules with the sample size used was problematical. Nevertheless,
Myrica pensylvanica
, the common bayberry, was found to have sufficient diversity to serve as a reservoir host for
Frankia
strains that infect plants from other actinorhizal families.
Myrica gale
, sweet gale, yielded a few dominant sequences, indicating either symbiont specialization or niche selection of particular ecotypes. Strains in
Comptonia peregrina
nodules had an intermediate level of diversity and were all from a single major group of
Frankia
.
Characterization of a Tetrameric Inositol Monophosphatase from the Hyperthermophilic Bacterium
Thermotoga maritima
Authors: Chen Liangjing , Roberts Mary F. 
Published: December 2019

ABSTRACT

Inositol monophosphatase (I-1-Pase) catalyzes the dephosphorylation step in the de novo biosynthetic pathway of inositol and is crucial for all inositol-dependent processes. An extremely heat-stable tetrameric form of I-1-Pase from the hyperthermophilic bacterium
Thermotoga maritima
was overexpressed in
Escherichia coli
. In addition to its different quaternary structure (all other known I-1-Pases are dimers), this enzyme displayed a 20-fold higher rate of hydrolysis of
d
-inositol 1-phosphate than of the
l
isomer. The homogeneous recombinant
T. maritima
I-1-Pase (containing 256 amino acids with a subunit molecular mass of 28 kDa) possessed an unusually high
V
max
(442 μmol min
−1
mg
−1
) that was much higher than the
V
max
of the same enzyme from another hyperthermophile,
Methanococcus jannaschii
. Although
T. maritima
is a eubacterium, its I-1-Pase is more similar to archaeal I-1-Pases than to the other known bacterial or mammalian I-1-Pases with respect to substrate specificity, Li
+
inhibition, inhibition by high Mg
2+
concentrations, metal ion activation, heat stability, and activation energy. Possible reasons for the observed kinetic differences are discussed based on an active site sequence alignment of the human and
T. maritima
I-1-Pases.
Protective Role of Catalase in
Pseudomonas aeruginosa
Biofilm Resistance to Hydrogen Peroxide
Authors: Elkins James G. , Hassett Daniel J. , Stewart Philip S. , Schweizer Herbert P. , McDermott Timothy R. 
Published: December 2019

ABSTRACT

The role of the two known catalases in
Pseudomonas aeruginosa
in protecting planktonic and biofilm cells against hydrogen peroxide (H
2
O
2
) was investigated. Planktonic cultures and biofilms formed by the wild-type strain PAO1 and the
katA
and
katB
catalase mutants were compared for their susceptibility to H
2
O
2
. Over the course of 1 h, wild-type cell viability decreased steadily in planktonic cells exposed to a single dose of 50 mM H
2
O
2
, whereas biofilm cell viability remained at approximately 90% when cells were exposed to a flowing stream of 50 mM H
2
O
2
. The
katB
mutant, lacking the H
2
O
2
-inducible catalase KatB, was similar to the wild-type strain with respect to H
2
O
2
resistance. The
katA
mutant possessed undetectable catalase activity. Planktonic
katA
mutant cultures were hypersusceptible to a single dose of 50 mM H
2
O
2
, while biofilms displayed a 10-fold reduction in the number of culturable cells after a 1-h exposure to 50 mM H
2
O
2
. Catalase activity assays, activity stains in nondenaturing polyacrylamide gels, and
lacZ
reporter genes were used to characterize the oxidative stress responses of planktonic cultures and biofilms. Enzyme assays and catalase activity bands in nondenaturing polyacrylamide gels showed significant KatB catalase induction occurred in biofilms after a 20-min exposure to H
2
O
2
, suggesting that biofilms were capable of a rapid adaptive response to the oxidant. Reporter gene data obtained with a
katB
::
lacZ
transcriptional reporter strain confirmed
katB
induction and that the increase in total cellular catalase activity was attributable to KatB. Biofilms upregulated the reporter in the constant presence of 50 mM H
2
O
2
, while planktonic cells were overwhelmed by a single 50 mM dose and were unable to make detectable levels of β-galactosidase. The results of this study demonstrated the following: the constitutively expressed KatA catalase is important for resistance of planktonic and biofilm
P. aeruginosa
to H
2
O
2
, particularly at high H
2
O
2
concentrations; KatB is induced in both planktonic and biofilm cells in response to H
2
O
2
insult, but plays a relatively small role in biofilm resistance; and KatB is important to either planktonic cells or biofilm cells for acquired antioxidant resistance when initial levels of H
2
O
2
are sublethal.
Production of Chymotrypsin-Resistant
Bacillus thuringiensis
Cry2Aa1 δ-Endotoxin by Protein Engineering
Authors: Audtho Mongkon , Valaitis Algimantas P. , Alzate Oscar , Dean Donald H. 
Published: December 2019

ABSTRACT

Cleavage of the Cry2Aa1 protoxin (molecular mass, 63 kDa) from
Bacillus thuringiensis
by midgut juice of gypsy moth (
Lymantria dispar
) larvae resulted in two major protein fragments: a 58-kDa fragment which was highly toxic to the insect and a 49-kDa fragment which was not toxic. In the midgut juice, the protoxin was processed into a 58-kDa toxin within 1 min, but after digestion for 1 h, the 58-kDa fragment was further cleaved within domain I, resulting in the protease-resistant 49-kDa fragment. Both the 58-kDa and nontoxic 49-kDa fragments were also found in vivo when
125
I-labeled toxin was fed to the insects. N-terminal sequencing revealed that the protease cleavage sites are at the C termini of Tyr49 and Leu144 for the active fragment and the smaller fragment, respectively. To prevent the production of the nontoxic fragment during midgut processing, five mutant proteins were constructed by replacing Leu144 of the toxin with Asp (L144D), Ala (L144A), Gly (L144G), His (L144H), or Val (L144V) by using a pair of complementary mutagenic oligonucleotides in PCR. All of the mutant proteins were highly resistant to the midgut proteases and chymotrypsin. Digestion of the mutant proteins by insect midgut extract and chymotrypsin produced only the active 58-kDa fragment, except that L144H was partially cleaved at residue 144.
Toxigenic Strains of
Bacillus licheniformis
Related to Food Poisoning
Authors: Salkinoja-Salonen M. S. , Vuorio R. , Andersson M. A. , Kämpfer P. , Andersson M. C. , Honkanen-Buzalski T. , Scoging A. C. 
Published: December 2019

ABSTRACT

Toxin-producing isolates of
Bacillus licheniformis
were obtained from foods involved in food poisoning incidents, from raw milk, and from industrially produced baby food. The toxin detection method, based on the inhibition of boar spermatozoan motility, has been shown previously to be a sensitive assay for the emetic toxin of
Bacillus cereus
, cereulide. Cell extracts of the toxigenic
B. licheniformis
isolates inhibited sperm motility, damaged cell membrane integrity, depleted cellular ATP, and swelled the acrosome, but no mitochondrial damage was observed. The responsible agent from the
B. licheniformis
isolates was partially purified. It showed physicochemical properties similar to those of cereulide, despite having very different biological activity. The toxic agent was nonproteinaceous; soluble in 50 and 100% methanol; and insensitive to heat, protease, and acid or alkali and of a molecular mass smaller than 10,000 g mol
−1
. The toxic
B. licheniformis
isolates inhibited growth of
Corynebacterium renale
DSM 20688
T
, but not all inhibitory isolates were sperm toxic. The food poisoning-related isolates were beta-hemolytic, grew anaerobically and at 55°C but not at 10°C, and were nondistinguishable from the type strain of
B. licheniformis
, DSM 13
T
, by a broad spectrum of biochemical tests. Ribotyping revealed more diversity; the toxin producers were divided among four ribotypes when cut with
Pvu
II and among six when cut with
Eco
RI, but many of the ribotypes also contained nontoxigenic isolates. When ribotyped with
Pvu
II, most toxin-producing isolates shared bands at 2.8 ± 0.2, 4.9 ± 0.3, and 11.7 ± 0.5 or 13.1 ± 0.8 kb.
Diversity of Sulfate-Reducing Bacteria in Oxic and Anoxic Regions of a Microbial Mat Characterized by Comparative Analysis of Dissimilatory Sulfite Reductase Genes
Authors: Minz Dror , Flax Jodi L. , Green Stefan J. , Muyzer Gerard , Cohen Yehuda , Wagner Michael , Rittmann Bruce E. , Stahl David A. 
Published: December 2019

ABSTRACT

Sequence analysis of genes encoding dissimilatory sulfite reductase (DSR) was used to identify sulfate-reducing bacteria in a hypersaline microbial mat and to evaluate their distribution in relation to levels of oxygen. The most highly diverse DSR sequences, most related to those of the
Desulfonema
-like organisms within the δ-proteobacteria, were recovered from oxic regions of the mat. This observation extends those of previous studies by us and others associating
Desulfonema
-like organisms with oxic habitats.
Aerobic Degradation of 1,1,1-Trichloroethane by
Mycobacterium
spp. Isolated from Soil
Authors: Yagi Osami , Hashimoto Akiko , Iwasaki Kazuhiro , Nakajima Mutsuyasu 
Published: December 2019

ABSTRACT

Two strains of 1,1,1-trichloroethane (TCA)-degrading bacteria, TA5 and TA27, were isolated from soil and identified as
Mycobacterium
spp. Strains TA5 and TA27 could degrade 25 and 75 mg · liter of TCA
−1
cometabolically in the presence of ethane as a carbon source, respectively. The compound 2,2,2-trichloroethanol was produced as a metabolite of the degradation process.