bluuebunny/crossref_metadata_2025_split huggingface dataset:
Apoptosis Induced by Aminoglycosides in LLC-PK1 Cells: Comparative Study of Neomycin, Gentamicin, Amikacin, and Isepamicin Using Electroporation
Authors: Denamur Sophie , Van Bambeke Françoise , Mingeot-Leclercq Marie-Paule , Tulkens Paul M. 
Published: April 2008

ABSTRACT
Levels of apoptosis induction (4′,6′-diamidino-2-phenylindole staining, activation of caspase 3) for aminoglycosides were compared by using renal LLC-PK1 cells. Amikacin caused less apoptosis than gentamicin in incubated cells. In electroporated cells, neomycin B and gentamicin caused apoptosis in the 0.03 to 0.1 mM range, isepamicin required larger concentrations (0.2 mM), and amikacin was without effect.
Characterization of Replication and Conjugation of
Streptomyces
Circular Plasmids pFP1 and pFP11 and Their Ability To Propagate in Linear Mode with Artificially Attached Telomeres
Authors: Zhang Ran , Zeng Ana , Fang Ping , Qin Zhongjun 
Published: April 2008

ABSTRACT

Many
Streptomyces
species harbor circular plasmids (8 to 31 kb) as well as linear plasmids (12 to 1,700 kb). We report the characterization of two newly detected circular plasmids, pFP11 (35,139 bp) and pFP1 (39,360 bp). As on linear plasmids, their replication loci comprise
repA
genes and adjacent iterons, to which RepA proteins bind specifically in vitro. Plasmids containing the minimal iterons plus the
repA
locus of pFP11 were inherited extremely unstably;
par
and additional loci were required for stable inheritance. Surprisingly, plasmids containing replication loci from pFP11 or
Streptomyces
circular plasmid SCP2 but not from pFP1, SLP1, or pIJ101 propagated in a stable linear mode when the telomeres of a linear plasmid were attached. These results indicate bidirectional replication for pFP11 and SCP2. Both pFP11 and pFP1 contain, for plasmid transfer, a major functional
traB
gene (encoding a DNA translocase typical for
Streptomyces
plasmids) as well as, surprisingly, a putative
traA
gene (encoding a DNA nickase, characteristic of single-stranded DNA transfer of gram-negative plasmids), but this did not appear to be functional, at least in isolation.
Transcriptional Analysis of
l
-Methionine Catabolism in the Cheese-Ripening Yeast
Yarrowia lipolytica
in Relation to Volatile Sulfur Compound Biosynthesis
Authors: Cholet Orianne , Hénaut Alain , Hébert Agnès , Bonnarme Pascal 
Published: April 2008

ABSTRACT

Yarrowia lipolytica
is one of the yeasts most frequently isolated from the surface of ripened cheeses. In previous work, it has been shown that this yeast is able to convert
l
-methionine into various volatile sulfur compounds (VSCs) that may contribute to the typical flavors of several cheeses. In the present study, we show that
Y. lipolytica
does not assimilate lactate in the presence of
l
-methionine in a cheeselike medium. Nineteen presumptive genes associated with
l
-methionine catabolism or pyruvate metabolism in
Y. lipolytica
were transcriptionally studied in relation to
l
-methionine degradation. The expression levels of the Yl
ARO8
(YALI0E20977g), Yl
BAT1
(YALI0D01265g), and Yl
BAT2
(YALI0F19910g) genes (confirmed by real-time PCR experiments) were found to be strongly up-regulated by
l
-methionine, and a greater variety and larger amounts of VSCs, such as methanethiol and its autooxidation products (dimethyl disulfide and dimethyl trisulfide), were released in the medium when
Y. lipolytica
was grown in the presence of a high concentration of
l
-methionine. In contrast, other genes related to pyruvate metabolism were found to be down-regulated in the presence of
l
-methionine; two exceptions were the Yl
PDB1
(YALI0E27005g) and Yl
PDC6
(YALI0D06930g) genes, which encode a pyruvate dehydrogenase and a pyruvate decarboxylase, respectively. Both transcriptional and biochemical results corroborate the view that transamination is the first step of the enzymatic conversion of
l
-methionine to VSCs in
Y. lipolytica
and that the Yl
ARO8
, Yl
BAT1
, and Yl
BAT2
genes could play a key role in this process.
Inactivation of
Bacillus anthracis
Spores by a Combination of Biocides and Heating under High-Temperature Short-Time Pasteurization Conditions
Authors: Xu Sa , Labuza Theodore P. , Diez-Gonzalez Francisco 
Published: April 2008

ABSTRACT

The milk supply is considered a primary route for a bioterrorism attack with
Bacillus anthracis
spores because typical high-temperature short-time (HTST) pasteurization conditions cannot inactivate spores. In the event of intentional contamination, an effective method to inactivate the spores in milk under HTST processing conditions is needed. This study was undertaken to identify combinations and concentrations of biocides that can inactivate
B. anthracis
spores at temperatures in the HTST range in less than 1 min. Hydrogen peroxide (HP), sodium hypochlorite (SH), and peroxyacetic acid (PA) were evaluated for their efficacy in inactivating spores of strains 7702, ANR-1, and 9131 in milk at 72, 80, and 85°C using a sealed capillary tube technique. Strains ANR-1 and 9131 were more resistant to all of the biocide treatments than strain 7702. Addition of 1,260 ppm SH to milk reduced the number of viable spores of each strain by 6 log CFU/ml in less than 90 and 60 s at 72 and 80°C, respectively. After neutralization, 1,260 ppm SH reduced the time necessary to inactivate 6 log CFU/ml (TTI6-log) at 80°C to less than 20 s. Treatment of milk with 7,000 ppm HP resulted in a similar level of inactivation in 60 s. Combined treatment with 1,260 ppm SH and 1,800 ppm HP inactivated spores of all strains in less than 20 s at 80°C. Mixing 15 ppm PA with milk containing 1,260 ppm SH resulted in TTI6-log of 25 and 12 s at 72 and 80°C, respectively. TTI6-log of less than 20 s were also achieved at 80°C by using two combinations of biocides: 250 ppm SH, 700 ppm HP, and 150 ppm PA; and 420 ppm SH (pH 7), 1,100 ppm HP, and 15 ppm PA. These results indicated that different combinations of biocides could consistently result in 6-log reductions in the number of
B. anthracis
spores in less than 1 min at temperatures in the HTST range. This information could be useful for developing more effective thermal treatment strategies which could be used in HTST milk plants to process contaminated milk for disposal and decontamination, as well as for potential protective measures.
Characterization and Genomic Analysis of Phage asccφ28, a Phage of the Family
Podoviridae
Infecting
Lactococcus lactis
Authors: Kotsonis Steven E. , Powell Ian B. , Pillidge Christopher J. , Limsowtin Gaëtan K. Y. , Hillier Alan J. , Davidson Barrie E. 
Published: April 2008

ABSTRACT

Bacteriophage asccφ28 infects dairy fermentation strains of
Lactococcus lactis
. This report describes characterization of asccφ28 and its full genome sequence. Phage asccφ28 has a prolate head, whiskers, and a short tail (C2 morphotype). This morphology and DNA hybridization to
L. lactis
phage P369 DNA showed that asccφ28 belongs to the P034 phage species, a group rarely encountered in the dairy industry. The burst size of asccφ28 was found to be 121 ± 18 PFU per infected bacterial cell after a latent period of 44 min. The linear genome (18,762 bp) contains 28 possible open reading frames (ORFs) comprising 90% of the total genome. The ORFs are arranged bidirectionally in recognizable functional modules. The genome contains 577 bp inverted terminal repeats (ITRs) and putatively eight promoters and four terminators. The presence of ITRs, a phage-encoded DNA polymerase, and a terminal protein that binds to the DNA, along with BLAST and morphology data, show that asccφ28 more closely resembles streptococcal phage Cp-1 and the φ29-like phages that infect
Bacillus subtilis
than it resembles common lactococcal phages. The sequence of this phage is the first published sequence of a P034 species phage genome.
Factors Controlling the Distribution of Archaeal Tetraethers in Terrestrial Hot Springs
Authors: Pearson Ann , Pi Yundan , Zhao Weidong , Li WenJun , Li Yiliang , Inskeep William , Perevalova Anna , Romanek Christopher , Li Shuguang , Zhang Chuanlun L. 
Published: April 2008

ABSTRACT

Glycerol dialkyl glycerol tetraethers (GDGTs) found in hot springs reflect the abundance and community structure of
Archaea
in these extreme environments. The relationships between GDGTs, archaeal communities, and physical or geochemical variables are underexamined to date and when reported often result in conflicting interpretations. Here, we examined profiles of GDGTs from pure cultures of
Crenarchaeota
and from terrestrial geothermal springs representing a wide distribution of locations, including Yellowstone National Park (United States), the Great Basin of Nevada and California (United States), Kamchatka (Russia), Tengchong thermal field (China), and Thailand. These samples had temperatures of 36.5 to 87°C and pH values of 3.0 to 9.2. GDGT abundances also were determined for three soil samples adjacent to some of the hot springs. Principal component analysis identified four factors that accounted for most of the variance among nine individual GDGTs, temperature, and pH. Significant correlations were observed between pH and the GDGTs crenarchaeol and GDGT-4 (four cyclopentane rings,
m
/
z
1,294); pH correlated positively with crenarchaeol and inversely with GDGT-4. Weaker correlations were observed between temperature and the four factors. Three of the four GDGTs used in the marine TEX
86
paleotemperature index (GDGT-1 to -3, but not crenarchaeol isomer) were associated with a single factor. No correlation was observed for GDGT-0 (acyclic caldarchaeol): it is effectively its own variable. The biosynthetic mechanisms and exact archaeal community structures leading to these relationships remain unknown. However, the data in general show promise for the continued development of GDGT lipid-based physiochemical proxies for archaeal evolution and for paleo-ecology or paleoclimate studies.
Comparison of
Campylobacter
Populations in Wild Geese with Those in Starlings and Free-Range Poultry on the Same Farm
Authors: Colles F. M. , Dingle K. E. , Cody A. J. , Maiden M. C. J. 
Published: April 2008

ABSTRACT

Wild geese are a potential source of
Campylobacter
infection for humans and farm animals and have been implicated in at least two large waterborne disease outbreaks. There have been few investigations into the population biology of
Campylobacter
in geese, carriage rates are reported to vary (0 to 100%), and no genetic characterization of isolates has been performed. Fecal samples collected from wild geese in Oxfordshire, United Kingdom, were culture positive for
C. jejuni
(50.2%) and
C. coli
(0.3%). The
C. jejuni
(
n
= 166) isolates were characterized by using multilocus sequence typing and were compared with isolates collected from free-range broiler chickens and wild starlings sampled at the same location. A total of 38 STs, six clonal complexes, and 23
flaA
SVR nucleotide STs were identified. The ST-21 and ST-45 complexes (5.4% of isolates) were the only complexes to be identified among isolates from the geese and the other bird species sampled in the same location. These clonal complexes were also identified among human disease isolates collected in the same health care region. The results indicate that large numbers of wild geese carry
Campylobacter
; however, there was limited mixing of
Campylobacter
populations among the different sources examined, and the host source could be predicted with high probability from the allelic profile of a
C. jejuni
isolate. In conclusion, genotypes of
C. jejuni
isolated from geese are highly host specific, and a comparison with isolates from Oxfordshire cases of human disease revealed that while geese cannot be excluded as a source of infection for humans and farm animals, their contribution is likely to be minor.
Bayesian-Integrated Microbial Forensics
Authors: Jarman Kristin H. , Kreuzer-Martin Helen W. , Wunschel David S. , Valentine Nancy B. , Cliff John B. , Petersen Catherine E. , Colburn Heather A. , Wahl Karen L. 
Published: April 2008

ABSTRACT

In the aftermath of the 2001 anthrax letters, researchers have been exploring ways to predict the production environment of unknown-source microorganisms. Culture medium, presence of agar, culturing temperature, and drying method are just some of the broad spectrum of characteristics an investigator might like to infer. The effects of many of these factors on microorganisms are not well understood, but the complex way in which microbes interact with their environments suggests that numerous analytical techniques measuring different properties will eventually be needed for complete characterization. In this work, we present a Bayesian statistical framework for integrating disparate analytical measurements. We illustrate its application to the problem of characterizing the culture medium of
Bacillus
spores using three different mass spectral techniques. The results of our study suggest that integrating data in this way significantly improves the accuracy and robustness of the analyses.
High-Yield Production of Secreted Active Proteins by the
Pseudomonas aeruginosa
Type III Secretion System
Authors: Derouazi M. , Toussaint B. , Quénée L. , Epaulard O. , Guillaume M. , Marlu R. , Polack B. 
Published: April 2008

ABSTRACT

The
Escherichia coli
system is the system of choice for recombinant protein production because it is possible to obtain a high protein yield in inexpensive media. The accumulation of protein in an insoluble form in inclusion bodies remains a major disadvantage. Use of the
Pseudomonas aeruginosa
type III secretion system can avoid this problem, allowing the production of soluble secreted proteins.
Characterization of Endogenous Plasmids from
Lactobacillus salivarius
UCC118
Authors: Fang Fang , Flynn Sarah , Li Yin , Claesson Marcus J. , van Pijkeren Jan-Peter , Collins J. Kevin , van Sinderen Douwe , O'Toole Paul W. 
Published: April 2008

ABSTRACT

The genome of
Lactobacillus salivarius
UCC118 comprises a 1.83-Mb chromosome, a 242-kb megaplasmid (pMP118), and two smaller plasmids of 20 kb (pSF118-20) and 44 kb (pSF118-44). Annotation and bioinformatic analyses suggest that both of the smaller plasmids replicate by a theta replication mechanism. Furthermore, it appears that they are transmissible, although neither possesses a complete set of conjugation genes. Plasmid pSF118-20 encodes a toxin-antitoxin system composed of
pemI
and
pemK
homologs, and this plasmid could be cured when PemI was produced in
trans
. The minimal replicon of pSF118-20 was determined by deletion analysis. Shuttle vector derivatives of pSF118-20 were generated that included the replication region (pLS203) and the replication region plus mobilization genes (pLS208). The plasmid pLS203 was stably maintained without selection in
Lactobacillus plantarum
,
Lactobacillus fermentum
, and the pSF118-20-cured derivative strain of
L. salivarius
UCC118 (strain LS201). Cloning in pLS203 of genes encoding luciferase and green fluorescent protein, and expression from a constitutive
L. salivarius
promoter, demonstrated the utility of this vector for the expression of heterologous genes in
Lactobacillus
. This study thus expands the knowledge base and vector repertoire of probiotic lactobacilli.
Improvement of the Glutaryl-7-Aminocephalosporanic Acid Acylase Activity of a Bacterial γ-Glutamyltranspeptidase
Authors: Yamada Chiaki , Kijima Kyoko , Ishihara Sayaka , Miwa Chinatsu , Wada Kei , Okada Toshihiro , Fukuyama Keiichi , Kumagai Hidehiko , Suzuki Hideyuki 
Published: April 2008

ABSTRACT7-Aminocephalosporanic acid (7-ACA) is an important material in the production of semisynthetic cephalosporins, which are the best-selling antibiotics worldwide. 7-ACA is produced from cephalosporin C via glutaryl-7-ACA (GL-7-ACA) by a bioconversion process usingd-amino acid oxidase and cephalosporin acylase (or GL-7-ACA acylase). Previous studies demonstrated that a single amino acid substitution, D433N, provided GL-7-ACA acylase activity for γ-glutamyltranspeptidase (GGT) ofEscherichia coliK-12. In this study, based on its three-dimensional structure, residues involved in substrate recognition ofE. coliGGT were rationally mutagenized, and effective mutations were then combined. A novel screening method, activity staining followed by a GL-7-ACA acylase assay with whole cells, was developed, and it enabled us to obtain mutant enzymes with enhanced GL-7-ACA acylase activity. The best mutant enzyme for catalytic efficiency, with akcat/Kmvalue for GL-7-ACA almost 50-fold higher than that of the D433N enzyme, has three amino acid substitutions: D433N, Y444A, and G484A. We also suggest that GGT fromBacillus subtilis168 can be another source of GL-7-ACA acylase for industrial applications.
Complete Genome Sequence of
Nitrosospira multiformis
, an Ammonia-Oxidizing Bacterium from the Soil Environment
Authors: Norton Jeanette M. , Klotz Martin G. , Stein Lisa Y. , Arp Daniel J. , Bottomley Peter J. , Chain Patrick S. G. , Hauser Loren J. , Land Miriam L. , Larimer Frank W. , Shin Maria W. , Starkenburg Shawn R. 
Published: April 2008

ABSTRACT

The complete genome of the ammonia-oxidizing bacterium
Nitrosospira multiformis
(ATCC 25196
T
) consists of a circular chromosome and three small plasmids totaling 3,234,309 bp and encoding 2,827 putative proteins. Of the 2,827 putative proteins, 2,026 proteins have predicted functions and 801 are without conserved functional domains, yet 747 of these have similarity to other predicted proteins in databases. Gene homologs from
Nitrosomonas europaea
and
Nitrosomonas eutropha
were the best match for 42% of the predicted genes in
N. multiformis
. The
N. multiformis
genome contains three nearly identical copies of
amo
and
hao
gene clusters as large repeats. The features of
N. multiformis
that distinguish it from
N. europaea
include the presence of gene clusters encoding urease and hydrogenase, a ribulose-bisphosphate carboxylase/oxygenase-encoding operon of distinctive structure and phylogeny, and a relatively small complement of genes related to Fe acquisition. Systems for synthesis of a pyoverdine-like siderophore and for acyl-homoserine lactone were unique to
N. multiformis
among the sequenced genomes of ammonia-oxidizing bacteria. Gene clusters encoding proteins associated with outer membrane and cell envelope functions, including transporters, porins, exopolysaccharide synthesis, capsule formation, and protein sorting/export, were abundant. Numerous sensory transduction and response regulator gene systems directed toward sensing of the extracellular environment are described. Gene clusters for glycogen, polyphosphate, and cyanophycin storage and utilization were identified, providing mechanisms for meeting energy requirements under substrate-limited conditions. The genome of
N. multiformis
encodes the core pathways for chemolithoautotrophy along with adaptations for surface growth and survival in soil environments.
Dynamics of
Legionella
spp. and Bacterial Populations during the Proliferation of
L. pneumophila
in a Cooling Tower Facility
Authors: Wéry Nathalie , Bru-Adan Valérie , Minervini Céline , Delgénes Jean-Philippe , Garrelly Laurent , Godon Jean-Jacques 
Published: April 2008

ABSTRACT

The dynamics of
Legionella
spp. and of dominant bacteria were investigated in water from a cooling tower plant over a 9-month period which included several weeks when
Legionella pneumophila
proliferated. The structural diversity of both the bacteria and the
Legionella
spp. was monitored by a fingerprint technique, single-strand conformation polymorphism, and
Legionella
spp. and
L. pneumophila
were quantified by real-time quantitative PCR. The structure of the bacterial community did not change over time, but it was perturbed periodically by chemical treatment or biofilm detachment. In contrast, the structure of the
Legionella
sp. population changed in different periods, its dynamics at times showing stability but also a rapid major shift during the proliferation of
L. pneumophila
in July. The dynamics of the
Legionella
spp. and of dominant bacteria were not correlated. In particular, no change in the bacterial community structure was observed during the proliferation of
L. pneumophila. Legionella
spp. present in the cooling tower system were identified by cloning and sequencing of 16S rRNA genes. A high diversity of
Legionella
spp. was observed before proliferation, including
L. lytica, L. fallonii
, and other
Legionella
-like amoebal pathogen types, along with as-yet-undescribed species. During the proliferation of
L. pneumophila, Legionella
sp. diversity decreased significantly,
L. fallonii
and
L. pneumophila
being the main species recovered.
Evolutionary Relationships of “
Candidatus
Endobugula” Bacterial Symbionts and Their
Bugula
Bryozoan Hosts
Authors: Lim-Fong Grace E. , Regali Lindsay A. , Haygood Margo G. 
Published: April 2008

ABSTRACT

Ribosomal gene sequences were obtained from bryozoans in the genus
Bugula
and their bacterial symbionts; analyses of host and symbiont phylogenetic trees did not support a history of strict cospeciation. Symbiont-derived compounds known to defend host larvae from predation were only detected in two out of four symbiotic
Bugula
species.
Characterization of the RND-Type Multidrug Efflux Pump MexAB-OprM of the Plant Pathogen
Pseudomonas syringae
Authors: Stoitsova Savina O. , Braun Yvonne , Ullrich Matthias S. , Weingart Helge 
Published: April 2008

ABSTRACT

In gram-negative bacteria, transporters belonging to the RND family are the transporters most relevant for resistance to antimicrobial compounds. In
Pseudomonas aeruginosa
, a clinically important pathogen, the RND-type pump MexAB-OprM has been recognized as one of the major multidrug efflux systems. Here, homologues of MexAB-OprM in the plant pathogens
Pseudomonas syringae
pv. phaseolicola 1448A,
P. syringae
pv. syringae B728a, and
P. syringae
pv. tomato DC3000 were identified, and
mexAB-oprM
-deficient mutants were generated. Determination of MICs revealed that mutation of MexAB-OprM dramatically reduced the tolerance to a broad range of antimicrobials. Moreover, the ability of the
mexAB
-
oprM
-deficient mutants to multiply in planta was reduced. RNA dot blot hybridization revealed growth-dependent regulation of the
mexAB-oprM
operon in
P. syringae
; the expression of this operon was maximal in early exponential phase and decreased gradually during further growth.