bluuebunny/crossref_metadata_2025_split huggingface dataset:
Initial Reaction(s) in Biotransformation of CL-20 Is Catalyzed by Salicylate 1-Monooxygenase from
Pseudomonas
sp. Strain ATCC 29352
Authors: Bhushan Bharat , Halasz Annamaria , Spain Jim C. , Hawari Jalal 
Published: July 2004

ABSTRACT

CL-20 (2,4,6,8,10,12-hexanitro-2,4,6,8,10,12-hexaazaisowurtzitane) (C
6
H
6
N
12
O
12
), a future-generation high-energy explosive, is biodegradable by
Pseudomonas
sp. strain FA1 and
Agrobacterium
sp. strain JS71; however, the nature of the enzyme(s) involved in the process was not understood. In the present study, salicylate 1-monooxygenase, a flavin adenine dinucleotide (FAD)-containing purified enzyme from
Pseudomonas
sp. strain ATCC 29352, biotransformed CL-20 at rates of 0.256 ± 0.011 and 0.043 ± 0.003 nmol min
−1
mg of protein
−1
under anaerobic and aerobic conditions, respectively. The disappearance of CL-20 was accompanied by the release of nitrite ions. Using liquid chromatography/mass spectrometry in the negative electrospray ionization mode, we detected a metabolite with a deprotonated mass ion [M − H]
−
at 345 Da, corresponding to an empirical formula of C
6
H
6
N
10
O
8
, produced as a result of two sequential N denitration steps on the CL- 20 molecule. We also detected two isomeric metabolites with [M − H]
−
at 381 Da corresponding to an empirical formula of C
6
H
10
N
10
O
10
. The latter was a hydrated product of the metabolite C
6
H
6
N
10
O
8
with addition of two H
2
O molecules, as confirmed by tests using
18
O-labeled water. The product stoichiometry showed that each reacted CL-20 molecule produced about 1.7 nitrite ions, 3.2 molecules of nitrous oxide, 1.5 molecules of formic acid, and 0.6 ammonium ion. Diphenyliodonium-mediated inhibition of salicylate 1-monooxygenase and a comparative study between native, deflavo, and reconstituted enzyme(s) showed that FAD site of the enzyme was involved in the biotransformation of CL-20 catalyzed by salicylate 1-monooxygenase. The data suggested that salicylate 1-monooxygenase catalyzed two oxygen-sensitive single-electron transfer steps necessary to release two nitrite ions from CL-20 and that this was followed by the secondary decomposition of this energetic chemical.
A Single Species,
Micromonas pusilla
(Prasinophyceae), Dominates the Eukaryotic Picoplankton in the Western English Channel
Authors: Not Fabrice , Latasa Mikel , Marie Dominique , Cariou Thierry , Vaulot Daniel , Simon Nathalie 
Published: July 2004

ABSTRACT

The class Prasinophyceae (Chlorophyta) contains several photosynthetic picoeukaryotic species described from cultured isolates. The ecology of these organisms and their contributions to the picoeukaryotic community in aquatic ecosystems have received little consideration. We have designed and tested eight new 18S ribosomal DNA oligonucleotide probes specific for different Prasinophyceae clades, genera, and species. Using fluorescent in situ hybridization associated with tyramide signal amplification, these probes, along with more general probes, have been applied to samples from a marine coastal site off Roscoff (France) collected every 2 weeks between July 2000 and September 2001. The abundance of eukaryotic picoplankton remained high (>10
3
cells ml
−1
) during the sampling period, with maxima in summer (up to 2 × 10
4
cells ml
−1
), and a single green algal species,
Micromonas pusilla
(Prasinophyceae), dominated the community all year round. Members of the order Prasinococcales and the species
Bathycoccus prasinos
(Mamiellales) displayed sporadic occurrences, while the abundances of all other
Prasinophyceae
groups targeted remained negligible.
Structural Characterization of Lignin during
Pinus taeda
Wood Treatment with
Ceriporiopsis subvermispora
Authors: Guerra Anderson , Mendonça Régis , Ferraz André , Lu Fachuang , Ralph John 
Published: July 2004

ABSTRACT

Pinus taeda
wood chips were biotreated with
Ceriporiopsis subvermispora
under solid-state fermentation for periods varying from 15 to 90 days. Milled wood lignins extracted from sound and biotreated wood samples were characterized by wet-chemical and spectroscopic techniques. Treatment of the lignins by derivatization followed by reductive cleavage (DFRC) made it possible to detect DFRC monomers and dimers that are diagnostic of the occurrence of arylglycerol-β-
O
-aryl and β-β, β-5, β-1, and 4-
O
-5 units in the lignin structure. Quantification of these DFRC products indicated that β-
O
-aryl cleavage was a significant route for lignin biodegradation but that β-β, β-5, β-1, and 4-
O
-5 linkages were more resistant to the biological attack. The amount of aromatic hydroxyls did not increase with the split of β-
O
-4 linkages, suggesting that the β-
O
-4 cleavage products remain as quinone-type structures as detected by UV and visible spectroscopy. Nuclear magnetic resonance techniques also indicated the formation of new substructures containing nonoxygenated, saturated aliphatic carbons (CH
2
and CH
3
) in the side chains of lignins extracted from biotreated wood samples.
Replication of the Endosymbiotic Bacterium
Blochmannia floridanus
Is Correlated with the Developmental and Reproductive Stages of Its Ant Host
Authors: Wolschin Florian , Hölldobler Bert , Gross Roy , Zientz Evelyn 
Published: July 2004

ABSTRACT

The dynamics of replication of the intracellular endosymbiotic bacterium
Blochmannia floridanus
was determined during the larval development of its host ant
Camponotus floridanus
by real-time quantitative PCR. The bacteria were found to proliferate during pupation and immediately after the eclosion of the imagines (adult ants). In older workers the number of bacteria present in the midgut bacteriocytes decreased significantly. In contrast, the bacterial population in the ovaries was dependent on the reproductive state of the animal. An age-dependent degeneration of the midgut bacteriocytes was also investigated by microscopic techniques in males and female castes of the closely related ant species
C. herculeanus
and
C. sericeiventris
, respectively, with similar results and supports the concept of age-dependent degeneration of the midgut bacteriocytes in all castes.
Diversity and Dynamics of a North Atlantic Coastal
Vibrio
Community
Authors: Thompson Janelle R. , Randa Mark A. , Marcelino Luisa A. , Tomita-Mitchell Aoy , Lim Eelin , Polz Martin F. 
Published: July 2004

ABSTRACT

Vibrios are ubiquitous marine bacteria that have long served as models for heterotrophic processes and have received renewed attention because of the discovery of increasing numbers of facultatively pathogenic strains. Because the occurrence of specific vibrios has frequently been linked to the temperature, salinity, and nutrient status of water, we hypothesized that seasonal changes in coastal water bodies lead to distinct vibrio communities and sought to characterize their level of differentiation. A novel technique was used to quantify shifts in 16S rRNA gene abundance in samples from Barnegat Bay, N.J., collected over a 15-month period. Quantitative PCR (QPCR) with primers specific for the genus
Vibrio
was combined with separation and quantification of amplicons by constant denaturant capillary electrophoresis (CDCE).
Vibrio
populations identified by QPCR-CDCE varied between summer and winter samples, suggesting distinct warm-water and year-round populations. Identification of the CDCE populations by cloning and sequencing of 16S rRNA genes from two summer and two winter samples confirmed this distinction. It further showed that CDCE populations corresponded in most cases to ∼98% rRNA similarity groups and suggested that the abundance of these follows temperature trends. Phylogenetic comparison yielded closely related cultured and often pathogenic representatives for most sequences, and the temperature ranges of these isolates confirmed the trends seen in the environmental samples. Overall, this suggests that temperature is a good predictor of the occurrence of closely related vibrios but that considerable microdiversity of unknown significance coexists within this trend.
CO
2
- and Anaerobiosis-Induced Changes in Physiology and Gene Expression of Different
Listeria monocytogenes
Strains
Authors: Jydegaard-Axelsen Anne-Marie , Høiby Poul Erik , Holmstrøm Kim , Russell Nicholas , Knøchel Susanne 
Published: July 2004

ABSTRACT

Although carbon dioxide (CO
2
) is known to inhibit growth of most bacteria, very little is known about the cellular response. The food-borne pathogen
Listeria monocytogenes
is characterized by its ability to grow in high CO
2
concentrations at refrigeration temperatures. We examined the listerial responses of different strains to growth in air, 100% N
2
, and 100% CO
2
. The CO
2
-induced changes in membrane lipid fatty acid composition and expression of selected genes were strain dependent. The acid-tolerant
L. monocytogenes
LO28 responded in the same manner to CO
2
as to other anaerobic, slightly acidic environments (100% N
2
, pH 5.7). An increase in the expression of the genes encoding glutamate decarboxylase (essential for survival in strong acid) as well as an increased amount of branched-chain fatty acids in the membrane was observed in both atmospheres. In contrast, the acid-sensitive
L. monocytogenes
strain EGD responded differently to CO
2
and N
2
at the same pH. In a separate experiment with
L. monocytogenes
412, an increased isocitrate dehydrogenase activity level was observed for cells grown in CO
2
-containing atmospheres. Together, our findings demonstrate that the CO
2
-response is a partly strain-dependent complex mechanism. The possible links between the CO
2
-dependent changes in isocitrate dehydrogenase activity, glutamate metabolism and branched fatty acid biosynthesis are discussed.
Use of the Riboflavin Synthase Gene (
ribC
) as a Model for Development of an Essential Gene Disruption and Complementation System for
Haemophilus influenzae
Authors: Saeed-Kothe Amna , Yang Wei , Mills Scott D. 
Published: July 2004

ABSTRACT

We have developed a system for rapid and reliable assessment of gene essentiality in
Haemophilus influenzae
Rd strain KW20. We constructed two “suicide” complementation vectors (pASK5 and pASK6) containing 5′ and 3′ regions of the nonessential
ompP1
gene flanking a multiple cloning site and a selectable marker (a chloramphenicol resistance gene or a tetracycline resistance cassette). Transformation of
H. influenzae
with the complementation constructs directs chromosomal integration of a gene of interest into the
ompP1
locus, where the strong, constitutive
ompP1
promoter drives its expression. This single-copy, chromosome-based complementation system is useful for confirming the essentiality of disrupted genes of interest. It allows genetic analysis in a background free of interference from any upstream or downstream genetic elements and enables conclusive assignment of essentiality. We validated this system by using the riboflavin synthase gene (
ribC
), a component of the riboflavin biosynthetic pathway. Our results confirmed the essentiality of
ribC
for survival of
H. influenzae
Rd strain KW20 and demonstrated that a complementing copy of
ribC
placed under control of the
ompP1
promoter reverses the lethal phenotype of a strain with
ribC
deleted.
Respiration Strategies Utilized by the Gill Endosymbiont from the Host Lucinid
Codakia orbicularis
(Bivalvia: Lucinidae)
Authors: Duplessis Melinda R. , Ziebis Wiebke , Gros Olivier , Caro Audrey , Robidart Julie , Felbeck Horst 
Published: July 2004

ABSTRACT

The large tropical lucinid clam
Codakia orbicularis
has a symbiotic relationship with intracellular, sulfide-oxidizing chemoautotrophic bacteria. The respiration strategies utilized by the symbiont were explored using integrative techniques on mechanically purified symbionts and intact clam-symbiont associations along with habitat analysis. Previous work on a related symbiont species found in the host lucinid
Lucinoma aequizonata
showed that the symbionts obligately used nitrate as an electron acceptor, even under oxygenated conditions. In contrast, the symbionts of
C. orbicularis
use oxygen as the primary electron acceptor while evidence for nitrate respiration was lacking. Direct measurements obtained by using microelectrodes in purified symbiont suspensions showed that the symbionts consumed oxygen; this intracellular respiration was confirmed by using the redox dye CTC (5-cyano-2,3-ditolyl tetrazolium chloride). In the few intact chemosymbioses tested in previous studies, hydrogen sulfide production was shown to occur when the animal-symbiont association was exposed to anoxia and elemental sulfur stored in the thioautotrophic symbionts was proposed to serve as an electron sink in the absence of oxygen and nitrate. However, this is the first study to show by direct measurements using sulfide microelectrodes in enriched symbiont suspensions that the symbionts are the actual source of sulfide under anoxic conditions.
Effect of Substratum Surface Chemistry and Surface Energy on Attachment of Marine Bacteria and Algal Spores
Authors: Ista Linnea K. , Callow Maureen E. , Finlay John A. , Coleman Sarah E. , Nolasco Aleece C. , Simons Robin H. , Callow James A. , Lopez Gabriel P. 
Published: July 2004

ABSTRACT

Two series of self-assembled monolayers (SAMs) of ω-substituted alkanethiolates on gold were used to systematically examine the effects of varying substratum surface chemistry and energy on the attachment of two model organisms of interest to the study of marine biofouling, the bacterium
Cobetia marina
(formerly
Halomonas marina
) and zoospores of the alga
Ulva linza
(formerly
Enteromorpha linza
). SAMs were formed on gold-coated glass slides from solutions containing mixtures of methyl- and carboxylic acid-terminated alkanethiols and mixtures of methyl- and hydroxyl-terminated alkanethiols.
C. marina
attached in increasing numbers to SAMs with decreasing advancing water contact angles (θ
AW
), in accordance with equation-of-state models of colloidal attachment. Previous studies of
Ulva
zoospore attachment to a series of mixed methyl- and hydroxyl-terminated SAMs showed a similar correlation between substratum θ
AW
and zoospore attachment. When the hydrophilic component of the SAMs was changed to carboxylate, however, the profile of attachment of
Ulva
was significantly different, suggesting that a more complex model of interfacial energetics is required.
Epidemic Clone I-Specific Genetic Markers in Strains of
Listeria monocytogenes
Serotype 4b from Foods
Authors: Yildirim Suleyman , Lin Wen , Hitchins Anthony D. , Jaykus Lee-Ann , Altermann Eric , Klaenhammer Todd R. , Kathariou Sophia 
Published: July 2004

ABSTRACT

Listeria monocytogenes
contamination of ready-to-eat foods has been implicated in numerous outbreaks of food-borne listeriosis. However, the health hazards posed by
L. monocytogenes
detected in foods may vary, and speculations exist that strains actually implicated in illness may constitute only a fraction of those that contaminate foods. In this study, examination of 34 serogroup 4 (putative or confirmed serotype 4b) isolates of
L. monocytogenes
obtained from various foods and food-processing environments, without known implication in illness, revealed that many of these strains had methylation of cytosines at GATC sites in the genome, rendering their DNA resistant to digestion by the restriction endonuclease Sau3AI. These strains also harbored a gene cassette with putative restriction-modification system genes as well as other, genomically unlinked genetic markers characteristic of the major epidemic-associated lineage of
L. monocytogenes
(epidemic clone I), implicated in numerous outbreaks in Europe and North America. This may reflect a relatively high fitness of strains with these genetic markers in foods and food-related environments relative to other serotype 4b strains and may partially account for the repeated involvement of such strains in human food-borne listeriosis.
New Real-Time Quantitative PCR Procedure for Quantification of Bifidobacteria in Human Fecal Samples
Authors: Gueimonde Miguel , Tölkkö Satu , Korpimäki Teemu , Salminen Seppo 
Published: July 2004

ABSTRACT

The application of a real-time quantitative PCR method (5′ nuclease assay), based on the use of a probe labeled at its 5′ end with a stable, fluorescent lanthanide chelate, for the quantification of human fecal bifidobacteria was evaluated. The specificities of the primers and the primer-probe combination were evaluated by conventional PCR and real-time PCR, respectively. The results obtained by real-time PCR were compared with those obtained by fluorescent in situ hybridization, the current gold standard for intestinal microbiota quantification. In general, a good correlation between the two methods was observed. In order to determine the detection limit and the accuracy of the real-time PCR procedure, germfree rat feces were spiked with known amounts of bifidobacteria and analyzed by both methods. The detection limit of the method used in this study was found to be about 5 × 10
4
cells per g of feces. Both methods, real-time PCR and fluorescent in situ hybridization, led to an accurate quantification of the spiked samples with high levels of bifidobacteria, but real-time PCR was more accurate for samples with low levels. We conclude that the real-time PCR procedure described here is a specific, accurate, rapid, and easy method for the quantification of bifidobacteria in feces.
Chloromethane-Dependent Expression of the
cmu
Gene Cluster of
Hyphomicrobium chloromethanicum
Authors: Borodina Elena , McDonald Ian R. , Murrell J. Colin 
Published: July 2004

ABSTRACT

The methylotrophic bacterium
Hyphomicrobium chloromethanicum
CM2 can utilize chloromethane (CH
3
Cl) as the sole carbon and energy source. Previously genes
cmuB
,
cmuC
,
cmuA
, and
folD
were shown to be essential for the growth of
Methylobacterium chloromethanicum
on CH
3
Cl. These CH
3
Cl-specific genes were subsequently detected in
H. chloromethanicum
. Transposon and marker exchange mutagenesis studies were carried out to identify the genes essential for CH
3
Cl metabolism in
H. chloromethanicum
. New developments in genetic manipulation of
Hyphomicrobium
are presented in this study. An electroporation protocol has been optimized and successfully applied for transformation of mutagenesis plasmids into
H. chloromethanicum
to generate stable CH
3
Cl-negative mutants. Both transposon and marker exchange mutageneses were highly applicable for genetic analysis of
Hyphomicrobium
. A reliable and reproducible selection procedure for screening of CH
3
Cl utilization-negative mutants has also been developed. Mutational inactivation of
cmuB
,
cmuC
, or
hutI
resulted in strains that were unable to utilize CH
3
Cl or to express the CH
3
Cl-dependent polypeptide CmuA. Reverse transcription-PCR analysis indicated that
cmuB
,
cmuC
,
cmuA
,
fmdB
,
paaE
,
hutI
, and
metF
formed a single
cmuBCA
-
metF
operon and were coregulated and coexpressed in
H. chloromethanicum
. This finding led to the conclusion that, in
cmuB
and
cmuC
mutants, impaired expression of
cmuA
was likely to be due to a polar effect of the defective gene (
cmuB
or
cmuC
) located upstream (5′) of
cmuA
. The detrimental effect of mutation in
hutI
on the upstream (5′)-located
cmuA
is not clear but indicated that all the genes located within the
cmuBCA
-
metF
operon are coordinately expressed. Expression of the
cmuBCA
-
metF
transcript was also shown to be strictly CH
3
Cl inducible and was not repressed by the alternative C
1
substrate methanol. Sequence analysis of a transposon mutant (D20) led to the discovery of the previously undetected
hutI
and
metF
genes located 3′ of the
paaE
gene in
H. chloromethanicum
. MetF, a putative methylene-tetrahydrofolate reductase, had 27% identity to MetF from
M. chloromethanicum
. Mutational and transcriptional analysis data indicated that, in
H. chloromethanicum
, CH
3
Cl is metabolized via a corrinoid-specific (
cmuA
) and tetrahydrofolate-dependent (
metF
,
purU
,
folD
) methyltransfer system.
Regulation of
Vibrio anguillarum empA
Metalloprotease Expression and Its Role in Virulence
Authors: Denkin Steven M. , Nelson David R. 
Published: July 2004

ABSTRACT

Atlantic salmon (
Salmo salar
) were challenged with
Vibrio anguillarum
strains M93Sm and NB10 and
empA
null mutants M99 and NB12. Both wild types were virulent when administered by intraperitoneal (i.p.) injection or anal intubation. NB12 was avirulent via either route of infection. M99 virulence was attenuated when delivered by intubation, but fully virulent by i.p. injection. Northern blot analysis revealed
empA
expression in M93Sm and NB10 cells incubated in mucus, while incubation in Luria-Bertani broth plus 2% NaCl (LB20) induced
empA
expression only in NB10. Nucleotide differences between M93Sm and NB10
empA
sequences were found in regions located 207 and 229 bp upstream of the
empA
translational start. Reverse transcription-PCR and 5′ rapid amplification of cDNA ends revealed the
empA
transcriptional start site 85 bp upstream of the translational start for both strains. A putative σ
S
-dependent promoter was identified upstream of the transcriptional start in both strains. Site-directed mutagenesis was used to create
rpoS
mutants of M93Sm and NB10. Neither
rpoS
mutant exhibited protease activity. Since
empA
is expressed during stationary phase, the effects of conditioned medium on protease activity were examined. M99 conditioned LB20 supernatants stimulated protease activity in NB10 while allowing M93Sm to produce protease in LB20. Neither acyl homoserine lactones nor AI-2 induced protease activity. Conditioned LB20 supernatant from a
V. anguillarum luxS
mutant caused a more rapid induction of protease activity in wild-type cells. Our data show that expression of
empA
is differentially regulated in
V. anguillarum
strains NB10 and M93Sm and requires σ
S
, quorum-sensing molecules, and gastrointestinal mucus.
Host-AdaptedCryptosporidiumspp. in Canada Geese (Branta canadensis)
Authors: Zhou Ling , Kassa Hailu , Tischler Monica L. , Xiao Lihua 
Published: July 2004

ABSTRACTThe prevalence and distribution ofCryptosporidiumspp. in the fecal droppings of the free-living waterfowl Canada geese were examined at 13 sites in Ohio and Illinois. On the basis of the analysis of the small-subunit rRNA gene by PCR, followed by restriction fragment length polymorphism analysis and DNA sequencing, 49 (23.4%) of 209 fecal specimens collected from 10 sites (76.9%) were positive forCryptosporidiumspp. The following fiveCryptosporidiumspecies and genotypes were identified:Cryptosporidiumgoose genotype I (in 36 specimens),Cryptosporidiumgoose genotype II (in 9 specimens),Cryptosporidiumduck genotype (in 1 specimen),Cryptosporidium parvum(in 4 specimens), andC. hominis(in 2 specimens).Cryptosporidiumgoose genotype I was the most prevalent parasite and was found at all fiveCryptosporidium-positive sites in Ohio and at four of five positive sites in Illinois, followed byCryptosporidiumgoose genotype II, which was found at two of five positive sites in Ohio and at four of five positive sites in Illinois.Cryptosporidiumgoose genotype II was detected for the first time, and it is phylogenetically related to goose genotype I and the duck genotype. All three genotypes have not so far been reported in humans, and their pathogenicity in geese has not been determined. Only 10.2% of theCryptosporidium-positive specimens hadC. parvumandC. hominis. The results of this study indicate that Canada geese might only serve as accidental carriers of cryptosporidia infectious to humans and probably play a minor role in the animal-to-human transmission cycle of the pathogen.