bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prediction of the Adaptability of
Pseudomonas putida
DOT-T1E to a Second Phase of a Solvent for Economically Sound Two-Phase Biotransformations
Authors: Neumann Grit , Kabelitz Nadja , Zehnsdorf Andreas , Miltner Anja , Lippold Holger , Meyer Daniel , Schmid Andreas , Heipieper Hermann J. 
Published: November 2005

ABSTRACT

The strain
Pseudomonas putida
DOT-T1E was tested for its ability to tolerate second phases of different alkanols for their use as solvents in two-liquid-phase biotransformations. Although 1-decanol showed an about 10-fold higher toxicity to the cells than 1-octanol, the cells were able to adapt completely to 1-decanol only and could not be adapted in order to grow stably in the presence of a second phase of 1-octanol. The main explanation for this observation can be seen in the higher water and membrane solubility of 1-octanol. The hydrophobicity (log P) of a substance correlates with a certain partitioning of that compound into the membrane. Combining the log P value with the water solubility, the maximum membrane concentration of a compound can be calculated. With this simple calculation, it is possible to predict the property of an organic chemical for its potential applicability as a solvent for two-liquid-phase biotransformations with solvent-tolerant
P. putida
strains. Only compounds that show a maximum membrane concentration of less than 400 mM, such as 1-decanol, seem to be tolerated by these bacterial strains when applied in supersaturating concentrations to the medium. Taking into consideration that a solvent for a two-liquid-phase system should possess partitioning properties for potential substrates and products of a fine chemical synthesis, it can be seen that 1-decanol is a suitable solvent for such biotransformation processes. This was also demonstrated in shake cultures, where increasing amounts of a second phase of 1-decanol led to bacteria tolerating higher concentrations of the model substrate 3-nitrotoluene. Transferring this example to a 5-liter-scale bioreactor with 10% (vol/vol) 1-decanol, the amount of 3-nitrotoluene tolerated by the cells is up to 200-fold higher than in pure aqueous medium. The system demonstrates the usefulness of two-phase biotransformations utilizing solvent-tolerant bacteria.
Comparison of Minisatellite Polymorphisms in the
Bacillus cereus
Complex: a Simple Assay for Large-Scale Screening and Identification of Strains Most Closely Related to
Bacillus anthracis
Authors: Valjevac Samina , Hilaire Valérie , Lisanti Olivier , Ramisse Françoise , Hernandez Eric , Cavallo Jean-Didier , Pourcel Christine , Vergnaud Gilles 
Published: November 2005

ABSTRACT

Polymorphism of five tandem repeats that are monomorphic in
Bacillus anthracis
was investigated in 230 isolates of the
B. cereus
group and in 5 sequenced
B. cereus
genomes in search for markers allowing identification of
B. cereus
and
B. thuringiensis
strains most closely related to
B. anthracis
. Using this multiple-locus variable number of tandem repeat analysis (MLVA), a cluster of 30 strains was selected for further characterization. Eventually, six of these were characterized by multilocus sequence type analysis. One of the strains is only six point mutations (of almost 3,000 bp) away from
B. anthracis
and was also proposed to be closest to
B. anthracis
by MLVA analysis. However, this strain remains separated from
B. anthracis
by a number of significant genetic events observed in
B. anthracis
, including the loss of the hemolysin activity, the presence of four prophages, and the presence of the two virulence plasmids, pXO1 and pXO2. One particular minisatellite marker provides an efficient assay to identify the subset of
B. cereus
and
B. thuringiensis
strains closely related to
B. anthracis
. Based on these results, a very simple assay is proposed that allows the screening of hundreds of strains from the
B. cereus
complex, with modest equipment and at a low cost, to eventually fill the gap with
B. anthracis
and better understand the origin and making of this dangerous pathogen.
Insights into
Actinobacillus succinogenes
Fermentative Metabolism in a Chemically Defined Growth Medium
Authors: McKinlay James B. , Zeikus J. Gregory , Vieille Claire 
Published: November 2005

ABSTRACT

Chemically defined media allow for a variety of metabolic studies that are not possible with undefined media. A defined medium, AM3, was created to expand the experimental opportunities for investigating the fermentative metabolism of succinate-producing
Actinobacillus succinogenes
. AM3 is a phosphate-buffered medium containing vitamins, minerals, NH
4
Cl as the main nitrogen source, and glutamate, cysteine, and methionine as required amino acids.
A. succinogenes
growth trends and end product distributions in AM3 and rich medium fermentations were compared. The effects of NaHCO
3
concentration in AM3 on end product distribution, growth rate, and metabolic rates were also examined. The
A. succinogenes
growth rate was 1.3 to 1.4 times higher at an NaHCO
3
concentration of 25 mM than at any other NaHCO
3
concentration, likely because both energy-producing metabolic branches (i.e., the succinate-producing branch and the formate-, acetate-, and ethanol-producing branch) were functioning at relatively high rates in the presence of 25 mM bicarbonate. To improve the accuracy of the
A. succinogenes
metabolic map, the reasons for
A. succinogenes
glutamate auxotrophy were examined by enzyme assays and by testing the ability of glutamate precursors to support growth. Enzyme activities were detected for glutamate synthesis that required glutamine or α-ketoglutarate. The inability to synthesize α-ketoglutarate from glucose indicates that at least two tricarboxylic acid cycle-associated enzyme activities are absent in
A. succinogenes
.
Identification ofShewanella balticaas the Most Important H2S-Producing Species during Iced Storage of Danish Marine Fish
Authors: Vogel Birte Fonnesbech , Venkateswaran Kasthuri , Satomi Masataka , Gram Lone 
Published: November 2005

ABSTRACTShewanella putrefacienshas been considered the main spoilage bacteria of low-temperature stored marine seafood. However, psychrotropicShewanellahave been reclassified during recent years, and the purpose of the present study was to determine whether any of the newShewanellaspecies are important in fish spoilage. More than 500 H2S-producing strains were isolated from iced stored marine fish (cod, plaice, and flounder) caught in the Baltic Sea during winter or summer time. All strains were identified asShewanellaspecies by phenotypic tests. DifferentShewanellaspecies were present on newly caught fish. During the warm summer months the mesophilic human pathogenicS. algaedominated the H2S-producing bacterial population. After iced storage, a shift in theShewanellaspecies was found, and most of the H2S-producing strains were identified asS. baltica. The 16S rRNA gene sequence analysis confirmed the identification of these two major groups. Several isolates could only be identified to the genusShewanellalevel and were separated into two subgroups with low (44%) and high (47%) G+C mol%. The low G+C% group was isolated during winter months, whereas the high G+C% group was isolated on fish caught during summer and only during the first few days of iced storage. Phenotypically, these strains were different from the type strains ofS. putrefaciens,S. oneidensis,S. colwelliana, andS. affinis, but the high G+C% group clustered close toS. colwellianaby 16S rRNA gene sequence comparison. The low G+C% group may constitute a new species.S. baltica, and the low G+C% group ofShewanellaspp. strains grew well in cod juice at 0°C, but three high G+CShewanellaspp. were unable to grow at 0°C. In conclusion, the spoilage reactions of iced Danish marine fish remain unchanged (i.e., trimethylamine-N-oxide reduction and H2S production); however, the main H2S-producing organism was identified asS. baltica.
Impact of Bt Corn on Rhizospheric and Soil Eubacterial Communities and on Beneficial Mycorrhizal Symbiosis in Experimental Microcosms
Authors: Castaldini M. , Turrini A. , Sbrana C. , Benedetti A. , Marchionni M. , Mocali S. , Fabiani A. , Landi S. , Santomassimo F. , Pietrangeli B. , Nuti M. P. , Miclaus N. , Giovannetti M. 
Published: November 2005

ABSTRACTA polyphasic approach has been developed to gain knowledge of suitable key indicators for the evaluation of environmental impact of genetically modified Bt 11 and Bt 176 corn lines on soil ecosystems. We assessed the effects of Bt corn (which constitutively expresses the insecticidal toxin fromBacillus thuringiensis, encoded by the truncatedCry1Abgene) and non-Bt corn plants and their residues on rhizospheric and bulk soil eubacterial communities by means of denaturing gradient gel electrophoresis analyses of 16S rRNA genes, on the nontarget mycorrhizal symbiontGlomus mosseae, and on soil respiration. Microcosm experiments showed differences in rhizospheric eubacterial communities associated with the three corn lines and a significantly lower level of mycorrhizal colonization in Bt 176 corn roots. In greenhouse experiments, differences between Bt and non-Bt corn plants were detected in rhizospheric eubacterial communities (both total and active), in culturable rhizospheric heterotrophic bacteria, and in mycorrhizal colonization. Plant residues of transgenic plants, plowed under at harvest and kept mixed with soil for up to 4 months, affected soil respiration, bacterial communities, and mycorrhizal establishment by indigenous endophytes. The multimodal approach utilized in our work may be applied in long-term field studies aimed at monitoring the real hazard of genetically modified crops and their residues on nontarget soil microbial communities.
Cloning, Biochemical Properties, and Distribution of Mycobacterial Haloalkane Dehalogenases
Authors: Jesenská Andrea , Pavlová Martina , Strouhal Michal , Chaloupková Radka , Těšínská Iva , Monincová Marta , Prokop Zbyněk , Bartoš Milan , Pavlík Ivo , Rychlík Ivan , Möbius Petra , Nagata Yuji , Damborský Jiři 
Published: November 2005

ABSTRACTHaloalkane dehalogenases are enzymes that catalyze the cleavage of the carbon-halogen bond by a hydrolytic mechanism. Genomes ofMycobacterium tuberculosisandM. boviscontain at least two open reading frames coding for the polypeptides showing a high sequence similarity with biochemically characterized haloalkane dehalogenases. We describe here the cloning of the haloalkane dehalogenase genesdmbAanddmbBfromM. bovis5033/66 and demonstrate the dehalogenase activity of their translation products. Both of these genes are widely distributed among species of theM. tuberculosiscomplex, includingM. bovis,M. bovisBCG,M. africanum,M. caprae,M. microti, andM. pinnipedii, as shown by the PCR screening of 48 isolates from various hosts. DmbA and DmbB proteins were heterologously expressed inEscherichia coliand purified to homogeneity. The DmbB protein had to be expressed in a fusion with thioredoxin to obtain a soluble protein sample. The temperature optimum of DmbA and DmbB proteins determined with 1,2-dibromoethane is 45°C. The melting temperature assessed by circular dichroism spectroscopy of DmbA is 47°C and DmbB is 57°C. The pH optimum of DmbA depends on composition of a buffer with maximal activity at 9.0. DmbB had a single pH optimum at pH 6.5. Mycobacteria are currently the only genus known to carry more than one haloalkane dehalogenase gene, although putative haloalkane dehalogenases can be inferred in more then 20 different bacterial species by comparative genomics. The evolution and distribution of haloalkane dehalogenases among mycobacteria is discussed.
Abundance, Activity, and Community Structure of Pelagic Methane-Oxidizing Bacteria in Temperate Lakes
Authors: Sundh Ingvar , Bastviken David , Tranvik Lars J. 
Published: November 2005

ABSTRACT

The abundance and activity of methane-oxidizing bacteria (MOB) in the water column were investigated in three lakes with different contents of nutrients and humic substances. The abundance of MOB was determined by analysis of group-specific phospholipid fatty acids from type I and type II MOB, and in situ activity was measured with a
14
CH
4
transformation method. The fatty acid analyses indicated that type I MOB most similar to species of
Methylomonas
,
Methylomicrobium
, and
Methylosarcina
made a substantial contribution (up to 41%) to the total bacterial biomass, whereas fatty acids from type II MOB generally had very low concentrations. The MOB biomass and oxidation activity were positively correlated and were highest in the hypo- and metalimnion during summer stratification, whereas under ice during winter, maxima occurred close to the sediments. The methanotroph biomass-specific oxidation rate (
V
) ranged from 0.001 to 2.77 mg CH
4
-C mg
−1
C day
−1
and was positively correlated with methane concentration, suggesting that methane supply largely determined the activity and biomass distribution of MOB. Our results demonstrate that type I MOB often are a large component of pelagic bacterial communities in temperate lakes. They represent a potentially important pathway for reentry of carbon and energy into pelagic food webs that would otherwise be lost as evasion of CH
4
.
Detection of Infectious
Cryptosporidium
Oocysts by Cell Culture Immunofluorescence Assay: Applicability to Environmental Samples
Authors: Schets F. M. , Engels G. B. , During M. , de Roda Husman A. M. 
Published: November 2005

ABSTRACT

In the past few years many waterborne outbreaks related to
Cryptosporidium
have been described. Current methods for detection of
Cryptosporidium
in water for the most part rely on viability assays which are not informative concerning the infectivity of oocysts. However, for estimation of the risk of infection with
Cryptosporidium
this information is required. For environmental samples the oocyst counts are often low, and the oocysts have been exposed to unfavorable conditions. Therefore, determination of the infectivity of environmental oocysts requires an assay with a high level of sensitivity. We evaluated the applicability of in vitro cell culture immunofluorescence assays with HCT-8 and Caco-2 cells for determination of oocyst infectivity in naturally contaminated water samples. Cell culture assays were compared with other viability and infectivity assays. Experiments with
Cryptosporidium
oocysts from different sources revealed that there was considerable variability in infectivity, which was illustrated by variable 50% infective doses, which ranged from 40 to 614 oocysts, and the results indicated that not only relatively large numbers of fresh oocysts but also aged oocysts produced infection in cell cultures. Fifteen Dutch surface water samples were tested, and the cell culture immunofluorescence assays were not capable of determining the infectivity for the low numbers of naturally occurring
Cryptosporidium
oocysts present in the samples. A comparison with other viability assays, such as the vital dye exclusion assay, demonstrated that surrogate methods overestimate the number of infectious oocysts and therefore the risk of infection with
Cryptosporidium
. For accurate risk assessment, further improvement of the method for detection of
Cryptosporidium
in water is needed.
Growth and Grazing Mortality Rates of Phylogenetic Groups of Bacterioplankton in Coastal Marine Environments
Authors: Yokokawa Taichi , Nagata Toshi 
Published: November 2005

ABSTRACT

Dilution culture experiments were conducted in western North Pacific coastal regions to determine growth and grazing mortality rates of bacterial phylogenetic groups (α-, β-, and γ-proteobacteria and the
Cytophaga-Flavobacter
cluster) detected by fluorescent in situ hybridization. Growth rates varied greatly (1.2- to 4.0-fold) among different groups, and they were related to environmental variables (chlorophyll
a
concentrations and temperature) in a group-specific fashion. Growth rates of α-proteobacteria, the most abundant group in all the samples examined, were generally lower than those of less abundant groups, including the
Cytophaga-Flavobacter
cluster and γ-proteobacteria. Grazing mortality rates and mean cell volumes varied little among different groups. These results provide insights into factors that affect distributions of different groups, but growth and grazing mortality alone did not fully explain bacterial community compositions at a broad phylogenetic level.
A Propionate-Inducible Expression System for Enteric Bacteria
Authors: Lee Sung Kuk , Keasling Jay D. 
Published: November 2005

ABSTRACT

A series of new expression vectors (pPro) have been constructed for the regulated expression of genes in
Escherichia coli
. The pPro vectors contain the
prpBCDE
promoter (P

prpB

) responsible for expression of the propionate catabolic genes (
prpBCDE
) and
prpR
encoding the positive regulator of this promoter. The efficiency and regulatory properties of the
prpR
-P

prpB

system were measured by placing the gene encoding the green fluorescent protein (
gfp
) under the control of the inducible P

prpB

of
E. coli
. This system provides homogenous expression in individual cells, highly regulatable expression over a wide range of propionate concentrations, and strong expression (maximal 1,500-fold induction) at high propionate concentrations. Since the
prpBCDE
promoter has CAP-dependent activation, the
prpR
-P

prpB

system exhibited negligible basal expression by addition of glucose to the medium.
Common, but Complex, Mode of Resistance of
Plutella xylostella
to
Bacillus thuringiensis
Toxins Cry1Ab and Cry1Ac
Authors: Sayyed Ali H. , Gatsi Roxani , Ibiza-Palacios M. Sales , Escriche Baltasar , Wright Denis J. , Crickmore Neil 
Published: November 2005

ABSTRACT

A field collected population of
Plutella xylostella
(SERD4) was selected in the laboratory with
Bacillus thuringiensis
endotoxins Cry1Ac (Cry1Ac-SEL) and Cry1Ab (Cry1Ab-SEL). Both subpopulations showed similar phenotypes: high resistance to the Cry1A toxins and little cross-resistance to Cry1Ca or Cry1D. A previous analysis of the Cry1Ac-SEL showed incompletely dominant resistance to Cry1Ac with more than one factor, at least one of which was sex influenced. In the present study reciprocal mass crosses between Cry1Ab-SEL and a laboratory susceptible population (ROTH) provided evidence that Cry1Ab resistance was also inherited as incompletely dominant trait with more than one factor, and at least one of the factors was sex influenced. Analysis of single pair mating indicated that Cry1Ab-SEL was still heterogeneous for Cry1Ab resistance genes, showing genes with different degrees of dominance. Binding studies showed a large reduction of specific binding of Cry1Ab and Cry1Ac to midgut membrane vesicles of the Cry1Ab-SEL subpopulation. Cry1Ab-SEL was found to be more susceptible to trypsin-activated Cry1Ab toxin than protoxin, although no defect in toxin activation was found. Present and previous results indicate a common basis of resistance to both Cry1Ab and Cry1Ac in selected subpopulations and suggest that a similar set of resistance genes are responsible for resistance to Cry1Ab and Cry1Ac and are selected whichever toxin was used. The possibility of an incompletely dominant trait of resistant to these toxins should be taken into account when considering refuge resistance management strategies.
Reciprocal Regulation of Pyoluteorin Production with Membrane Transporter Gene Expression in
Pseudomonas fluorescens
Pf-5
Authors: Brodhagen Marion , Paulsen Ian , Loper Joyce E. 
Published: November 2005

ABSTRACT

Pyoluteorin is a chlorinated polyketide antibiotic secreted by the rhizosphere bacterium
Pseudomonas fluorescens
Pf-5. Genes encoding enzymes and transcriptional regulators involved in pyoluteorin production are clustered in the genome of Pf-5. Sequence analysis of genes adjacent to the known pyoluteorin biosynthetic gene cluster revealed the presence of an ABC transporter system. We disrupted two putative ABC transporter genes by inserting transcriptional fusions to an ice nucleation reporter gene. Mutations in
pltI
and
pltJ
, which are predicted to encode a membrane fusion protein and an ATP-binding cassette of the ABC transporter, respectively, greatly reduced pyoluteorin production by Pf-5. During the transition from exponential growth to stationary phase, populations of a
pltI
mutant were lower than those of a
pltI
+
strain in a culture medium containing pyoluteorin, suggesting a role for the transport system in efflux and the resistance of Pf-5 to the antibiotic. Although
pltI
or
pltJ
mutant strains displayed low pyoluteorin production, they did not accumulate proportionately more of the antibiotic intracellularly, indicating that
pltI
and
pltJ
do not encode an exclusive exporter for pyoluteorin. Transcription of the putative pyoluteorin efflux genes
pltI
and
pltJ
was enhanced by exogenous pyoluteorin. These new observations parallel an earlier finding that pyoluteorin enhances the transcription of pyoluteorin biosynthesis genes and pyoluteorin production in Pf-5. This report provides evidence of a coordination of pyoluteorin production and the transcription of genes encoding a linked transport apparatus, wherein each requires the other for optimal expression.
Photodynamic Inactivation of
Bacillus
Spores, Mediated by Phenothiazinium Dyes
Authors: Demidova Tatiana N. , Hamblin Michael R. 
Published: November 2005

ABSTRACT

Spore formation is a sophisticated mechanism by which some bacteria survive conditions of stress and starvation by producing a multilayered protective capsule enclosing their condensed DNA. Spores are highly resistant to damage by heat, radiation, and commonly employed antibacterial agents. Previously, spores have also been shown to be resistant to photodynamic inactivation using dyes and light that easily destroy the corresponding vegetative bacteria. We have discovered that
Bacillus
spores are susceptible to photoinactivation by phenothiazinium dyes and low doses of red light. Dimethylmethylene blue, methylene blue, new methylene blue, and toluidine blue O are all effective, while alternative photosensitizers such as Rose Bengal, polylysine chlorin(e6) conjugate, a tricationic porphyrin, and a benzoporphyrin derivative, which easily kill vegetative cells, are ineffective. Spores of
Bacillus cereus
and
B. thuringiensis
are most susceptible,
B. subtilis
and
B. atrophaeus
are also killed, and
B. megaterium
is resistant. Photoinactivation is most effective when excess dye is washed from the spores, showing that the dye binds to the spores and that excess dye in solution can quench light delivery. The relatively mild conditions needed for spore killing could have applications for treating wounds contaminated by anthrax spores, for which conventional sporicides would have unacceptable tissue toxicity.
Identifying Components of the NF-κB Pathway in the Beneficial
Euprymna scolopes
-
Vibrio fischeri
Light Organ Symbiosis
Authors: Goodson Michael S. , Kojadinovic Mila , Troll Joshua V. , Scheetz Todd E. , Casavant Thomas L. , Soares M. Bento , McFall-Ngai Margaret J. 
Published: November 2005

ABSTRACT

The Toll/NF-κB pathway is a common, evolutionarily conserved innate immune pathway that modulates the responses of animal cells to microbe-associated molecular patterns (MAMPs). Because MAMPs have been implicated as critical elements in the signaling of symbiont-induced development, an expressed sequence tag library from the juvenile light organ of
Euprymna scolopes
was used to identify members of the Toll/NF-κB pathway. Full-length transcripts were identified by using 5′ and 3′ RACE PCR. Seven transcripts critical for MAMP-induced triggering of the Toll/NF-κB phosphorylation cascade have been identified, including receptors, signal transducers, and a transcription factor. Further investigations should elucidate the role of the Toll/NF-κB pathway in the initiation of the beneficial symbiosis between
E. scolopes
and
Vibrio fischeri
.