bluuebunny/crossref_metadata_2025_split huggingface dataset:
In Vitro Antiplasmodium Effects of Dermaseptin S4 Derivatives
Authors: Dagan Arie , Efron Leah , Gaidukov Leonid , Mor Amram , Ginsburg Hagai 
Published: July 2002

ABSTRACT

The 13-residue dermaseptin S4 derivative K
4
S4(1-13)a (P) was previously shown to kill intraerythrocytic malaria parasites through the lysis of the host cells. In this study, we have sought peptides that will kill the parasite without lysing the erythrocyte. To produce such peptides, 26 compounds of variable structure and size were attached to the N terminus of P and screened for antiplasmodium and hemolytic activities in cultures of
Plasmodium falciparum
. Results from this screen indicated that increased hydrophobicity results in amplified antiplasmodium effect, irrespective of the linearity or bulkiness of the additive. However, increased hydrophobicity also was generally associated with increased hemolysis, with the exception of two derivatives: propionyl-P (C3-P) and isobutyryl-P (iC4-P). Both acyl-peptides were more effective than P, with 50% growth inhibition at 3.8, 4.3, and 7.7 μM, respectively. The antiparasitic effect was time dependent and totally irreversible, implying a cytotoxic effect. The peptides were also investigated in parallel for their ability to inhibit parasite growth and to induce hemolysis in infected and uninfected erythrocytes. Whereas the dose dependence of growth inhibition and hemolysis of infected cells overlapped when cells were treated with P, the acyl-peptides exerted 50% growth inhibition at concentrations that did not cause hemolysis. Noticeably, the acyl derivatives, but not P, were able to dissipate the parasite plasma membrane potential and cause depletion of intraparasite potassium under nonhemolytic conditions. These results clearly demonstrate that the acyl-peptides can affect parasite viability in a manner that is dissociated from lysis of the host cell. Overall, the data indicate the potential usefulness of this strategy for development of selective peptides as investigative tools and eventually as antimalarial agents.
Rapid Mineralization of Benzo[a]pyrene by a Microbial Consortium Growing on Diesel Fuel
Authors: Kanaly Robert A. , Bartha Richard , Watanabe Kazuya , Harayama Shigeaki 
Published: July 2002

ABSTRACTA microbial consortium which rapidly mineralized the environmentally persistent pollutant benzo[a]pyrene was recovered from soil. The consortium cometabolically converted [7-14C]benzo[a]pyrene to14CO2when it was grown on diesel fuel, and the extent of benzo[a]pyrene mineralization was dependent on both diesel fuel and benzo[a]pyrene concentrations. Addition of diesel fuel at concentrations ranging from 0.007 to 0.2% (wt/vol) stimulated the mineralization of 10 mg of benzo[a]pyrene per liter 33 to 65% during a 2-week incubation period. When the benzo[a]pyrene concentration was 10 to 100 mg liter−1and the diesel fuel concentration was 0.1% (wt/vol), an inoculum containing 1 mg of cell protein per liter (small inoculum) resulted in mineralization of up to 17.2 mg of benzo[a]pyrene per liter in 16 days. This corresponded to 35% of the added radiolabel when the concentration of benzo[a]pyrene was 50 mg liter−1. A radiocarbon mass balance analysis recovered 25% of the added benzo[a]pyrene solubilized in the culture suspension prior to mineralization. Populations growing on diesel fuel most likely promoted emulsification of benzo[a]pyrene through the production of surface-active compounds. The consortium was also analyzed by PCR-denaturing gradient gel electrophoresis of 16S rRNA gene fragments, and 12 dominant bands, representing different sequence types, were detected during a 19-day incubation period. The onset of benzo[a]pyrene mineralization was compared to changes in the consortium community structure and was found to correlate with the emergence of at least four sequence types. DNA from 10 sequence types were successfully purified and sequenced, and that data revealed that eight of the consortium members were related to the classProteobacteriabut that the consortium also included members which were related to the generaMycobacteriumandSphingobacterium.
Metabolic Engineering of an Aerobic Sulfate Reduction Pathway and Its Application to Precipitation of Cadmium on the Cell Surface
Authors: Wang Clifford L. , Maratukulam Priya D. , Lum Amy M. , Clark Douglas S. , Keasling J. D. 
Published: July 2002

ABSTRACT
The conversion of sulfate to an excess of free sulfide requires stringent reductive conditions. Dissimilatory sulfate reduction is used in nature by sulfate-reducing bacteria for respiration and results in the conversion of sulfate to sulfide. However, this dissimilatory sulfate reduction pathway is inhibited by oxygen and is thus limited to anaerobic environments. As an alternative, we have metabolically engineered a novel aerobic sulfate reduction pathway for the secretion of sulfides. The assimilatory sulfate reduction pathway was redirected to overproduce cysteine, and excess cysteine was converted to sulfide by cysteine desulfhydrase. As a potential application for this pathway, a bacterium was engineered with this pathway and was used to aerobically precipitate cadmium as cadmium sulfide, which was deposited on the cell surface. To maximize sulfide production and cadmium precipitation, the production of cysteine desulfhydrase was modulated to achieve an optimal balance between the production and degradation of cysteine.
Comparison of Acid Mine Drainage Microbial Communities in Physically and Geochemically Distinct Ecosystems
Authors: Bond Philip L. , Druschel Greg K. , Banfield Jillian F. 
Published: July 2002

ABSTRACT

This study presents population analyses of microbial communities inhabiting a site of extreme acid mine drainage (AMD) production. The site is the inactive underground Richmond mine at Iron Mountain, Calif., where the weathering of a massive sulfide ore body (mostly pyrite) produces solutions with pHs of ∼0.5 to ∼1.0. Here we used a suite of oligonucleotide probes, designed from molecular data recently acquired from the site, to analyze a number of microbial environments by fluorescent in situ hybridization. Microbial-community analyses were correlated with geochemical and mineralogical data from those environments. The environments investigated were within the ore body and thus at the site of pyrite dissolution, as opposed to environments that occur downstream of the dissolution. Few organism types, as defined by the specificities of the oligonucleotide probes, dominated the microbial communities. The majority of the dominant organisms detected were newly discovered or organisms only recently associated with acid-leaching environments. “
Ferroplasma
” spp. were detected in many of the communities and were particularly dominant in environments of lowest pH and highest ionic strength.
Leptospirillum
spp. were also detected in many slime and pyrite-dominated environments. In samples of an unusual subaerial slime, a new uncultured
Leptospirillum
sp. dominated.
Sulfobacillus
spp. were detected as a prominent inhabitant in warmer (∼43°C) environments. The information gathered here is critical for determining organisms important to AMD production at Iron Mountain and for directing future studies of this process. The findings presented here also have relevance to the microbiology of industrial bioleaching and to the understanding of geochemical iron and sulfur cycles.
Influence of Infected Cell Growth State on Bacteriophage Reactivation Levels
Authors: Kadavy Dana R. , Shaffer Julie J. , Lott Susan E. , Wolf Thomas A. , Bolton Cathy E. , Gallimore William H. , Martin Eugene L. , Nickerson Kenneth W. , Kokjohn Tyler A. 
Published: July 2002

ABSTRACT

Reactivation of UV-C-inactivated
Pseudomonas aeruginosa
bacteriophages D3C3, F116, G101, and UNL-1 was quantified in host cells infected during the exponential phase, during the stationary phase, and after starvation (1 day, 1 and 5 weeks) under conditions designed to detect dark repair and photoreactivation. Our experiments revealed that while the photoreactivation capacity of stationary-phase or starved cells remained about the same as that of exponential-phase cells, in some cases their capacity to support dark repair of UV-inactivated bacteriophages increased over 10-fold. This enhanced reactivation capacity was correlated with the ca. 30-fold-greater UV-C resistance of
P. aeruginosa
host cells that were in the stationary phase or exposed to starvation conditions prior to irradiation. The dark repair capacity of
P. aeruginosa
cells that were infected while they were starved for prolonged periods depended on the bacteriophage examined. For bacteriophage D3C3 this dark repair capacity declined with prolonged starvation, while for bacteriophage G101 the dark repair capacity continued to increase when cells were starved for 24 h or 1 week prior to infection. For G101, the reactivation potentials were 16-, 18-, 10-, and 3-fold at starvation intervals of 1 day, 1 week, 5 weeks, and 1.5 years, respectively. Exclusive use of exponential-phase cells to quantify bacteriophage reactivation should detect only a fraction of the true phage reactivation potential.
Bacterial Cell Surface Display of an Enzyme Library for Selective Screening of Improved Cellulase Variants
Authors: Kim Yong-Sung , Jung Heung-Chae , Pan Jae-Gu 
Published: July 2002

ABSTRACT
The bacterial surface display method was used to selectively screen for improved variants of carboxymethyl cellulase (CMCase). A library of mutated CMCase genes generated by DNA shuffling was fused to the ice nucleation protein (Inp) gene so that the resulting fusion proteins would be displayed on the bacterial cell surface. Some cells displaying mutant proteins grew more rapidly on carboxymethyl cellulose plates than controls, forming heterogeneous colonies. In contrast, cells displaying the nonmutated parent CMCase formed uniform tiny colonies. These variations in growth rate were assumed to result from altered availability of glucose caused by differences in the activity of variant CMCases at the cell surface. Staining assays indicate that large, rapidly growing colonies have increased CMCase activity. Increased CMCase activity was confirmed by assaying the specific activities of cell extracts after the expression of unfused forms of the variant genes in the cytoplasm. The best-evolved CMCases showed about a 5- and 2.2-fold increase in activity in the fused and free forms, respectively. Sequencing of nine evolved CMCase variant genes showed that most amino acid substitutions occurred within the catalytic domain of the enzyme. These results demonstrate that the bacterial surface display of enzyme libraries provides a direct way to correlate evolved enzyme activity with cell growth rates. This technique will provide a useful technology platform for directed evolution and high-throughput screening of industrial enzymes, including hydrolases.
Biomarker Evidence for Widespread Anaerobic Methane Oxidation in Mediterranean Sediments by a Consortium of Methanogenic Archaea and Bacteria
Authors: Pancost Richard D. , Sinninghe Damsté Jaap S. , de Lint Saskia , van der Maarel Marc J. E. C. , Gottschal Jan C. ,   The Medinaut Shipboard Scientific Party
Published: July 2002

ABSTRACT

Although abundant geochemical data indicate that anaerobic methane oxidation occurs in marine sediments, the linkage to specific microorganisms remains unclear. In order to examine processes of methane consumption and oxidation, sediment samples from mud volcanoes at two distinct sites on the Mediterranean Ridge were collected via the submersible
Nautile
. Geochemical data strongly indicate that methane is oxidized under anaerobic conditions, and compound-specific carbon isotope analyses indicate that this reaction is facilitated by a consortium of archaea and bacteria. Specifically, these methane-rich sediments contain high abundances of methanogen-specific biomarkers that are significantly depleted in
13
C (δ
13
C values are as low as −95‰). Biomarkers inferred to derive from sulfate-reducing bacteria and other heterotrophic bacteria are similarly depleted. Consistent with previous work, such depletion can be explained by consumption of
13
C-depleted methane by methanogens operating in reverse and as part a consortium of organisms in which sulfate serves as the terminal electron acceptor. Moreover, our results indicate that this process is widespread in Mediterranean mud volcanoes and in some localized settings is the predominant microbiological process.
rRNA Operon Copy Number Reflects Ecological Strategies of Bacteria
Authors: Klappenbach Joel A. , Dunbar John M. , Schmidt Thomas M. 
Published: July 2002

ABSTRACT

Although natural selection appears to favor the elimination of gene redundancy in prokaryotes, multiple copies of each rRNA-encoding gene are common on bacterial chromosomes. Despite this conspicuous deviation from single-copy genes, no phenotype has been consistently associated with rRNA gene copy number. We found that the number of rRNA genes correlates with the rate at which phylogenetically diverse bacteria respond to resource availability. Soil bacteria that formed colonies rapidly upon exposure to a nutritionally complex medium contained an average of 5.5 copies of the small subunit rRNA gene, whereas bacteria that responded slowly contained an average of 1.4 copies. In soil microcosms pulsed with the herbicide 2,4-dichlorophenoxyacetic acid (2,4-D), indigenous populations of 2,4-D-degrading bacteria with multiple rRNA genes (

x

¯

= 5.4) became dominant, whereas populations with fewer rRNA genes (

x

¯

= 2.7) were favored in unamended controls. These findings demonstrate phenotypic effects associated with rRNA gene copy number that are indicative of ecological strategies influencing the structure of natural microbial communities.
Effects of Acid Adaptation, Product pH, and Heating on Survival of
Escherichia coli
O157:H7 in Pepperoni
Authors: R. Riordan Denise C. , Duffy Geraldine , Sheridan James J. , Whiting Richard C. , Blair Ian S. , McDowell David A. 
Published: July 2002

ABSTRACT

The thermotolerance of
E. coli
O157:H7 cells (strain 380-94) heated in pepperoni is reported. Information on the pattern of thermal inactivation of
E. coli
O157:H7 in pepperoni was applied in the development of heating processes designed to reduce
E. coli
O157:H7 numbers therein by 5 log
10
units.
Genetic and Biochemical Characterization of a Highly Thermostable α-
l
-Arabinofuranosidase from
Thermobacillus xylanilyticus
Authors: Debeche Takoua , Cummings Nicola , Connerton Ian , Debeire Philippe , O'Donohue Michael J. 
Published: July 2002

ABSTRACT

The gene encoding an α-
l
-arabinofuranosidase from
Thermobacillus xylanilyticus
D3, AbfD3, was isolated. Characterization of the purified recombinant α-
l
-arabinofuranosidase produced in
Escherichia coli
revealed that it is highly stable with respect to both temperature (up to 90°C) and pH (stable in the pH range 4 to 12). On the basis of amino acid sequence similarities, this 56,071-Da enzyme could be assigned to family 51 of the glycosyl hydrolase classification system. However, substrate specificity analysis revealed that AbfD3, unlike the majority of F51 members, displays high activity in the presence of polysaccharides.
Characterization of a Novel Integrative Element, ICE
St1
, in the Lactic Acid Bacterium
Streptococcus thermophilus
Authors: Burrus Vincent , Roussel Yvonne , Decaris Bernard , Guédon Gérard 
Published: July 2002

ABSTRACT

The 35.5-kb ICE
St1
element of
Streptococcus thermophilus
CNRZ368 is bordered by a 27-bp repeat and integrated into the 3′ end of a gene encoding a putative fructose-1,6-biphosphate aldolase. This element encodes site-specific integrase and excisionase enzymes related to those of conjugative transposons Tn
5276
and Tn
5252
. The integrase was found to be involved in a site-specific excision of a circular form. ICE
St1
also encodes putative conjugative transfer proteins related to those of the conjugative transposon Tn
916
. Therefore, ICE
St1
could be or could be derived from an integrative conjugative element.
Coexistence of Two Different O Demethylation Systems in Lignin Metabolism by
Sphingomonas paucimobilis
SYK-6: Cloning and Sequencing of the Lignin Biphenyl-Specific
O
-Demethylase (LigX) Gene
Authors: Sonoki Tomonori , Obi Takahiro , Kubota Sachiko , Higashi Motoo , Masai Eiji , Katayama Yoshihiro 
Published: July 2002

ABSTRACT

Sphingomonas paucimobilis
SYK-6 can grow on several dimeric model compounds of lignin as a carbon and energy source. It has O demethylation systems on three kinds of substrates: 5,5′-dehydrodivanillic acid (DDVA), syringate, and vanillate. We previously reported the cloning of a gene involved in the tetrahydrofolate-dependent O demethylation of syringate and vanillate. In the study reported here, we cloned the gene responsible for DDVA O demethylation. Using nitrosoguanidine mutagenesis, a mutant strain, NT-1, which could not degrade DDVA but could degrade syringate and vanillate, was isolated and was used to clone the gene responsible for the O demethylation of DDVA by complementation. Sequencing analysis showed an open reading frame (designated
ligX
) of 1,266 bp in this fragment. The deduced amino acid sequence of LigX had similarity to class I type oxygenases. LigX was involved in O demethylation activity on DDVA but not on vanillate and syringate. DDVA O demethylation activity in
S. paucimobilis
SYK-6 cell extracts was inhibited by addition of the LigX polyclonal antiserum. Thus, LigX is an essential enzyme for DDVA O demethylation in SYK-6.
S. paucimobilis
SYK-6 has two O demethylation systems: one is an oxygenative demethylase system, and the other is a tetrahydrofolate-dependent methyltransferase system.
Biotransformation of Hydroxylaminobenzene and Aminophenol by
Pseudomonas putida
2NP8 Cells Grown in the Presence of 3-Nitrophenol
Authors: Zhao Jian-Shen , Singh Ajay , Huang Xiao-Dong , Ward Owen P. 
Published: July 2002

ABSTRACT

Biotransformation products of hydroxylaminobenzene and aminophenol produced by 3-nitrophenol-grown cells of
Pseudomonas putida
2NP8, a strain grown on 2- and 3-nitrophenol, were characterized. Ammonia, 2-aminophenol, 4-aminophenol, 4-benzoquinone,
N
-acetyl-4-aminophenol,
N
-acetyl-2-aminophenol, 2-aminophenoxazine-3-one, 4-hydroquinone, and catechol were produced from hydroxylaminobenzene. Ammonia,
N
-acetyl-2-aminophenol, and 2-aminophenoxazine-3-one were produced from 2-aminophenol. All of these metabolites were also found in the nitrobenzene transformation medium, and this demonstrated that they were metabolites of nitrobenzene transformation via hydroxylaminobenzene. Production of 2-aminophenoxazine-3-one indicated that oxidation of 2-aminophenol via imine occurred. Rapid release of ammonia from 2-aminophenol transformation indicated that hydrolysis of the imine intermediate was the dominant reaction. The low level of 2-aminophenoxazine-3-one indicated that formation of this compound was probably due to a spontaneous reaction accompanying oxidation of 2-aminophenol via imine. 4-Hydroquinone and catechol were reduction products of 2- and 4-benzoquinones. Based on these transformation products, we propose a new ammonia release pathway via oxidation of aminophenol to benzoquinone monoimine and subsequent hydrolysis for transformation of nitroaromatic compounds by 3-nitrophenol-grown cells of
P. putida
2NP8. We propose a parallel mechanism for 3-nitrophenol degradation in
P. putida
2NP8, in which all of the possible intermediates are postulated.
Differential Effects of Permeating and Nonpermeating Solutes on the Fatty Acid Composition of
Pseudomonas putida
Authors: Halverson Larry J. , Firestone Mary K. 
Published: July 2002

ABSTRACT

We examined the effect of reduced water availability on the fatty acid composition of
Pseudomonas putida
strain mt-2 grown in a defined medium in which the water potential was lowered with the permeating solutes NaCl or polyethylene glycol (PEG) with a molecular weight of 200 (PEG 200) or the nonpermeating solute PEG 8000. Transmission electron microscopy showed that −1.0-MPa PEG 8000-treated cells had convoluted outer membranes, whereas −1.0-MPa NaCl-treated or control cells did not. At the range of water potential (−0.25 to −1.5 MPa) that we examined, reduced water availability imposed by PEG 8000, but not by NaCl or PEG 200, significantly altered the amounts of
trans
and
cis
isomers of monounsaturated fatty acids that were present in whole-cell fatty acid extracts. Cells grown in basal medium or under the −0.25-MPa water potential imposed by NaCl or PEG 200 had a higher
trans
:
cis
ratio than −0.25-MPa PEG 8000-treated cells. As the water potential was lowered further with PEG 8000 amendments, there was an increase in the amount of
trans
isomers, resulting in a higher
trans
:
cis
ratio. Similar results were observed in cells grown physically separated from PEG 8000, indicating that these changes were not due to PEG toxicity. When cells grown in −1.5-MPa PEG 8000 amendments were exposed to a rapid water potential increase of 1.5 MPa or to a thermodynamically equivalent concentration of the permeating solute, NaCl, there was a decrease in the amount of
trans
fatty acids with a corresponding increase in the
cis
isomer. The decrease in the
trans/cis
ratio following hypoosomotic shock did not occur in the presence of the lipid synthesis inhibitor cerulenin or the growth inhibitors chloramphenicol and rifampicin, which indicates a constitutively operating enzyme system. These results indicate that thermodynamically equivalent concentrations of permeating and nonpermeating solutes have unique effects on membrane fatty acid composition.