bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reaction of Acylated Homoserine Lactone Bacterial Signaling Molecules with Oxidized Halogen Antimicrobials
Authors: Borchardt S. A. , Allain E. J. , Michels J. J. , Stearns G. W. , Kelly R. F. , McCoy W. F. 
Published: July 2002

ABSTRACTOxidized halogen antimicrobials, such as hypochlorous and hypobromous acids, have been used extensively for microbial control in industrial systems. Recent discoveries have shown that acylated homoserine lactone cell-to-cell signaling molecules are important for biofilm formation inPseudomonas aeruginosa, suggesting that biofouling can be controlled by interfering with bacterial cell-to-cell communication. This study was conducted to investigate the potential for oxidized halogens to react with acylated homoserine lactone-based signaling molecules. Acylated homoserine lactones containing a 3-oxo group were found to rapidly react with oxidized halogens, while acylated homoserine lactones lacking the 3-oxo functionality did not react. TheChromobacterium violaceumCV026 bioassay was used to determine the effects of such reactions on acylated homoserine lactone activity. The results demonstrated that 3-oxo acyl homoserine lactone activity was rapidly lost upon exposure to oxidized halogens; however, acylated homoserine lactones lacking the 3-oxo group retained activity. Experiments with the marine algaLaminaria digitatademonstrated that natural haloperoxidase systems are capable of mediating the deactivation of acylated homoserine lactones. This may illustrate a natural defense mechanism to prevent biofouling on the surface of this marine alga. TheChromobacterium violaceumactivity assay illustrates that reactions between 3-oxo acylated homoserine lactone molecules and oxidized halogens do occur despite the presence of biofilm components at much greater concentrations. This work suggests that oxidized halogens may control biofilm not only via a cidal mechanism, but also by possibly interfering with 3-oxo acylated homoserine lactone-based cell signaling.
Biotransformation of Various Substituted Aromatic Compounds to Chiral Dihydrodihydroxy Derivatives
Authors: Raschke Henning , Meier Michael , Burken Joel G. , Hany Roland , Müller Markus D. , Van Der Meer Jan Roelof , Kohler Hans-Peter E. 
Published: July 2002

ABSTRACT

The biotransformation of four different classes of aromatic compounds by the
Escherichia coli
strain DH5α(pTCB 144), which contained the chlorobenzene dioxygenase (CDO) from
Pseudomonas
sp. strain P51, was examined. CDO oxidized biphenyl as well as monochlorobiphenyls to the corresponding
cis
-2,3-dihydro-2,3-dihydroxy derivatives, whereby oxidation occurred on the unsubstituted ring. No higher substituted biphenyls were oxidized. The absolute configurations of several monosubstituted
cis
-benzene dihydrodiols formed by CDO were determined. All had an
S
configuration at the carbon atom in
meta
position to the substituent on the benzene nucleus. With one exception, the enantiomeric excess of several 1,4-disubstituted
cis
-benzene dihydrodiols formed by CDO was higher than that of the products formed by two toluene dioxygenases. Naphthalene was oxidized to enantiomerically pure (+)-
cis
-(1
R
,2
S
)-dihydroxy-1,2-dihydronaphthalene. All absolute configurations were identical to those of the products formed by toluene dioxygenases of
Pseudomonas putida
UV4 and
P. putida
F39/D. The formation rate of (+)-
cis
-(1
R
,2
S
)-dihydroxy-1,2-dihydronaphthalene was significantly higher (about 45 to 200%) than those of several monosubstituted
cis
-benzene dihydrodiols and more than four times higher than the formation rate of
cis
-benzene dihydrodiol. A new gas chromatographic method was developed to determine the enantiomeric excess of the oxidation products.
Differentiation of
Lactobacillus plantarum,
L. pentosus,
and
L. paraplantarum
by
recA
Gene Sequence Analysis and Multiplex PCR Assay with
recA
Gene-Derived Primers
Authors: Torriani Sandra , Felis Giovanna E. , Dellaglio Franco 
Published: July 2002

ABSTRACT

In this study, we succeeded in differentiating
Lactobacillus plantarum,
Lactobacillus pentosus,
and
Lactobacillus paraplantarum
by means of
recA
gene sequence comparison. Short homologous regions of about 360 bp were amplified by PCR with degenerate consensus primers, sequenced, and analyzed, and 322 bp were considered for the inference of phylogenetic trees. Phylograms, obtained by parsimony, maximum likelihood, and analysis of data matrices with the neighbor-joining model, were coherent and clearly separated the three species. The validity of the
recA
gene and RecA protein as phylogenetic markers is discussed. Based on the same sequences, species-specific primers were designed, and a multiplex PCR protocol for the simultaneous distinction of these bacteria was optimized. The sizes of the amplicons were 318 bp for
L. plantarum
, 218 bp for
L. pentosus,
and 107 bp for
L. paraplantarum
. This strategy permitted the unambiguous identification of strains belonging to
L. plantarum,
L. pentosus,
and
L. paraplantarum
in a single reaction, indicating its applicability to the speciation of isolates of the
L. plantarum
group.
Presence of Nitrate-Accumulating Sulfur Bacteria and Their Influence on Nitrogen Cycling in a Shallow Coastal Marine Sediment
Authors: Sayama Mikio 
Published: July 2002

ABSTRACTNitrate flux between sediment and water, nitrate concentration profile at the sediment-water interface, and in situ sediment denitrification activity were measured seasonally at the innermost part of Tokyo Bay, Japan. For the determination of sediment nitrate concentration, undisturbed sediment cores were sectioned into 5-mm depth intervals and each segment was stored frozen at −30°C. The nitrate concentration was determined for the supernatants after centrifuging the frozen and thawed sediments. Nitrate in the uppermost sediment showed a remarkable seasonal change, and its seasonal maximum of up to 400 μM was found in October. The directions of the diffusive nitrate fluxes predicted from the interfacial concentration gradients were out of the sediment throughout the year. In contrast, the directions of the total nitrate fluxes measured by the whole-core incubation were into the sediment at all seasons. This contradiction between directions indicates that a large part of the nitrate pool extracted from the frozen surface sediments is not a pore water constituent, and preliminary examinations demonstrated that the nitrate was contained in the intracellular vacuoles of filamentous sulfur bacteria dwelling on or in the surface sediment. Based on the comparison between in situ sediment denitrification activity and total nitrate flux, it is suggested that intracellular nitrate cannot be directly utilized by sediment denitrification, and the probable fate of the intracellular nitrate is hypothesized to be dissimilatory reduction to ammonium. The presence of nitrate-accumulating sulfur bacteria therefore may lower nature's self-purification capacity (denitrification) and exacerbate eutrophication in shallow coastal marine environments.
Isolation of
Gemmata
-Like and
Isosphaera
-Like Planctomycete Bacteria from Soil and Freshwater
Authors: Wang Jenny , Jenkins Cheryl , Webb Richard I. , Fuerst John A. 
Published: July 2002

ABSTRACT

New cultured strains of the planctomycete division (order
Planctomycetales
) of the domain
Bacteria
related to species in the genera
Gemmata
and
Isosphaera
were isolated from soil, freshwater, and a laboratory ampicillin solution. Phylogenetic analysis of the 16S rRNA gene from eight representative isolates showed that all the isolates were members of the planctomycete division. Six isolates clustered with
Gemmata obscuriglobus
and related strains, while two isolates clustered with
Isosphaera pallida
. A double-membrane-bounded nucleoid was observed in
Gemmata
-related isolates but not in
Isosphaera
-related isolates, consistent with the ultrastructures of existing species of each genus. Two isolates from this study represent the first planctomycetes successfully cultivated from soil.
Identification ofCryptosporidium parvumOocysts by an Artificial Neural Network Approach
Authors: Widmer Kenneth W. , Oshima Kevin H. , Pillai Suresh D. 
Published: July 2002

ABSTRACTMicroscopic detection ofCryptosporidium parvumoocysts is time-consuming, requires trained analysts, and is frequently subject to significant human errors. Artificial neural networks (ANN) were developed to help identify immunofluorescently labeledC. parvumoocysts. A total of 525 digitized images of immunofluorescently labeled oocysts, fluorescent microspheres, and other miscellaneous nonoocyst images were employed in the training of the ANN. The images were cropped to a 36- by 36-pixel image, and the cropped images were placed into two categories, oocyst and nonoocyst images. The images were converted to grayscale and processed into a histogram of gray color pixel intensity. Commercially available software was used to develop and train the ANN. The networks were optimized by varying the number of training images, number of hidden neurons, and a combination of these two parameters. The network performance was then evaluated using a set of 362 unique testing images which the network had never “seen” before. Under optimized conditions, the correct identification of authentic oocyst images ranged from 81 to 97%, and the correct identification of nonoocyst images ranged from 78 to 82%, depending on the type of fluorescent antibody that was employed. The results indicate that the ANN developed were able to generalize the training images and subsequently discern previously unseen oocyst images efficiently and reproducibly. Thus, ANN can be used to reduce human errors associated with the microscopic detection ofCryptosporidiumoocysts.
Novel
Bacillus thuringiensis
Binary Insecticidal Crystal Proteins Active on Western Corn Rootworm,
Diabrotica virgifera virgifera
LeConte
Authors: Ellis R. Tracy , Stockhoff Brian A. , Stamp Lisa , Schnepf H. Ernest , Schwab George E. , Knuth Mark , Russell Josh , Cardineau Guy A. , Narva Kenneth E. 
Published: July 2002

ABSTRACT

A new family of insecticidal crystal proteins was discovered by screening sporulated
Bacillus thuringiensis
cultures for oral activity against western corn rootworm (WCR) larvae.
B. thuringiensis
isolates PS80JJ1, PS149B1, and PS167H2 have WCR insecticidal activity attributable to parasporal inclusion bodies containing proteins with molecular masses of ca. 14 and 44 kDa. The genes encoding these polypeptides reside in apparent operons, and the 14-kDa protein open reading frame (ORF) precedes the 44-kDa protein ORF. Mutagenesis of either gene in the apparent operons dramatically reduced insecticidal activity of the corresponding recombinant
B. thuringiensis
strain. Bioassays performed with separately expressed, biochemically purified 14- and 44-kDa polypeptides also demonstrated that both proteins are required for WCR mortality. Sequence comparisons with other known
B. thuringiensis
insecticidal proteins failed to reveal homology with previously described Cry, Cyt, or Vip proteins. However, there is evidence that the 44-kDa polypeptide and the 41.9- and 51.4-kDa binary dipteran insecticidal proteins from
Bacillus sphaericus
are evolutionarily related. The 14- and 44-kDa polypeptides from isolates PS80JJ1, PS149B1, and PS167H2 have been designated Cry34Aa1, Cry34Ab1, and Cry34Ac1, respectively, and the 44-kDa polypeptides from these isolates have been designated Cry35Aa1, Cry35Ab1, and Cry35Ac1, respectively.
Induction, Isolation, and Characterization of Two Laccases from the White Rot BasidiomyceteCoriolopsis rigida
Authors: Saparrat Mario C. N. , Guillén Francisco , Arambarri Angélica M. , Martínez Angel T. , Martínez María Jesús 
Published: July 2002

ABSTRACTPrevious work has shown that the white rot fungusCoriolopsis rigidadegraded wheat straw lignin and both the aliphatic and aromatic fractions of crude oil from contaminated soils. To better understand these processes, we studied the enzymatic composition of the ligninolytic system of this fungus. Since laccase was the sole ligninolytic enzyme found, we paid attention to the oxidative capabilities of this enzyme that would allow its participation in the mentioned degradative processes. We purified two laccase isoenzymes to electrophoretic homogeneity from copper-induced cultures. Both enzymes are monomeric proteins, with the same molecular mass (66 kDa), isoelectric point (3.9), N-linked carbohydrate content (9%), pH optima of 3.0 on 2,6-dimethoxyphenol (DMP) and 2.5 on 2,2′-azinobis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS), absorption spectrum, and N-terminal amino acid sequence. They oxidized 4-anisidine and numerous phenolic compounds, including methoxyphenols, hydroquinones, and lignin-derived aldehydes and acids. Phenol red, an unusual substrate of laccase due to its high redox potential, was also oxidized. The highest enzyme affinity and efficiency were obtained with ABTS and, among phenolic compounds, with 2,6-dimethoxyhydroquinone (DBQH2). The presence of ABTS in the laccase reaction expanded the substrate range ofC. rigidalaccases to nonphenolic compounds and that of MBQH2extended the reactions catalyzed by these enzymes to the production of H2O2, the oxidation of Mn2+, the reduction of Fe3+, and the generation of hydroxyl radicals. These results confirm the participation of laccase in the production of oxygen free radicals, suggesting novel uses of this enzyme in degradative processes.
Analysis of Bacteria Contaminating Ultrapure Water in Industrial Systems
Authors: Kulakov Leonid A. , McAlister Morven B. , Ogden Kimberly L. , Larkin Michael J. , O'Hanlon John F. 
Published: July 2002

ABSTRACT

Bacterial populations inhabiting ultrapure water (UPW) systems were investigated. The analyzed UPW systems included pilot scale, bench scale, and full size UPW plants employed in the semiconductor and other industries. Bacteria present in the polishing loop of the UPW systems were enumerated by both plate counts and epifluorescence microscopy. Assessment of bacterial presence in UPW by epifluorescence microscopy (cyanotolyl tetrazolium chloride [CTC] and DAPI [4′,6′-diamidino-2-phenylindole] staining) showed significantly higher numbers (10 to 100 times more bacterial cells were detected) than that determined by plate counts. A considerable proportion of the bacteria present in UPW (50 to 90%) were cells that did not give a positive signal with CTC stain. Bacteria isolated from the UPW systems were mostly gram negative, and several groups seem to be indigenous for all of the UPW production systems studied. These included
Ralstonia pickettii
,
Bradyrhizobium
sp.,
Pseudomonas saccharophilia
, and
Stenotrophomonas
strains. These bacteria constituted a significant part of the total number of isolated strains (≥20%). Two sets of primers specific to
R. pickettii
and
Bradyrhizobium
sp. were designed and successfully used for the detection of the corresponding bacteria in the concentrated UPW samples. Unexpectedly,
nifH
gene sequences were found in
Bradyrhizobium
sp. and some
P. saccharophilia
strains isolated from UPW. The widespread use of nitrogen gas in UPW plants may be associated with the presence of nitrogen-fixing genes in these bacteria.
Responses of
Listeria monocytogenes
to Acid Stress and Glucose Availability Revealed by a Novel Combination of Fluorescence Microscopy and Microelectrode Ion-Selective Techniques
Authors: Shabala Lana , Budde Birgitte , Ross Tom , Siegumfeldt Henrik , Jakobsen Mogens , McMeekin Tom 
Published: July 2002

ABSTRACT

Fluorescence ratio imaging microscopy and microelectrode ion flux estimation techniques were combined to study mechanisms of pH homeostasis in
Listeria monocytogenes
subjected to acid stress at different levels of glucose availability. This novel combination provided a unique opportunity to measure changes in H
+
at either side of the bacterial membrane in real time and therefore to evaluate the rate of H
+
flux across the bacterial plasma membrane and its contribution to bacterial pH homeostasis. Responses were assessed at external pHs (pH
o
) between 3.0 and 6.0 for three levels of glucose (0, 1, and 10 mM) in the medium. Both the intracellular pH (pH
i
) and net H
+
fluxes were affected by the glucose concentration in the medium, with the highest absolute values corresponding to the highest glucose concentration. In the presence of glucose, the pH
i
remained above 7.0 within a pH
o
range of 4 to 6 and decreased below pH
o
4. Above pH
o
4, H
+
extrusion increased correspondingly, with the maximum value at pH
o
5.5, and below pH
o
4, a net H
+
influx was observed. Without glucose in the medium, the pH
i
decreased, and a net H
+
influx was observed below pH
o
5.5. A high correlation (
R
= 0.75 to 0.92) between the pH
i
and net H
+
flux changes is reported, indicating that the two processes are complementary. The results obtained support other reports indicating that membrane transport processes are the main contributors to the process of pH
i
homeostasis in
L. monocytogenes
subjected to acid stress.
Towards Growth of Arbuscular Mycorrhizal Fungi Independent of a Plant Host
Authors: Hildebrandt Ulrich , Janetta Katharina , Bothe Hermann 
Published: July 2002

ABSTRACTWhen surface-sterilized spores of the arbuscular mycorrhizal fungus (AMF)Glomus intraradicesSy167 were germinated on agar plates in the slightly modified minimum mineral medium described by G. Bécard and J. A. Fortin (New Phytol. 108:211-218, 1988), slime-forming bacteria, identified asPaenibacillus validus, frequently grew up. These bacteria were able to support growth of the fungus on the agar plates. In the presence ofP. validus, hyphae branched profusely and formed coiled structures. These were much more densely packed than the so-called arbuscule-like structures which are formed by AMF grown in coculture with carrot roots transformed with T-DNA fromAgrobacterium rhizogenes. The presence ofP. validusalone also enabledG. intraradicesto form new spores, mainly at the densely packed hyphal coils. The new spores were not as abundant as and were smaller than those formed by AMF in the monoxenic culture with carrot root tissues, but they also contained lipid droplets and a large number of nuclei. In these experimentsP. validuscould not be replaced by bacteria such asEscherichia coliK-12 orAzospirillum brasilenseSp7. Although no conditions under which the daughter spores regerminate and colonize plants have been found yet, and no factor(s) fromP. validuswhich stimulates fungal growth has been identified, the present findings might be a significant step forward toward growth of AMF independent of any plant host.
Bradyrhizobia from Wild
Phaseolus
,
Desmodium
, and
Macroptilium
Species in Northern Mexico
Authors: Parker Matthew A. 
Published: July 2002

ABSTRACT

rRNA genetic markers were analyzed in 97 isolates of nodule bacteria from six legume species in Chihuahua, Mexico. The most common genotypes were widely shared across host species and had 16S rRNA sequences identical to those of strains from an eastern North American legume (
Amphicarpaea
) that are closely related to
Bradyrhizobium elkanii.
An NADH:Quinone Oxidoreductase Active during Biodegradation by the Brown-Rot Basidiomycete
Gloeophyllum trabeum
Authors: Jensen, Kenneth A. , Ryan Zachary C. , Vanden Wymelenberg Amber , Cullen Daniel , Hammel Kenneth E. 
Published: July 2002

ABSTRACT

The brown-rot basidiomycete
Gloeophyllum trabeum
uses a quinone redox cycle to generate extracellular Fenton reagent, a key component of the biodegradative system expressed by this highly destructive wood decay fungus. The hitherto uncharacterized quinone reductase that drives this cycle is a potential target for inhibitors of wood decay. We have identified the major quinone reductase expressed by
G. trabeum
under conditions that elicit high levels of quinone redox cycling. The enzyme comprises two identical 22-kDa subunits, each with one molecule of flavin mononucleotide. It is specific for NADH as the reductant and uses the quinones produced by
G. trabeum
(2,5-dimethoxy-1,4-benzoquinone and 4,5-dimethoxy-1,2-benzoquinone) as electron acceptors. The affinity of the reductase for these quinones is so high that precise kinetic parameters were not obtainable, but it is clear that
k
cat
/

K
m

for the quinones is greater than 10
8
M
−1
s
−1
. The reductase is encoded by a gene with substantial similarity to NAD(P)H:quinone reductase genes from other fungi. The
G. trabeum
quinone reductase may function in quinone detoxification, a role often proposed for these enzymes, but we hypothesize that the fungus has recruited it to drive extracellular oxyradical production.
Metabolic Engineering of Glycerol Production inSaccharomyces cerevisiae
Authors: Overkamp Karin M. , Bakker Barbara M. , Kötter Peter , Luttik Marijke A. H. , van Dijken Johannes P. , Pronk Jack T. 
Published: July 2002

ABSTRACTInactivation ofTPI1, theSaccharomyces cerevisiaestructural gene encoding triose phosphate isomerase, completely eliminates growth on glucose as the sole carbon source. Intpi1-null mutants, intracellular accumulation of dihydroxyacetone phosphate might be prevented if the cytosolic NADH generated in glycolysis by glyceraldehyde-3-phosphate dehydrogenase were quantitatively used to reduce dihydroxyacetone phosphate to glycerol. We hypothesize that the growth defect oftpi1-null mutants is caused by mitochondrial reoxidation of cytosolic NADH, thus rendering it unavailable for dihydroxyacetone-phosphate reduction. To test this hypothesis, atpi1Δnde1Δnde2Δgut2Δ quadruple mutant was constructed.NDE1andNDE2encode isoenzymes of mitochondrial external NADH dehydrogenase;GUT2encodes a key enzyme of the glycerol-3-phosphate shuttle. It has recently been demonstrated that these two systems are primarily responsible for mitochondrial oxidation of cytosolic NADH inS. cerevisiae. Consistent with the hypothesis, the quadruple mutant grew on glucose as the sole carbon source. The growth on glucose, which was accompanied by glycerol production, was inhibited at high-glucose concentrations. This inhibition was attributed to glucose repression of respiratory enzymes as, in the quadruple mutant, respiratory pyruvate dissimilation is essential for ATP synthesis and growth. Serial transfer of the quadruple mutant on high-glucose media yielded a spontaneous mutant with much higher specific growth rates in high-glucose media (up to 0.10 h−1at 100 g of glucose · liter−1). In aerated batch cultures grown on 400 g of glucose · liter−1, this engineeredS. cerevisiaestrain produced over 200 g of glycerol · liter−1, corresponding to a molar yield of glycerol on glucose close to unity.
Relationship between IS901in theMycobacterium aviumComplex Strains Isolated from Birds, Animals, Humans, and the Environment and Virulence for Poultry
Authors: Pavlik Ivo , Svastova Petra , Bartl Jiri , Dvorska Lenka , Rychlik Ivan 
Published: July 2002

ABSTRACTA total of 738 strains ofMycobacterium aviumcomplex (MAC) were examined in biological experiments on poultry by use of PCR methods with primers for detection of the insertion sequence IS901. Serotype strains of MAC from all known 28 serotypes were examined. Further strains were isolated from human immunodeficiency virus (HIV)-negative and HIV-positive patients, 6 animal species, 17 bird species, and the environment. Of 165 strains virulent for poultry, characterized by generalized tuberculosis, 164 strains contained IS901, a result which is statistically highly significant (P, 0.01). The remaining 573 strains were nonvirulent; however, IS901was present in 24 strains. From among 20 strains of serotypes 1, 2, and 3, IS901was found in 15 strains, only 5 of which were virulent for poultry. The remaining 111 strains, of serotypes 4 to 28, were nonvirulent and did not incorporate IS901. None of the 152 strains isolated from humans was virulent for poultry, including 12 strains which were IS901positive.