bluuebunny/crossref_metadata_2025 huggingface dataset:
Molecular Relationship between Two Groups of the Genus
Leptospirillum
and the Finding that
Leptospirillum ferriphilum
sp. nov. Dominates South African Commercial Biooxidation Tanks That Operate at 40°C
Authors: Coram Nicolette J. , Rawlings Douglas E.
Published: February 2003

Iron-oxidizing bacteria belonging to the genus
Leptospirillum
are of great importance in continuous-flow commercial biooxidation reactors, used for extracting metals from minerals, that operate at 40°C or less. They also form part of the microbial community responsible for the generation of acid mine drainage. More than 16 isolates of leptospirilla were included in this study, and they were clearly divisible into two major groups. Group I leptospirilla had G+C moles percent ratios within the range 49 to 52% and had three copies of
rrn
genes, and based on 16S rRNA sequence data, these isolates clustered together with the
Leptospirillum ferrooxidans
type strain (DSM2705 or L15). Group II leptospirilla had G+C moles percent ratios of 55 to 58% and had two copies of
rrn
genes, and based on 16S rRNA sequence data, they form a separate cluster. Genome DNA-DNA hybridization experiments indicated that three similarity subgroups were present among the leptospirilla tested, with two DNA-DNA hybridization similarity subgroups found within group I. The two groups could also be distinguished based on the sizes of their 16S-23S rRNA gene spacer regions. We propose that the group II leptospirilla should be recognized as a separate species with the name
Leptospirillum ferriphilum
sp. nov. Members of the two species can be rapidly distinguished from each other by amplification of their 16S rRNA genes and by carrying out restriction enzyme digests of the products. Several, but not all, isolates of the group II leptospirilla, but none from group I (
L. ferrooxidans
), were capable of growth at 45°C. All the leptospirilla isolated from commercial biooxidation tanks in South Africa were from group II.
Calnexin Overexpression Increases Manganese Peroxidase Production in
Aspergillus niger
Authors: Conesa Ana , Jeenes David , Archer David B. , van den Hondel Cees A. M. J. J. , Punt Peter J.
Published: February 2003

Heme-containing peroxidases from white rot basidiomycetes, in contrast to most proteins of fungal origin, are poorly produced in industrial filamentous fungal strains. Factors limiting peroxidase production are believed to operate at the posttranslational level. In particular, insufficient availability of the prosthetic group which is required for peroxidase biosynthesis has been proposed to be an important bottleneck. In this work, we analyzed the role of two components of the secretion pathway, the chaperones calnexin and binding protein (BiP), in the production of a fungal peroxidase. Expression of the
Phanerochaete chrysosporium
manganese peroxidase (MnP) in
Aspergillus niger
resulted in an increase in the expression level of the
clxA
and
bipA
genes. In a heme-supplemented medium, where MnP was shown to be overproduced to higher levels, induction of
clxA
and
bipA
was also higher. Overexpression of these two chaperones in an MnP-producing strain was analyzed for its effect on MnP production. Whereas
bipA
overexpression seriously reduced MnP production, overexpression of calnexin resulted in a four- to fivefold increase in the extracellular MnP levels. However, when additional heme was provided in the culture medium, calnexin overexpression had no synergistic effect on MnP production. The possible function of these two chaperones in MnP maturation and production is discussed.
Identical Ring Cleavage Products during Anaerobic Degradation of Naphthalene, 2-Methylnaphthalene, and Tetralin Indicate a New Metabolic Pathway
Authors: Annweiler Eva , Michaelis Walter , Meckenstock Rainer U.
Published: February 2003

Anaerobic degradation of naphthalene, 2-methylnaphthalene, and tetralin (1,2,3,4-tetrahydronaphthalene) was investigated with a sulfate-reducing enrichment culture obtained from a contaminated aquifer. Degradation studies with tetralin revealed 5,6,7,8-tetrahydro-2-naphthoic acid as a major metabolite indicating activation by addition of a C
1
unit to tetralin, comparable to the formation of 2-naphthoic acid in anaerobic naphthalene degradation. The activation reaction was specific for the aromatic ring of tetralin; 1,2,3,4-tetrahydro-2-naphthoic acid was not detected. The reduced 2-naphthoic acid derivatives tetrahydro-, octahydro-, and decahydro-2-naphthoic acid were identified consistently in supernatants of cultures grown with either naphthalene, 2-methylnaphthalene, or tetralin. In addition, two common ring cleavage products were identified. Gas chromatography-mass spectrometry (GC-MS) and high-resolution GC-MS analyses revealed a compound with a cyclohexane ring and two carboxylic acid side chains as one of the first ring cleavage products. The elemental composition was C
11
H
16
O
4
(C
11
H
16
O
4
-diacid), indicating that all carbon atoms of the precursor 2-naphthoic acid structure were preserved in this ring cleavage product. According to the mass spectrum, the side chains could be either an acetic acid and a propenic acid, or a carboxy group and a butenic acid side chain. A further ring cleavage product was identified as 2-carboxycyclohexylacetic acid and was assumed to be formed by
β
-oxidation of one of the side chains of the C
11
H
16
O
4
-diacid. Stable isotope-labeling growth experiments with either
13
C-labeled naphthalene, per-deuterated naphthalene-
d
8
, or a
13
C-bicarbonate-buffered medium showed that the ring cleavage products derived from the introduced carbon source naphthalene. The series of identified metabolites suggests that anaerobic degradation of naphthalenes proceeds via reduction of the aromatic ring system of 2-naphthoic acid to initiate ring cleavage in analogy to the benzoyl-coenzyme A pathway for monoaromatic hydrocarbons. Our findings provide strong indications that further degradation goes through saturated compounds with a cyclohexane ring structure and not through monoaromatic compounds. A metabolic pathway for anaerobic degradation of bicyclic aromatic hydrocarbons with 2-naphthoic acid as the central intermediate is proposed.
Biotransformation and Bioconcentration of Steroid Estrogens by
Chlorella vulgaris
Authors: Lai K. M. , Scrimshaw M. D. , Lester J. N.
Published: February 2003

The biotransformation and bioconcentration of natural and synthetic steroid estrogens by
Chlorella vulgaris
were investigated by using batch-shaking experiments with incubation for 48 h in the light or dark. Estradiol and estrone were interconvertible in both light and dark conditions; however, this biotransformation showed a preference for estrone. In the light, 50% estradiol was further metabolized to an unknown product. Apart from biotransformation, estrone, as well as hydroxyestrone, estriol, and ethinylestradiol, was relatively stable in the algal culture, whereas estradiol valerate was hydrolyzed to estradiol and then to estrone within 3 h of incubation. All of the tested estrogens exhibited a degree of partitioning to
C. vulgaris
; however, the concentrations of estriol, hydroxyestrone, ethinylestradiol, and estradiol valerate were always below the quantification limits. For estradiol and estrone, the partitioning of these estrogens in the algal extracts to the filtrates was <6% of the total amount present. The average concentration factor for estrone was ca. 27; however, the concentration factor for estradiol was not reported since no equilibrium was reached between the aqueous solution and that within the cells due to continuing biotransformation.
Highly Different Levels of Natural Transformation Are Associated with Genomic Subgroups within a Local Population of
Pseudomonas stutzeri
from Soil
Authors: Sikorski Johannes , Teschner Nicole , Wackernagel Wilfried
Published: February 2003

A highly sensitive and specific PCR-based method of monitoring 16S rRNA genes of
Pseudomonas stutzeri
was developed for searching
P. stutzeri
DNA in environmental samples. This monitoring was combined with a reliable and sensitive method for isolating
P. stutzeri
colony formers from soil and sediment, depending on their utilization of ethylene glycol, starch, and maltose. With these techniques,
P. stutzeri
populations (
n
= 2 to 170) were obtained from five of six sites giving positive PCR signals (including three marine sediment and two soil samples). The phylogenetic positions of isolates from the five sites, based on their 16S ribosomal DNA sequences, indicated that the environmental isolates were affiliated with different genomovars of
P. stutzeri
. Using the broad-host-range plasmid pNS1 with kanamycin and gentamicin resistance determinants as the transforming DNA, naturally transformable strains were identified among the isolates from all sites. For one population from soil, the genetic relationship of the 120 members was determined by randomly amplified polymorphic DNA-PCR with three PCR primers. Among the population members which are taxonomically closely related as determined by 16S sequence comparisons of group representatives, a rather high genetic diversity and a characteristic clustering into subgroups were found. Remarkably, within the population, nontransformability and different levels of transformability (a frequency between about 10
−9
and 10
−4
per cell) were often associated with distinct genetic subgroups. It is concluded that transformability is widespread among environmental
P. stutzeri
strains and that its specific level is a heritable trait that may vary strongly within a local population.
Enzymatic Manganese(II) Oxidation by Metabolically Dormant Spores of Diverse
Bacillus
Species
Authors: Francis Chris A. , Tebo Bradley M.
Published: February 2003

Bacterial spores are renowned for their longevity, ubiquity, and resistance to environmental insults, but virtually nothing is known regarding whether these metabolically dormant structures impact their surrounding chemical environments. In the present study, a number of spore-forming bacteria that produce dormant spores which enzymatically oxidize soluble Mn(II) to insoluble Mn(IV) oxides were isolated from coastal marine sediments. The highly charged and reactive surfaces of biogenic metal oxides dramatically influence the oxidation and sorption of both trace metals and organics in the environment. Prior to this study, the only known Mn(II)-oxidizing sporeformer was the marine
Bacillus
sp. strain SG-1, an extensively studied bacterium in which Mn(II) oxidation is believed to be catalyzed by a multicopper oxidase, MnxG. Phylogenetic analysis based on 16S rRNA and
mnxG
sequences obtained from 15 different Mn(II)-oxidizing sporeformers (including SG-1) revealed extensive diversity within the genus
Bacillus
, with organisms falling into several distinct clusters and lineages. In addition, active Mn(II)-oxidizing proteins of various sizes, as observed in sodium dodecyl sulfate-polyacrylamide electrophoresis gels, were recovered from the outer layers of purified dormant spores of the isolates. These are the first active Mn(II)-oxidizing enzymes identified in spores or gram-positive bacteria. Although extremely resistant to denaturation, the activities of these enzymes were inhibited by azide and
o
-phenanthroline, consistent with the involvement of multicopper oxidases. Overall, these studies suggest that the commonly held view that bacterial spores are merely inactive structures in the environment should be revised.
Transcriptional and Proteomic Analysis of a Ferric Uptake Regulator (Fur) Mutant of
Shewanella oneidensis
: Possible Involvement of Fur in Energy Metabolism, Transcriptional Regulation, and Oxidative Stress
Authors: Thompson Dorothea K. , Beliaev Alexander S. , Giometti Carol S. , Tollaksen Sandra L. , Khare Tripti , Lies Douglas P. , Nealson Kenneth H. , Lim Hanjo , Yates John , Brandt Craig C. , Tiedje James M. , Zhou Jizhong
Published: February 2003

The iron-directed, coordinate regulation of genes depends on the
fur
(ferric uptake regulator) gene product, which acts as an iron-responsive, transcriptional repressor protein. To investigate the biological function of a
fur
homolog in the dissimilatory metal-reducing bacterium
Shewanella oneidensis
MR-1, a
fur
knockout strain (FUR1) was generated by suicide plasmid integration into this gene and characterized using phenotype assays, DNA microarrays containing 691 arrayed genes, and two-dimensional polyacrylamide gel electrophoresis. Physiological studies indicated that FUR1 was similar to the wild-type strain when they were compared for anaerobic growth and reduction of various electron acceptors. Transcription profiling, however, revealed that genes with predicted functions in electron transport, energy metabolism, transcriptional regulation, and oxidative stress protection were either repressed (
ccoNQ
,
etrA
, cytochrome
b
and
c
maturation-encoding genes,
qor
,
yiaY
,
sodB
,
rpoH
,
phoB
, and
chvI
) or induced (
yggW
,
pdhC
,
prpC
,
aceE
,
fdhD
, and
ppc
) in the
fur
mutant. Disruption of
fur
also resulted in derepression of genes (
hxuC
,
alcC
,
fhuA
,
hemR
,
irgA
, and
ompW
) putatively involved in iron uptake. This agreed with the finding that the
fur
mutant produced threefold-higher levels of siderophore than the wild-type strain under conditions of sufficient iron. Analysis of a subset of the FUR1 proteome (i.e., primarily soluble cytoplasmic and periplasmic proteins) indicated that 11 major protein species reproducibly showed significant (
P
< 0.05) differences in abundance relative to the wild type. Protein identification using mass spectrometry indicated that the expression of two of these proteins (SodB and AlcC) correlated with the microarray data. These results suggest a possible regulatory role of
S. oneidensis
MR-1 Fur in energy metabolism that extends the traditional model of Fur as a negative regulator of iron acquisition systems.
Characterization and Description of
Anaeromyxobacter dehalogenans
gen. nov., sp. nov., an Aryl-Halorespiring Facultative Anaerobic Myxobacterium
Authors: Sanford Robert A. , Cole James R. , Tiedje James M.
Published: February 2003

Five strains were isolated which form a physiologically and phylogenetically coherent group of chlororespiring microorganisms and represent the first taxon in the
Myxobacteria
capable of anaerobic growth. The strains were enriched and isolated from various soils and sediments based on their ability to grow using acetate as an electron donor and 2-chlorophenol (2-CPh) as an electron acceptor. They are slender gram-negative rods with a bright red pigmentation that exhibit gliding motility and form spore-like structures. These unique chlororespiring myxobacteria also grow with 2,6-dichlorophenol, 2,5-dichlorophenol, 2-bromophenol, nitrate, fumarate, and oxygen as terminal electron acceptors, with optimal growth occurring at low concentrations (<1 mM) of electron acceptor. 2-CPh is reduced by all strains as an electron acceptor in preference to nitrate, which is reduced to ammonium. Acetate, H
2
, succinate, pyruvate, formate, and lactate were used as electron donors. None of the strains grew by fermentation. The 16S ribosomal DNA (rDNA) sequences of the five strains form a coherent cluster deeply branching within the family
Myxococcaceae
within the class
Myxobacteria
and are mostly closely associated with the
Myxococcus
subgroup. With the exception of anaerobic growth and lack of a characteristic fruiting body, these strains closely resemble previously characterized myxobacteria and therefore should be considered part of the
Myxococcus
subgroup. The anaerobic growth and 9.0% difference in 16S rDNA sequence from those of other myxobacterial genera are sufficient to place these strains in a new genus and species designated
Anaeromyxobacter dehalogenans
. The type strain is 2CP-1 (ATCC BAA-258).
Assessment of Fluorochromes for Two-Photon Laser Scanning Microscopy of Biofilms
Authors: Neu Thomas R. , Kuhlicke Ute , Lawrence John R.
Published: February 2003

A major limitation for the use of two-proton laser scanning microscopy (2P-LSM) in biofilm and other studies is the lack of a thorough understanding of the excitation-emission responses of potential fluorochromes. In order to use 2P-LSM, the utility of various fluorochromes and probes specific for a range of biofilm constituents must be evaluated. The fluorochromes tested in this study included classical nucleic acid-specific stains, such as acridine orange (AO) and 4",6"-diamidino-2-phenylindole (DAPI), as well as recently developed stains. In addition, stains specific for biofilm extracellular polymeric substances (EPS matrix components) were tested. Two-photon excitation with a Ti/Sapphire laser was carried out at wavelengths from 760 to 900 nm in 10-nm steps. It was found that autofluorescence of phototrophic organisms (cyanobacteria and green algae) resulted in strong signals for the entire excitation range. In addition, the coenzyme F420-related autofluorescence of methanogenic bacteria could be used to obtain images of dense aggregates (excitation wavelength, 780 nm). The intensities of the emission signals for the nucleic acid-specific fluorochromes varied. For example, the intensities were similar for excitation wavelengths ranging from 780 to 900 nm for AO but were higher for a narrower range, 780 to 810 nm, for DAPI. In selective excitation, fading, multiple staining, and combined single-photon-two-photon studies, the recently developed nucleic acid-specific fluorochromes proved to be more suitable regardless of whether they are intended for living or fixed samples. Probes specific for proteins and glycoconjugates allowed two-photon imaging of polymeric biofilm constituents. Selective excitation-emission was observed for Calcofluor White M2R (780 to 800 nm) and SyproOrange (880 to 900 nm). In addition, fluor-conjugated concanavalin A lectins were examined and provided acceptable two-photon emission signals at wavelengths ranging from 780 to 800 nm. Finally, CellTracker, a fluorochrome suitable for long-term labeling of microbial eucaryote cells, was found to give strong emission at wavelengths ranging from 770 to 810 nm. If fluorochromes have the same two-photon excitation cross section, they are suitable for multiple staining and multichannel recording. Generally, if an appropriate excitation wavelength and fluorochrome were used, it was possible to obtain more highly resolved images for thick biofilm samples with two-photon laser microscopy than with conventional single-photon laser microscopy. Due to its potential for higher resolution in light-scattering tissue-like material, such as biofilms, and extremely localized excitation, 2P-LSM is a valuable addition to conventional confocal laser scanning microscopy with single-photon excitation. However, further development of the method and basic research are necessary to take full advantage of nonlinear excitation in studies of interfacial microbial ecology.
Production and Targeting of theBrucella abortusAntigen L7/L12 inLactococcus lactis: a First Step towards Food-Grade Live Vaccines against Brucellosis
Authors: Ribeiro Luciana A. , Azevedo Vasco , Le Loir Yves , Oliveira Sergio C. , Dieye Yakhya , Piard Jean-Christophe , Gruss Alexandra , Langella Philippe
Published: February 2003

Brucella abortusis a facultative intracellular gram-negative bacterial pathogen that infects humans and animals by entry mainly through the digestive tract.B. abortuscauses abortion in pregnant cattle and undulant fever in humans. The immunogenicB. abortusribosomal protein L7/L12 is a promising candidate antigen for the development of oral live vaccines against brucellosis, using food-grade lactic acid bacteria (LAB) as a carrier. TheL7/L12gene was expressed inLactococcus lactis, the model LAB, under the nisin-inducible promoter. Using different signals, L7/L12 was produced in cytoplasmic, cell-wall-anchored, and secreted forms. Cytoplasmic production of L7/L12 gave a low yield, estimated at 0.5 mg/liter. Interestingly, a secretable form of this normally cytoplasmic protein via fusion with a signal peptide resulted in increased yield of L7/L12 to 3 mg/liter; secretion efficiency (SE) was 35%. A fusion between the mature moiety of the staphylococcal nuclease (Nuc) and L7/L12 further increased yield to 8 mg/liter. Fusion with a synthetic propeptide (LEISSTCDA) previously described as an enhancer for heterologous protein secretion inL. lactis(Y. Le Loir, A. Gruss, S. D. Ehrlich, and P. Langella, J. Bacteriol. 180:1895-1903, 1998) raised the yield to 8 mg/liter and SE to 50%. A surface-anchored L7/L12 form inL. lactiswas obtained by fusing the cell wall anchor ofStreptococcus pyogenesM6 protein to the C-terminal end of L7/L12. The fusions described allow the production and targeting of L7/L12 in three different locations inL. lactis. This is the first example of aB. abortusantigen produced in a food-grade bacterium and opens new perspectives for alternative vaccine strategies against brucellosis.
Production of Human Papillomavirus Type 16 E7 Protein in
Lactococcus lactis
Authors: Bermúdez-Humarán L. G. , Langella P. , Miyoshi A. , Gruss A. , Guerra R. Tamez , Montes de Oca-Luna R. , Le Loir Y.
Published: February 2003

The E7 protein of human papillomavirus type 16 was produced in
Lactococcus lactis.
Secretion allowed higher production yields than cytoplasmic production. In stationary phase, amounts of cytoplasmic E7 were reduced, while amounts of secreted E7 increased, suggesting a phase-dependent intracellular proteolysis. Fusion of E7 to the staphylococcal nuclease, a stable protein, resulted in a highly stable cytoplasmic protein. This work provides new candidates for development of viral screening systems and for oral vaccine against cervical cancer.
Heavy Metal Resistance Patterns of
Frankia
Strains
Authors: Richards Joel W. , Krumholz Glenn D. , Chval Matthew S. , Tisa Louis S.
Published: February 2003

The sensitivity of 12
Frankia
strains to heavy metals was determined by a growth inhibition assay. In general, all of the strains were sensitive to low concentrations (<0.5 mM) of Ag
1+
, AsO
2
1−
, Cd
2+
, SbO
2
1−
, and Ni
2+
, but most of the strains were less sensitive to Pb
2+
(6 to 8 mM), CrO
4
2−
(1.0 to 1.75 mM), AsO
4
3−
(>50 mM), and SeO
2
2−
(1.5 to 3.5 mM). While most strains were sensitive to 0.1 mM Cu
2+
, four strains were resistant to elevated levels of Cu
2+
(2 to 5 mM and concentrations as high as 20 mM). The mechanism of SeO
2
2−
resistance seems to involve reduction of the selenite oxyanion to insoluble elemental selenium, whereas Pb
2+
resistance and Cu
2+
resistance may involve sequestration or binding mechanisms. Indications of the resistance mechanisms for the other heavy metals were not as clear.
Natural Communities of Novel Archaea and Bacteria with a String-of-Pearls-Like Morphology: Molecular Analysis of the Bacterial Partners
Authors: Moissl Christine , Rudolph Christian , Huber Robert
Published: February 2003

A recently discovered bacterial/archaeal association, growing in a string-of-pearls-like structure, thrives in the cold (∼10°C) sulfidic marsh water of the Sippenauer Moor near Regensburg, Bavaria, Germany. It forms characteristic, macroscopically visible globules, the pearls, containing microcolonies of novel euryarchaeota, which are surrounded by mainly filamentous bacteria (C. Rudolph, G. Wanner, and R. Huber, Appl. Environ. Microbiol. 67:2336-2344, 2001). Single pearls in series are connected by white threads. Here we report the first detailed molecular investigations of the taxonomic affiliation of the bacteria contributing to the strings of pearls. Phylogenetic analysis showed the dominance of a single phylotype (clone sipK4) within single pearls most closely related to
Thiothrix unzii
. The presence of
Thiothrix
sipK4 as a major constituent of single pearls and of the pearl-connecting white threads was verified by fluorescence in situ hybridization.
Streptococcus thermophilus
Is Able To Produce a β-Galactosidase Active during Its Transit in the Digestive Tract of Germ-Free Mice
Authors: Drouault Sophie , Anba Jamila , Corthier Gérard
Published: February 2003

This work presents data on the application of a bacterial luciferase used to monitor gene expression of
Streptococcus thermophilus
in the digestive tract. The main result is that the bacterium was able to produce an active β-galactosidase in the digestive tract, although it did not multiply during its transit. This production was enhanced when lactose (the inducer) was added to the diet.
Genetic and Immunochemical Characterization of Thiocyanate-Degrading Bacteria in Lake Water
Authors: Yamasaki Manabu , Matsushita Yasuhiko , Namura Motonobu , Nyunoya Hiroshi , Katayama Yoko
Published: February 2003

Natural aquatic and soil samples were screened for the presence of thiocyanate-degrading bacteria. Using thiocyanate supplementation, we established an enrichment culture containing such bacteria from lake water. The dominant bacteria had the
scnC-LS5
gene encoding thiocyanate hydrolase, which was closely related to the enzyme found previously in
Thiobacillus thioparus
THI115 isolated from activated sludge.
Two Forms of NAD-Dependent
d
-Mandelate Dehydrogenase in
Enterococcus faecalis
IAM 10071
Authors: Tamura Yusuke , Ohkubo Atsuko , Iwai Saho , Wada Yoichiro , Shinoda Takeshi , Arai Kazuhito , Mineki Shigeru , Iida Mitsugi , Taguchi Hayao
Published: February 2003

Two forms of NAD-dependent
d
-mandelate dehydrogenase (
d
-ManDHs) were purified from
Enterococcus faecalis
IAM 10071. While these two enzymes consistently exhibited high activity toward large 2-ketoacid substrates that were branched at the C3 or C4 position, they gave distinctly different

K
m

and
V
max
values for these substrates and had distinct molecular weights by gel electrophoresis and gel filtration.
Rapid Two-Step Procedure for Large-Scale Purification of Pediocin-Like Bacteriocins and Other Cationic Antimicrobial Peptides from Complex Culture Medium
Authors: Uteng Marianne , Hauge Håvard Hildeng , Brondz Ilia , Nissen-Meyer Jon , Fimland Gunnar
Published: February 2003

A rapid and simple two-step procedure suitable for both small- and large-scale purification of pediocin-like bacteriocins and other cationic peptides has been developed. In the first step, the bacterial culture was applied directly on a cation-exchange column (1-ml cation exchanger per 100-ml cell culture). Bacteria and anionic compounds passed through the column, and cationic bacteriocins were subsequently eluted with 1 M NaCl. In the second step, the bacteriocin fraction was applied on a low-pressure, reverse-phase column and the bacteriocins were detected as major optical density peaks upon elution with propanol. More than 80% of the activity that was initially in the culture supernatant was recovered in both purification steps, and the final bacteriocin preparation was more than 90% pure as judged by analytical reverse-phase chromatography and capillary electrophoresis.
Coexistence of Two Distinct Copies of Naphthalene Degradation Genes in
Pseudomonas
Strains Isolated from the Western Mediterranean Region
Authors: Ferrero Marcela , Llobet-Brossa Enrique , Lalucat Jorge , García-Valdés Elena , Rosselló-Mora Ramón , Bosch Rafael
Published: February 2003

We analyzed the occurrence of the naphthalene degradation upper-pathway (
nah
) genes in the western Mediterranean region. The amplification, restriction, and sequence analysis of internal fragments for several
nah
genes (
nahAc
,
nahB
,
nahC
, and
nahE
) from naphthalene-degrading strains isolated from this geographical area proved the coexistence of two distinct sets of
nah
genes.
Microbial Growth Inside Insulated External Walls as an Indoor Air Biocontamination Source
Authors: Pessi Anna-Mari , Suonketo Jommi , Pentti Matti , Kurkilahti Mika , Peltola Kaija , Rantio-Lehtimäki Auli
Published: February 2003

The association between moisture-related microbial growth (mesophilic fungi and bacteria) within insulated exterior walls and microbial concentrations in the indoor air was studied. The studied apartment buildings with precast concrete external walls were situated in a subarctic zone. Actinomycetes in the insulation layer were found to have increased concentrations in the indoor air. The moisture content of the indoor air significantly affected all measurable airborne concentrations.
Chemotaxis of
Ralstonia eutropha
JMP134(pJP4) to the Herbicide 2,4-Dichlorophenoxyacetate
Authors: Hawkins Andrew C. , Harwood Caroline S.
Published: February 2003

Ralstonia eutropha
JMP134(pJP4) and several other species of motile bacteria can degrade the herbicide 2,4-dichlorophenoxyacetate (2,4-D), but it was not known if bacteria could sense and swim towards 2,4-D by the process of chemotaxis. Wild-type
R. eutropha
cells were chemotactically attracted to 2,4-D in swarm plate assays and qualitative capillary assays. The chemotactic response was induced by growth with 2,4-D and depended on the presence of the catabolic plasmid pJP4, which harbors the
tfd
genes for 2,4-D degradation. The
tfd
cluster also encodes a permease for 2,4-D named TfdK. A
tfdK
mutant was not chemotactic to 2,4-D, even though it grew at wild-type rates on 2,4-D.
Isolation and Characterization of Bacteriophages from Fermenting Sauerkraut
Authors: Yoon S. S. , Barrangou-Poueys R. , Breidt F. , Klaenhammer T. R. , Fleming H. P.
Published: February 2003

This paper presents the first report of bacteriophage isolated from commercial vegetable fermentations. Nine phages were isolated from two 90-ton commercial sauerkraut fermentations. These phages were active against fermentation isolates and selected
Leuconostoc mesenteroides
and
Lactobacillus plantarum
strains, including a starter culture. Phages were characterized as members of the
Siphoviridae
and
Myoviridae
families. All
Leuconostoc
phages reported previously, primarily of dairy origin, belonged to the
Siphoviridae
family.
Rapid Identification of Probiotic Lactobacillus Biosurfactant Proteins by ProteinChip Tandem Mass Spectrometry Tryptic Peptide Sequencing
Authors: Reid Gregor , Gan Bing Siang , She Yi-Min , Ens Werner , Weinberger Scot , Howard Jeffrey C.
Published: February 2003

A novel ProteinChip-interfaced tandem mass spectrometer was employed to identify collagen binding proteins from biosurfactant produced by
Lactobacillus fermentum
RC-14. On-chip tryptic digestion of the captured collagen binding proteins resulted in rapid sequence identification of five novel tryptic peptide sequences via collision-induced dissociation tandem mass spectrometry.
Effect of Oxidizing Disinfectants (Chlorine, Monochloramine, and Ozone) on
Helicobacter pylori
Authors: Baker Katherine H. , Hegarty John P. , Redmond Brady , Reed Nathan A. , Herson Diane S.
Published: February 2003

The susceptibility of
Helicobacter pylori
to disinfectants was compared to that of
Escherichia coli
.
H. pylori
is more resistant than
E. coli
to chlorine and ozone but not monochloramine.
H. pylori
may be able to tolerate disinfectants in distribution systems and, therefore, may be transmitted by a waterborne route.
Involvement of
glnB, glnZ
, and
glnD
Genes in the Regulation of Poly-3-Hydroxybutyrate Biosynthesis by Ammonia in
Azospirillum brasilense
Sp7
Authors: Sun Jun , Van Dommelen Anne , Van Impe Jan , Vanderleyden Jos
Published: February 2003

The role of three key nitrogen regulatory genes,
glnB
(encoding the P
II
protein),
glnZ
(encoding the P
z
protein), and
glnD
(encoding the GlnD protein), in regulation of poly-3-hydroxybutyrate (PHB) biosynthesis by ammonia in
Azospirillum brasilense
Sp7 was investigated. It was observed that
glnB glnZ
and
glnD
mutants produce substantially higher amounts of PHB than the wild type produces during the active growth phase.
glnB
and
glnZ
mutants have PHB production phenotypes similar to that of the wild type. Our results indicate that the P
II
-P
z
system is apparently involved in nitrogen-dependent regulation of PHB biosynthesis in
A. brasilense
Sp7.
Novel Clade of
Rickettsia
spp. from Leeches
Authors: Kikuchi Yoshitomo , Sameshima Shinya , Kitade Osamu , Kojima Junichi , Fukatsu Takema
Published: February 2003

Intracellular rickettsia-like structures were found in the tissues of a glossiphoniid leech,
Torix tagoi
, by transmission electron microscopy. Diagnostic PCR analysis using specific primers suggested that of the nine glossiphoniid species examined, two species,
T. tagoi
and
Hemicrepsis marginata
, harbored bacteria of the genus
Rickettsia
. A 1.5-kb eubacterial 16S rRNA gene segment obtained from each of these species was amplified by PCR, cloned, and sequenced. Phylogenetic analysis of the 16S rRNA gene demonstrated that the
Rickettsia
species found in the leeches constituted a novel clade that is distinct from the clade of arthropod-associated
Rickettsia
species. In natural populations, 97.7% (43 of 44) of
T. tagoi
leeches and 100% (9 of 9) of
H. marginata
leeches carried
Rickettsia
, suggesting that infection with
Rickettsia
is prevalent in these leeches. This is the first report of
Rickettsia
found in annelids.
Effects of ISSo
2
Insertions in Structural and Regulatory Genes of the Trimethylamine Oxide Reductase of
Shewanella oneidensis
Authors: Bordi Christophe , Iobbi-Nivol Chantal , Méjean Vincent , Patte Jean-Claude
Published: March 2003

We have isolated three
Shewanella oneidensis
mutants specifically impaired in trimethylamine oxide (TMAO) respiration. The mutations arose from insertions of an ISSo
2
element into
torA
,
torR
, and
torS
, encoding, respectively, the TMAO reductase TorA, the response regulator TorR, and the sensor TorS. Although TorA is not the sole enzyme reducing TMAO in
S. oneidensis
, growth analysis showed that it is the main respiratory TMAO reductase. Use of a plasmid-borne
torE
′-
lacZ
fusion confirmed that the TorS-TorR phosphorelay mediates TMAO induction of the
torECAD
operon.
Performance of indicators derived from abundance estimates for detecting the impact of fishing on a fish community
Authors: Trenkel Verena M , Rochet Marie-Joëlle
Published: March 2003

Population and community indicators for the impact of fishing are often estimated using abundance estimates instead of raw sampling observations. Methods are presented for testing null hypotheses of nonsignificant impacts and, where possible, for calculating the statistical power. The indicators considered concern populations (intrinsic growth rate, total mortality, exploitation rate, and a new indicator, the change in fishing mortality required to reverse population growth) and communities (k- and partial-dominance curves, a biodiversity index, size spectrum, and proportions of various population groups). The performance of these indicators is compared for the Celtic Sea groundfish community based on achieved precision, statistical power, and availability and estimation method of reference points. Among population indicators, mean length of catch was most precisely estimated and the corresponding hypothesis tests had consistently large powers. Total mortality performed reasonably well. In contrast, both the intrinsic population growth rate and the exploitation rate gave unreliable results. All tested community indicators performed similarly well. Indicators for which the direction of change caused by fishing is predictable, such as the proportion of noncommercial species or piscivores in the community, are promising indicators at the community level.
Predation on stocked Atlantic salmon (Salmo salar) fry
Authors: Henderson J Nathan , Letcher Benjamin H
Published: March 2003

We studied predatorprey interactions between juvenile Atlantic salmon (Salmo salar) and trout in three Massachusetts, U.S.A., streams and in artificial streams. We sampled stomach contents of age-1+ and older salmon and trout (Salvelinus fontinalis, Salmo trutta) following salmon fry stocking in the spring of 1997 and 1998. Between 4.3 and 48.6% of the stocked fry were consumed within the first 2 days after stocking, and total fry mortality from predation varied from 4.3 to 60.7%. No significant differences were found between stomach weights of predators ( without fry weight) that consumed fry and those that did not. Artificial stream experiments testing effects of habitat complexity and predator species on predator consumption rates revealed that consumption rates were not different between brook (S. fontinalis) and brown (S. trutta) trout (p = 0.59). Predation rate tended to decrease as the percentage of riffle habitat increased but the decrease was not significant (p = 0.22). Our results indicate that predation on stocked Atlantic salmon fry can be substantial (up to 60%), appears to be short lived (2 days), and is not related in a simple way to abiotic and biotic factors.
Semiclassical and quantum-mechanical study of the reaction mechanism for the N2 + N2+ electron transfer system
Authors: Xing Yu-Mei , Chen Lan , Zhang Chong , Cai Zun-Sheng , Zhao Xue-Zhuang
Published: March 2003

Density functional theory (DFT) calculations, including electron correlation, were carried out on the N2 + N2+ electron transfer system. Six geometries of the precursor complex were assumed and their stabilities were calculated and compared. The activation energy, the electronic transmission factor, and the electronic coupling matrix element in the electron transfer process were also calculated. The electronic transmission factor for this system was far less than unity (ca. 0.006~0.09); thus, the electron transfer reaction was considered to be diabatic in nature. Therefore, the electron transfer rate for the selected structures was calculated using semiclassical and quantum-mechanical theories. The calculated values were compared with each other and were in good agreement with the experimental value.Key words: N2 + N2+ electron transfer reaction, semiclassical and quantum-mechanical theories, electronic transmission factor, electronic coupling matrix element, B3LYP.
Outer-sphere electron transfer reactions of aqua(5,5,7,12,12,14-hexamethyl-1,4,8,11-tetraazacyclotetradecane-1-acetato) nickel(II) and (III).
Authors: Haines Robert I , Hutchings Dean R
Published: March 2003

The outer-sphere oxidation of the nickel(II) complex of the deprotonated pendant-arm macrocycle, 5,5,7,12,12,14-hexamethyl-1,4,8,11-tetraazacyclotetradecane-1-acetate, [NiL1(OH2)]+ by bis-(1,4,7-triazacyclononane)nickel(III), [Ni(tacn)2]3+ has been studied in aqueous perchlorate media. The reaction displays reversible second-order behaviour and the kinetic study reveals the forward and reverse rate constants for the reaction:

[Formula: see text]

The kinetics show the forward reaction to be acid dependent, a feature that is attributed to protonation of the acetato group of the nickel(II) complex. Using Marcus theory, the self-exchange rate for the [NiL1(OH2)]+/2+ couple has been calculated. The nickel(II/III) electron transfer is a reversible one electron process with E° = 1.04 V (vs. S.H.E.). The formation of the authentic nickel(III) product has been confirmed by esr spectroscopy. The kinetics of reduction of the [NiL1(OH2)]2+ species by Fe2+(aq) exhibits a second-order rate law, the reaction being independent of acid. Using the calculated self-exchange rate for the nickel complex, its reaction with Fe2+(aq) has been examined in terms of an inner- versus outer-sphere mechanism. Key words: nickel(III), pendant-arm macrocycles, hexaaquairon(II), outer sphere, kinetics, Marcus theory.
MONOTONICITY OF QUANTUM RELATIVE ENTROPY REVISITED
Authors: PETZ DÉNES
Published: February 2003

Monotonicity under coarse-graining is a crucial property of the quantum relative entropy. The aim of this paper is to investigate the condition of equality in the monotonicity theorem and in its consequences as the strong sub-additivity of von Neumann entropy, the Golden–Thompson trace inequality and the monotonicity of the Holevo quantitity. The relation to quantum Markov states is briefly indicated.
SELF ORGANIZATION IN THE LOW TEMPERATURE REGION OF A SPIN GLASS MODEL
Authors: TALAGRAND MICHEL
Published: February 2003

We obtain an almost complete description of the structure of the p-spin interaction model down to temperatures that decrease exponentially with p. We prove in particular the spontaneous creation of pure states, and we describe the distribution of their weights. This confirms the picture of "one step of symmetry breaking" predicted by the physicists. Similar results are obtained when a small external field is added, provided one accepts to add a lower order "generic" perturbation to the Hamiltonian.
ON BROADCASTING TIME
Authors: DIMAKOPOULOS VASSILIOS V. , DIMOPOULOS NIKITAS J.
Published: February 2003

Broadcasting is an information dissemination problem in which a particular node in a network must transmit an item of information to all the other nodes. In this work we present new lower bounds for the time needed to complete this process in arbitrary graphs. In particular we generalize a result of P. Fraigniaud and E. Lazard [Discrete Applied Mathematics, 53 (1994) 79–133] which states that if in a graph there are at least two vertices in distance equal to the diameter from the originator, then broadcasting requires time at least equal to the diameter plus one.
COMPARISON OF HEURISTICS FOR ONE-TO-ALL AND ALL-TO-ALL COMMUNICATIONS IN PARTIAL MESHES
Authors: FRAIGNIAUD PIERRE , VIAL SANDRINE
Published: February 2003

Broadcasting (one-to-all) and gossiping (all-to-all) are two major communication paradigms that were considered from both practical and theoretical points of view. Indeed, such communication patterns frequently appear in parallel programming, and therefore are included in most of the communication libraries (e.g., MPI or PVM). Also, broadcasting and gossiping times of graphs are important parameters yielding lots of fundamental results.

For most of the communication models, the corresponding decision problems are NP-complete in general. Therefore, in this paper, we consider broadcasting and gossiping heuristics. We study the performances of several heuristics applied to partial meshes, that is to connected subgraphs of the mesh. This choice of topology is motivated by the fact that a regularly connected multicomputer can be shared by many users, each of them dealing with an irregular sub-topology of the original network.

The result of our comparison is that, although they were defined for arbitrary topologies, the matching-based heuristics offer the best performances for partial meshes compared to sophisticated heuristics defined specifically for these networks (we derive a new heuristic for this class of topologies), or for graphs with [Formula: see text]-diameter. Since matching-based heuristics are simple, and do not require intensive computation, they appear to be the best candidates to solve broadcasting and gossiping problems in multi-user mesh architectures.
FAULT DIAMETER FOR SUPERCUBES
Authors: SHEU JYH-JIAN , HSU LIH-HSING
Published: February 2003

Assume that N and s are positive integers with 2s < N ≤ 2s+1. It is claimed by Auletta, Rescigno, and Scarano that the fault diameter of the supercube with N nodes, is exactly s+1 if N∉{2s+1-1, 2s+1 - 2, 2s-1+1}, and s+2 otherwise. In this paper, we will argue that the above claim is not correct. Instead, we will show that the fult diameter of the supercube with N nodes is s+2 if N ∈ {2s+1 - 2i+1|0 ≤ i ≤ s-1}.
SIMPLE OPTIMAL ALGORITHMS FOR RECTILINEAR LINK PATH AND POLYGON SEPARATION PROBLEMS
Authors: MAHESHWARI ANIL , SACK JÖRG-RÜDIGER
Published: February 2003

The link metric, defined on a constrained region R of the plane, sets the distance between a pair of points in R to equal the minimum number of line segments or links needed to construct a path in R between the point pair. The minimum rectilinear link path problem considered here is to compute a rectilinear path consisting of the minimum number of links between two points in R, when R is inside an n-sided rectilinear simple polygon. In this paper we present optimal sequential and parallel algorithms to compute a minimum rectilinear link path in a trapezoided region R. Our parallel algorithm requires O( log n) time using a total of O(n) operations. The complexity of our algorithm matches that of the algorithm of McDonald and Peters [19]. By exploiting the dual structure of the trapezoidation of R, we obtain a conceptually simple and easy to implement algorithm. As applications of our techniques we provide an optimal solution to the minimum nested polygon problem and the minimum polygon separation problem. The minimum nested polygon problem asks for finding a rectilinear polygon, with minimum number of sides, that is nested between two given rectilinear polygons one of which is contained in the other. The minimum polygon separation problem asks for computing a minimum number of orthogonal lines and line segments that separate two given non-intersecting simple rectilinear polygons. All parallel algorithms are deterministic, designed to run on the exclusive read exclusive write parallel random access machine (EREW PRAM), and are optimal.
EFFICIENT PARALLEL ALGORITHMS ON DISTANCE HEREDITARY GRAPHS
Authors: HSIEH SUN-YUAN , HO CHIN-WEN , HSU TSAN-SHENG , KO MING-TAT , CHEN GEN-HUEY
Published: February 2003

Distance hereditary graphs are graphs in which every two vertices have the same distance in every connected induced subgraph containing them. In this paper, we study properties of distance hereditary graphs from the view point of parallel computations. We present efficient parallel algorithms for finding a minimum weighted connected dominating set, a minimum weighted Steiner tree, which take O( log n) time using O(n + m) processors on CRCW PRAM, where n and m are the number of vertices and edges of a given graph, respectively. We also find a maximum weighted clique of a distance hereditary graph in O( log 2 n) time using O(n + m) processors on a CREW PRAM.
CONSTRUCTION OF TIME-RELAXED MINIMAL BROADCAST NETWORKS
Authors: DINNEEN MICHAEL J. , VENTURA JOSE A. , WILSON MARK C. , ZAKERI GOLBON
Published: February 2003

In broadcasting, or one-to-all communication, a message originally held in one node of the network must be transmitted to all the other nodes. A minimal broadcast network is a communication network that can transmit a message originated at any node to all other nodes of the network in minimum time. In this paper, we present a compound method to construct sparse, time-relaxed, minimal broadcast networks (t-mbn), in which broadcasting can be accomplished in slightly more than the minimum time. The proposed method generates a new network by connecting a subset of nodes from several copies of a t1-mbn using the structure of another t2-mbn. The objective is to construct a network as sparse as possible satisfying the desired broadcasting time constraint. Computational results illustrate the effectiveness of the proposed method.
EFFICIENT DETERMINISTIC SORTING ON THE BSP MODEL
Authors: GERBESSIOTIS ALEXANDROS V. , SINIOLAKIS CONSTANTINOS J.
Published: February 2003

We present a new algorithm for deterministic sorting on the Bulk-Synchronous Parallel (BSP) model of computation. We sort n keys using a partitioning scheme that achieves the requirements of efficiency (one-optimality) and insensitivity against initial key distribution. Although we employ sampling to realize efficiency, we give a precise worst-case estimation of the maximum imbalance which might occur. The algorithm is one-optimal for a wide range of the BSP parameters in the sense that its speedup on p processors is asymptotically (1 - o(1))p.
A CONSTANT TIME PARALLEL DETECTION OF REPETITIONS
Authors: DELACOURT EMMANUEL , MYOUPO JEAN-FREDERIC , SEME DAVID
Published: February 2003

Recently Akl and al. introduced a new model of parallel computation, called BSR (broadcasting with selective reduction) and showed that it is more powerful than any CRCW PRAM and yet requires no more resources (asymptotically) for implementation than even EREW PRAM [2,3,4]. The model allows constant time solutions to sorting, parallel prefix and other problems. In this paper, we describe constant time solution to the detection of repetitions (with overlapping) problem using the one criterion BSR model. This is the first constant time solution to this problem on any model of computation. If the problem is only to detect the existence of any repetition then n processors suffice, where n is the length of the string. If all repetitions are to be found then [Formula: see text] processors suffice in our algorithm.