bluuebunny/crossref_metadata_2025 huggingface dataset:
Identification and Characterization of Di- and Tripeptide Transporter DtpT of
Listeria monocytogenes
EGD-e
Authors: Wouters Jeroen A. , Hain Torsten , Darji Ajub , Hüfner Eric , Wemekamp-Kamphuis Henrike , Chakraborty Trinad , Abee Tjakko
Published: October 2005

Listeria monocytogenes
is a gram-positive intracellular pathogen responsible for opportunistic infections in humans and animals. Here we identified and characterized the
dtpT
gene (lmo0555) of
L. monocytogenes
EGD-e, encoding the di- and tripeptide transporter, and assessed its role in growth under various environmental conditions as well as in the virulence of
L. monocytogenes
. Uptake of the dipeptide Pro-[
14
C]Ala was mediated by the DtpT transporter and was abrogated in a Δ
dtpT
isogenic deletion mutant. The DtpT transporter was shown to be required for growth when the essential amino acids leucine and valine were supplied as peptides. The protective effect of glycine- and proline-containing peptides during growth in defined medium containing 3% NaCl was noted only in
L. monocytogenes
EGD-e, not in the Δ
dtpT
mutant strain, indicating that the DtpT transporter is involved in salt stress protection. Infection studies showed that DtpT contributes to pathogenesis in a mouse infection model but has no role in bacterial growth following infection of J774 macrophages. These studies reveal that DptT may contribute to the virulence of
L. monocytogenes
.
Vertical and Seasonal Variations of Bacterioplankton Subgroups with Different Nucleic Acid Contents: Possible Regulation by Phosphorus
Authors: Nishimura Yoko , Kim Chulgoo , Nagata Toshi
Published: October 2005

We used flow cytometry to examine seasonal variations in basin-scale distributions of bacterioplankton in Lake Biwa, Japan, a large mesotrophic freshwater lake with an oxygenated hypolimnion. The bacterial communities were divided into three subgroups: bacteria with very high nucleic acid contents (VHNA bacteria), bacteria with high nucleic acid contents (HNA bacteria), and bacteria with low nucleic acid contents (LNA bacteria). During the thermal stratification period, the relative abundance of VHNA bacteria (%VHNA) increased with depth, while the reverse trend was evident for LNA bacteria. Seasonally, the %VHNA was strongly positively correlated (
r
= 0.87;
P
< 0.001) with the concentration of dissolved inorganic phosphorus, but not with the concentration of chlorophyll
a
. The growth of VHNA bacteria was significantly enhanced by addition of phosphate or phosphate plus glucose but not by addition of glucose alone. Although the growth of VHNA and HNA bacteria generally exceeded that of LNA bacteria, our data also revealed that LNA bacteria grew faster than and were grazed as fast as VHNA bacteria in late August, when nutrient limitation was presumably severe. Based on these results, we hypothesize that in severely P-limited environments such as Lake Biwa, P limitation exerts more severe constraints on the growth of bacterial groups with higher nucleic acid contents, which allows LNA bacteria to be competitive and become an important component of the microbial loop.
Development of a Method for Markerless Genetic Exchange in
Enterococcus faecalis
and Its Use in Construction of a
srtA
Mutant
Authors: Kristich Christopher J. , Manias Dawn A. , Dunny Gary M.
Published: October 2005

Enterococcus faecalis
is a gram-positive commensal bacterium of the gastrointestinal tract and an important opportunistic pathogen. Despite the increasing clinical significance of the enterococci, genetic analysis of these organisms has thus far been limited in scope due to the lack of advanced genetic tools. To broaden the repertoire of genetic tools available for manipulation of
E.faecalis
, we investigated the use of phosphoribosyl transferases as elements of a counterselection strategy. We report here the development of a counterselectable markerless genetic exchange system based on the
upp
-encoded uracil phosphoribosyl transferase of
E. faecalis
. Whereas wild-type
E. faecalis
is sensitive to growth inhibition by the toxic base analog 5-fluorouracil (5-FU), a mutant bearing an in-frame deletion of
upp
is resistant to 5-FU. When a cloned version of
upp
was ectopically introduced into the deletion mutant, sensitivity to 5-FU growth inhibition was restored, thereby providing the basis for a two-step integration and excision strategy for the transfer of mutant alleles to the enterococcal chromosome by recombination. This method was validated by the construction of a Δ
srtA
mutant of
E. faecalis
and by the exchange of the surface protein Asc10, encoded on the pheromone-responsive conjugative plasmid pCF10, with a previously isolated mutant allele. Analysis of the Δ
srtA
mutant indicated that SrtA anchors Asc10 to the enterococcal cell wall, facilitating the pheromone-induced aggregation of
E. faecalis
cells required for high-frequency conjugative plasmid transfer in liquid matings. The system of markerless exchange reported here will facilitate detailed genetic analysis of these important pathogens.
Genetic Diversity of Small Eukaryotes in Lakes Differing by Their Trophic Status
Authors: Lefranc Marie , Thénot Aurélie , Lepère Cécile , Debroas Didier
Published: October 2005

Small eukaryotes, cells with a diameter of less than 5 μm, are fundamental components of lacustrine planktonic systems. In this study, small-eukaryote diversity was determined by sequencing cloned 18S rRNA genes in three libraries from lakes of differing trophic status in the Massif Central, France: the oligotrophic Lake Godivelle, the oligomesotrophic Lake Pavin, and the eutrophic Lake Aydat. This analysis shows that the least diversified library was in the eutrophic lake (12 operational taxonomic units [OTUs]) and the most diversified was in the oligomesotrophic lake (26 OTUs). Certain groups were present in at least two ecosystems, while the others were specific to one lake on the sampling date. Cryptophyta, Chrysophyceae, and the strictly heterotrophic eukaryotes, Ciliophora and fungi, were identified in the three libraries. Among the small eukaryotes found only in two lakes, Choanoflagellida and environmental sequences (LKM11) were not detected in the eutrophic system whereas Cercozoa were confined to the oligomesotrophic and eutrophic lakes. Three OTUs, linked to the Perkinsozoa, were detected only in the Aydat library, where they represented 60% of the clones of the library. Chlorophyta and Haptophyta lineages were represented by a single clone and were present only in Godivelle and Pavin, respectively. Of the 127 clones studied, classical pigmented organisms (autotrophs and mixotrophs) represented only a low proportion regardless of the library's origin. This study shows that the small-eukaryote community composition may differ as a function of trophic status; certain lineages could be detected only in a single ecosystem.
Effects of Dichloroethene Isomers on the Induction and Activity of Butane Monooxygenase in the Alkane-Oxidizing Bacterium “
Pseudomonas butanovora
”
Authors: Doughty D. M. , Sayavedra-Soto L. A. , Arp D. J. , Bottomley P. J.
Published: October 2005

We examined cooxidation of three different dichloroethenes (1,1-DCE, 1,2-
trans
DCE, and 1,2-
cis
DCE) by butane monooxygenase (BMO) in the butane-utilizing bacterium “
Pseudomonas butanovora
.” Different organic acids were tested as exogenous reductant sources for this process. In addition, we determined if DCEs could serve as surrogate inducers of BMO gene expression. Lactic acid supported greater rates of oxidation of the three DCEs than the other organic acids tested. The impacts of lactic acid-supported DCE oxidation on BMO activity differed among the isomers. In intact cells, 50% of BMO activity was irreversibly lost after consumption of ∼20 nmol mg protein
−1
of 1,1-DCE and 1,2-
trans
DCE in 0.5 and 5 min, respectively. In contrast, a comparable loss of activity required the oxidation of 120 nmol 1,2-
cis
DCE mg protein
−1
. Oxidation of similar amounts of each DCE isomer (∼20 nmol mg protein
−1
) produced different negative effects on lactic acid-dependent respiration. Despite 1,1-DCE being consumed 10 times faster than 1,2,-
trans
DCE, respiration declined at similar rates, suggesting that the product(s) of oxidation of 1,2-
trans
DCE was more toxic to respiration than 1,1-DCE. Lactate-grown “
P. butanovora
” did not express BMO activity but gained activity after exposure to butane, ethene, 1,2-
cis
DCE, or 1,2-
trans
DCE. The products of BMO activity, ethene oxide and 1-butanol, induced
lac
Z in a reporter strain containing
lac
Z fused to the BMO promoter, whereas butane, ethene, and 1,2-
cis
DCE did not. 1,2-
trans
DCE was unique among the BMO substrates tested in its ability to induce
lac
Z expression.
Alternative Lactose Catabolic Pathway in
Lactococcus lactis
IL1403
Authors: Aleksandrzak-Piekarczyk Tamara , Kok Jan , Renault Pierre , Bardowski Jacek
Published: October 2005

In this study, we present a glimpse of the diversity of
Lactococcus lactis
subsp.
lactis
IL1403
β
-galactosidase phenotype-negative mutants isolated by negative selection on solid media containing cellobiose or lactose and X-Gal (5-bromo-4-chloro-3-indolyl-β-
d
-galactopyranoside), and we identify several genes essential for lactose assimilation. Among these are
ccpA
(encoding catabolite control protein A),
bglS
(encoding phospho-
β
-glucosidase), and several genes from the Leloir pathway gene cluster encoding proteins presumably essential for lactose metabolism. The functions of these genes were demonstrated by their disruption and testing of the growth of resultant mutants in lactose-containing media. By examining the
ccpA
and
bglS
mutants for phospho-
β
-galactosidase activity, we showed that expression of
bglS
is not under strong control of CcpA. Moreover, this analysis revealed that although BglS is homologous to a putative phospho-
β
-glucosidase, it also exhibits phospho-
β
-galactosidase activity and is the major enzyme in
L. lactis
IL1403 involved in lactose hydrolysis.
Bioaerosol Mass Spectrometry for Rapid Detection of Individual Airborne
Mycobacterium tuberculosis
H37Ra Particles
Authors: Tobias Herbert J. , Schafer Millie P. , Pitesky Maurice , Fergenson David P. , Horn Joanne , Frank Matthias , Gard Eric E.
Published: October 2005

Single-particle laser desorption/ionization time-of-flight mass spectrometry, in the form of bioaerosol mass spectrometry (BAMS), was evaluated as a rapid detector for individual airborne, micron-sized,
Mycobacterium tuberculosis
H37Ra particles, comprised of a single cell or a small number of clumped cells. The BAMS mass spectral signatures for aerosolized
M. tuberculosis
H37Ra particles were found to be distinct from
M. smegmatis
,
Bacillus atrophaeus
, and
B. cereus
particles, using a distinct biomarker. This is the first time a potentially unique biomarker was measured in
M. tuberculosis
H37Ra on a single-cell level. In addition,
M. tuberculosis
H37Ra and
M. smegmatis
were aerosolized into a bioaerosol chamber and were sampled and analyzed using BAMS, an aerodynamic particle sizer, a viable Anderson six-stage sampler, and filter cassette samplers that permitted direct counts of cells. In a background-free environment, BAMS was able to sample and detect
M. tuberculosis
H37Ra at airborne concentrations of >1
M. tuberculosis
H37Ra-containing particles/liter of air in 20 min as determined by direct counts of filter cassette-sampled particles, and concentrations of >40
M. tuberculosis
H37Ra CFU/liter of air in 1 min as determined by using viable Andersen six-stage samplers. This is a first step toward the development of a rapid, stand-alone airborne
M. tuberculosis
particle detector for the direct detection of
M. tuberculosis
bioaerosols generated by an infectious patient. Additional instrumental development is currently under way to make BAMS useful in realistic environmental and respiratory particle backgrounds expected in tuberculosis diagnostic scenarios.
Identification of Bacteria Potentially Responsible for Oxic and Anoxic Sulfide Oxidation in Biofilters of a Recirculating Mariculture System
Authors: Cytryn Eddie , van Rijn Jaap , Schramm Andreas , Gieseke Armin , de Beer Dirk , Minz Dror
Published: October 2005

Bacteria presumably involved in oxygen- or nitrate-dependent sulfide oxidation in the biofilters of a recirculating marine aquaculture system were identified using a new application of reverse transcription-PCR denaturing gradient gel electrophoresis (DGGE) analysis termed differential-transcription (DT)-DGGE. Biofilter samples were incubated in various concentrations of sulfide or thiosulfate (0 to 5 mM) with either oxygen or nitrate as the sole electron acceptor. Before and after short-term incubations (10 to 20 h), total DNA and RNA were extracted, and a 550-bp fragment of the 16S rRNA genes was PCR amplified either directly or after reverse transcription. DGGE analysis of DNA showed no significant change of the original microbial consortia upon incubation. In contrast, DGGE of cDNA revealed several phylotypes whose relative band intensities markedly increased or decreased in response to certain incubation conditions, indicating enhanced or suppressed rRNA transcription and thus implying metabolic activity under these conditions. Specifically, species of the gammaproteobacterial genus
Thiomicrospira
and phylotypes related to symbiotic sulfide oxidizers could be linked to oxygen-dependent sulfide oxidation, while members of the
Rhodobacteraceae
(genera
Roseobacter
,
Rhodobacter
, and
Rhodobium
) were putatively active in anoxic, nitrate-dependent sulfide oxidation. For all these organisms, the physiology of their closest cultured relatives matches their DT-DGGE-inferred function. In addition, higher band intensities following exposure to 5 mM sulfide and nitrate were observed for
Thauera-
,
Hydrogenophaga-
, and
Dethiosulfovibrio-
like phylotypes. For these genera, nitrate-dependent sulfide oxidation has not been documented previously and therefore DT-DGGE might indicate a higher relative tolerance to high sulfide concentrations than that of other community members. We anticipate that DT-DGGE will be of general use in tracing functionally equivalent yet phylogenetically diverse microbial populations in nature.
Correlation between Anammox Activity and Microscale Distribution of Nitrite in a Subtropical Mangrove Sediment
Authors: Meyer Rikke Louise , Risgaard-Petersen Nils , Allen Diane Elizabeth
Published: October 2005

The distribution of anaerobic ammonium oxidation (anammox) in nature has been addressed by only a few environmental studies, and our understanding of how anammox bacteria compete for substrates in natural environments is therefore limited. In this study, we measure the potential anammox rates in sediment from four locations in a subtropical tidal river system. Porewater profiles of NO
x
−
(NO
2
−
plus NO
3
−
) and NO
2
−
were measured with microscale biosensors, and the availability of NO
2
−
was compared with the potential for anammox activity. The potential rate of anammox increased with increasing distance from the mouth of the river and correlated strongly with the production of nitrite in the sediment and with the average concentration or total pool of nitrite in the suboxic sediment layer. Nitrite accumulated both from nitrification and from NO
x
−
reduction, though NO
x
−
reduction was shown to have the greatest impact on the availability of nitrite in the suboxic sediment layer. This finding suggests that denitrification, though using NO
2
−
as a substrate, also provides a substrate for the anammox process, which has been suggested in previous studies where microscale NO
2
−
profiles were not measured.
Patterns ofCryptosporidiumOocyst Shedding by Eastern Grey Kangaroos Inhabiting an Australian Watershed
Authors: Power Michelle L. , Sangster Nicholas C. , Slade Martin B. , Veal Duncan A.
Published: October 2005

The occurrence ofCryptosporidiumoocysts in feces from a population of wild eastern grey kangaroos inhabiting a protected watershed in Sydney, Australia, was investigated. Over a 2-year period,Cryptosporidiumoocysts were detected in 239 of the 3,557 (6.7%) eastern grey kangaroo fecal samples tested by using a combined immunomagnetic separation and flow cytometric technique. The prevalence ofCryptosporidiumin this host population was estimated to range from 0.32% to 28.5%, with peaks occurring during the autumn months. Oocyst shedding intensity ranged from below 20 oocysts/g feces to 2.0 × 106oocysts/g feces, and shedding did not appear to be associated with diarrhea. Although morphologically similar to the human-infectiveCryptosporidium hominisand theCryptosporidium parvum“bovine” genotype oocysts, the oocysts isolated from kangaroo feces were identified as theCryptosporidium“marsupial” genotype I or “marsupial” genotype II. Kangaroos are the predominant large mammal inhabiting Australian watersheds and are potentially a significant source ofCryptosporidiumcontamination of drinking water reservoirs. However, this host population was predominantly shedding the marsupial-derived genotypes, which to date have been identified only in marsupial host species.
Phylum- and Class-Specific PCR Primers for General Microbial Community Analysis
Authors: Blackwood Christopher B. , Oaks Adam , Buyer Jeffrey S.
Published: October 2005

Amplification of a particular DNA fragment from a mixture of organisms by PCR is a common first step in methods of examining microbial community structure. The use of group-specific primers in community DNA profiling applications can provide enhanced sensitivity and phylogenetic detail compared to domain-specific primers. Other uses for group-specific primers include quantitative PCR and library screening. The purpose of the present study was to develop several primer sets targeting commonly occurring and important groups. Primers specific for the 16S ribosomal sequences of
Alphaproteobacteria
,
Betaproteobacteria
,
Bacilli
,
Actinobacteria
, and
Planctomycetes
and for parts of both the 18S ribosomal sequence and the internal transcribed spacer region of
Basidiomycota
were examined. Primers were tested by comparison to sequences in the ARB 2003 database, and chosen primers were further tested by cloning and sequencing from soil community DNA. Eighty-five to 100% of the sequences obtained from clone libraries were found to be placed with the groups intended as targets, demonstrating the specificity of the primers under field conditions. It will be important to reevaluate primers over time because of the continual growth of sequence databases and revision of microbial taxonomy.
Analysis of Genes Involved in Arsenic Resistance in
Corynebacterium glutamicum
ATCC 13032
Authors: Ordóñez Efrén , Letek Michal , Valbuena Noelia , Gil José A. , Mateos Luis M.
Published: October 2005

Corynebacterium glutamicum
is able to grow in media containing up to 12 mM arsenite and 500 mM arsenate and is one of the most arsenic-resistant microorganisms described to date. Two operons (
ars1
and
ars2
) involved in arsenate and arsenite resistance have been identified in the complete genome sequence of
Corynebacterium glutamicum
. The operons
ars1
and
ars2
are located some distance from each other in the bacterial chromosome, but they are both composed of genes encoding a regulatory protein (
arsR
), an arsenite permease (
arsB
), and an arsenate reductase (
arsC
); operon
ars1
contains an additional arsenate reductase gene (
arsC1′
) located immediately downstream from
arsC1
. Additional arsenite permease and arsenate reductase genes (
arsB3
and
arsC4
) scattered on the chromosome were also identified. The involvement of
ars
operons in arsenic resistance in
C. glutamicum
was confirmed by gene disruption experiments of the three arsenite permease genes present in its genome. Wild-type and
arsB3
insertional mutant
C. glutamicum
strains were able to grow with up to 12 mM arsenite, whereas
arsB1
and
arsB2 C. glutamicum
insertional mutants were resistant to 4 mM and 9 mM arsenite, respectively. The double
arsB1-arsB2
insertional mutant was resistant to only 0.4 mM arsenite and 10 mM arsenate. Gene amplification assays of operons
ars1
and
ars2
in
C. glutamicum
revealed that the recombinant strains containing the
ars1
operon were resistant to up to 60 mM arsenite, this being one of the highest levels of bacterial resistance to arsenite so far described, whereas recombinant strains containing operon
ars2
were resistant to only 20 mM arsenite. Northern blot and reverse transcription-PCR analysis confirmed the presence of transcripts for all the
ars
genes, the expression of
arsB3
and
arsC4
being constitutive, and the expression of
arsR1
,
arsB1
,
arsC1
,
arsC1′
,
arsR2
,
arsB2
, and
arsC2
being inducible by arsenite.
Trichoderma Mitogen-Activated Protein Kinase Signaling Is Involved in Induction of Plant Systemic Resistance
Authors: Viterbo Ada , Harel Michal , Horwitz Benjamin A. , Chet Ilan , Mukherjee Prasun K.
Published: October 2005

The role of a mitogen-activated protein kinase (MAPK) TmkA in inducing systemic resistance in cucumber against the bacterial pathogen
Pseudomonas syringae
pv.
lacrymans
was investigated by using
tmkA
loss-of-function mutants of
Trichoderma virens
. In an assay where
Trichoderma
spores were germinated in proximity to cucumber roots, the mutants were able to colonize the plant roots as effectively as the wild-type strain but failed to induce full systemic resistance against the leaf pathogen. Interactions with the plant roots enhanced the level of
tmkA
transcript in
T. virens
and its homologue in
Trichoderma asperellum
. At the protein level, we could detect the activation of two forms reacting to the phospho-p44/42 MAPK antibody. Biocontrol experiments demonstrated that the
tmkA
mutants retain their biocontrol potential against
Rhizoctonia solani
in soil but are not effective against
Sclerotium rolfsii
in reducing disease incidence. Our results show that, unlike in many plant-pathogen interactions,
Trichoderma
TmkA MAPK is not involved in limited root colonization.
Trichoderma
, however, needs MAPK signaling in order to induce full systemic resistance in the plant.
Pyrimidine Nucleoside Salvage Confers an Advantage to
Xenorhabdus nematophila
in Its Host Interactions
Authors: Orchard Samantha S. , Goodrich-Blair Heidi
Published: October 2005

Xenorhabdus nematophila
is a mutualist of entomopathogenic nematodes and a pathogen of insects. To begin to examine the role of pyrimidine salvage in nutrient exchange between
X. nematophila
and its hosts, we identified and mutated an
X. nematophila tdk
homologue.
X. nematophila tdk
mutant strains had reduced virulence toward
Manduca sexta
insects and a competitive defect for nematode colonization in plate-based assays. Provision of a wild-type
tdk
allele in
trans
corrected the defects of the mutant strain. As in
Escherichia coli
,
X. nematophila tdk
encodes a deoxythymidine kinase, which converts salvaged deoxythymidine and deoxyuridine nucleosides to their respective nucleotide forms. Thus, nucleoside salvage may confer a competitive advantage to
X. nematophila
in the nematode intestine and be important for normal entomopathogenicity.
Functional Characterization of the Proteolytic System ofLactobacillus sanfranciscensisDSM 20451Tduring Growth in Sourdough
Authors: Vermeulen Nicoline , Pavlovic Melanie , Ehrmann Matthias A. , Gänzle Michael G. , Vogel Rudi F.
Published: October 2005

Protein hydrolysis and amino acid metabolism contribute to the beneficial effects of sourdough fermentation on bread quality. In this work, genes ofLactobacillus sanfranciscensisstrain DSM 20451 involved in peptide uptake and hydrolysis were identified and their expression during growth in sourdough was determined. Screening of theL. sanfranciscensisgenome with degenerate primers targetingprtand analysis of proteolytic activity in vitro provided no indication for proteolytic activity. Proteolysis in aseptic doughs and sourdoughs fermented withL. sanfranciscensiswas inhibited upon the addition of an aspartic protease inhibitor. These results indicate that proteolysis was not linked to the presence ofL. sanfranciscensisDSM 20451 and that this strain does not harbor a proteinase. Genes encoding the peptide transport systems Opp and DtpT and the intracellular peptidases PepT, PepR, PepC, PepN, and PepX were identified. Both peptide uptake systems and the genespepN,pepX,pepC, andpepTwere expressed byL. sanfranciscensisgrowing exponentially in sourdough, whereaspepXwas not transcribed. The regulation of the expression of Opp, DtpT, and PepT during growth ofL. sanfranciscensisin sourdough was investigated. Expression of Opp and DtpT was reduced approximately 17-fold when the peptide supply in dough was increased. The expression of PepT was dependent on the peptide supply to a lesser extent. Thus, the accumulation of amino nitrogen byL. sanfranciscensisin dough is attributable to peptide hydrolysis rather than proteolysis and amino acid metabolism byL. sanfranciscensisduring growth in sourdough is limited by the peptide availability.
Novel Vip3-Related Protein from
Bacillus thuringiensis
Authors: Rang Cécile , Gil Patricia , Neisner Nathalie , Van Rie Jeroen , Frutos Roger
Published: October 2005

A novel
vip3
-related gene was identified in
Bacillus thuringiensis
. This novel gene is 2,406 bp long and codes for a 91-kDa protein (801 amino acids). This novel protein exhibits between 61 and 62% similarity with Vip3A proteins and is designated Vip3Ba1. Vip3Ba1 has several specific features. Differences between Vip3Ba1 and the Vip3A proteins are spread throughout the sequence but are more frequent in the C-terminal part from amino acid 456 onward. The regions containing the two proteolytic processing sites, which are highly conserved among the Vip3A toxins, are markedly different in Vip3Ba1. The pattern DCCEE (Asp Cys Cys Glu Glu) is repeated four times between position 463 and 483 in Vip3Ba1, generating the sequence 463-DCCEEDCCEEDCCEEDCCEE-483. This sequence, which is rich in negatively charged amino acids, also contains 73% of the cysteines present in Vip3Ba1. This repeated sequence is not present in Vip3A proteins. The Vip3Ba1protein was produced in
Escherichia coli
and tested against
Ostrinia nubilalis
and
Plutella xylostella
, and it generated significant growth delays but had no larvicidal effect, indicating that its host range might be different than that of Vip3A proteins.
Intracellular Screen To Identify Metagenomic Clones That Induce or Inhibit a Quorum-Sensing Biosensor
Authors: Williamson Lynn L. , Borlee Bradley R. , Schloss Patrick D. , Guan Changhui , Allen Heather K. , Handelsman Jo
Published: October 2005

The goal of this study was to design and evaluate a rapid screen to identify metagenomic clones that produce biologically active small molecules. We built metagenomic libraries with DNA from soil on the floodplain of the Tanana River in Alaska. We extracted DNA directly from the soil and cloned it into fosmid and bacterial artificial chromosome vectors, constructing eight metagenomic libraries that contain 53,000 clones with inserts ranging from 1 to 190 kb. To identify clones of interest, we designed a high throughput “intracellular” screen, designated METREX, in which metagenomic DNA is in a host cell containing a biosensor for compounds that induce bacterial quorum sensing. If the metagenomic clone produces a quorum-sensing inducer, the cell produces green fluorescent protein (GFP) and can be identified by fluorescence microscopy or captured by fluorescence-activated cell sorting. Our initial screen identified 11 clones that induce and two that inhibit expression of GFP. The intracellular screen detected quorum-sensing inducers among metagenomic clones that a traditional overlay screen would not. One inducing clone carries a LuxI homologue that directs the synthesis of an
N
-acyl homoserine lactone quorum-sensing signal molecule. The LuxI homologue has 62% amino acid sequence identity to its closest match in GenBank, AmfI from
Pseudomonas fluorescens
, and is on a 78-kb insert that contains 67 open reading frames. Another inducing clone carries a gene with homology to homocitrate synthase. Our results demonstrate the power of an intracellular screen to identify functionally active clones and biologically active small molecules in metagenomic libraries.
Production of an Engineered Killer Peptide inNicotiana benthamianaby Using aPotato virus XExpression System
Authors: Donini Marcello , Lico Chiara , Baschieri Selene , Conti Stefania , Magliani Walter , Polonelli Luciano , Benvenuto Eugenio
Published: October 2005

The decapeptide killer peptide (KP) derived from the sequence of a single-chain, anti-idiotypic antibody acting as a functional internal image of a microbicidal, broad-spectrum yeast killer toxin (KT) was shown to exert a strong microbicidal activity against human pathogens. With the aim to exploit this peptide to confer resistance to plant pathogens, we assayed its antimicrobial activity against a broad spectrum of phytopathogenic bacteria and fungi. Synthetic KP exhibited antimicrobial activity in vitro towardsPseudomonas syringae,Erwinia carotovora,Botrytis cinerea, andFusarium oxysporum. KP was also expressed in plants by using aPotato virus X(PVX)-derived vector as a fusion to the viral coat protein, yielding chimeric virus particles (CVPs) displaying the heterologous peptide. Purified CVPs showed enhanced antimicrobial activity against the above-mentioned plant pathogens and human pathogens such asStaphylococcus aureusandCandida albicans. Moreover, in vivo assays designed to challenge KP-expressing plants (as CVPs) withPseudomonas syringaepv. tabaci showed enhanced resistance to bacterial attack. The results indicate that the PVX-based display system is a high-yield, rapid, and efficient method to produce and evaluate antimicrobial peptides in plants, representing a milestone for the large-scale production of high-added-value peptides through molecular farming. Moreover, KP is a promising molecule to be stably engineered in plants to confer broad-spectrum resistance to phytopathogens.
Assessment of the Ability of the Bioelectric Effect To Eliminate Mixed-Species Biofilms
Authors: Shirtliff Mark E. , Bargmeyer Alex , Camper Anne K.
Published: October 2005

Microbes have been able to persist in water distribution systems through the development of multicellular communities known as biofilms. This study evaluated the usefulness of the bioelectric effect for the elimination of water distribution system biofilms from annular reactors. The bioelectric effect did not have any bactericidal action either alone or when coupled with free chlorine.
Simple Colorimetric Method for Detecting Degenerate Strains of the Cultivated Basidiomycete
Flammulina velutipes
(Enokitake)
Authors: Magae Yumi , Akahane Kobun , Nakamura Kimiyoshi , Tsunoda Shigeyuki
Published: October 2005

Degeneration of cultivated strains of
Flammulina velutipes
is a serious problem. We developed a simple colorimetric method to detect degenerate strains by using a liquid medium supplemented with bromothymol blue and lactose. The ability of a strain to develop normal mushrooms could be determined by the color of the medium.
Metabolically Improved Exopolysaccharide Production by
Streptococcus thermophilus
and Its Influence on the Rheological Properties of Fermented Milk
Authors: Svensson Malin , Waak Elisabet , Svensson Ulla , Rådström Peter
Published: October 2005

Altered levels of enzymes in the central carbon metabolism in
Streptococcus thermophilus
increased the exopolysaccharide (EPS) production 3.3 times over that of the parent strain. The influence of enhanced EPS production on the rheological properties of fermented milk is described for engineered strains of
S. thermophilus
which produce different levels of EPSs.
Disinfection of Microorganisms by Use of Electrochemically Regenerated Periodate
Authors: Okochi Mina , Yokokawa Hiroshi , Lim Tae-Kyu , Taguchi Tomoyuki , Takahashi Hiromichi , Yokouchi Hiroko , Kaiho Tatsuo , Sakuma Akira , Matsunaga Tadashi
Published: October 2005

A new method for disinfection of microorganisms by electrochemically regenerated periodate was developed. Oxidation of iodate to periodate was observed at 1.25 V versus a silver/silver chloride electrode in a cyclic voltammogram of potassium iodate. When 1.25 V was applied in 1.0 mM potassium iodate, approximately 4-log inactivation of
Escherichia coli
was observed in 30 min.
Chloroethene Biodegradation in Sediments at 4°C
Authors: Bradley P. M. , Richmond S. , Chapelle F. H.
Published: October 2005

Microbial reductive dechlorination of [1,2-
14
C]trichloroethene to [
14
C]
cis
-dichloroethene and [
14
C]vinyl chloride was observed at 4°C in anoxic microcosms prepared with cold temperature-adapted aquifer and river sediments from Alaska. Microbial anaerobic oxidation of [1,2-
14
C]
cis
-dichloroethene and [1,2-
14
C]vinyl chloride to
14
CO
2
also was observed under these conditions.
Comparison of Rectoanal Mucosal Swab Cultures and Fecal Cultures for Determining Prevalence of
Escherichia coli
O157:H7 in Feedlot Cattle
Authors: Greenquist M. A. , Drouillard J. S. , Sargeant J. M. , Depenbusch B. E. , Shi Xiaorong , Lechtenberg K. F. , Nagaraja T. G.
Published: October 2005

We compared fecal samples with samples collected with rectoanal mucosa swabs (RAMS) to determine the prevalence of
Escherichia coli
O157 in feedlot cattle (
n
= 747).
Escherichia coli
O157 was detected in 9.5% of samples collected with RAMS and 4.7% of samples tested by fecal culture. Pulsed-field gel electrophoresis analysis of isolates suggested that the strains colonizing the rectoanal junction were the same as those from the feces. Mucosal swab sampling was more sensitive than fecal sampling for determining the prevalence of
E. coli
O157 in feedlot cattle.
Aquaporin Expression and Freeze Tolerance in
Candida albicans
Authors: Tanghe An , Carbrey Jennifer M. , Agre Peter , Thevelein Johan M. , Van Dijck Patrick
Published: October 2005

Aquaporins are members of the major intrinsic protein superfamily of integral membrane proteins which enable the transport of water, glycerol, and other solutes across membranes in various organisms. In microorganisms, the physiological role of aquaporins is not yet defined. We found a clear correlation between expression of the
Candida albicans
aquaporin-encoding gene
AQY1
and freeze tolerance. A connection with the function for the aquaporin in the natural environment of
C. albicans
is, however, not obvious.
Production of Ethanol from Starch by Respiration-Deficient Recombinant
Saccharomyces cerevisiae
Authors: Toksoy Öner Ebru , Oliver Stephen G. , Kırdar Betül
Published: October 2005

A 100%-respiration-deficient nuclear petite amylolytic
Saccharomyces cerevisiae
NPB-G strain was generated, and its employment for direct fermentation of starch into ethanol was investigated. In a comparison of ethanol fermentation performances with the parental respiration-sufficient WTPB-G strain, the NPB-G strain showed an increase of ca. 48% in both ethanol yield and ethanol productivity.
FREE EXPANSION OF IMPENETRABLE BOSONS ON ONE-DIMENSIONAL OPTICAL LATTICES
Authors: RIGOL MARCOS , MURAMATSU ALEJANDRO
Published: October 2005

We review recent exact results for the free expansion of impenetrable bosons on one-dimensional lattices, after switching off a confining potential. When the system is initially in a superfluid state, far from the regime in which the Mott-insulator appears in the middle of the trap, the momentum distribution of the expanding bosons rapidly approaches the momentum distribution of non-interacting fermions. Remarkably, no loss in coherence is observed in the system as reflected by a large occupation of the lowest eigenstate of the one-particle density matrix. In the opposite limit, when the initial system is a pure Mott insulator with one particle per lattice site, the expansion leads to the emergence of quasicondensates at finite momentum. In this case, one-particle correlations like the ones shown to be universal in the equilibrium case develop in the system. We show that the out-of-equilibrium behavior of the Shannon information entropy in momentum space, and its contrast with one of non-interacting fermions, allows to differentiate the two different regimes of interest. It also helps in understanding the crossover between them.
"NON-IDENTITY-CHECK" IS QMA-COMPLETE
Authors: JANZING DOMINIK , WOCJAN PAWEL , BETH THOMAS
Published: October 2005

We describe a computational problem that is complete for the complexity class QMA, a quantum generalization of NP. It arises as a natural question in quantum computing and quantum physics. "Non-identity-check" is the following decision problem: Given a classical description of a quantum circuit (a sequence of elementary gates), determine whether it is almost equivalent to the identity. Explicitly, the task is to decide whether the corresponding unitary is close to a complex multiple of the identity matrix with respect to the operator norm. We show that this problem is QMA-complete. A generalization of this problem is "non-equivalence check": given two descriptions of quantum circuits and a description of a common invariant subspace, decide whether the restrictions of the circuits to this subspace almost coincide. We show that non-equivalence check is also in QMA and hence QMA-complete.
FLUCTUATIONS OF QUANTUM RANDOM WALKS ON CIRCLES
Authors: INUI NORIO , KONISHI YOSHINAO , KONNO NORIO , SOSHI TAKAHIRO
Published: October 2005

Temporal fluctuations in the Hadamard walk on circles are studied. A temporal standard deviation of probability that a quantum random walker is positive at a given site is introduced to manifest striking differences between quantum and classical random walks. An analytical expression of the temporal standard deviation on a circle with odd sites is shown and its asymptotic behavior is considered for large system size. In contrast with classical random walks, the temporal fluctuation of quantum random walks depends on the position and initial conditions, since temporal standard deviation of the classical case is zero for any site. It indicates that the temporal fluctuation of the Hadamard walk can be controlled.
QUANTUM GATES AND PROTOCOLS WITH SPHERICAL WIGNER FUNCTIONS
Authors: KÁLMÁN ORSOLYA , BENEDICT MIHÁLY G.
Published: October 2005

The fundamental concepts and operations of quantum information theory are considered in the framework of a phase space formulation of quantum mechanics, where the states of one or several qubits are represented by a specific continuous quasiprobability distribution function on the Bloch sphere or on its generalizations. The function we use is the spherical Wigner function. It is shown that the usual transformations of quantum information theory are certain rotations or more general transformations of this Wigner function. We show that the standard teleportation and dense coding protocols can be appropriately formulated in terms of the Wigner function.
IMPOSSIBILITY OF REVERSING OR COMPLEMENTING AN UNKNOWN QUANTUM STATE AND A GENERAL NO-CLONING PRINCIPLE
Authors: LI DAFA , LI XIANGRONG , HUANG HONGTAO , LI XINXIN
Published: October 2005

We show the impossibility of reversing or complementing any quantum state and give the generalization of the no-cloning theorem to other forbidden evolutions and impossible processes.
STABILITY OF THE QUANTUM FOURIER TRANSFORMATION ON THE ISING QUANTUM COMPUTER
Authors: CELARDO GIUSEPPE LUCA , PINEDA CARLOS , ŽNIDARIČ MARKO
Published: October 2005

We analyze the influence of errors on the implementation of the quantum Fourier transformation. Two kinds of errors are studied: (i) systematic errors due to off-resonant transitions and (ii) errors due to an external perturbation. The scaling of errors with system parameters and the number of qubits is analyzed. To suppress off-resonant transitions, we use correcting pulses while in order to suppress errors due to an external perturbation, we use an improved quantum Fourier transformation algorithm. As a result, the fidelity of quantum computation is increased by several orders of magnitude and is thus stable in a much wider range of physical parameters.
EXPERIMENTAL DEMONSTRATION OF THE PERFORMANCE OF QUANTUM KEY DISTRIBUTION SYSTEM AT 1550 nm
Authors: GUI YOUZHEN , MO XIAOFAN , HAN ZHENGFU , GUO GUANGCAN
Published: October 2005

We analyze some of the critical factors that confine the transmission length for a quantum key distribution system under a certain Quantum Bit Error Rate (QBER). Emphasis was placed on the relationship between transmission length and QBER. Relationships between the minimum QBER and transmission length in theory for ideal M–Z interferometers and for the real case in theory according to the parameters of our system are given. The relationship between them as obtained by experiment was also given. The results showed that our system is very close to the performance of an ideal experimental system.
Angiotensin-Converting Enzyme 2 (ACE2) and ACE Activities Display Tissue-Specific Sensitivity to Undernutrition-Programmed Hypertension in the Adult Rat
Authors: Rivière Guillaume , Michaud Annie , Breton Christophe , VanCamp Gilles , Laborie Christine , Enache Mihaela , Lesage Jean , Deloof Sylvie , Corvol Pierre , Vieau Didier
Published: October 2005

Human epidemiological studies have shown that low birth weight is associated with hypertension in adulthood. Rodent models of intrauterine growth retardation (IUGR) support these findings because offspring from undernourished dams develop hypertension. Angiotensin-converting enzyme 2 (ACE2) is a newly described renin-angiotensin system (RAS) component that competes with ACE for angiotensin peptide hydrolysis and therefore may modulate blood pressure. However, ACE2 potential participation in hypertension programming remains unknown, although RAS alterations were reported in IUGR models. Hence, we first investigated the tissue distribution of ACE2 and ACE in the rat and then whether hypertension programming differentially affects both enzymes. Using multiplex RT-PCR and in situ hybridization, we show that ACE2 mRNA is widely expressed and coregionalized with ACE. Moreover, tissues involved in blood pressure homeostasis (lung, heart, and kidney) express high levels of both enzymes. Enzymatic assays reveal that ACE2 and ACE are coactive in these tissues. Adult (4-month-old) offspring from 70% food-restricted dams throughout gestation (FR30 rats) present mild hypertension, impaired renal morphology, as well as elevated plasma angiotensin II and aldosterone, suggesting alterations of the systemic RAS. In FR30 rats, we show that ACE2 and ACE activities are increased only in the lung, whereas their mRNA expression is not significantly altered, showing that the enzymes display tissue-specific sensitivity to programming. Our results indicate that ACE2 and ACE are coexpressed in numerous rat tissues and that their increased activity in the lung of FR30 rats may participate in hypertension programming.
Combined QT Interval and Voltage Criteria Improve Left Ventricular Hypertrophy Detection in Resistant Hypertension
Authors: Salles Gil , Leocádio Sharon , Bloch Katia , Nogueira Armando R. , Muxfeldt Elizabeth
Published: October 2005

QT interval parameters have been associated with left ventricular hypertrophy (LVH) in hypertensive patients. The aim of this study is to assess this relationship in resistant hypertension and, in particular, to evaluate whether any QT interval parameter could provide additive information for LVH beyond that obtained from the best electrocardiographic voltage criterion. In a cross-sectional study, 471 resistant hypertensives were submitted to standard 12-lead ECGs, 24-hour ambulatory blood pressure monitoring, and 2D echocardiographic examinations. QT interval durations and QRS voltages were measured, and maximum rate–corrected QT interval duration (QTc
max
) and dispersion (QTd), and Sokolow’s and Cornell’s voltage product were calculated. Statistical analyses involved bivariate tests and multivariate logistic regression, with LVH as the dependent variable. A total of 383 patients (81%) had echocardiographic LVH. In bivariate comparisons, both QT interval parameters showed a predictive performance for LVH similar to Cornell’s product, the best ECG voltage criterion. In multivariate analysis, QT parameters and Cornell’s product were independently associated with LVH, after adjustment for other LVH determinants. QTc interval >440 ms
1/2
and dispersion >60 ms were associated with a 2-fold (95% confidence interval [CI], 1.1 to 3.8) greater chance of having LVH, whereas Cornell’s product >240 mV·ms implied a 2.6-fold (95% CI, 1.2 to 6.1) increased chance of LVH. The combination of prolonged QT interval and increased Cornell’s product was associated with a 5.3- to 9.3-fold higher chance of having LVH. Hence, although in isolation, no QT interval parameter performs better for LVH detection than simpler Cornell’s product, it provides additive information and can be used in combination with voltage criteria to refine LVH risk stratification in resistant hypertension.
High-Resolution Spiral Computed Tomography Coronary Angiography in Patients Referred for Diagnostic Conventional Coronary Angiography
Authors: Mollet Nico R. , Cademartiri Filippo , van Mieghem Carlos A.G. , Runza Giuseppe , McFadden Eugène P. , Baks Timo , Serruys Patrick W. , Krestin Gabriel P. , de Feyter Pim J.
Published: October 2005

Background—

The diagnostic performance of the latest 64-slice CT scanner, with increased temporal (165 ms) and spatial (0.4 mm
3
) resolution, to detect significant stenoses in the clinically relevant coronary tree is unknown.

Methods and Results—

We studied 52 patients (34 men; mean age, 59.6±12.1 years) with atypical chest pain, stable or unstable angina pectoris, or non–ST-segment elevation myocardial infarction scheduled for diagnostic conventional coronary angiography. All patients had stable sinus rhythm. Patients with initial heart rates ≥70 bpm received β-blockers. Mean scan time was 13.3±0.9 seconds. The CT scans were analyzed by 2 observers unaware of the results of invasive coronary angiography, which was used as the standard of reference. All available coronary segments, regardless of size, were included in the evaluation. Lesions with ≥50 luminal narrowing were considered significant stenoses. Invasive coronary angiography demonstrated the absence of significant disease in 25% (13 of 52), single-vessel disease in 31% (16 of 52), and multivessel disease in 45% (23 of 52) of patients. One unsuccessful CT scan was classified as inconclusive. Ninety-four significant stenoses were present in the remaining 51 patients. Sensitivity, specificity, and positive and negative predictive values of CT for detecting significant stenoses on a segment-by-segment analysis were 99% (93 of 94; 95% CI, 94 to 99), 95% (601 of 631; 95% CI, 93 to 96), 76% (93 of 123; 95% CI, 67 to 89), and 99% (601 of 602; 95% CI, 99 to 100), respectively.

Conclusions—

Noninvasive 64-slice CT coronary angiography accurately detects coronary stenoses in patients in sinus rhythm and presenting with atypical chest pain, stable or unstable angina, or non–ST-segment elevation myocardial infarction.