bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

ABSTRACT

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

ABSTRACT

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

ABSTRACT

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

ABSTRACTThe 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

ABSTRACT

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

ABSTRACT

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

ABSTRACT

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

ABSTRACT

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

ABSTRACTProtein 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

ABSTRACT

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

ABSTRACT

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

ABSTRACTThe 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

ABSTRACT
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

ABSTRACT

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

ABSTRACT

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

ABSTRACT

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

ABSTRACT

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

ABSTRACT

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.