bluuebunny/crossref_metadata_2025 huggingface dataset:
Source Bioaerosol Concentration and rRNA Gene-Based Identification of Microorganisms Aerosolized at a Flood Irrigation Wastewater Reuse Site
Authors: Paez-Rubio Tania , Viau Emily , Romero-Hernandez Socorro , Peccia Jordan
Published: February 2005

Reuse of partially treated domestic wastewater for agricultural irrigation is a growing practice in arid regions throughout the world. A field sampling campaign to determine bioaerosol concentration, culturability, and identity at various wind speeds was conducted at a flooded wastewater irrigation site in Mexicali, Baja California, Mexico. Direct fluorescent microscopy measurements for total microorganisms, culture-based assays for heterotrophs and gram-negative enteric bacteria, and small-subunit rRNA gene-based cloning were used for microbial characterizations of aerosols and effluent wastewater samples. Bioaerosol results were divided into two wind speed regimens: (i) below 1.9 m/s, average speed 0.5 m/s, and (ii) above 1.9 m/s, average speed 4.5 m/s. Average air-borne concentration of total microorganisms, culturable heterotrophs, and gram-negative enteric bacteria were, respectively, 1.1, 4.2, and 6.2 orders of magnitude greater during the high-wind-speed regimen. Small-subunit rRNA gene clone libraries processed from samples from air and the irrigation effluent wastewater during a high-wind sampling event indicate that the majority of air clone sequences were more than 98% similar to clone sequences retrieved from the effluent wastewater sample. Overall results indicate that wind is a potential aerosolization mechanism of viable wastewater microorganisms at flood irrigation sites.
Low-Temperature Growth of
Shewanella oneidensis
MR-1
Authors: Abboud Randa , Popa Radu , Souza-Egipsy Virginia , Giometti Carol S. , Tollaksen Sandra , Mosher Jennifer J. , Findlay Robert H. , Nealson Kenneth H.
Published: February 2005

Shewanella oneidensis
MR-1 is a mesophilic bacterium with a maximum growth temperature of ≈35°C but the ability to grow over a wide range of temperatures, including temperatures near zero. At room temperature (≈22°C) MR-1 grows with a doubling time of about 40 min, but when moved from 22°C to 3°C, MR-1 cells display a very long lag phase of more than 100 h followed by very slow growth, with a doubling time of ≈67 h. In comparison to cells grown at 22°C, the cold-grown cells formed long, motile filaments, showed many spheroplast-like structures, produced an array of proteins not seen at higher temperature, and synthesized a different pattern of cellular lipids. Frequent pilus-like structures were observed during the transition from 3 to 22°C.
Effect of Nutrient Addition and Environmental Factors on Prophage Induction in Natural Populations of Marine
Synechococcus
Species
Authors: McDaniel L. , Paul J. H.
Published: February 2005

A series of experiments were conducted with samples collected in both Tampa Bay and the Gulf of Mexico to assess the impact of nutrient addition on cyanophage induction in natural populations of
Synechococcus
sp. The samples were virus reduced to decrease the background level of cyanophage and then either left untreated or amended with nitrate, ammonium, urea, or phosphate. Replicate samples were treated with mitomycin C to stimulate cyanophage induction. In five of the nine total experiments performed, cyanophage induction was present in the non-nutrient-amended control samples. Stimulation of cyanophage induction in response to nutrient addition (phosphate) occurred in only one Tampa Bay sample. Nutrient additions caused a decrease in lytic (or control) phage production in three of three offshore stations, in one of three estuarine experiments, and in a lysogenic marine
Synechococcus
in culture. These results suggest that the process of cyanophage induction as an assay of
Synechococcus
lysogeny was not inorganically nutrient limited, at least in the samples examined. More importantly, it was observed that the level of cyanophage induction (cyanophage milliliter
−1
) was inversely correlated to
Synechococcus
and cyanophage abundance. Thus, the intensity of the prophage induction response is defined by ambient population size and cyanophage abundance. This corroborates prior observations that lysogeny in
Synechococcus
is favored during times of low host abundance.
Role of the
bga1
-Encoded Extracellular β-Galactosidase of
Hypocrea jecorina
in Cellulase Induction by Lactose
Authors: Seiboth Bernhard , Hartl Lukas , Salovuori Noora , Lanthaler Karin , Robson Geoff D. , Vehmaanperä Jari , Penttilä Merja E. , Kubicek Christian P.
Published: February 2005

Lactose is the only soluble and economically feasible carbon source for the production of cellulases or heterologous proteins regulated by cellulase expression signals by
Hypocrea jecorina
(
Trichoderma reesei
). We investigated the role of the major β-galactosidase of
H. jecorina
in lactose metabolism and cellulase induction. A genomic copy of the
bga1
gene was cloned, and this copy encodes a 1,023-amino-acid protein with a 20-amino-acid signal sequence. This protein has a molecular mass of 109.3 kDa, belongs to glycosyl hydrolase family 35, and is the major extracellular β-galactosidase during growth on lactose. Its transcript was abundant during growth on
l
-arabinose and
l
-arabinitol but was much less common when the organism was grown on lactose,
d
-galactose, galactitol,
d
-xylose, and xylitol. Δ
bga1
strains grow more slowly and accumulate less biomass on lactose, but the cellobiohydrolase I and II gene expression and the final cellulase yields were comparable to those of the parental strain. Overexpression of
bga1
under the control of the pyruvate kinase promoter reduced the lag phase, increased growth on lactose, and limited transcription of cellobiohydrolases. We detected an additional extracellular β-galactosidase activity that was not encoded by
bga1
but no intracellular β-galactosidase activity. In conclusion, cellulase production on lactose occurs when β-galactosidase activity levels are low but decreases as the β-galactosidase activities increase. The data indicate that
bga1
-encoded β-galactosidase activity is a critical factor for cellulase production on lactose.
Comparison of Ileum Microflora of Pigs Fed Corn-, Wheat-, or Barley-Based Diets by Chaperonin-60 Sequencing and Quantitative PCR
Authors: Hill Janet E. , Hemmingsen Sean M. , Goldade Blair G. , Dumonceaux Tim J. , Klassen Jonathan , Zijlstra Ruurd T. , Goh Swee Han , Van Kessel Andrew G.
Published: February 2005

We have combined the culture-independent methods of high-throughput sequencing of chaperonin-60 PCR product libraries and quantitative PCR to profile and quantify the small-intestinal microflora of pigs fed diets based on corn, wheat, or barley. A total of 2,751 chaperonin-60 PCR product clones produced from samples of ileum digesta were examined. The majority (81%) of these clones contained sequences independently recovered from all three libraries; 372 different nucleotide sequences were identified, but only 14% of the 372 different sequences were recovered from all three libraries. Taxonomic assignments of the library sequences were made by comparison to a reference database of chaperonin-60 sequences combined with phylogenetic analysis. The taxa identified are consistent with previous reports of pig ileum microflora. Frequencies of each sequence in each library were calculated to identify taxa that varied in frequency between the corn, barley, and wheat libraries. The chaperonin-60 sequence inventory was used as a basis for designing PCR primer sets for taxon-specific quantitative PCR. Results of quantitative PCR analysis of ileum digesta confirmed the relative abundances of targeted taxa identified with the library sequencing approach. The results of this study indicate that chaperonin-60 clone libraries can be valid profiles of complex microbial communities and can be used as the basis for producing quantitative PCR assays to measure the abundance of taxa of interest during experimentally induced or natural changes in a community.
Metabolism of Bismuth Subsalicylate and Intracellular Accumulation of Bismuth by
Fusarium
sp. Strain BI
Authors: Dodge Anthony G. , Wackett Lawrence P.
Published: February 2005

Enrichment cultures were conducted using bismuth subsalicylate as the sole source of carbon and activated sludge as the inoculum. A pure culture was obtained and identified as a
Fusarium
sp. based on spore morphology and partial sequences of 18S rRNA, translation elongation factor 1-α, and β-tubulin genes. The isolate, named
Fusarium
sp. strain BI, grew to equivalent densities when using salicylate or bismuth subsalicylate as carbon sources. Bismuth nitrate at concentrations of up to 200 μM did not limit growth of this organism on glucose. The concentration of soluble bismuth in suspensions of bismuth subsalicylate decreased during growth of
Fusarium
sp. strain BI. Transmission electron microscopy and energy-dispersive spectroscopy revealed that the accumulated bismuth was localized in phosphorus-rich granules distributed in the cytoplasm and vacuoles. Long-chain polyphosphates were extracted from fresh biomass grown on bismuth subsalicylate, and inductively coupled plasma optical emission spectrometry showed that these fractions also contained high concentrations of bismuth. Enzyme activity assays of crude extracts of
Fusarium
sp. strain BI showed that salicylate hydroxylase and catechol 1,2-dioxygenase were induced during growth on salicylate, indicating that this organism degrades salicylate by conversion of salicylate to catechol, followed by
ortho
cleavage of the aromatic ring. Catechol 2,3-dioxygenase activity was not detected.
Fusarium
sp. strain BI grew with several other aromatic acids as carbon sources: benzoate, 3-hydroxybenzoate, 4-hydroxybenzoate, gentisate,
d
-mandelate,
l
-phenylalanine,
l
-tyrosine, phenylacetate, 3-hydroxyphenylacetate, 4-hydroxyphenylacetate, and phenylpropionate.
Detection and Discrimination of
Cryptosporidium parvum
and
C. hominis
in Water Samples by Immunomagnetic Separation-PCR
Authors: Ochiai Yoshitsugu , Takada Chieko , Hosaka Mitsugu
Published: February 2005

Cryptosporidium parvum
and
C. hominis
have been the cause of large and serious outbreaks of waterborne cryptosporidiosis. A specific and sensitive recovery-detection method is required for control of this pathogen in drinking water. In the present study, nested PCR-restriction fragment length polymorphism (RFLP), which targets the divergent
Cpgp40/15
gene, was developed. This nested PCR detected only the gene derived from
C. parvum
and
C. hominis
strains, and RFLP was able to discriminate between the PCR products from
C. parvum
and
C. hominis
. To evaluate the sensitivity of nested PCR,
C. parvum
oocysts inoculated in water samples of two different turbidities were recovered by immunomagnetic separation (IMS) and detected by nested PCR and fluorescent antibody assay (FA). Genetic detection by nested PCR and oocyst number confirmed by FA were compared, and the results suggested that detection by nested PCR depends on the confirmed oocyst number and that nested PCR in combination with IMS has the ability to detect a single oocyst in a water sample. We applied an agitation procedure with river water solids to which oocysts were added to evaluate the recovery and detection by the procedure in environmental samples and found some decrease in the rate of detection by IMS.
Unique Kinetic Properties of Phenol-Degrading
Variovorax
Strains Responsible for Efficient Trichloroethylene Degradation in a Chemostat Enrichment Culture
Authors: Futamata Hiroyuki , Nagano Yayoi , Watanabe Kazuya , Hiraishi Akira
Published: February 2005

A chemostat enrichment of soil bacteria growing on phenol as the sole carbon source has been shown to exhibit quite high trichloroethylene (TCE)-degrading activities (H. Futamata, S. Harayama, and K. Watanabe, Appl. Environ. Microbiol.
67:
4671-4677, 2001). To identify the bacterial populations responsible for the high TCE-degrading activity, a multidisciplinary survey of the chemostat enrichment was conducted by employing molecular-ecological and culture-dependent approaches. Three chemostat enrichment cultures were newly developed under different phenol-loading conditions (0.25, 0.75, and 1.25 g liter
−1
day
−1
) in this study, and the TCE-degrading activities of the enrichments were measured. Among them, the enrichment at 0.75 g liter
−1
day
−1
(enrichment 0.75) expressed the highest activity. Denaturing gradient gel electrophoresis of PCR-amplified 16S rRNA gene fragments detected a
Variovorax
ribotype as the strongest band in enrichment 0.75; however, it was not a major ribotype in the other samples. Bacteria were isolated from enrichment 0.75 by direct plating, and their 16S rRNA genes and genes encoding the largest subunit of phenol hydroxylase (LmPHs) were analyzed. Among the bacteria isolated, several strains were affiliated with the genus
Variovorax
and were shown to have high-affinity-type LmPHs. The LmPH of the
Variovorax
strains was also detected as the major genotype in enrichment 0.75. Kinetic analyses of phenol and TCE degradation revealed, however, that these strains exhibited quite low affinity for phenol compared to other phenol-degrading bacteria, while they showed quite high specific TCE-degrading activities and relatively high affinity for TCE. Owing to these unique kinetic traits, the
Variovorax
strains can obviate competitive inhibition of TCE degradation by the primary substrate of the catabolic enzyme (i.e., phenol), contributing to the high TCE-degrading activity of the chemostat enrichments. On the basis of physiological information, mechanisms accounting for the way the
Variovorax
population overgrew the chemostat enrichment are discussed.
Adhesion-Aggregation and Inactivation of
Poliovirus 1
in Groundwater Stored in a Hydrophobic Container
Authors: Gassilloud Benoît , Gantzer Christophe
Published: February 2005

Viral inactivation and adhesion-aggregation in water are often studied as separate phenomena. When the focus is placed on viral adhesion-aggregation, inactivation is neglected because the phenomena under investigation occur over a short period measured in days. When viral inactivation is studied, adhesion-aggregation phenomena are considered to be negligible because viral survival is traced over several days or months. In the present work, we took a global approach, examining the relative contributions of each of these processes in a complex system composed of groundwater,
Poliovirus 1
, and a hydrophobic container (polypropylene) maintained in a dark environment at 20°C. We demonstrated that infectious viral load fell off 2.8 log
10
during the first 20 days. During this time, adhesion was far from negligible because it accounted for most of the decline, 1.5 log
10
. Adhesion was undoubtedly favored by the presence of divalent ions in the groundwater. After 20 days, aggregation may also have been the cause of 0.66 to 0.92 log
10
of viral loss. Finally, viral inactivation was quantitatively the lowest phenomena because it only explained 0.38 to 0.64 log
10
of the viral loss. This study thus clearly demonstrated that estimates of viral survival in a given system must always take into account adhesion-aggregation phenomena which may be responsible for the majority of viral loss in the aqueous phase. Adhesion and aggregation are reversible processes which may lead to an underestimation of viral load in certain studies.
High Motility Reduces Grazing Mortality of Planktonic Bacteria
Authors: Matz Carsten , Jürgens Klaus
Published: February 2005

We tested the impact of bacterial swimming speed on the survival of planktonic bacteria in the presence of protozoan grazers. Grazing experiments with three common bacterivorous nanoflagellates revealed low clearance rates for highly motile bacteria. High-resolution video microscopy demonstrated that the number of predator-prey contacts increased with bacterial swimming speed, but ingestion rates dropped at speeds of >25 μm s
−1
as a result of handling problems with highly motile cells. Comparative studies of a moderately motile strain (<25 μm s
−1
) and a highly motile strain (>45 μm s
−1
) further revealed changes in the bacterial swimming speed distribution due to speed-selective flagellate grazing. Better long-term survival of the highly motile strain was indicated by fourfold-higher bacterial numbers in the presence of grazing compared to the moderately motile strain. Putative constraints of maintaining high swimming speeds were tested at high growth rates and under starvation with the following results: (i) for two out of three strains increased growth rate resulted in larger and slower bacterial cells, and (ii) starved cells became smaller but maintained their swimming speeds. Combined data sets for bacterial swimming speed and cell size revealed highest grazing losses for moderately motile bacteria with a cell size between 0.2 and 0.4 μm
3
. Grazing mortality was lowest for cells of >0.5 μm
3
and small, highly motile bacteria. Survival efficiencies of >95% for the ultramicrobacterial isolate CP-1 (≤0.1 μm
3
, >50 μm s
−1
) illustrated the combined protective action of small cell size and high motility. Our findings suggest that motility has an important adaptive function in the survival of planktonic bacteria during protozoan grazing.
Genomic and Phylogenetic Characterization of Luminous Bacteria Symbiotic with the Deep-Sea FishChlorophthalmus albatrossis(Aulopiformes: Chlorophthalmidae)
Authors: Dunlap Paul V. , Ast Jennifer C.
Published: February 2005

Bacteria forming light-organ symbiosis with deep-sea chlorophthalmid fishes (Aulopiformes: Chlorophthalmidae) are considered to belong to the speciesPhotobacterium phosphoreum. The identification of these bacteria asP. phosphoreum, however, was based exclusively on phenotypic traits, which may not discriminate between phenetically similar but evolutionarily distinct luminous bacteria. Therefore, to test the species identification of chlorophthalmid symbionts, we carried out a genomotypic (repetitive element palindromic PCR genomic profiling) and phylogenetic analysis on strains isolated from the perirectal light organ ofChlorophthalmus albatrossis. Sequence analysis of the 16S rRNA gene of 10 strains from 5 fish specimens placed these bacteria in a cluster related to but phylogenetically distinct from the type strain ofP. phosphoreum, ATCC 11040T, and the type strain ofPhotobacterium iliopiscarium, ATCC 51760T. Analysis ofgyrBresolved theC. albatrossisstrains as a strongly supported clade distinct fromP. phosphoreumandP. iliopiscarium. Genomic profiling of 109 strains from the 5C. albatrossisspecimens revealed a high level of similarity among strains but allowed identification of genomotypically different types from each fish. Representatives of each type were then analyzed phylogenetically, using sequence of theluxABFEgenes. As withgyrB, analysis ofluxABFEresolved theC. albatrossisstrains as a robustly supported clade distinct fromP. phosphoreum. Furthermore, other strains of luminous bacteria reported asP. phosphoreum, i.e., NCIMB 844, from the skin ofMerluccius capensis(Merlucciidae), NZ-11D, from the light organ ofNezumia aequalis(Macrouridae), andpjapo.1.1, from the light organ ofPhysiculus japonicus(Moridae), grouped phylogenetically bygyrBandluxABFEwith theC. albatrossisstrains, not with ATCC 11040T. These results demonstrate that luminous bacteria symbiotic withC. albatrossis, together with certain other strains of luminous bacteria, form a clade, designated thekishitaniiclade, that is related to but evolutionarily distinct fromP. phosphoreum. Members of thekishitaniiclade may constitute the major or sole bioluminescent symbiont of several families of deep-sea luminous fishes.
Bacterial Degradation of Cyanide and Its Metal Complexes under Alkaline Conditions
Authors: Luque-Almagro Víctor M. , Huertas María-J. , Martínez-Luque Manuel , Moreno-Vivián Conrado , Roldán M. Dolores , García-Gil L. Jesús , Castillo Francisco , Blasco Rafael
Published: February 2005

A bacterial strain able to use cyanide as the sole nitrogen source under alkaline conditions has been isolated. The bacterium was classified as
Pseudomonas pseudoalcaligenes
by comparison of its 16S RNA gene sequence to those of existing strains and deposited in the Colección Española de Cultivos Tipo (Spanish Type Culture Collection) as strain CECT5344. Cyanide consumption is an assimilative process, since (i) bacterial growth was concomitant and proportional to cyanide degradation and (ii) the bacterium stoichiometrically converted cyanide into ammonium in the presence of
l
-methionine-
d
,
l
-sulfoximine, a glutamine synthetase inhibitor. The bacterium was able to grow in alkaline media, up to an initial pH of 11.5, and tolerated free cyanide in concentrations of up to 30 mM, which makes it a good candidate for the biological treatment of cyanide-contaminated residues. Both acetate and
d
,
l
-malate were suitable carbon sources for cyanotrophic growth, but no growth was detected in media with cyanide as the sole carbon source. In addition to cyanide,
P. pseudoalcaligenes
CECT5344 used other nitrogen sources, namely ammonium, nitrate, cyanate, cyanoacetamide, nitroferricyanide (nitroprusside), and a variety of cyanide-metal complexes. Cyanide and ammonium were assimilated simultaneously, whereas cyanide strongly inhibited nitrate and nitrite assimilation. Cyanase activity was induced during growth with cyanide or cyanate, but not with ammonium or nitrate as the nitrogen source. This result suggests that cyanate could be an intermediate in the cyanide degradation pathway, but alternative routes cannot be excluded.
Bias in the
Listeria monocytogenes
Enrichment Procedure: Lineage 2 Strains Outcompete Lineage 1 Strains in University of Vermont Selective Enrichments
Authors: Bruhn Jesper Bartholin , Vogel Birte Fonnesbech , Gram Lone
Published: February 2005

Listeria monocytogenes
can be isolated from a range of food products and may cause food-borne outbreaks or sporadic cases of listeriosis.
L. monocytogenes
is divided into three genetic lineages and 13 serotypes. Strains of three serotypes (1/2a, 1/2b, and 4b) are associated with most human cases of listeriosis. Of these, strains of serotypes 1/2b and 4b belong to lineage 1, whereas strains of serotype 1/2a and many other strains isolated from foods belong to lineage 2.
L. monocytogenes
is isolated from foods by selective enrichment procedures and from patients by nonselective methods. The aim of the present study was to investigate if the selective enrichment procedure results in a true representation of the subtypes of
L. monocytogenes
present in a sample. Eight
L. monocytogenes
strains (four lineage 1 strains and four lineage 2 strains) and one
Listeria innocua
strain grew with identical growth rates in the nonselective medium brain heart infusion (BHI), but differed in their growth rate in the selective medium University of Vermont medium I (UVM I). When coinoculated in UVM I, some strains completely outgrew other strains. This outcome was dependent on the lineage of
L. monocytogenes
rather than the individual growth rate of the strains. When inoculated at identical cell densities in UVM I,
L. innocua
outcompeted
L. monocytogenes
lineage 1 strains but not lineage 2 strains. In addition, lineage 2
L. monocytogenes
strains outcompeted lineage 1
L. monocytogenes
strains in all combinations tested, indicating a bias in strains selected by the enrichment procedures. Bias also occurred when coinoculating two lineage 2 or lineage 1 strains; however, it did not appear to correlate with origin (clinical versus food). Identical coinoculation experiments in BHI suggested that the selective compounds in UVM I and II influenced this bias. The results of the present study demonstrate that the selective procedures used for isolation of
L. monocytogenes
may not allow a true representation of the types present in foods. Our results could have a significant impact on epidemiological studies, as lineage 1 strains, which are often isolated from clinical cases of listeriosis, may be suppressed during enrichment by other
L. monocytogenes
lineages present in a food sample.
Screening for
Bacillus
Isolates in the Broiler Gastrointestinal Tract
Authors: Barbosa Teresa M. , Serra Cláudia R. , La Ragione Roberto M. , Woodward Martin J. , Henriques Adriano O.
Published: February 2005

Spores from a number of different
Bacillus
species are currently being used as human and animal probiotics, although their mechanisms of action remain poorly understood. Here we describe the isolation of 237 presumptive gut-associated
Bacillus
spp. isolates that were obtained by heat and ethanol treatment of fecal material from organically reared broilers followed by aerobic plating. Thirty-one representative isolates were characterized according to their morphological, physiological, and biochemical properties as well as partial 16S rRNA gene sequences and screening for the presence of plasmid DNA. The
Bacillus
species identified included
B. subtilis
,
B. pumilus
,
B. licheniformis
,
B. clausii
,
B. megaterium
,
B. firmus
, and species of the
B. cereus
group, whereas a number of our isolates could not be classified. Intrinsic properties of potential importance for survival in the gut that could be advantageous for spore-forming probiotics were further investigated for seven isolates belonging to five different species. All isolates sporulated efficiently in the laboratory, and the resulting spores were tolerant to simulated gastrointestinal tract conditions. They also exhibited antimicrobial activity against a broad spectrum of bacteria, including food spoilage and pathogenic organisms such as
Bacillus
spp.,
Clostridium perfringens
,
Staphylococcus aureus
, and
Listeria monocytogenes
. Importantly, the isolates were susceptible to most of the antibiotics tested, arguing that they would not act as donors for resistance determinants if introduced in the form of probiotic preparations. Together, our results suggest that some of the sporeformers isolated in this study have the potential to persist in or transiently associate with the complex gut ecosystem.
A High-Molecular-Mass Surface Protein (Lsp) and Methionine Sulfoxide Reductase B (MsrB) Contribute to the Ecological Performance of
Lactobacillus reuteri
in the Murine Gut
Authors: Walter Jens , Chagnaud Patrice , Tannock Gerald W. , Loach Diane M. , Dal Bello Fabio , Jenkinson Howard F. , Hammes Walter P. , Hertel Christian
Published: February 2005

Members of the genus
Lactobacillus
are common inhabitants of the gut, yet little is known about the traits that contribute to their ecological performance in gastrointestinal ecosystems.
Lactobacillus reuteri
100-23 persists in the gut of the reconstituted
Lactobacillus
-free mouse after a single oral inoculation. Recently, three genes of this strain that were specifically induced (in vivo induced) in the murine gut were identified (38). We report here the detection of a gene of
L. reuteri
100-23 that encodes a high-molecular-mass surface protein (Lsp) that shows homology to proteins involved in the adherence of other bacteria to epithelial cells and in biofilm formation. The three in vivo-induced genes and
lsp
of
L. reuteri
100-23 were inactivated by insertional mutagenesis in order to study their biological importance in the murine gastrointestinal tract. Competition experiments showed that mutation of
lsp
and a gene encoding methionine sulfoxide reductase (MsrB) reduced ecological performance. Mutation of
lsp
impaired the adherence of the bacteria to the epithelium of the mouse forestomach and altered colonization dynamics. Homologues of
lsp
and
msrB
are present in the genomes of several strains of
Lactobacillus
and may play an important role in the maintenance of these bacteria in gut ecosystems.
Assessment of Genotypic Diversity of Antibiotic-Producing
Pseudomonas
Species in the Rhizosphere by Denaturing Gradient Gel Electrophoresis
Authors: Bergsma-Vlami M. , Prins M. E. , Staats M. , Raaijmakers J. M.
Published: February 2005

The genotypic diversity of antibiotic-producing
Pseudomonas
spp. provides an enormous resource for identifying strains that are highly rhizosphere competent and superior for biological control of plant diseases. In this study, a simple and rapid method was developed to determine the presence and genotypic diversity of 2,4-diacetylphloroglucinol (DAPG)-producing
Pseudomonas
strains in rhizosphere samples. Denaturing gradient gel electrophoresis (DGGE) of 350-bp fragments of
phlD
, a key gene involved in DAPG biosynthesis, allowed discrimination between genotypically different
phlD
+
reference strains and indigenous isolates. DGGE analysis of the
phlD
fragments provided a level of discrimination between
phlD
+
genotypes that was higher than the level obtained by currently used techniques and enabled detection of specific
phlD
+
genotypes directly in rhizosphere samples with a detection limit of approximately 5 × 10
3
CFU/g of root. DGGE also allowed simultaneous detection of multiple
phlD
+
genotypes present in mixtures in rhizosphere samples. DGGE analysis of 184 indigenous
phlD
+
isolates obtained from the rhizospheres of wheat, sugar beet, and potato plants resulted in the identification of seven
phlD
+
genotypes, five of which were not described previously based on sequence and phylogenetic analyses. Subsequent bioassays demonstrated that eight genotypically different
phlD
+
genotypes differed substantially in the ability to colonize the rhizosphere of sugar beet seedlings. Collectively, these results demonstrated that DGGE analysis of the
phlD
gene allows identification of new genotypic groups of specific antibiotic-producing
Pseudomonas
with different abilities to colonize the rhizosphere of sugar beet seedlings.
Use of ecological study designs for injury prevention
Authors: Stevenson M , McClure R
Published: February 2005

This paper provides an overview of the ecological study design and its application to injury prevention. The advantages and disadvantages of ecological designs are described and the principle characteristics of the ecological design are highlighted. The paper concludes by highlighting the pivotal role that ecological studies can have in our understanding of the complex interaction between the environment and injury, and the application of this design in elucidating key population based strategies for injury prevention.
Injury outcome indicators: the development of a validation tool: Table 1
Authors: Cryer C , Langley J D , Jarvis S N , Mackenzie S G , Stephenson S C R , Heywood P
Published: February 2005

Background:Researchers have previously expressed concern about some national indicators of injury incidence and have argued that indicators should be validated before their introduction.

Aims:To develop a tool to assess the validity of indicators of injury incidence and to carry out initial testing of the tool to explore consistency on application.

Methods:Previously proposed criteria were shared for comment with members of the International Collaborative Effort on Injury Statistics (ICE) Injury Indicators Group over a period of six months. Immediately after, at a meeting of Injury ICE in Washington, DC in April 2001, revised criteria were agreed over two days of meetings. The criteria were applied, by three raters, to six non-fatal indicators that underpin the national road safety targets for Canada, New Zealand, and the United Kingdom. Consistency of ratings were judged.

Consensus outcome:The development process resulted in a validation tool that comprised criteria relating to: (1) case definition, (2) a focus on serious injury, (3) unbiased case ascertainment, (4) source data for the indicator being representative of the target population, (5) availability of data to generate the indicator, and (6) the existence of a full written specification for the indicator. On application of these criteria to the six road safety indicators, some problems of agreement between raters were identified.

Conclusion:This paper has presented an early step in the development of a tool for validating injury indicators, as well as some directions that can be taken in its further development.
Effect of recall on estimation of non-fatal injury rates: a community based study in Tanzania
Authors: Moshiro C , Heuch I , Åstrøm A N , Setel P , Kvåle G
Published: February 2005

Study objective:To investigate the effect of recall on estimation of non-fatal injury rates in Tanzania.

Design:Retrospective population based survey.

Setting:Eight branches in an urban area and six villages in a relatively prosperous rural area in Tanzania.

Subjects:Individuals of all ages living in households selected by cluster sampling.

Main outcome measures:Estimated non-fatal injury rates calculated at each of the 12 recall periods (one to 12 months before the interview).

Results:Out of a population of 15 223 persons, 509 individuals reported 516 injuries during the preceding year. Of these 313 (61.5%) were males and 196 (38.5%) females. The data showed notable declining incidence rates from 72 per 1000 person-years when based on a one month recall period to 32.7 per 1000 person-years for a 12 month recall period (55% decline). The decline was found for injuries resulting in fewer than 30 days of disability whereas rates for severe injuries (disability of 30 days or more) did not show a consistent variation with recall period. Decline in injury rates by recall period was higher in rural than in urban areas. Age, sex, and education did not notably affect recall.

Conclusions:Longer recall periods underestimate injury rates compared with shorter recall periods. For severe injuries, a recall period of up to 12 months does not affect the rate estimates. It is essential that a recall period of less than three months be used to calculate injury rates for less severe injuries.
Ability of parents to recall the injuries of their young children
Authors: Cummings P , Rivara F P , Thompson R S , Reid R J
Published: February 2005

Objective:To estimate the ability of parents to recall the injuries of their children.

Design:Comparison of parent recall with computerized medical records.

Setting:A health maintenance organization in Washington State during 2003.

Subjects:Parents of children younger than 6 years.

Main outcome measures:The ratio of recalled injuries to injuries in computerized data.

Results:Telephone interviews were completed with a parent of 1672 young children who had computerized medical data for at least one injury in the last year. Counting the three most recent treated injuries, the 1672 children had 1896 separate new injuries in the year before interview and parents recalled 1150 of these: recall ratio 0.61 (95% confidence interval (CI) 0.58 to 0.63). The recall ratio decreased from 0.82 (95% CI 0.79 to 0.85) for injuries one day before interview to 0.37 (95% CI 0.32 to 0.40) at 365 days before interview. For 341 major injuries the recall ratio was 0.80 (95% CI 0.76 to 0.84), for 202 minor injuries treated in an emergency department or hospital it was 0.77 (95% CI 0.71 to 0.82), for 597 minor injuries treated in urgent care it was 0.70 (95% CI 0.65 to 0.73), and for 756 minor injuries treated in a clinic it was 0.43 (95% CI 0.39 to 0.47).

Conclusions:Recall decreased with time. Recall was best for major injuries, intermediate for minor injuries treated in a hospital, emergency department, or urgent care center, and worst for minor injuries treated in a clinic.
A comparison of two surveillance systems for deaths related to violent injury
Authors: Comstock R D , Mallonee S , Jordan F
Published: February 2005

Objective:To compare violent injury death reporting by the statewide Medical Examiner and Vital Statistics Office surveillance systems in Oklahoma.

Methods:Using a standard study definition for violent injury death, the sensitivity and predictive value positive (PVP) of the Medical Examiner and Vital Statistics violent injury death reporting systems in Oklahoma in 2001 were evaluated.

Results:Altogether 776 violent injury deaths were identified (violent injury death rate: 22.4 per 100 000 population) including 519 (66.9%) suicides, 248 (32.0%) homicides, and nine (1.2%) unintentional firearm deaths. The Medical Examiner system over-reported homicides and the Vital Statistics system under-reported homicides and suicides and over-reported unintentional firearm injury deaths. When compared with the standard, the Medical Examiner and Vital Statistics systems had sensitivities of 99.2% and 90.7% (respectively) and PVPs of 95.0% and 99.1% for homicide, sensitivities of 99.2% and 93.1% and PVPs of 100% and 99.0% for suicide, and sensitivities of 100% and 100% and PVPs of 100% and 31.0% for unintentional firearm deaths.

Conclusions:Both the Vital Statistics and Medical Examiner systems contain valuable data and when combined can work synergistically to provide violent injury death information while also serving as quality control checks for each other. Preventable errors within both systems can be reduced by increasing training, addressing sources of human error, and expanding computer quality assurance programming. A standardized nationwide Medical Examiners’ coding system and a national violent death reporting system that merges multiple public health and criminal justice datasets would enhance violent injury surveillance and prevention efforts.
DENSE STEREO CORRESPONDENCE USING QUARTERS OF WAVELET TRANSFORM
Authors: RÉGIS SÉBASTIEN , DONCESCU ANDREI , MOREAU GUILLAUME , FUCHS PHILIPPE
Published: February 2005

In stereo research the construction of a dense disparity map is a complicated task when the scene contains a lot of occlusions. In this case in the neighborhood of occlusions, we could consider that the images have a non-stationary behavior. In this paper we propose a new method for computing a dense disparity map using the decomposition of the 2D wavelet transform in four quarters allowing us to find a corresponding pixel in the case of occlusion as well. Our algorithm constructs in each pixel of two images four estimators corresponding to each quarter. The matching of the four wavelet coefficient estimators in the right image with the other four in the left image allow us to construct a dense map disparity map in each pixel of an image.
A HYBRID LANGUAGE MODEL BASED ON STATISTICS AND LINGUISTIC RULES
Authors: WANG XIAOLONG , YEUNG DANIEL S. , LIU JAMES N. K. , LUK ROBERT , WANG XUAN
Published: February 2005

Language modeling is a current research topic in many domains including speech recognition, optical character recognition, handwriting recognition, machine translation and spelling correction. There are two main types of language models, the mathematical and the linguistic. The most widely used mathematical language model is the n-gram model inferred from statistics. This model has three problems: long distance restriction, recursive nature and partial language understanding. Language models based on linguistics present many difficulties when applied to large scale real texts. We present here a new hybrid language model that combines the advantages of the n-gram statistical language model with those of a linguistic language model which makes use of grammatical or semantic rules. Using suitable rules, this hybrid model can solve problems such as long distance restriction, recursive nature and partial language understanding. The new language model has been effective in experiments and has been incorporated in Chinese sentence input products for Windows and Macintosh OS.
TERMINAL RELIABILITY IMPROVEMENT OF SHUFFLE-EXCHANGE NETWORK SYSTEMS
Authors: FARD NASSER S. , GUNAWAN INDRA
Published: February 2005

Multistage Interconnection Networks (MINs) are communication network systems that provide fast and efficient information transitions among N processors and N memory modules of systems. A typical MIN consists of layers of switching elements that are connected together in a predefined topology. The routing capability of a network depends on its specific topology. A shuffle-exchange network (SEN), a specific type of MIN that consists of 2 × 2 switching elements, has been widely considered a practical interconnection system. In this paper, a modified shuffle-exchange network with 1 × 2 switching elements at the input (source) stage, 2 × 2 switching elements at the intermediate stages, and 2 × 1 switching elements at the output (terminal) stage is proposed. The proposed network shows an improvement in the terminal reliability of SEN. The terminal reliability evaluation of the SEN and the modified SEN are demonstrated through numerical examples for different sizes of networks. The reliability evaluation of MINs is important, as it determines the usability and efficiency of the network to provide services. It is shown that the proposed modified SEN provides higher terminal reliability for network sizes larger than 4 inputs and 4 outputs (4 × 4).
RELIABILITY ANALYSIS OF STIFFNESS DEGRADATION IN AUTOMOTIVE SPOT-WELDED JOINTS
Authors: MAHADEVAN SANKARAN , HOLLANDER BRIAN , NI KAN , MAO HONGYIN
Published: February 2005

This paper develops a reliability-based methodology for the evaluation of stiffness degradation of spot-welded joints under high mileage. A global-local finite element analysis is used, with the loads on the detailed three-dimensional joint model coming from finite element analysis of the entire car model with proving ground loads. Probabilistic fatigue crack propagation analysis is developed for multi-axial variable amplitude loading history on the joint. Multiple spot welds contribute to the stiffness of the joint. Hence the problem is addressed through system reliability techniques. The effect of spot-weld separation on joint stiffness, and on global vehicle stiffness, is incorporated. This results in the computation of the statistics of vehicle stiffness degradation with mileage.
AUTOMATIC ELASTIC MEDICAL IMAGE REGISTRATION BASED ON IMAGE INTENSITY
Authors: WANG XIUYING , FENG DAVID DAGAN
Published: February 2005

An automatic elastic medical image registration approach is proposed, based on image intensity. The algorithm is divided into two steps. In Step 1, global affine registration is first used to establish an initial guess and the resulting images can be assumed to have only small local elastic deformations. The mapped images are then used as inputs in Step 2, during which, the study image is modeled as elastic sheet by being divided into sub-images. Moving the individual sub-image in the reference image, the local displacement vectors are found and the global elastic transformation is achieved by assimilating all of the local transformation into a continuous transformation. The algorithm has been validated by simulated data, noisy data and clinical tomographic data. Both experiments and theoretical analysis have demonstrated that the proposed algorithm has a superior computational performance and can register images automatically with an improved accuracy.
AN EFFICIENT 3D PLENOPTIC REPRESENTATION FOR APPROXIMATING A PATH OF MOTION TO A CURVED LINE
Authors: BING CHENG , YING WANG , NANNING ZHENG , ZHENGZHONG BIAN
Published: February 2005

We constrain camera motion to a curved line, and capture panoramic images at discrete points along the line. An efficient 3D plenoptic representation is created using the panoramic images. The method does not need to recover geometric models of the scene and the new view is gotten directly from the sampled images of the scene. Moreover, the user can observe significant parallax and lighting changes at a point away from the sampling line. Compared with 4D plenoptic representation, such as lumigraph or light field, the amount of data is much decreased. By combining this 3D plenoptic function with the other plenoptic functions (3D or 4D), a larger scene can be represented. This representation has good storage and computational efficiency, and is very easy to capture. This paper discusses a complete working system, from capturing and construction to rendering of linear mosaics, using synthetic environments and real scenes.
NONPHOTOREALISTIC VIRTUAL ENVIRONMENT NAVIGATION FROM IMAGES
Authors: KANG HYUNG W.
Published: February 2005

This paper presents a novel scheme based on a hybrid NPR/IBMR approach, for providing non-photorealistic virtual environment navigation from images. As a preprocess, we first divide the background and the foreground components in the image and then construct a simple 3D scene model consisting of background model and foreground object models, together with the corresponding non-photorealistic texture maps. Thus, through interactive navigation at runtime, non-photorealistic walk-through images for novel viewpoints can be generated in real time. To reduce visual artifacts in the resulting animation, we propose an effective method for generating multiresolution and view-dependent non-photorealistic texture maps that preserve the stroke size and coherence across different viewing resolutions and angles.
PERMANENCE AND THE EXISTENCE OF THE PERIODIC SOLUTION OF THE NON-AUTONOMOUS TWO-SPECIES COMPETITIVE MODEL WITH STAGE STRUCTURE
Authors: ZENG GUANGZHAO , CHEN LANSUN , SUN LIHUA , LIU YING
Published: February 2005

This paper considers a non-autonomous competitive two-species model with stage structure in one species. The conditions of permanence obtained. Furthermore, the existence and asymptotic stability of the periodic solution are proved under some assumptions if this model turns out to be a periodic system.
HUMAN FACE DETECTION IN COLOR IMAGES
Authors: ZAQOUT IHAB , ZAINUDDIN ROZIATI , BABA SAPIAN
Published: February 2005

In this paper we have used a simple and efficient color-based approach to segment human skin pixels from background, using a 2D histogram-based approach as a preprocess stage for human face detection. For skin segmentation, a total of 446,007 skin samples from the training set is manually cropped from the RGB color images, to calculate three lookup tables based on the relationship between each pair of the triple components (R, G, B). Derivation of skin classifier rules from the lookup tables are based on how often each attribute value (interval) occurs, and their associated certainty values. For face detection, we assume the face-appearance as blob-like, and that the face has an approximately elliptical shape. Accordingly, an ellipse-fitting algorithm is appropriate, which is based on statistical moments, and those blobs that have an elliptical shape are retained as face candidates.
COMPACTNESS AND CYCLES IN SIGNAL TRANSDUCTION AND TRANSCRIPTIONAL REGULATION NETWORKS: A SIGNATURE OF NATURAL SELECTION?
Authors: WAGNER ANDREAS , WRIGHT JEREMIAH
Published: February 2005

We ask whether natural selection has shaped three biologically important features of 15 signal transduction networks and two genome-scale transcriptional regulation networks. These features are regulatory cycles, the lengths of the longest pathways through a network — a measure of network compactness — and the abundance of node pairs connected by many alternative regulatory pathways. We determine whether these features are significantly more or less abundant in biological networks than in randomized networks with the same distribution of incoming and outgoing connections per network node. We find that autoregulatory cycles are of exceptionally high abundance in transcriptional regulation networks. All other cycles, however, are significantly less abundant in several signal transduction networks. This suggests that the multistability caused by complex feedback loops in a network may interfere with the functioning of such networks. We also find that several of the networks we examine are more compact than expected by chance alone. This raises the possibility that the transmission of information through such networks, which is fastest in compact networks, is a biologically important characteristic of such networks.
A CELLULAR AUTOMATA MODEL FOR A LEARNING PROCESS
Authors: HE MING-FENG , DENG CHENG-RUI , FENG LIN , TIAN BO-WEN
Published: February 2005

Ideas on educational psychology suggest that a learning process occurs when people participate within social communities. A model is constructed based on two primary factors in the learning process : knowledge storage and interactive ability of each person. Results of simulations are consistent with some actual phenomena including the average knowledge achieved and different educational effects under different conditions. Functions of two main factors and teachers' influences are also studied and discussed.