bluuebunny/crossref_metadata_2025 huggingface dataset:
Secondary Metabolites Help Biocontrol Strain
Pseudomonas fluorescens
CHA0 To Escape Protozoan Grazing
Authors: Jousset Alexandre , Lara Enrique , Wall Luis G. , Valverde Claudio
Published: November 2006

In soil ecosystems, bacteria must cope with predation activity, which is attributed mainly to protists. The development of antipredation strategies may help bacteria maintain higher populations and persist longer in the soil. We analyzed the interaction between the root-colonizing and biocontrol strain
Pseudomonas fluorescens
CHA0 and three different protist isolates (an amoeba, a flagellate, and a ciliate). CHA0 produces a set of antibiotics, HCN, and an exoprotease. We observed that protists cannot grow on CHA0 but can multiply on isogenic regulatory mutants that do not produce the extracellular metabolites. The in vitro responses to CHA0 cells and its exoproducts included growth inhibition, encystation, paralysis, and cell lysis. By analyzing the responses of protists to bacterial supernatants obtained from different isogenic mutants whose production of one or more exometabolites was affected and also to culture extracts with antibiotic enrichment, we observed different contributions of the phenolic antifungal compound 2,4-diacetylphloroglucinol (DAPG) and the extracellular protease AprA to CHA0 toxicity for protists and to the encystation-reactivation cycle. The grazing pressure artificially produced by a mixture of the three protists in a microcosm system resulted in reduced colonization of cucumber roots by a regulatory isogenic CHA0 mutant unable to produce toxins. These results suggest that exometabolite production in biocontrol strain CHA0 may contribute to avoidance of protist grazing and help sustain higher populations in the rhizosphere, which may be a desirable and advantageous trait for competition with other bacteria for available resources.
Quantifying Substrate Uptake by Individual Cells of Marine Bacterioplankton by Catalyzed Reporter Deposition Fluorescence In Situ Hybridization Combined with Microautoradiography
Authors: Sintes Eva , Herndl Gerhard J.
Published: November 2006

Catalyzed reporter deposition fluorescence in situ hybridization combined with microautoradiography (MICRO-CARD-FISH) is increasingly being used to obtain qualitative information on substrate uptake by individual members of specific prokaryotic communities. Here we evaluated the potential for using this approach quantitatively by relating the measured silver grain area around cells taking up
3
H-labeled leucine to bulk leucine uptake measurements. The increase in the silver grain area over time around leucine-assimilating cells of coastal bacterial assemblages was linear during 4 to 6 h of incubation. By establishing standardized conditions for specific activity levels and concomitantly performing uptake measurements with the bulk community, MICRO-CARD-FISH can be used quantitatively to determine uptake rates on a single-cell level. Therefore, this approach allows comparisons of single-cell activities for bacterial communities obtained from different sites or growing under different ecological conditions.
Intraspecific Variation in Growth and Morphology of the Bloom-Forming Cyanobacterium
Microcystis aeruginosa
Authors: Wilson Alan E. , Wilson Whitney A. , Hay Mark E.
Published: November 2006

In the laboratory, we documented large variation in the morphology, toxicity, and maximum population growth rates for 32
Microcystis aeruginosa
strains isolated from 12 lakes. Growth rates and mean colony sizes varied significantly across strains and were positively correlated. However, growth rates were unrelated to toxin production.
Increased Abundance of IncP-1β Plasmids and Mercury Resistance Genes in Mercury-Polluted River Sediments: First Discovery of IncP-1β Plasmids with a Complex
mer
Transposon as the Sole Accessory Element
Authors: Smalla Kornelia , Haines Anthony S. , Jones Karen , Krögerrecklenfort Ellen , Heuer Holger , Schloter Michael , Thomas Christopher M.
Published: November 2006

Although it is generally assumed that mobile genetic elements facilitate the adaptation of microbial communities to environmental stresses, environmental data supporting this assumption are rare. In this study, river sediment samples taken from two mercury-polluted (A and B) and two nonpolluted or less-polluted (C and D) areas of the river Nura (Kazakhstan) were analyzed by PCR for the presence and abundance of mercury resistance genes and of broad-host-range plasmids. PCR-based detection revealed that mercury pollution corresponded to an increased abundance of mercury resistance genes and of IncP-1β replicon-specific sequences detected in total community DNA. The isolation of IncP-1β plasmids from contaminated sediments was attempted in order to determine whether they carry mercury resistance genes and thus contribute to an adaptation of bacterial populations to Hg pollution. We failed to detect IncP-1β plasmids in the genomic DNA of the cultured Hg-resistant bacterial isolates. However, without selection for mercury resistance, three different IncP-1β plasmids (pTP6, pTP7, and pTP8) were captured directly from contaminated sediment slurry in
Cupriavidus necator
JMP228 based on their ability to mobilize the IncQ plasmid pIE723. These plasmids hybridized with the
merRT
Δ
P
probe and conferred Hg resistance to their host. A broad host range and high stability under conditions of nonselective growth were observed for pTP6 and pTP7. The full sequence of plasmid pTP6 was determined and revealed a backbone almost identical to that of the IncP-1β plasmids R751 and pB8. However, this is the first example of an IncP-1β plasmid which had acquired only a mercury resistance transposon but no antibiotic resistance or biodegradation genes. This transposon carries a rather complex set of
mer
genes and is inserted between Tra1 and Tra2.
Polyphosphate Stores Enhance the Ability of
Vibrio cholerae
To Overcome Environmental Stresses in a Low-Phosphate Environment
Authors: Jahid Iqbal K. , Silva Anisia J. , Benitez Jorge A.
Published: November 2006

Vibrio cholerae
, the causative agent of Asiatic cholera, has been reported to make large quantities of polyphosphate. Inorganic polyphosphate is a ubiquitous molecule with a variety of functions in prokaryotic and eukaryotic cells. We constructed a
V. cholerae
mutant with a deletion in the polyphosphate kinase (
ppk
) gene. The mutant was defective in polyphosphate biosynthesis. Deletion of
ppk
had no significant effect on production of cholera toxin, hemagglutinin/protease, motility, biofilm formation, and colonization of the suckling mouse intestine. The wild type and mutant had similar growth rates in rich and minimal medium and exhibited similar phosphate uptake and alkaline phosphatase induction. In contrast to
ppk
mutants from other gram-negative bacteria, the
V. cholerae
mutant survived prolonged starvation in LB medium and artificial seawater basal salts. The
ppk
mutant was significantly more sensitive to low pH, high salinity, and oxidative stress when it was cultured in low-phosphate minimal medium.
T
he
ppk
mutant failed to induce catalase when it was downshifted to phosphorus-limiting conditions. Furthermore, the increased sensitivity of the
ppk
mutant to environmental stressors in phosphate-limited medium correlated with a diminished capacity to synthesize ATP from intracellular reservoirs. We concluded that polyphosphate protects
V. cholerae
from environmental stresses under phosphate limitation conditions. It has been proposed that toxigenic
V. cholerae
can survive in estuaries and brackish waters in which phosphorus and/or nitrogen can be a limiting nutrient. Thus, synthesis of large polyphosphate stores could enhance the ability of
V. cholerae
to survive in the aquatic environment.
Effect of Sheep Urine Deposition on the Bacterial Community Structure in an Acidic Upland Grassland Soil
Authors: Rooney Deirdre , Kennedy Nabla , Deering Louise , Gleeson Deirdre , Clipson Nicholas
Published: November 2006

The effect of the addition of synthetic sheep urine (SSU) and plant species on the bacterial community composition of upland acidic grasslands was studied using a microcosm approach. Low, medium, and high concentrations of SSU were applied to pots containing plant species typical of both unimproved (
Agrostis capillaris
) and agriculturally improved (
Lolium perenne
) grasslands, and harvests were carried out 10 days and 50 days after the addition of SSU. SSU application significantly increased both soil pH (
P
< 0.005), with pH values ranging from pH 5.4 (zero SSU) to pH 6.4 (high SSU), and microbial activity (
P
< 0.005), with treatment with medium and high levels of SSU displaying significantly higher microbial activity (triphenylformazan dehydrogenase activity) than treatment of soil with zero or low concentrations of SSU. Microbial biomass, however, was not significantly altered by any of the SSU applications. Plant species alone had no effect on microbial biomass or activity. Bacterial community structure was profiled using bacterial automated ribosomal intergenic spacer analysis. Multidimensional scaling plots indicated that applications of high concentrations of SSU significantly altered the bacterial community composition in the presence of plant species but at different times: 10 days after application of high concentrations of SSU, the bacterial community composition of
L. perenne
-planted soils differed significantly from those of any other soils, whereas in the case of
A. capillaris
-planted soils, the bacterial community composition was different 50 days after treatment with high concentrations of SSU. Canonical correspondence analysis also highlighted the importance of interactions between SSU addition, plant species, and time in the bacterial community structure. This study has shown that the response of plants and bacterial communities to sheep urine deposition in grasslands is dependent on both the grass species present and the concentration of SSU applied, which may have important ecological consequences for agricultural grasslands.
RecombinantEscherichia coliStrain Produces a ZZ Domain Displaying Biopolyester Granules Suitable for Immunoglobulin G Purification
Authors: Brockelbank Jane A. , Peters Verena , Rehm Bernd H. A.
Published: November 2006

The immunoglobulin G (IgG) binding ZZ domain of protein A fromStaphylococcus aureuswas fused to the N terminus of the polyhydroxyalkanoate (PHA) synthase fromCupriavidus necator. The fusion protein was confirmed by matrix-assisted laser desorption ionization-time-of-flight mass spectrometry and mediated formation of ZZ domain-displaying PHA granules in recombinantEscherichia coli. The IgG binding capacity of isolated granules was assessed using enzyme-linked immunosorbent assay and could be enhanced by the overproduction of the ZZ-PHA synthase. ZZ-PHA granules enabled efficient purification of IgG from human serum.
Enhancement of Chilling Resistance of Inoculated Grapevine Plantlets with a Plant Growth-Promoting Rhizobacterium,Burkholderia phytofirmansStrain PsJN
Authors: Ait Barka Essaid , Nowak Jerzy , Clément Christophe
Published: November 2006

In vitro inoculation ofVitis viniferaL. cv. Chardonnay explants with a plant growth-promoting rhizobacterium,Burkholderia phytofirmansstrain PsJN, increased grapevine growth and physiological activity at a low temperature. There was a relationship between endophytic bacterial colonization of the grapevine plantlets and their growth at both ambient (26°C) and low (4°C) temperatures and their sensitivities to chilling. The major benefits of bacterization were observed on root growth (11.8- and 10.7-fold increases at 26°C and 4°C, respectively) and plantlet biomass (6- and 2.2-fold increases at 26°C and 4°C, respectively). The inoculation with PsJN also significantly improved plantlet cold tolerance compared to that of the nonbacterized control. In nonchilled plantlets, bacterization enhanced CO2fixation and O2evolution 1.3 and 2.2 times, respectively. The nonbacterized controls were more sensitive to exposure to low temperatures than were the bacterized plantlets, as indicated by several measured parameters. Moreover, relative to the noninoculated controls, bacterized plantlets had significantly increased levels of starch, proline, and phenolics. These increases correlated with the enhancement of cold tolerance of the grapevine plantlets. In summary,B. phytofirmansstrain PsJN inoculation stimulates grapevine growth and improves its ability to withstand cold stress.
Degradation of Fluorobenzene by
Rhizobiales
Strain F11 via
ortho
Cleavage of 4-Fluorocatechol and Catechol
Authors: Carvalho Maria F. , Ferreira Maria Isabel M. , Moreira Irina S. , Castro Paula M. L. , Janssen Dick B.
Published: November 2006

The aerobic metabolism of fluorobenzene by
Rhizobiales
sp. strain F11 was investigated. Liquid chromatography-mass spectrometry analysis showed that 4-fluorocatechol and catechol were formed as intermediates during fluorobenzene degradation by cell suspensions. Both these compounds, unlike 3-fluorocatechol, supported growth and oxygen uptake. Cells grown on fluorobenzene contained enzymes for the
ortho
pathway but not for
meta
ring cleavage of catechols. The results suggest that fluorobenzene is predominantly degraded via 4-fluorocatechol with subsequent
ortho
cleavage and also partially via catechol.
A Disulfide Bond-Containing Alkaline Phosphatase Triggers a BdbC-Dependent Secretion Stress Response in
Bacillus subtilis
Authors: Darmon Elise , Dorenbos Ronald , Meens Jochen , Freudl Roland , Antelmann Haike , Hecker Michael , Kuipers Oscar P. , Bron Sierd , Quax Wim J. , Dubois Jean-Yves F. , van Dijl Jan Maarten
Published: November 2006

The gram-positive bacterium
Bacillus subtilis
secretes high levels of proteins into its environment. Most of these secretory proteins are exported from the cytoplasm in an unfolded state and have to fold efficiently after membrane translocation. As previously shown for α-amylases of
Bacillus
species, inefficient posttranslocational protein folding is potentially detrimental and stressful. In
B. subtilis
, this so-called secretion stress is sensed and combated by the CssRS two-component system. Two known members of the CssRS regulon are the
htrA
and
htrB
genes, encoding potential extracytoplasmic chaperone proteases for protein quality control. In the present study, we investigated whether high-level production of a secretory protein with two disulfide bonds, PhoA of
Escherichia coli
, induces secretion stress in
B. subtilis
. Our results show that
E. coli
PhoA production triggers a relatively moderate CssRS-dependent secretion stress response in
B. subtilis
. The intensity of this response is significantly increased in the absence of BdbC, which is a major determinant for posttranslocational folding of disulfide bond-containing proteins in
B. subtilis
. Our findings show that BdbC is required to limit the PhoA-induced secretion stress. This conclusion focuses interest on the BdbC-dependent folding pathway for biotechnological production of proteins with disulfide bonds in
B. subtilis
and related bacilli.
Use of Native Lactococci as Vehicles for Delivery of DNA into Mammalian Epithelial Cells
Authors: Guimarães Valéria Dellaretti , Innocentin Silvia , Lefèvre François , Azevedo Vasco , Wal Jean-Michel , Langella Philippe , Chatel Jean-Marc
Published: November 2006

The use of the food-grade bacterium
Lactococcus lactis
as a DNA delivery vehicle at the mucosal level is an attractive DNA vaccination strategy. Previous experiments showed that recombinant
L. lactis
expressing the
Listeria monocytogenes inlA
gene can deliver a functional gene into mammalian cells. Here, we explored the potential use of noninvasive
L. lactis
strains as a DNA delivery vehicle. We constructed two
Escherichia coli-L. lactis
shuttle plasmids, pLIG:BLG1 and pLIG:BLG2, containing a eukaryotic expression cassette with the cDNA of bovine β-lactoglobulin (BLG). The greatest BLG expression after transfection of Cos-7 cells was obtained with pLIG:BLG1, which was then used to transform
L. lactis
MG1363. The resulting
L. lactis
strain MG1363(pLIG:BLG1) was not able to express BLG. The potential of
L. lactis
as a DNA delivery vehicle was analyzed by detection of BLG in Caco-2 human colon carcinoma cells after 3 h of coincubation with (i) purified pLIG:BLG1, (ii) MG1363(pLIG:BLG1), (iii) a mix of MG1363(pLIG) and purified pLIG:BLG1, and (iv) MG1363. Both BLG cDNA and BLG expression were detected only in Caco-2 cells coincubated with MG1363(pLIG:BLG1). There was a decrease in the BLG cDNA level in Caco-2 cells between 24 and 48 h after coincubation. BLG expression by Caco-2 cells started at 24 h and increased between 24 and 72 h. BLG secretion by Caco-2 cells started 48 h after coincubation with MG1363(pLIG:BLG1). We conclude that lactococci can deliver BLG cDNA into mammalian epithelial cells, demonstrating their potential to deliver in vivo a DNA vaccine.
Analysis of Novel Soluble Chromate and Uranyl Reductases and Generation of an Improved Enzyme by Directed Evolution
Authors: Barak Y. , Ackerley D. F. , Dodge C. J. , Banwari L. , Alex C. , Francis A. J. , Matin A.
Published: November 2006

Most polluted sites contain mixed waste. This is especially true of the U.S. Department of Energy (DOE) waste sites which hold a complex mixture of heavy metals, radionuclides, and organic solvents. In such environments enzymes that can remediate multiple pollutants are advantageous. We report here evolution of an enzyme, ChrR6 (formerly referred to as Y6), which shows a markedly enhanced capacity for remediating two of the most serious and prevalent DOE contaminants, chromate and uranyl. ChrR6 is a soluble enzyme and reduces chromate and uranyl intracellularly. Thus, the reduced product is at least partially sequestered and nucleated, minimizing the chances of reoxidation. Only one amino acid change,
Tyr
128
Asn
, was responsible for the observed improvement. We show here that ChrR6 makes
Pseudomonas putida
and
Escherichia coli
more efficient agents for bioremediation if the cellular permeability barrier to the metals is decreased.
Construction of a Library of Human Glycosyltransferases Immobilized in the Cell Wall ofSaccharomyces cerevisiae
Authors: Shimma Yoh-ichi , Saito Fumie , Oosawa Fumi , Jigami Yoshifumi
Published: November 2006

Fifty-one human glycosyltransferases were expressed inSaccharomyces cerevisiaeas immobilized enzymes and were assayed for enzymatic activities. The stem and catalytic regions of sialyl-, fucosyl-, galactosyl-,N-acetylgalactosaminyl-, andN-acetylglucosaminyltransferases were fused with yeast cell wall Pir proteins, which anchor glycosyltransferases at the yeast cell wall glucan. More than 75% of expressed recombinant glycosyltransferases retained their enzymatic activities in the yeast cell wall fraction and will be used as a human glycosyltransferase library. In increasing the enzymatic activities of immobilized glycosyltransferases, several approaches were found to be effective. Additional expression of yeast protein disulfide isomerase increased the expression levels and activities of polypeptideN-acetylgalactosaminyltransferases and other glycosyltransferases. PIR3 and/or PIR4 was more effective than PIR1 as a cell wall anchor when the Pir-glycosyltransferase fusions were expressed under the control of the constitutive glyceraldehyde-3-phosphate dehydrogenase promoter. Oligosaccharides such as Lewis x, Lewis y, and H antigen were successfully synthesized using this immobilized glycosyltransferase library, indicating that the Pir-fused glycosyltransferases are useful for the production of various human oligosaccharides.
Biofilm and Nanowire Production Leads to Increased Current in
Geobacter sulfurreducens
Fuel Cells
Authors: Reguera Gemma , Nevin Kelly P. , Nicoll Julie S. , Covalla Sean F. , Woodard Trevor L. , Lovley Derek R.
Published: November 2006

Geobacter sulfurreducens
developed highly structured, multilayer biofilms on the anode surface of a microbial fuel cell converting acetate to electricity. Cells at a distance from the anode remained viable, and there was no decrease in the efficiency of current production as the thickness of the biofilm increased. Genetic studies demonstrated that efficient electron transfer through the biofilm required the presence of electrically conductive pili. These pili may represent an electronic network permeating the biofilm that can promote long-range electrical transfer in an energy-efficient manner, increasing electricity production more than 10-fold.
Genetic Variability of
Spodoptera frugiperda
Smith (Lepidoptera: Noctuidae) Populations from Latin America Is Associated with Variations in Susceptibility to
Bacillus thuringiensis
Cry Toxins
Authors: Monnerat Rose , Martins Erica , Queiroz Paulo , Ordúz Sergio , Jaramillo Gabriela , Benintende Graciela , Cozzi Jorge , Real M. Dolores , Martinez-Ramirez Amparo , Rausell Carolina , Cerón Jairo , Ibarra Jorge E. , Del Rincon-Castro M. Cristina , Espinoza Ana M. , Meza-Basso Luis , Cabrera Lizbeth , Sánchez Jorge , Soberon Mario , Bravo Alejandra
Published: November 2006

Bacillus thuringiensis
strains isolated from Latin American soil samples that showed toxicity against three
Spodoptera frugiperda
populations from different geographical areas (Mexico, Colombia, and Brazil) were characterized on the basis of their insecticidal activity, crystal morphology, sodium dodecyl sulfate-polyacrylamide gel electrophoresis of parasporal crystals, plasmid profiles, and
cry
gene content. We found that the different
S. frugiperda
populations display different susceptibilities to the selected
B. thuringiensis
strains and also to pure preparations of Cry1B, Cry1C, and Cry1D toxins. Binding assays performed with pure toxin demonstrated that the differences in the toxin binding capacities of these insect populations correlated with the observed differences in susceptibility to the three Cry toxins analyzed. Finally, the genetic variability of the three insect populations was analyzed by random amplification of polymorphic DNA-PCR, which showed significant genetic diversity among the three
S. frugiperda
populations analyzed. The data presented here show that the genetic variability of
S. frugiperda
populations should be carefully considered in the development of insect pest control strategies, including the deployment of genetically modified maize in different geographical regions.
Transcriptional Regulation of the
pdt
Gene Cluster of
Pseudomonas stutzeri
KC Involves an AraC/XylS Family Transcriptional Activator (PdtC) and the Cognate Siderophore Pyridine-2,6-Bis(Thiocarboxylic Acid)
Authors: Morales Sergio E. , Lewis Thomas A.
Published: November 2006

In order to gain an understanding of the molecular mechanisms dictating production of the siderophore and dechlorination agent pyridine-2,6-bis(thiocarboxylic acid) (PDTC), we have begun characterization of a gene found in the
pdt
gene cluster of
Pseudomonas stutzeri
KC predicted to have a regulatory role. That gene product is an AraC family transcriptional activator, PdtC. Quantitative reverse transcription-PCR and expression of transcriptional reporter fusions were used to assess a role for
pdtC
in the transcription of
pdt
genes. PdtC and an upstream, promoter-proximal DNA segment were required for wild-type levels of expression from the promoter of a predicted biosynthesis operon (P

pdt
F

). At least two other transcriptional units within the
pdt
cluster were also dependent upon
pdtC
for expression at wild-type levels. The use of a heterologous,
Pseudomonas putida
host demonstrated that
pdtC
and an exogenously added siderophore were necessary and sufficient for expression from the
pdtF
promoter, i.e., none of the PDTC utilization genes within the
pdt
cluster were required for transcriptional signaling. Tests using the promoter of the
pdtC
gene in transcriptional reporter fusions indicated siderophore-dependent negative autoregulation similar to that seen with other AraC-type regulators of siderophore biosynthesis and utilization genes. The data increase the repertoire of siderophore systems known to be regulated by this type of transcriptional activator and have implications for PDTC signaling.
Fermentation of High Concentrations of Maltose by
Saccharomyces cerevisiae
Is Limited by the COMPASS Methylation Complex
Authors: Houghton-Larsen Jens , Brandt Anders
Published: November 2006

In
Saccharomyces cerevisiae
, genes encoding maltose permeases and maltases are located in the telomeric regions of different chromosomes. The COMPASS methylation complex, which methylates lysine 4 on histone H3, controls the silencing of telomeric regions. Yeast strains deleted for
SWD1
,
SWD3
,
SDC1
,
SET1
,
BRE2
, or
SPP1
, encoding components of the COMPASS complex, fermented a medium containing 22% maltose with noticeably higher attenuation than did the wild type, resulting in production of up to 29% more ethanol. The least effective strain was
spp1
. Absence of COMPASS components had no effect on the fermentation of media with 20% glucose, 20% sucrose, or 16% maltose. Deletion of
SWD3
resulted in larger amounts of
MAL12
transcript, encoding maltase, at the late stages of fermentation of 22% maltose. A similar effect on maltase activity and maltose uptake capability was seen. The lysine 4 residue of histone H3 was trimethylated in wild-type cells at the late stages, while only small amounts of the dimethylated form were detected. Trimethylation and dimethylation of this residue were not detected in strains deleted for
SWD1
,
SWD3
,
SET1
,
BRE2
, or
SDC1
. Trimethylated lysine 4 was apparent only at the early stages (48 and 96 h) of fermentation in an
spp1
strain. This work indicates that the COMPASS complex represses the expression of maltose utilization genes during the late stages of fermentation of a high concentration of maltose.
Molecular Characterization of
Cryptosporidium
spp. from Children in Kolkata, India
Authors: Das Pradeep , Roy Seuli Saha , MitraDhar Kakali , Dutta Phalguni , Bhattacharya Mihir K. , Sen Abhik , Ganguly Sandipan , Bhattacharya Sujit K. , Lal Altaf A. , Xiao Lihua
Published: November 2006

The intracellular parasite
Cryptosporidium
is responsible for severe diarrhea in immunocompromised persons in developing countries. Few studies on the characterization of the parasite in India are available. In this study, molecular characterization of the parasite from diarrheic children was carried out by PCR-restriction fragment length polymorphism analysis. At least three genotypes were identified. Out of 40 positive samples, 35 were positive for
C. hominis
, 4 were positive for
C. parvum
, and 1 was positive for
C. felis
. This study clearly suggests that cryptosporidiosis in this region is caused largely by anthroponotic transmission.
High Prevalence of Human Enterovirus A Infections in Natural Circulation of Human Enteroviruses
Authors: Witsø Elisabet , Palacios Gustavo , Cinek Ondrej , Stene Lars C. , Grinde Bjørn , Janowitz Diana , Lipkin W. Ian , Rønningen Kjersti S.
Published: November 2006

Human enterovirus (HEV) infections can be asymptomatic or cause only mild illness; recent evidence may implicate HEV infection in type 1 diabetes mellitus and myocarditis. Here, we report the molecular characterization of HEV obtained in serial monthly collections from healthy Norwegian infants. A total of 1,255 fecal samples were collected from 113 healthy infants beginning at age 3 months and continuing to 28 months. The samples were analyzed for HEV nucleic acid by real-time PCR. Fifty-eight children (51.3%) had HEV infections. One hundred forty-five positive samples were typed directly by nucleotide sequencing of the VP1 region. HEV-A was detected most frequently, with an overall prevalence of 6.8%. HEV-B was present in 4.8% of the samples and HEV-C in only 0.2% of the samples. No poliovirus or HEV-D group viruses were detected. Twenty-two different serotypes were detected in the study period: the most common were EV71 (14.5%), CAV6 (10.5%), CAV4 (8.9%), E18 (8.9%), and CBV3 (7.3%). These findings suggest that the prevalence of HEV infections in general, and HEV-A infections in particular, has been underestimated in epidemiological studies based on virus culture.
Comparison of a PCR-Restriction Fragment Length Polymorphism (PCR-RFLP) Assay to Pulsed-Field Gel Electrophoresis To Determine the Effect of Repeated Subculture and Prolonged Storage on RFLP Patterns of Shiga Toxin-Producing
Escherichia coli
O157:H7
Authors: Shima Kensuke , Wu Yuluo , Sugimoto Norihiko , Asakura Masahiro , Nishimura Kazuhiko , Yamasaki Shinji
Published: November 2006

In this study, we compared a recently developed PCR-restriction fragment length polymorphism (PCR-RFLP) assay with pulsed-field gel electrophoresis (PFGE) using three different Shiga toxin-producing
Escherichia coli
(STEC) strains to understand whether repeated subculture in vitro and prolonged storage at room temperature affect the RFLP patterns of STEC. The PFGE profiles of the STEC strains changed by 1 to 8 fragments after repeated subculture and prolonged storage; one strain was no longer clonal after repeated subculture compared to the original isolate according to the Tenover criteria. In contrast, RFLP patterns obtained by PCR-RFLP were identical after repeated subculture and prolonged storage. These data clearly indicate that the PCR-RFLP assay which is based on the diversity of region V, a regulatory region of Stx-phage, was not affected by repeated subculture and prolonged storage and is a more practical and reliable method for molecular typing of STEC strains.
Effects of
Bifidobacterium lactis
Bb12 Supplementation on Intestinal Microbiota of Preterm Infants: a Double-Blind, Placebo-Controlled, Randomized Study
Authors: Mohan Ruchika , Koebnick Corinna , Schildt Janko , Schmidt Sabine , Mueller Manfred , Possner Mike , Radke Michael , Blaut Michael
Published: November 2006

The gastrointestinal microbiota of preterm infants in a neonatal intensive care unit differs from that of term infants. In particular, the colonization of preterm infants by bifidobacteria is delayed. A double-blind, placebo-controlled, randomized clinical study was performed on 69 preterm infants to investigate the role of
Bifidobacterium lactis
Bb12 supplementation in modifying the gut microbiota. Both culture-dependent and culture-independent approaches were used to study the gut microbiota. Bifidobacterial numbers, determined by fluorescence in situ hybridization, were significantly higher in the probiotic than in the placebo group (log
10
values per g of fecal wet weight: probiotic, 8.18 + 0.54 [standard error of the mean]; placebo, 4.82 + 0.51;
P
< 0.001). A similar trend for bifidobacterial numbers was also obtained with the culture-dependent method. The infants supplemented with Bb12 also had lower viable counts of
Enterobacteriaceae
(log
10
values of CFU per g of fecal wet weight: probiotic, 7.80 + 0.34; placebo, 9.03 + 0.35;
P
= 0.015) and
Clostridium
spp. (probiotic, 4.89 + 0.30; placebo, 5.99 + 0.32;
P
= 0.014) than the infants in the placebo group. Supplementation of
B. lactis
Bb12 did not reduce the colonization by antibiotic-resistant organisms in the study population. However, the probiotic supplementation increased the cell counts of bifidobacteria and reduced the cell counts of enterobacteria and clostridia.
In Vitro Antifungal-Drug Susceptibilities of Mycelial and Yeast Forms of
Penicillium marneffei
Isolates in Cambodia
Authors: Sar Borann , Boy Sambo , Keo Chantary , Ngeth Chan Chhaya , Prak Narom , Vann Mich , Monchy Didier , Sarthou Jean Louis
Published: November 2006

Penicillium marneffei
infection is an important disease among human immunodeficiency virus patients in Southeast Asia. The in vitro antifungal-drug susceptibilities of 29 clinical isolates and 5 isolates from bamboo rats collected from 2002 to 2004 were determined. The
P. marneffei
yeast form is more susceptible than the mycelial form to amphotericin B and ketoconazole, while the mycelial and yeast forms displayed similar susceptibilities to flucytosine and itraconazole. The MICs of fluconazole were higher for both mycelial and yeast forms.
Detection of Rare G3P[19] Porcine Rotavirus Strains in Chiang Mai, Thailand, Provides Evidence for Origin of the VP4 Genes of Mc323 and Mc345 Human Rotaviruses
Authors: Maneekarn Niwat , Khamrin Pattara , Chan-it Wisoot , Peerakome Supatra , Sukchai Sujin , Pringprao Kidsadagon , Ushijima Hiroshi
Published: November 2006

Among 175 fecal specimens collected from diarrheic piglets during a surveillance of porcine rotavirus (PoRV) strains in Chiang Mai, Thailand, 39 (22.3%) were positive for group A rotaviruses. Of these, 33.3% (13 of 39) belonged to G3P[19], which was a rare P genotype seldom reported. Interestingly, their VP4 nucleotide sequences were most closely related to human P[19] strains (Mc323 and Mc345) isolated in 1989 from the same geographical area where these PoRV strains were isolated. These P[19] PoRV strains were also closely related to another human P[19] strain (RMC321), isolated from India in 1990. The VP4 sequence identities with human P[19] were 95.4% to 97.4%, while those to a porcine P[19] strain (4F) were only 87.6 to 89.1%. Phylogenetic analysis of the VP4 gene revealed that PoRV P[19] strains clustered with human P[19] strains in a monophyletic branch separated from strain 4F. Analysis of the VP7 gene confirmed that these strains belonged to the G3 genotype and shared 97.7% to 98.3% nucleotide identities with other G3 PoRV strains circulating in the regions. This close genetic relationship was also reflected in the phylogenetic analysis of their VP7 genes. Altogether, the findings provided peculiar evidence that supported the porcine origin of VP4 genes of Mc323 and Mc345 human rotaviruses.
Genotyping Hepatitis C Viruses from Southeast Asia by a Novel Line Probe Assay That Simultaneously Detects Core and 5′ Untranslated Regions
Authors: Noppornpanth Suwanna , Sablon Erwin , De Nys Kathy , Lien Truong Xuan , Brouwer Jan , Van Brussel Marianne , Smits Saskia L. , Poovorawan Yong , Osterhaus Albert D. M. E. , Haagmans Bart L.
Published: November 2006

Hepatitis C viruses (HCVs) display a high level of sequence diversity and are currently divided into six genotypes. A line probe assay (LiPA), which targets the 5′ untranslated region (5′UTR) of the HCV genome, is widely used for genotyping. However, this assay cannot distinguish many genotype 6 subtypes from genotype 1 due to high sequence similarity in the 5′UTR. We investigated the accuracy of a new generation LiPA (VERSANT HCV genotype 2.0 assay), in which genotyping is based on 5′UTR and core sequences, by testing 75 selected HCV RNA-positive sera from Southeast Asia (Vietnam and Thailand). For comparison, sera were tested on the 5′UTR based VERSANT HCV genotype assay and processed for sequence analysis of the 5′UTR-to-core and NS5b regions as well. Phylogenetic analysis of both regions revealed the presence of genotype 1, 2, 3, and 6 viruses. Using the new LiPA assay, genotypes 6c to 6l and 1a/b samples were more accurately genotyped than with the previous test only targeting the 5′UTR (96% versus 71%, respectively). These results indicate that the VERSANT HCV genotype 2.0 assay is able to discriminate genotypes 6c to 6l from genotype 1 and allows a more accurate identification of genotype 1a from 1b by using the genotype-specific core information.
Pyrosequencing, a High-Throughput Method for Detecting Single Nucleotide Polymorphisms in the Dihydrofolate Reductase and Dihydropteroate Synthetase Genes of
Plasmodium falciparum
Authors: Zhou Zhiyong , Poe Amanda C. , Limor Josef , Grady Katharine K. , Goldman Ira , McCollum Andrea M. , Escalante Ananias A. , Barnwell John W. , Udhayakumar Venkatachalam
Published: November 2006

A pyrosequencing protocol was developed as a rapid and reliable method to identify the mutations of the
dhfr
and
dhps
genes of
Plasmodium falciparum
that are associated with antifolate resistance. The accuracy and specificity of this method were tested using six laboratory-cultured
P. falciparum
isolates harboring known single nucleotide polymorphisms (SNPs) in the genes
dhfr
(codons 50, 51, 59, 108, and 164) and
dhps
(codons 436, 437, 540, 581, and 613). The lowest threshold for detection of all the SNPs tested by pyrosequencing was the equivalent of two to four parasite genomes. Also, this method was highly specific for
P. falciparum
, as it did not amplify any DNA products from the other species of human malaria parasites. We also mixed wild-type and mutant-type parasite DNAs in various proportions to determine how pyrosequencing, restriction fragment length polymorphism (RFLP), and direct conventional sequencing (for
dhfr
) compared with each other in detecting different SNPs in the mixture. In general, pyrosequencing and RFLP showed comparable sensitivities in detecting most of the SNPs in
dhfr
except for the 164L mutation, which required at least twice the amount of DNA for pyroseqencing as for RFLP. For detecting SNPs in
dhps
, pyrosequencing was slightly more sensitive than RFLP and direct sequencing. Overall, pyrosequencing was faster and less expensive than either RFLP or direct sequencing. Thus, pyrosequencing is a practical alternative method that can be used in a high-throughput format for molecular surveillance of antimalarial-drug resistance.
MultiCode-RTx Real-Time PCR System for Detection of Subpopulations of K65R Human Immunodeficiency Virus Type 1 Reverse Transcriptase Mutant Viruses in Clinical Samples
Authors: Svarovskaia Evguenia S. , Moser Michael J. , Bae Andrew S. , Prudent James R. , Miller Michael D. , Borroto-Esoda Katyna
Published: November 2006

We report a real-time PCR assay capable of detecting drug-resistant human immunodeficiency virus type 1 reverse transcriptase K65R mutant virus at a level of 0.5% in polymorphic patient plasma specimens. Fifty-three treatment-naïve and 20 treatment-experienced specimens were successfully genotyped with the new method. Results were in agreement with population sequencing and the labor-intensive single-genome sequencing method.
UNFOLDED FORM OF CONFORMAL EQUATIONS IN M DIMENSIONS AND 𝔬(M + 2)-MODULES
Authors: SHAYNKMAN O. V. , YU. TIPUNIN I. , VASILIEV M. A.
Published: November 2006

A constructive procedure is proposed for formulation of linear differential equations invariant under global symmetry transformations forming a semi-simple Lie algebra 𝔣. Under certain conditions, 𝔣-invariant systems of differential equations are shown to be associated with 𝔣-modules that are integrable with respect to some parabolic subalgebra of 𝔣. The suggested construction is motivated by the unfolded formulation of dynamical equations developed in the higher spin gauge theory and provides a starting point for generalization to the nonlinear case. It is applied to the conformal algebra 𝔬(M, 2) to classify all linear conformally invariant differential equations in the Minkowski space. Numerous examples of conformal equations are discussed from this perspective.
IMPLEMENTING CANONICAL SEESAW MECHANISM IN THE EXACT SOLUTION OF A 3-3-1 GAUGE MODEL WITHOUT EXOTIC ELECTRIC CHARGES
Authors: PALCU ADRIAN
Published: November 2006

We prove that, even at a low TeV scale, the canonical seesaw mechanism can be naturally implemented in the exact solution of a particular 3-3-1 gauge model, since a very small alteration ε in the parameter matrix of the Higgs sector is taken into account. Therefore, this new parameter can act as an appropriate mass source for neutrinos, while, due to the main parameter a, all the previously achieved results in the exact solution of the model are recovered. Moreover, this mathematical artifice does separate the boson mass spectrum from the neutrino mass issue, hence giving more flexibility in tuning the model. Possible phenomenological results and their implications — such as dark matter plausible candidates that can occur — are also briefly discussed.
TOPOLOGICAL HYPERMULTIPLET ON N = 2 TWISTED SUPERSPACE IN FOUR DIMENSIONS
Authors: KATO JUNJI , MIYAKE AKIKO
Published: November 2006

We propose an N = 2 twisted superspace formalism with a central charge in four dimensions by introducing a Dirac–Kähler twist. Using this formalism, we construct an off-shell twisted hypermultiplet action and find an explicit form of fermionic scalar, vector and tensor transformations. We construct an off-shell Donaldson–Witten theory coupled to the twisted hypermultiplet. We show that this action possesses N = 4 twisted supersymmetry at the on-shell level. It turns out that the four-dimensional Dirac–Kähler twist is equivalent to Marcus' twist.
INFLUENCE OF DISTORTION IN THE HOMOGENIZATION OF FIBER-REINFORCED COMPOSITES
Authors: BONNETIER ERIC , KHAYAT FATEN
Published: November 2006

We consider fiber-reinforced composites, where the fibers present some distortion in their longitudinal direction. The length scale of this distorsion is much larger than the spacing of the fibers. We derive asymptotic formulas for a conduction problem. Reiterated homogenization, i.e. homogenizing with respect to the smallest length scale, then with respect to the largest does not capture the effects of distortion. Instead, we use a representation formula to show how distortion influences the correction terms.
Diametrically contractive maps and fixed points
Authors: Baronti Marco , Casini Emanuele , Papini Pier Luigi
Published: November 2006

Contractive maps have nice properties concerning fixed points; a big amount of literature has been devoted to fixed points of nonexpansive maps. The class of shrinking (or strictly contractive) maps is slightly less popular: few specific results on them (not applicable to all nonexpansive maps) appear in the literature and some interesting problems remain open. As an attempt to fill this gap, a condition half way between shrinking and contractive maps has been studied recently. Here we continue the study of the latter notion, solving some open problems concerning these maps.
Strong convergence theorems for asymptotically nonexpansive mappings and asymptotically nonexpansive semigroups
Authors: Su Yongfu , Qin Xiaolong
Published: November 2006

Strong convergence theorems are obtained from modified Halpern iterative scheme for asymptotically nonexpansive mappings and asymptotically nonexpansive semigroups, respectively. Our results extend and improve the recent ones announced by Nakajo, Takahashi, Kim, Xu, and some others.
Effect of Bacterial Endotoxins on Superovulated Mouse Embryos In Vivo: Is CSF‐1 Involved in Endotoxin‐Induced Pregnancy Loss?
Authors: Jaiswal Yogesh Kumar , Chaturvedi Madan Mohan , Deb Kaushik
Published: November 2006

Mammalian embryonic development is regulated by several cytokines and growth factors from embryonic or maternal origins. Since CSF‐1 plays important role in embryonic development and implantation, we investigated its role in gram‐negative bacterial LPS‐induced implantation failure. The effect of LPS on normal (nonsuperovulated) and superovulated in vivo‐produced embryos was assessed by signs of morphological degeneration. A significantly similar number of morphologically degenerated embryos recovered from both nonsuperovulated and superovulated LPS treated animals on day 2.5 of pregnancy onwards were morphologically and developmentally abnormal as compared to their respective controls (P < .001. Normal CSF‐1 expression level and pattern were also altered through the preimplantation period in the mouse embryos and uterine horns after LPS treatment. This deviation from the normal pattern and level of CSF‐1 expression in the preimplantation embryos and uterine tissues suggest a role for CSF‐1 in LPS‐induced implantation failure.
Optimization of Spiral MRI Using a Perceptual Difference Model
Authors: Huo Donglai , Salem Kyle A. , Jiang Yuhao , Wilson David L.
Published: November 2006

We systematically evaluated a variety of MR spiral imaging acquisition and reconstruction schemes using a computational perceptual difference model (PDM) that models the ability of humans to perceive a visual difference between a degraded “fast” MRI image with subsampling ofk‐space and a “gold standard” image mimicking full acquisition. Human subject experiments performed using a modified double‐stimulus continuous‐quality scale (DSCQS) correlated well with PDM, over a variety of images. In a smaller set of conditions, PDM scores agreed very well with human detectability measurements of image quality. Having validated the technique, PDM was used to systematically evaluate 2016 spiral image conditions (six interleave patterns, seven sampling densities, three density compensation schemes, four reconstruction methods, and four noise levels). Voronoi (VOR) with conventional regridding gave the best reconstructions. At a fixed sampling density, more interleaves gave better results. With noise present more interleaves and samples were desirable. With PDM, conditions were determined where equivalent image quality was obtained with 50% sampling in noise‐free conditions. We conclude that PDM scoring provides an objective, useful tool for the assessment of fast MR image quality that can greatly aid the design of MR acquisition and signal processing strategies.
Transformation groups on real plane and their differential invariants
Authors: Nesterenko Maryna O.
Published: November 2006

Complete sets of bases of differential invariants, operators of invariant differentiation, and Lie determinants of continuous transformation groups acting on the real plane are constructed. As a necessary preliminary, realizations of finite‐dimensional Lie algebras on the real plane are revisited.
Some relations between variational‐like inequalities and efficientsolutions of certain nonsmooth optimization problems
Authors: Santos Lucelina Batista , Rojas-Medar Marko A. , Rufián-Lizana Antonio
Published: November 2006

We study the equivalence between the solutions of the
variational‐like inequality problem and the solutions of certain
nonsmooth and nonconvex vectorial optimization problem.
Existence of positive periodic solution of a periodic cooperativemodel with delays and impulses
Authors: Li Yongkun , Xing Wenya
Published: November 2006

Sufficient conditions are obtained for the existence of at least
one positive periodic solution of a periodic cooperative model
with delays and impulses by using Mawhin′s continuation theorem of
coincidence degree theory.
Invariant triple products
Authors: Deitmar Anton
Published: November 2006

It is shown that the space of invariant trilinear forms on smooth representations of a semisimple Lie group is finite dimensional if the group is a product of hyperbolic groups. Explicit upper bounds are given which are attained in the case of induced representations. Applications to automorphic coefficients are given.
Interaction between coefficient conditions and solution conditionsof differential equations in the unit disk
Authors: Fowler K. E. , Sons L. R.
Published: November 2006

The influence of the normality of the coefficient A(z) of the differential equation f(k) + A(z)f = 0 on a solution f and also the influence of the normality of a solution f on A(z) are investigated in the unit disk. In particular, an estimate of P.
Lappan is used to determine restrictions on the growth of a
meromorphic function A(z) when a solution f is α‐normal.
Structure of rings with certain conditions on zero divisors
Authors: Abu-Khuzam Hazar , Yaqub Adil
Published: November 2006

Let R be a ring such that every zero divisor x is expressible as a sum of a nilpotent element and a potent element of R : x = a + b, where a is nilpotent, b is potent, and ab = ba. We call such a ring a D*‐ring. We give the structure of periodic D*‐ring, weakly periodic D*‐ring, Artinian D*‐ring, semiperfect D*‐ring, and other classes of D*‐ring.
Existence and bifurcation for some elliptic problems on exteriorstrip domains
Authors: Hsu Tsing-San
Published: November 2006

We consider the semilinear elliptic problem −Δu + u = λK(x)up + f(x) in Ω, u > 0 in Ω, , where λ ≥ 0, N ≥ 3, 1 < p < (N + 2)/(N − 2), and
Ω is an exterior strip domain in ℝN. Under some suitable conditions on K(x) and f(x), we show that there exists a positive constant λ∗ such that the above semilinear elliptic problem has at least two solutions if λ ∈ (0, λ∗), a unique
positive solution if λ = λ∗, and no solution if
λ > λ∗. We also obtain some bifurcation results of the solutions at λ = λ∗.