bluuebunny/crossref_metadata_2025 huggingface dataset:
Molecular Analysis of an Inactive Aflatoxin Biosynthesis Gene Cluster in
Aspergillus oryzae
RIB Strains
Authors: Tominaga Mihoko , Lee Yun-Hae , Hayashi Risa , Suzuki Yuji , Yamada Osamu , Sakamoto Kazutoshi , Gotoh Kuniyasu , Akita Osamu
Published: January 2006

To help assess the potential for aflatoxin production by
Aspergillus oryzae
, the structure of an aflatoxin biosynthesis gene homolog cluster in
A. oryzae
RIB 40 was analyzed. Although most genes in the corresponding cluster exhibited from 97 to 99% similarity to those of
Aspergillus flavus
, three genes shared 93% similarity or less. A 257-bp deletion in the
aflT
region, a frameshift mutation in
norA
, and a base pair substitution in
verA
were found in
A. oryzae
RIB 40. In the
aflR
promoter, two substitutions were found in one of the three putative AreA binding sites and in the FacB binding site. PCR primers were designed to amplify homologs of
aflT
,
nor-1
,
aflR
,
norA
,
avnA
,
verB
, and
vbs
and were used to detect these genes in 210
A. oryzae
strains. Based on the PCR results, the
A. oryzae
RIB strains were classified into three groups, although most of them fell into two of the groups. Group 1, in which amplification of all seven genes was confirmed, contained 122 RIB strains (58.1% of examined strains), including RIB 40. Seventy-seven strains (36.7%) belonged to group 2, characterized by having only
vbs
,
verB
, and
avnA
in half of the cluster. Although slight expression of
aflR
was detected by reverse transcription-PCR in some group 1 strains, including RIB 40, other genes (
avnA
,
vbs
,
verB
, and
omtA
) related to aflatoxin production were not detected.
aflR
was not detected in group 2 strains by Southern analysis.
Deep Desulfurization of Diesel Oil and Crude Oils by a Newly Isolated
Rhodococcus erythropolis
Strain
Authors: Yu Bo , Xu Ping , Shi Quan , Ma Cuiqing
Published: January 2006

The soil-isolated strain XP was identified as
Rhodococcus erythropolis. R. erythropolis
XP could efficiently desulfurize benzonaphthothiophene, a complicated model sulfur compound that exists in crude oil. The desulfurization product of benzonaphthothiophene was identified as α-hydroxy-β-phenyl-naphthalene. Resting cells could desulfurize diesel oil (total organic sulfur, 259 ppm) after hydrodesulfurization. The sulfur content of diesel oil was reduced by 94.5% by using the resting cell biocatalyst for 24 h at 30°C. Biodesulfurization of crude oils was also investigated. After 72 h of treatment at 30°C, 62.3% of the total sulfur content in Fushun crude oil (initial total sulfur content, 3,210 ppm) and 47.2% of that in Sudanese crude oil (initial total sulfur, 1,237 ppm) were removed. Gas chromatography with pulsed-flame photometric detector analysis was used to evaluate the effect of
R. erythropolis
XP treatment on the sulfur content in Fushun crude oil, and it was shown that most organic sulfur compounds were eliminated after biodesulfurization.
Aerobic Anoxygenic Phototrophic Bacteria in the Mid-Atlantic Bight and the North Pacific Gyre
Authors: Cottrell Matthew T. , Mannino Antonio , Kirchman David L.
Published: January 2006

The abundance of aerobic anoxygenic phototrophic (AAP) bacteria, cyanobacteria, and heterotrophs was examined in the Mid-Atlantic Bight and the central North Pacific Gyre using infrared fluorescence microscopy coupled with image analysis and flow cytometry. AAP bacteria comprised 5% to 16% of total prokaryotes in the Atlantic Ocean but only 5% or less in the Pacific Ocean. In the Atlantic, AAP bacterial abundance was as much as 2-fold higher than that of
Prochlorococcus
spp. and 10-fold higher than that of
Synechococcus
spp. In contrast,
Prochlorococcus
spp. outnumbered AAP bacteria 5- to 50-fold in the Pacific. In both oceans, subsurface abundance maxima occurred within the photic zone, and AAP bacteria were least abundant below the 1% light depth. The abundance of AAP bacteria rivaled some groups of strictly heterotrophic bacteria and was often higher than the abundance of known AAP bacterial genera (
Erythrobacter
and
Roseobacter
spp.). Concentrations of bacteriochlorophyll
a
(BChl
a
) were low (∼1%) compared to those of chlorophyll
a
in the North Atlantic. Although the BChl
a
content of AAP bacteria per cell was typically 20- to 250-fold lower than the divinyl-chlorophyll
a
content of
Prochlorococcus
, the pigment content of AAP bacteria approached that of
Prochlorococcus
in shelf break water. Our results suggest that AAP bacteria can be quite abundant in some oceanic regimes and that their distribution in the water column is consistent with phototrophy.
Presence and Growth of Naturalized
Escherichia coli
in Temperate Soils from Lake Superior Watersheds
Authors: Ishii Satoshi , Ksoll Winfried B. , Hicks Randall E. , Sadowsky Michael J.
Published: January 2006

The presence of
Escherichia coli
in water is used as an indicator of fecal contamination, but recent reports indicate that soil populations can also be detected in tropical, subtropical, and some temperate environments. In this study, we report that viable
E. coli
populations were repeatedly isolated from northern temperate soils in three Lake Superior watersheds from October 2003 to October 2004. Seasonal variation in the population density of soilborne
E. coli
was observed; the greatest cell densities, up to 3 × 10
3
CFU/g soil, were found in the summer to fall (June to October), and the lowest numbers, ≤1 CFU/g soil, occurred during the winter to spring months (February to May). Horizontal, fluorophore-enhanced repetitive extragenic palindromic PCR (HFERP) DNA fingerprint analyses indicated that identical soilborne
E. coli
genotypes, those with ≥92% similarity values, overwintered in frozen soil and were present over time. Soilborne
E. coli
strains had HFERP DNA fingerprints that were unique to specific soils and locations, suggesting that these
E. coli
strains became naturalized, autochthonous members of the soil microbial community. In laboratory studies, naturalized
E. coli
strains had the ability to grow and replicate to high cell densities, up to 4.2 × 10
5
CFU/g soil, in nonsterile soils when incubated at 30 or 37°C and survived longer than 1 month when soil temperatures were ≤25°C. To our knowledge, this is the first report of the growth of naturalized
E. coli
in nonsterile, nonamended soils. The presence of significant populations of naturalized populations of
E. coli
in temperate soils may confound the use of this bacterium as an indicator of fecal contamination.
Involvement of NarK1 and NarK2 Proteins in Transport of Nitrate and Nitrite in the Denitrifying Bacterium
Pseudomonas aeruginosa
PAO1
Authors: Sharma Vandana , Noriega Chris E. , Rowe John J.
Published: January 2006

Two transmembrane proteins were tentatively classified as NarK1 and NarK2 in the
Pseudomonas
genome project and hypothesized to play an important physiological role in nitrate/nitrite transport in
Pseudomonas aeruginosa
. The
narK1
and
narK2
genes are located in a cluster along with the structural genes for the nitrate reductase complex. Our studies indicate that the transcription of all these genes is initiated from a single promoter and that the gene complex
narK1K2GHJI
constitutes an operon. Utilizing an isogenic
narK1
mutant, a
narK2
mutant, and a
narK1K2
double mutant, we explored their effect on growth under denitrifying conditions. While the Δ
narK1
::Gm mutant was only slightly affected in its ability to grow under denitrification conditions, both the Δ
narK2
::Gm and Δ
narK1K2
::Gm mutants were found to be severely restricted in nitrate-dependent, anaerobic growth. All three strains demonstrated wild-type levels of nitrate reductase activity. Nitrate uptake by whole-cell suspensions demonstrated both the
ΔnarK2
::Gm and Δ
narK1K2
::Gm mutants to have very low yet different nitrate uptake rates, while the Δ
narK1
::Gm mutant exhibited wild-type levels of nitrate uptake. Finally,
Escherichia coli narK
rescued both the Δ
narK2
::Gm and Δ
narK1K2
::Gm mutants with respect to anaerobic respiratory growth. Our results indicate that only the NarK2 protein is required as a nitrate/nitrite transporter by
Pseudomonas aeruginosa
under denitrifying conditions.
Involvement of Quinolinate Phosphoribosyl Transferase in Promotion of Potato Growth by a
Burkholderia
Strain
Authors: Wang Keri , Conn Kenneth , Lazarovits George
Published: January 2006

Burkholderia
sp. strain PsJN stimulates root growth of potato explants compared to uninoculated controls under gnotobiotic conditions. In order to determine the mechanism by which this growth stimulation occurs, we used Tn
5
mutagenesis to produce a mutant, H41, which exhibited no growth-promoting activity but was able to colonize potato plants as well as the wild-type strain. The gene associated with the loss of growth promotion in H41 was shown to exhibit 65% identity at the amino acid level to the
nadC
gene encoding quinolinate phosphoribosyltransferase (QAPRTase) in
Ralstonia solanacearum
. Complementation of H41 with QAPRTase restored growth promotion of potato explants by this mutant. Expression of the gene identified in
Escherichia coli
yielded a protein with QAPRTase activities that catalyzed the de novo formation of nicotinic acid mononucleotide (NaMN). Two other genes involved in the same enzymatic pathway,
nadA
and
nadB
, were physically linked to
nadC
. The
nadA
gene was cotranscribed with
nadC
as an operon in wild-type strain PsJN, while the
nadB
gene was located downstream of the
nadA
-
nadC
operon. Growth promotion by H41 was fully restored by addition of NaMN to the tissue culture medium. These data suggested that QAPRTase may play a role in the signal pathway for promotion of plant growth by PsJN.
Transmission of Nephridial Bacteria of the EarthwormEisenia fetida
Authors: Davidson Seana K. , Stahl David A.
Published: January 2006

The lumbricid earthworms (annelid family Lumbricidae) harbor gram-negative bacteria in their excretory organs, the nephridia. Comparative 16S rRNA gene sequencing of bacteria associated with the nephridia of several earthworm species has shown that each species of worm harbors a distinct bacterial species and that the bacteria from different species form a monophyletic cluster within the genusAcidovorax, suggesting that there is a specific association resulting from radiation from a common bacterial ancestor. Previous microscopy and culture studies revealed the presence of bacteria within the egg capsules and on the surface of embryos but did not demonstrate that the bacteria within the egg capsule were the same bacteria that colonized the nephridia. We present evidence, based on curing experiments, in situ hybridizations withAcidovorax-specific probes, and 16S rRNA gene sequence analysis, that the egg capsules contain high numbers of the bacterial symbiont and that juveniles are colonized during development within the egg capsule. Studies exposing aposymbiotic hatchlings to colonized adults and their bedding material suggested that juvenile earthworms do not readily acquire bacteria from the soil after hatching but must be colonized during development by bacteria deposited in the egg capsule. Whether this is due to the developmental stage of the host or the physiological state of the symbiont remains to be investigated.
Evolutionary Dynamics ofwAu-LikeWolbachiaVariants in NeotropicalDrosophilaspp
Authors: Miller Wolfgang J. , Riegler Markus
Published: January 2006

Wolbachiabacteria are common intracellular symbionts of arthropods and have been extensively studied inDrosophila. Most research focuses on two Old Word hosts,Drosophila melanogasterandDrosophila simulans, and does not take into account that some of theWolbachiaassociations in these species may have evolved only after their fast global expansion and after the exposure toWolbachiaof previously isolated habitats. Here we looked atWolbachiaof NeotropicalDrosophilaspecies. Seventy-one lines of 16 NeotropicalDrosophilaspecies sampled in different regions and at different time points were analyzed.Wolbachiais absent in lines ofDrosophila willistonicollected before the 1970s, but more recent samples are infected with a strain designatedwWil.Wolbachiais absent in all other species of the willistoni group. PolymorphicwWil-related strains were detected in some saltans group species, withD. septentriosaltansbeing coinfected with at least four variants. Based onwspandftsZsequence data,wWil ofD. willistoniis identical towAu, a strain isolated fromD. simulans, but can be discriminated when using a polymorphic minisatellite marker. In contrast towAu, which infects both germ line and somatic tissues ofD. simulans,wWil is found exclusively in the primordial germ line cells ofD. willistoniembryos. We report on a pool of closely relatedWolbachiastrains in NeotropicalDrosophilaspecies as a potential source for thewAu strain inD. simulans. Possible evolutionary scenarios reconstructing the infection history ofwAu-likeWolbachiain NeotropicalDrosophilaspecies and the Old World speciesD. simulansare discussed.
Transcriptomic and Proteomic Approach for Understanding the Molecular Basis of Adaptation of
Saccharomyces cerevisiae
to Wine Fermentation
Authors: Zuzuarregui Aurora , Monteoliva Lucía , Gil Concha , del Olmo Marcel·lí
Published: January 2006

Throughout alcoholic fermentation,
Saccharomyces cerevisiae
cells have to cope with several stress conditions that could affect their growth and viability. In addition, the metabolic activity of yeast cells during this process leads to the production of secondary compounds that contribute to the organoleptic properties of the resulting wine. Commercial strains have been selected during the last decades for inoculation into the must to carry out the alcoholic fermentation on the basis of physiological traits, but little is known about the molecular basis of the fermentative behavior of these strains. In this work, we present the first transcriptomic and proteomic comparison between two commercial strains with different fermentative behaviors. Our results indicate that some physiological differences between the fermentative behaviors of these two strains could be related to differences in the mRNA and protein profiles. In this sense, at the level of gene expression, we have found differences related to carbohydrate metabolism, nitrogen catabolite repression, and response to stimuli, among other factors. In addition, we have detected a relative increase in the abundance of proteins involved in stress responses (the heat shock protein Hsp26p, for instance) and in fermentation (in particular, the major cytosolic aldehyde dehydrogenase Ald6p) in the strain with better behavior during vinification. Moreover, in the case of the other strain, higher levels of enzymes required for sulfur metabolism (Cys4p, Hom6p, and Met22p) are observed, which could be related to the production of particular organoleptic compounds or to detoxification processes.
Gene Targeting in the Gram-Positive Bacterium
Lactococcus lactis
, Using Various Delta Ribozymes
Authors: Fiola Karine , Perreault Jean-Pierre , Cousineau Benoit
Published: January 2006

The
trans
-acting antigenomic delta ribozyme, isolated from the human hepatitis delta virus, was shown to be highly stable and active in vitro, as well as in mammalian cell lines. However, the stability and gene-targeting competence of this small ribozyme have not been studied previously in bacterial cells. In this paper we describe the use of two variants of the
trans
-acting antigenomic delta ribozyme targeting the abundant EF-Tu mRNA in the industrially important gram-positive bacterium
Lactococcus lactis
. These two delta ribozyme variants were expressed at significant levels and were shown to be highly stable in vivo. The half-life of the EF-Tu mRNA was slightly but consistently reduced in the presence of the classical delta ribozymes (7 to 13%). In contrast, delta ribozymes harboring a specific on/off riboswitch (SOFA-delta ribozymes) targeting the same sites on the EF-Tu mRNA considerably reduced the half-life of this mRNA (22 to 47%). The rates of catalysis of the SOFA-delta ribozymes in
L. lactis
were similar to the rates determined in vitro, showing that this new generation of delta ribozymes was highly efficient in these bacterial cells. Clearly, SOFA-delta ribozymes appear to be an ideal means for development of gene inactivation systems in bacteria.
Sensitive Determination of Microbial Growth by Nucleic Acid Staining in Aqueous Suspension
Authors: Martens-Habbena Willm , Sass Henrik
Published: January 2006

The determination of cell numbers or biomass in laboratory cultures or environmental samples is usually based on turbidity measurements, viable counts, biochemical determinations (e.g., protein and lipid measurements), microscopic counting, or recently, flow cytometric analysis. In the present study, we developed a novel procedure for the sensitive quantification of microbial cells in cultures and most-probable-number series. The assay combines fluorescent nucleic acid staining and subsequent fluorescence measurement in suspension. Six different fluorescent dyes (acridine orange, DAPI [4′,6′-diamidino-2-phenylindole], ethidium bromide, PicoGreen, and SYBR green I and II) were evaluated. SYBR green I was found to be the most sensitive dye and allowed the quantification of 50,000 to up to 1.5 × 10
8
Escherichia coli
cells per ml sample. The rapid staining procedure was robust against interference from rRNA, sample fixation by the addition of glutaric dialdehyde, and reducing agents such as sodium dithionite, sodium sulfide, and ferrous sulfide. It worked well with phylogenetically distant bacterial and archaeal strains. Excellent agreement with optical density measurements of cell increases was achieved during growth experiments performed with aerobic and sulfate-reducing bacteria. The assay offers a time-saving, more sensitive alternative to epifluorescence microscopy analysis of most-probable-number dilution series. This method simplifies the quantification of microbial cells in pure cultures as well as enrichments and is particularly suited for low cell densities.
Heat Resistance and Mechanism of Heat Inactivation in Thermophilic Campylobacters
Authors: Nguyen Hong T. T. , Corry Janet E. L. , Miles Christopher A.
Published: January 2006

The heat resistance of
Campylobacter jejuni
strains AR6 and L51 and the heat resistance of
Campylobacter coli
strains DR4 and L6 were measured over the temperature range from 50 to 60°C by two methods. Isothermal measurements yielded
D
55
values in the range from 4.6 to 6.6 min and
z
values in the range from 5.5 to 6.3°C. Dynamic measurements using differential scanning calorimetry (DSC) during heating at a rate of 10°C/min yielded
D
55
values of 2.5 min and 3.4 min and
z
values of 6.3°C and 6.5°C for AR6 and DR4, respectively. Both dynamic and isothermal methods yielded mean
D
55
values that were substantially greater than those reported previously (0.75 to 0.95 min). DSC analysis of each strain during heating at a rate of 10°C/min yielded a complex series of overlapping endothermic peaks, which were assigned to cell wall lipids, ribosomes, and DNA. Measurement of the decline in the numbers of CFU in calorimetric samples as they were heated showed that the maximum rate of cell death occurred at 56 to 57°C, which is close to the value predicted mathematically from the isothermal measurements of
D
and
z
(61°C). Both estimates were very close to the peak
m
1
values, 60 to 62°C, which were tentatively identified with unfolding of the 30S ribosome subunit, showing that cell death in
C. jejuni
and
C. coli
coincided with unfolding of the most thermally labile regions of the ribosome. Other measurements indicated that several essential proteins, including the α and β subunits of RNA polymerase, might also unfold at the same time and contribute to cell death.
Relating Cell Killing to Inactivation of Critical Components
Authors: Miles Christopher A.
Published: January 2006

In this paper I relate the loss of CFU following a life-threatening treatment to the inactivation of critical components. Equations are used to calculate the loss of CFU following isothermal and temperature-scanning treatments, and the results are discussed in relation to differential scanning calorimetry of bacteria.
Sequential Multiplex PCR Approach for Determining Capsular Serotypes of
Streptococcus pneumoniae
Isolates
Authors: Pai Rekha , Gertz Robert E. , Beall Bernard
Published: January 2006

Accurate serotyping is essential to monitor the changes in the seroepidemiology of
Streptococcus pneumoniae
. We devised a simple and schematic sequence-based system of seven multiplex PCRs, in a sequence order based upon Active Bacterial Core surveillance (ABCs) serotype distribution during 2002 to 2003, to reliably deduce specific pneumococcal serotypes. A total of 421 isolates from ABCs were randomly chosen to evaluate this system. Two hundred twenty-nine of the isolates (54.3%) were specifically assigned 1 of 17 serotypes by the multiplex PCR system, with the results in complete concordance with conventional serotyping. One hundred seventy-two additional isolates (40.9%) were assigned to 11 specific sets of 2 to 4 serotypes that with one exception (serotypes 6A and 6B) consisted of the single frequently occurring targeted serotype and 1 to 3 additional rare serotypes primarily within the same serogroup as the targeted serotype. Only 20 isolates (4.8%) could not be assigned specific serotypes or serotype sets, since they were either of rare serotypes not included in the assay design or were nonserotypeable. Overall, we found this system to be highly reliable, with the potential to greatly reduce our reliance upon conventional serotyping. Especially important is the capability of this system to give serotype-determining potential to any facility that lacks the expensive typing sera and expertise needed for conventional serotyping yet has the modest equipment necessary for DNA amplification and electrophoresis.
Molecular Characterization of
Haemophilus ducreyi
Isolates from Different Geographical Locations
Authors: Mbwana J. , Bölin I. , Lyamuya E. , Mhalu F. , Lagergård T.
Published: January 2006

The technique of random amplified polymorphic DNA (RAPD) was adapted and optimized to study
Haemophilus ducreyi
isolates. A panel of 43 strains isolated from chancroid patients from different countries in Africa, Europe, North America, and Asia were characterized. The strains were also studied with respect to lipooligosaccharide (LOS) migration and immunoblotting patterns and the presence of cytolethal distending toxin genes. The RAPD method with the OPJ20 primer generated nine banding patterns (1 to 9). The majority of the isolates were clustered into two major profiles, 14 and 13 strains into profiles 1 and 2, respectively, and just a few strains revealed patterns 3 and 4. The isolates from Thailand were exceptional in that they showed greater diversity and were represented by six different RAPD patterns, i.e., patterns 3 and 5 to 9. The LOS migration and immunoblotting analyses revealed two different patterns, which indicated long and short forms of LOS; the former was found in 20/23 tested strains. Two strains that expressed the short form of LOS were grouped into RAPD pattern 4. The absence of
cdtABC
genes was observed in only 4/23 strains, and three of these isolates were assigned to RAPD pattern 4. Our results showed limited genotypic and phenotypic variations among
H. ducreyi
strains, as supported by the conserved RAPD and LOS profiles shared by the majority of the studied strains. However, the RAPD method identified differences between strains, including those from different geographic areas, which indicate the potential of RAPD as an epidemiological tool for the typing of
H. ducreyi
isolates in countries where chancroid is endemic.
Evolution and Molecular Characterization of Methicillin-Resistant
Staphylococcus aureus
Epidemic and Sporadic Clones in Cordoba, Argentina
Authors: Sola Claudia , Cortes Paulo , Saka Hector A. , Vindel Ana , Bocco José Luis
Published: January 2006

Since 1999, a new, epidemic, methicillin-resistant
Staphylococcus aureus
(MRSA) strain, named the “Cordobes clone,” has emerged in Argentina and coexists with the pandemic Brazilian clone. The purpose of this study was to determine the stability over time of the new clone and to investigate its evolutionary relationship with epidemic international MRSA lineages and with other MRSA and methicillin-susceptible
S. aureus
(MSSA) major clones distributed in this region. One hundred three MRSA isolates recovered in 2001 from Cordoba, Argentina, hospitals and 31 MSSA strains collected from 1999 to 2002 were analyzed by their antibiotic resistance patterns, phage typing, and pulsed-field gel electrophoresis. Additionally, representative members of most MRSA defined genotypes (A, B, C, E, K, and I) were characterized by multilocus sequence typing (MLST) and
spaA
and SCC
mec
typing. The most prevalent MSSA pulsotypes were also analyzed by MLST. Our results support the displacement of the Brazilian clone (sequence type [ST] 239,
spaA
type WGKAOMQ, SCC
mec
type IIIA) by the Cordobes clone (ST5,
spaA
type TIMEMDMGMGMK, SCC
mec
type I) in the hospital environment. MRSA and MSSA isolates shared only ST5. The data support the origin of the Cordobes clone as a member of a lineage that includes the pediatric and New York/Japan international clones and that is genetically related to the British EMRSA-3 strain. Interestingly, the pediatric clone, isolated from most community-acquired infections in Cordoba, was characterized by ST100, a single-locus variant of ST5 and a new variant of SCC
mec
type related to SCC
mec
type IVc.
Community-Associated Methicillin-Resistant
Staphylococcus aureus
Epidemic Clone USA300 in Isolates from Florida and Washington
Authors: Roberts Jill C. , Krueger Robin L. , Peak K. Kealy , Veguilla William , Cannons Andrew C. , Amuso Philip T. , Cattani Jacqueline
Published: January 2006

We examined 299 methicillin-resistant, community-associated
Staphylococcus aureus
isolates from Florida and Washington State for the presence of the USA300 epidemic clone. Pulsed-field gel electrophoresis demonstrated the epidemic clone in 43% of our
S. aureus
strains and in isolates from both states. The majority of the USA300 isolates (88%) were from wound infections.
Novel PCR-Restriction Fragment Length Polymorphism Analysis for Rapid Typing of Staphylococcal Cassette Chromosome
mec
Elements
Authors: Yang Jin Ah , Park Dae Won , Sohn Jang Wook , Kim Min Ja
Published: January 2006

We developed a novel PCR-restriction fragment length polymorphism test for the
ccrB
gene by using HinfI and BsmI for rapid typing of staphylococcal cassette chromosome
mec
(SCC
mec
). When tested with reference strains and methicillin-resistant
Staphylococcus aureus
isolates, the method proved to be valid and useful for rapid identification of four SCC
mec
types, especially type IV.
Serological Evidence for Increased Human Exposure to
Burkholderia pseudomallei
following the Tsunami in Southern Thailand
Authors: Wuthiekanun Vanaporn , Chierakul Wirongrong , Rattanalertnavee Jurairat , Langa Sayan , Sirodom Damrong , Wattanawaitunechai Charnkij , Winothai Wut , White Nicholas J. , Day Nicholas , Peacock Sharon J.
Published: January 2006

A serological study was performed to determine recent human exposure to
Burkholderia pseudomallei
(the cause of melioidosis) in residents of southern Thailand affected by the tsunami of 26 December 2004. The findings were suggestive of increased recent exposure in both tsunami survivors and uninjured bystanders. Survivors of the Thailand tsunami may be at increased risk of melioidosis.
Use of Variations in Staphylococcal Interspersed Repeat Units for Molecular Typing of Methicillin-Resistant
Staphylococcus aureus
Strains
Authors: Hardy Katherine J. , Oppenheim Beryl A. , Gossain Savita , Gao Fang , Hawkey Peter M.
Published: January 2006

Staphylococcal interspersed repeat unit typing has previously been shown to have the ability to discriminate between epidemic methicillin-resistant
Staphylococcus aureus
strains in the United Kingdom. The current study illustrates its ability to distinguish between strains within an endemic setting thereby providing a rapid transportable typing method for the identification of transmission events.
Molecular Analysis of Human and Bovine Tubercle Bacilli from a Local Setting in Nigeria
Authors: Cadmus Simeon , Palmer Si , Okker Melissa , Dale James , Gover Karen , Smith Noel , Jahans Keith , Hewinson R. Glyn , Gordon Stephen V.
Published: January 2006

To establish a molecular epidemiological baseline for the strains causing tuberculosis in Nigeria, a survey of isolates from humans and cattle was carried out. Spoligotyping and variable-number tandem-repeat analysis revealed that the majority of tuberculosis disease in humans in Ibadan, southwestern Nigeria, is caused by a single, closely related group of
Mycobacterium tuberculosis
strains. Using deletion typing, we show that approximately 13% of the disease in humans in this sample was caused by strains of
Mycobacterium africanum
and
Mycobacterium bovis
rather than
M. tuberculosis
. Molecular analysis of strains of
M. bovis
recovered from Nigerian cattle show that they form a group of closely related strains that show similarity to strains from neighboring Cameroon. Surprisingly, the strains of
M. bovis
recovered from humans do not match the molecular type of the cattle strains, and possible reasons for this are discussed. This is the first molecular analysis of
M. tuberculosis
complex strains circulating among humans and cattle in Nigeria, the results of which have significant implications for disease control.
Development and Evaluation of a Real-Time PCR Assay Targeting the Type III Secretion System of
Burkholderia pseudomallei
Authors: Novak Ryan T. , Glass Mindy B. , Gee Jay E. , Gal Daniel , Mayo Mark J. , Currie Bart J. , Wilkins Patricia P.
Published: January 2006

Here we report on the development of a discriminatory real-time assay for the rapid identification of
Burkholderia pseudomallei
isolates and the evaluation of this assay for sensitivity against related species and detection in spiked human blood samples. The assay targets a 115-base-pair region within
orf2
of the
B. pseudomallei
type III secretion system gene cluster and distinguishes
B. pseudomallei
from other microbial species. Assay performance was evaluated with 224 geographically, temporally, and clinically diverse
B. pseudomallei
isolates from the Centers for Disease Control and Prevention strain collection. This represents the first real-time PCR for rapid and sensitive identification of
B. pseudomallei
that has been tested for cross-reactivity with 23
Burkholderia mallei
, 5
Burkholderia thailandensis
, and 35
Burkholderia
and 76 non
-Burkholderia
organisms which have historically presented diagnostic challenges. The assay performed with 100% specificity. The limit of detection was found to be 76 femtograms of DNA (equivalent to 5.2 × 10
3
genome equivalents per ml) in a single PCR. In spiked human blood, the assay could detect as few as 8.4 × 10
3
CFU per ml. This rapid assay is a valuable tool for identification of
B. pseudomallei
and may improve diagnosis in regions endemic for melioidosis.
ISOLATING COSTS IN SHARED MEMORY COMMUNICATION BUFFERING
Authors: BYNA SURENDRA , CAMERON KIRK W. , SUN XIAN-HE
Published: January 2006

Communication in parallel applications is a combination of data transfers internally at a source or destination and across the network. Previous research focused on quantifying network transfer costs has indirectly resulted in reduced overall communication cost. Optimized data transfer from source memory to the network interface has received less attention. In shared memory systems, such memory-to-memory transfers dominate communication cost. In distributed memory systems, memory-to-network interface transfers grow in significance as processor and network speeds increase at faster rates than memory latency speeds. Our objective is to minimize the cost of internal data transfers. The following examples illustrating the impact of memory transfers on communication, we present a methodology for classifying the effects of data size and data distribution on hardware, middleware, and application software performance. This cost is quantified using hardware counter event measurements on the SGI Origin 2000. For the SGI O2K, we empirically identify the cost caused by just copying data from one buffer to another and the middleware overhead. We use MPICH in our experiments, but our techniques are generally applicable to any communication implementation.
TOWARDS AN XML BASED DATAGRID DESCRIPTION LANGUAGE
Authors: SCHIKUTA ERICH
Published: January 2006

We present xDGDL, an approach towards a concise but comprehensive Datagrid description language. Our framework is based on XML and allows to store syntactical and semantical information together with arbitrary files. This information can be used to administer, locate, search and process data stored on the Grid.
THE IMPROVED PARALLEL ICGS METHOD FOR LARGE AND SPARSE UNSYMMETRIC LINEAR SYSTEMS
Authors: Yang Laurence Tianruo
Published: January 2006

For the solutions of large and sparse linear systems of equations with unsymmetric coefficient matrices, we propose an improved version of the Conjugate Gradient Squared method (ICGS) method. The algorithm is derived such that all inner products, matrix-vector multiplications and vector updates of a single iteration step are independent and communication time required for inner product can be overlapped efficiently with computation time of vector updates. Therefore, the cost of global communication on parallel distributed memory computers can be significantly reduced. The resulting ICGS algorithm maintains the favorable properties of the algorithm while not increasing computational costs. Data distribution suitable for both irregularly and regularly structured matrices based on the analysis of the non-zero matrix elements is also presented. Communication scheme is supported by overlapping execution of computation and communication to reduce waiting times. The efficiency of this method is demonstrated by numerical experimental results carried out on a parallel distributed memory system.
Solving the Independent-set Problem in a DNA-Based Supercomputer Model
Authors: CHANG WENG-LONG , GUO MINYI , WU JESSE
Published: January 2006

In this paper, it is demonstrated how the DNA (DeoxyriboNucleic Acid) operations presented by Adleman and Lipton can be used to develop the parallel genetic algorithm that solves the independent-set problem. The advantage of the genetic algorithm is the huge parallelism inherent in DNA based computing. Furthermore, this work represents obvious evidence for the ability of DNA based parallel computing to solve NP-complete problems.
OPTICAL PROPERTIES OF FUNCTIONALIZED POLYTHIOPHENES
Authors: SOMANATHAN N. , RADHAKRISHNAN S.
Published: January 2006

This review focuses on the interrelation between the influences of polymeric structure on the optical properties of polythiophene — a versatile polymer for opto-electronic applications. From the application's point of view, the polymer should either be melt- or solution-processible. Functionalization of polythiophenes really helps for the above. On the other hand, the functionalization at the 3 and/or 4 position of the thiophene ring modifies the band gap of the polymer, which in turn, modifies photo absorption, photo- and electro-emission characteristics of polythiophenes. The present work reviews the influence of the optical properties of polythiophene on the different functional groups present in the thiophene ring.
THERMAL STABILITY OF THE NEW SOLITON TRANSPORTED BIO-ENERGY UNDER INFLUENCE OF FLUCTUATIONS OF CHARACTERISTIC PARAMETERS AT BIOLOGICAL TEMPERATURE IN THE PROTEIN MOLECULES
Authors: PANG XIAO-FENG , ZHANG HUAI-WU , YU JIA-FENG , LUO YU-HUI
Published: January 2006

The dynamic behaviors of the new soliton in the improved Davydov model in the protein molecules at biological temperature have been numerically simulated by utilizing the dynamic equations for the bio-energy transport and the Runge–Kutta way. In this simulation the influences of the temperature and structure disorders of the protein molecules on the soliton transporting the bio-energy have been completely considered. We find that the new soliton is quite stable in the cases of motion of a long time of 300 ps and of disorders of the structures of the proteins at biological temperatures of 300 K–320 K. The disorders of the structures contain the disorder of mass sequence of amino acids and the fluctuations of the coupling constant, force constant and dipole- dipole interaction constant and ground state energy of the proteins, designating the features of its structure and interactions between the particles in it. However, the soliton disperses in the cases of higher temperature of 325 K and larger structure disorders. The numerical results show that the new soliton is very robust against the influences of the thermal perturbation and structure disorders at biological temperature 300 K, its lifetime and critical temperature are at least 300 ps at 300 K and 320 K, respectively. These results are also consistent with analytical data.
DYNAMICAL PHASE TRANSITION IN THE ISING MODEL ON A SCALE-FREE NETWORK
Authors: KRAWIECKI A.
Published: January 2006

Dynamical phase transition in the Ising model on a Barabási–Albert network under the influence of periodic magnetic field is studied using Monte-Carlo simulations. For a wide range of the system sizes N and the field frequencies, approximate phase borders between dynamically ordered and disordered phases are obtained on a plane h (field amplitude) versus T/Tc (temperature normalized to the static critical temperature without external field, Tc∝ ln N). On these borders, second- or first-order transitions occur, for parameter ranges separated by a tricritical point. For all frequencies of the magnetic field, position of the tricritical point is shifted toward higher values of T/Tc and lower values of h with increasing system size, i.e. the range of critical parameters corresponding to the first-order transition is broadened.
MODEL VALIDATION AND TREND STUDY OF A TWIN ELECTRO-RHEOLOGICAL (ER) CLUTCH MECHANISM FOR ROBOTIC APPLICATIONS
Authors: TAN K. P. , STANWAY R. , JOHNSON A. R. , BULLOUGH W. A.
Published: January 2006

Positioning accuracies of the robot arms are important at fast maneuvering speeds of the manipulators. In the past, many researchers had investigated the precisions of the robotic arms. They reported that these robotic positioning errors are caused by the dynamic inefficiencies of the robotic actuators; DC servomotors. Therefore, in order to resolve this actuator's issue, a twin electro-rheological (ER) clutch mechanism that consists of two counter-rotating ER clutches is employed. This is due to its output dynamics being unaffected by the output cogging torque of the driving motors. Also, this clutch mechanism can perform rapid reversal responses in bi-directional mode. In this present paper, two kinematics models that describe the output angular velocity and displacement behaviors of this clutch mechanism undergone validations. Next, the trend studies of these angular kinematics responses are conducted in order to determine the methodology to generate the fastest reversal motions of the clutch mechanism.
EFFECT OF METAL PARTICLES (Mo) INCLUSION INTO INSULATING MATRIX (Al2O3)
Authors: HUSSAIN SABINA , SBAIZERO ORFEO
Published: January 2006

The effect of metal particles ( Mo ) inclusion in an insulating matrix ( Al 2 O 3) has been investigated. The conducting phase ( Mo ) is dispersed in alumina in different amounts (00%, 5%, 10%, 20%, 25% in volume). Two types of Mo particles have been used: the first with an average particle size ≅0.56 μm, the other with an average particle size ≅10.0 μm. All specimens were fabricated by hot pressing. The bulk conductivities have been measured over temperatures ranging from 500°C to 900°C using two-probe impedance spectroscopy within the available frequency range (5 Hz–13 MHz). From the interpretation of the impedance spectra, it has been observed that the bulk conductivity for fine particles of Mo inclusion in alumina is higher than that for large particles of Mo inclusion in alumina. A microstructural study revealed that below 15 vol% of Mo inclusion in Al 2 O 3 samples had no-contact random patterns. Samples with metal contents higher than 20 vol% of Mo consistently showed metallic conductivity due to percolation effect.
EXTENDING SIMPLE WEIGHTED DENSITY APPROXIMATION FOR HARD SPHERE FLUID TO LENNARD–JONES FLUID (I): TEST
Authors: ZHOU SHIQI
Published: January 2006

A theoretical formalism which can be combined with any hard sphere density functional approximations (DFA) to construct DFA for non-hard sphere fluids with a hard or soft core subjected to diverse external potentials is proposed. To show validity and power of the present formalism, we employ a simple weighted density approximation as an illustrating example. It is found that the resultant DFA for Lennard–Jones fluid under influences of diverse extenal potentials is in generally satisfactory agreement with corresponding simulational results even though the co-existence bulk fluid in the particle reservoir with which the non-uniform fluid under consideration is connected, is situated at "dangerous" regions. The significance of the present formalism lies in that it can be combined with any other hard sphere DFAs to construct DFAs for any non-hard sphere fluids with a hard or soft core.
SEPARATING POINTS BY AXIS-PARALLEL LINES
Authors: CĂLINESCU GRUIA , DUMITRESCU ADRIAN , KARLOFF HOWARD , WAN PENG-JUN
Published: January 2006

We study the problem of separating n points in the plane, no two of which have the same x- or y-coordinate, using a minimum number of vertical and horizontal lines avoiding the points, so that each cell of the subdivision contains at most one point. Extending previous NP-hardness results due to Freimer et al. we prove that this problem and some variants of it are APX-hard. We give a 2-approximation algorithm for this problem, and a d-approximation algorithm for the d-dimensional variant, in which the points are to be separated using axis-parallel hyperplanes. To this end, we reduce the point separation problem to the rectangle stabbing problem studied by Gaur et al. Their approximation algorithm uses LP-rounding. We present an alternative LP-rounding procedure which also works for the rectangle stabbing problem. We show that the integrality ratio of the LP is exactly 2.
ON SURFACE-LINKS REPRESENTED BY DIAGRAMS WITH TWO OR THREE TRIPLE POINTS
Authors: TANAKA KOKORO
Published: January 2006

We define invariants of surface-links, called generalized fundamental classes, and determine the values which the generalized fundamental classes of surface-links represented by diagrams with two or three triple points can take.
EXTENDING REPRESENTATIONS OF BRAID GROUPS TO THE AUTOMORPHISM GROUPS OF FREE GROUPS
Authors: BARDAKOV VALERIJ G.
Published: January 2006

We construct a linear representation of the group IA (Fn) of IA-automorphisms of a free group Fn, an extension of the Gassner representation of the pure braid group Pn. Although the problem of faithfulness of the Gassner representation is still open for n > 3, we prove that the restriction of our representation to the group of basis conjugating automorphisms Cbn contains a non-trivial kernel even if n = 2. We construct also an extension of the Burau representation to the group of conjugating automorphisms Cn. This representation is not faithful for n ≥ 2.
Hutchison Whampoa: A Global 3G Giant in the Making?
Authors: Lim Ghee Soon
Published: January 2006

This case focuses on an unprecedented attempt by an Asian telecommunications company to capture a sizable share of the emerging, potentially lucrative global 3G (third-generation) mobile communication services market. It provides details on several crucial aspects of the huge risk-taking venture undertaken by Hong Kong-based Hutchison Whampoa for the period between 2000 and 2003. If successful, the endeavor would not only translate into huge monetary gains for Hutchison Whampoa, it would also show a contrarian style of investing and a far-sighted "gamble" could be systematically and skillfully planned and executed by ambitious enterprising decision makers. It would shed light on how real-life strategists could craft a corporate-level growth model by capitalizing on the synergy made possible by a portfolio of successful businesses available at hand.
Shanghai GM's Marketing Strategy for the China Market
Authors: Chen Ivy Siok Ngoh , Luk Sherriff Ting Kwong , Yip Leslie Sai Chung
Published: January 2006

Demand for passenger cars in China had been growing at more than 10% annually. Changing buyer expectations, increasing competition and an inefficient distribution system were challenges that car manufacturers faced as they sought to expand into China. This case describes the socio-economic developments in China, the competition and government policies affecting the passenger car industry. This case explores how Shanghai General Motors (SGM) adapted their brand and channel strategies to respond to these changes in the environment.
Crane Supari
Authors: Velayudhan Sanal Kumar
Published: January 2006

Crane Supari was a leading brand of betel nut pieces in South India. Crane Supari was perceived as a quality brand and was well accepted in urban areas, but this was not true in rural areas where the smaller brands dominated. The smaller brands had both effective and efficient distribution in rural markets. The servicing of the channel was superior in addition to the cost advantage for the small competitor. Betel nut pieces faced competition from other chewing products too. Faced with increasing category competition, the marketing manager of Crane Supari planned to tap the opportunity in the rural markets. This case explores the unique capabilities necessary to compete effectively in the rural market.
CHARGE TRANSPORT THROUGH THIOPHENE BITHIOL MOLECULE AS A MOLECULAR WIRE
Authors: JALILI SEIFOLLAH , MORADI FERESHTEH
Published: January 2006

The conductance properties of the thiophene bithiol molecular wire, a nano-wire connecting two metallic electrodes, were investigated using quantum-mechanical based methods such as Density Functional Theory, in conjunction with non-equilibrium Green's function formalism. Using the quantum mechanics methods, the Hamiltonians of the three main parts of system, i.e. the right lead, the device, the left lead and conductance properties of this molecular wire such as I-V curve, were calculated.
ELECTRON TRANSFER INDUCED DISSOCIATION OF CHLORO-CYANO-BENZENE RADICAL ANION: DRIVING CHEMICAL REACTIONS VIA CHARGE RESTRAINTS
Authors: SULPIZI MARIALORE , ROTHLISBERGER URSULA , LAIO ALESSANDRO
Published: January 2006

We introduce a new quantum mechanics/molecular mechanics based method to drive electron transfer reactions. Our approach uses the dynamically restrained electrostatic potential derived charges of the quantum atoms1 as a reaction coordinate, and allows an estimation of the free energy barrier of the electron transfer process. Moreover, it provides an accurate description of the electronic structure changes and of the nuclear reorganization associated with the reaction. We use the method to describe the electron-transfer induced dissociation of the m-chloro-cyano-benzene radical anion in aqueous solution. The reaction is triggered by solvent reorganization by a change in the coordination water shell around the cyano nitrogen atom. At the onset of the reaction, charge-spin segregation is observed. The negative charge is transferred to the leaving Cl , while the spin density localizes on the non-saturated carbon atom of the benzene ring. The calculated free energy barrier of dissociation is in good quantitative agreement with the experimental data.