bluuebunny/crossref_metadata_2025 huggingface dataset:
Influence of Different Filling, Cooling, and Storage Conditions on the Growth ofAlicyclobacillus acidoterrestrisCRA7152 in Orange Juice
Authors: Spinelli Ana Cláudia N. F. , Sant'Ana Anderson S. , Rodrigues-Junior Salatir , Massaguer Pilar R.
Published: October 2009

The prevention of spoilage byAlicyclobacillus acidoterrestrisis a current challenge for fruit juice and beverage industries worldwide due to the bacterium's acidothermophilic growth capability, heat resistance, and spoilage potential. This study examined the effect of storage temperature onA. acidoterrestrisgrowth in hot-filled orange juice. The evolution of theA. acidoterrestrispopulation was monitored under six different storage conditions after pasteurization (at 92°C for 10 s), maintenance at 85°C for 150 s, and cooling with water spray to 35°C in about 30 min and using two inoculum levels: <101and 101spores/ml. Final cooling and storage conditions were as follows: treatment 1, 30°C for the bottle cold point and storage at 35°C; treatment 2, 30°C for 48 h and storage at 35°C; treatment 3, 25°C for the bottle cold point and storage at 35°C; treatment 4, 25°C for 48 h and storage at 35°C; treatment 5, storage at 20°C (control); and treatment 6, filling and storage at 25°C. It was found that only in treatment 5 did the population remain inhibited during the 6 months of orange juice shelf life. By examining treatments 1 to 4, it was observed thatA. acidoterrestrispredicted growth parameters were significantly influenced (P< 0.05) either by inoculum level or cooling and storage conditions. The time required to reach a 104CFU/ml population ofA. acidoterrestriswas considered to be an adequate parameter to indicate orange juice spoilage byA. acidoterrestris. Therefore, hot-filled orange juice should be stored at or below 20°C to avoid spoilage by this microorganism. This procedure can be considered a safe and inexpensive alternative to other treatments proposed earlier.
Diversity of
nirK
Denitrifying Genes and Transcripts in an Agricultural Soil
Authors: Wertz Sophie , Dandie Catherine E. , Goyer Claudia , Trevors Jack T. , Patten Cheryl L.
Published: October 2009

Environmental conditions can change dramatically over a crop season and among locations in an agricultural field and can increase denitrification and emissions of the potent greenhouse gas nitrous oxide. In a previous study, changes in the overall size of the denitrifier community in a potato crop field were relatively small and did not correlate with variations in environmental conditions or denitrification rates. However, denitrifying bacteria are taxonomically diverse, and different members of the community may respond differently to environmental changes. The objective of this research was to understand which portion of the
nirK
denitrifying community is active and contributes to denitrification under conditions in a potato crop field. Denaturing gradient gel electrophoresis (DGGE) of
nirK
genes in soil-extracted DNA showed changes in the composition of the
nirK
denitrifier community over the growing season and among spatial locations in the field. By contrast, the composition of the active
nirK
denitrifier community, as determined by DGGE analysis of
nirK
transcripts derived from soil-extracted mRNA, changed very little over time, although differences in the relative abundance of some specific transcripts were observed between locations. Our results indicate that the soil denitrifier populations bearing
nirK
genes are not all contributing to denitrification and that the denitrifying populations that are active are among the most abundant and ubiquitous
nirK
-bearing denitrifiers. Changes in the community composition of the total and active
nirK
denitrifiers were not strongly correlated with changes in environmental factors and denitrification activity.
Dynamics of Clinical and Environmental
Vibrio parahaemolyticus
Strains during Seafood-Related Summer Diarrhea Outbreaks in Southern Chile
Authors: García Katherine , Torres Rafael , Uribe Paulina , Hernández Cristina , Rioseco M. Luisa , Romero Jaime , Espejo Romilio T.
Published: October 2009

Seafood consumption-related diarrhea became prevalent in Chile when the pandemic strain of
Vibrio parahaemolyticus
serotype O3:K6 reached a region in the south of Chile (Region de los Lagos) where approximately 80% of the country's seafood is produced. In spite of the large outbreaks of clinical infection, the load of
V. parahaemolyticus
in shellfish of this region is relatively low. The pandemic strain constitutes a small but relatively stable group of a diverse
V. parahaemolyticus
population, composed of at least 28 genetic groups. Outbreaks in Region de los Lagos began in 2004 and reached a peak in 2005 with 3,725 clinical cases, all associated with the pandemic strain. After 2005, reported cases steadily decreased to a total of 477 cases in 2007. At that time, 40% of the clinical cases were associated with a pandemic strain of a different serotype (O3:K59), and 27% were related to
V. parahaemolyticus
isolates unrelated to the pandemic strain. In the results published here, we report that in the summer of 2008, when reported cases unexpectedly increased from 477 to 1,143, 98% of the clinical cases were associated with the pandemic strain serotype O3:K6, a change from 2007. Nevertheless, in 2009, when clinical cases decreased to 441, only 64% were related to the pandemic strain; the remaining cases were related to a nonpandemic
tdh-
and
trh
-negative strain first identified in shellfish in 2006. Overall, our observations indicate that the pandemic strain has become a relatively stable subpopulation and that when the number of diarrhea cases related to the pandemic strain is low, previously undetected
V. parahaemolyticus
pathogenic strains become evident.
Phenotypic and Gene Expression Changes among Clonal Type I Strains of
Toxoplasma gondii
Authors: Khan Asis , Behnke Michael S. , Dunay Ildiko R. , White Michael W. , Sibley L. David
Published: October 2009

Toxoplasma gondii
has an unusual population structure consisting of three clonal lineages that predominate in North America and Europe. This simple pattern has encouraged the use of only a few laboratory isolates that are representative of each lineage. Principle among these is the type I RH strain, originally isolated from a child with encephalitis some 70 years ago. Comparison of different passages of the RH strain that have been propagated differently over the intervening time period revealed that the commonly used clonal line called RH-ERP was not representative of natural isolates of the type I lineage. Notably, RH-ERP formed much larger plaques than other type 1 strains, including a separate, earlier derived isolate of the RH strain. The RH-ERP variant also showed enhanced extracellular survival, faster growth, and decreased differentiation compared to the prototype type I strain GT1. Comparison of gene expression differences in the RH-ERP line revealed that several ABC transporters were upregulated, which may provide a growth advantage in vitro. These findings illustrate that dramatic phenotypic changes can arise in laboratory strains, emphasizing the need for comparison with recent clinical isolates.
Molecular Regulation of Arabinan and
l
-Arabinose Metabolism in
Hypocrea jecorina
(
Trichoderma reesei
)
Authors: Akel Eda , Metz Benjamin , Seiboth Bernhard , Kubicek Christian P.
Published: October 2009

Hypocrea jecorina
(anamorph:
Trichoderma reesei
) can grow on plant arabinans by the aid of secreted arabinan-degrading enzymes. This growth on arabinan and its degradation product
l
-arabinose requires the operation of the aldose reductase XYL1 and the
l
-arabinitol dehydrogenase LAD1. Growth on arabinan and
l
-arabinose is also severely affected in a strain deficient in the general cellulase and hemicellulase regulator XYR1, but this impairment can be overcome by constitutive expression of the
xyl1
encoding the aldose reductase. An inspection of the genome of
H. jecorina
reveals four genes capable of degrading arabinan, i.e., the α-
l
-arabinofuranosidase encoding genes
abf1
,
abf2
, and
abf3
and also
bxl1
, which encodes a β-xylosidase with a separate α-
l
-arabinofuranosidase domain and activity but no endo-arabinanase. Transcriptional analysis reveals that in the parent strain QM9414 the expression of all of these genes is induced by
l
-arabinose and to a lesser extent by
l
-arabinitol and absent on
d
-glucose. Induction by
l
-arabinitol, however, is strongly enhanced in a Δ
lad1
strain lacking
l
-arabinitol dehydrogenase activity and severely impaired in an aldose reductase (Δ
xyl1
) strain, suggesting a cross talk between
l
-arabinitol and the aldose reductase XYL1 in an α-
l
-arabinofuranosidase gene expression. Strains bearing a knockout in the cellulase regulator
xyr1
do not show any induction of
abf2
and
bxl1
, and this phenotype cannot be reverted by constitutive expression of
xyl1
. The loss of function of
xyr1
has also a slight effect on the expression of
abf1
and
abf3
. We conclude that the expression of the four α-
l
-arabinofuranosidases of
H. jecorina
for growth on arabinan requires an early pathway intermediate (
l
-arabinitol or
l
-arabinose), the first enzyme of the pathway XYL1, and in the case of
abf2
and
bxl1
also the function of the cellulase regulator XYR1.
Structure and Distribution of Organelles and Cellular Location of Calcium Transporters in
Neurospora crassa
Authors: Bowman Barry J. , Draskovic Marija , Freitag Michael , Bowman Emma Jean
Published: October 2009

We wanted to examine the cellular locations of four
Neurospora crassa
proteins that transport calcium. However, the structure and distribution of organelles in live hyphae of
N. crassa
have not been comprehensively described. Therefore, we made recombinant genes that generate translational fusions of putative organellar marker proteins with green or red fluorescent protein. We observed putative endoplasmic reticulum proteins, encoded by
grp-78
and
dpm
, in the nuclear envelope and associated membranes. Proteins of the vacuolar membrane, encoded by
vam-3
and
vma-1
, were in an interconnected network of small tubules and vesicles near the hyphal tip, while in more distal regions they were in large and small spherical vacuoles. Mitochondria, visualized with tagged ARG-4, were abundant in all regions of the hyphae. Similarly, we tagged the four
N. crassa
proteins that transport calcium with green or red fluorescent protein to examine their cellular locations. NCA-1 protein, a homolog of the SERCA-type Ca
2+
-ATPase of animal cells, colocalized with the endoplasmic reticulum markers. The NCA-2 and NCA-3 proteins are homologs of Ca
2+
-ATPases in the vacuolar membrane in yeast or in the plasma membrane in animal cells. They colocalized with markers in the vacuolar membrane, and they also occurred in the plasma membrane in regions of the hyphae more than 1 mm from the tip. The
cax
gene encodes a Ca
2+
/H
+
exchange protein found in vacuoles. As expected, the CAX protein localized to the vacuolar compartment. We observed, approximately 50 to 100 μm from the tip, a few spherical organelles that had high amounts of tagged CAX protein and tagged subunits of the vacuolar ATPase (VMA-1 and VMA-5). We suggest that this organelle, not described previously in
N. crassa
, may have a role in sequestering calcium.
Flexible Gates: Dynamic Topologies and Functions for FG Nucleoporins in Nucleocytoplasmic Transport
Authors: Terry Laura J. , Wente Susan R.
Published: October 2009

The nuclear envelope is a physical barrier between the nucleus and cytoplasm and, as such, separates the mechanisms of transcription from translation. This compartmentalization of eukaryotic cells allows spatial regulation of gene expression; however, it also necessitates a mechanism for transport between the nucleus and cytoplasm. Macromolecular trafficking of protein and RNA occurs exclusively through nuclear pore complexes (NPCs), specialized channels spanning the nuclear envelope. A novel family of NPC proteins, the FG-nucleoporins (FG-Nups), coordinates and potentially regulates NPC translocation. The extensive repeats of phenylalanine-glycine (FG) in each FG-Nup directly bind to shuttling transport receptors moving through the NPC. In addition, FG-Nups are essential components of the nuclear permeability barrier. In this review, we discuss the structural features, cellular functions, and evolutionary conservation of the FG-Nups.
Toll-Like Receptors 2 and 4 Contribute to Sepsis-Induced Depletion of Spleen Dendritic Cells
Authors: Pène Frédéric , Courtine Emilie , Ouaaz Fatah , Zuber Benjamin , Sauneuf Bertrand , Sirgo Gonzalo , Rousseau Christophe , Toubiana Julie , Balloy Viviane , Chignard Michel , Mira Jean-Paul , Chiche Jean-Daniel
Published: October 2009

Depletion of dendritic cells (DC) in secondary lymphoid organs is a hallmark of sepsis-induced immune dysfunction. In this setting, we investigated if Toll-like receptor (TLR)-dependent signaling might modulate the maturation process and the survival of DC. Using a model of sublethal polymicrobial sepsis induced by cecal ligation and puncture, we investigated the quantitative and functional features of spleen DC in wild-type, TLR2
−/−
, TLR4
−/−
, and TLR2
−/−
TLR4
−/−
mice. By 24 h, a decrease in the relative percentage of CD11c
high
spleen DC occurred in wild-type mice but was prevented in TLR2
−/−
, TLR4
−/−
, and TLR2
−/−
TLR4
−/−
mice. In wild-type mice, sepsis dramatically affected both CD11c
+
CD8α
+
and CD11c
+
CD8α
−
subsets. In all three types of knockout mice studied, the CD11c
+
CD8α
+
subset followed a depletion pattern similar to that for wild-type mice. In contrast, the loss of CD11c
+
CD8α
−
cells was attenuated in TLR2
−/−
and TLR4
−/−
mice and completely prevented in TLR2
−/−
TLR4
−/−
mice. Accordingly, apoptosis of spleen DC was increased in septic wild-type mice and inhibited in knockout mice. In addition we characterized the functional features of spleen DC obtained from septic mice. As shown by increased expression of major histocompatibility complex class II and CD86, polymicrobial sepsis induced maturation of DC, with subsequent increased capacity to prime T lymphocytes, similarly in wild-type and knockout mice. In response to CpG DNA stimulation, production of interleukin-12 was equally impaired in DC obtained from wild-type and knockout septic mice. In conclusion, although dispensable for the DC maturation process, TLR2 and TLR4 are involved in the mechanisms leading to depletion of spleen DC following polymicrobial sepsis.
The Glycosylphosphatidylinositol-Anchored Protease Sap9 Modulates the Interaction ofCandida albicanswith Human Neutrophils
Authors: Hornbach Anke , Heyken Antje , Schild Lydia , Hube Bernhard , Löffler Jürgen , Kurzai Oliver
Published: October 2009

Human polymorphonuclear neutrophils (PMNs) play a major role in the immune defense against invasiveCandida albicansinfection. This fungal pathogen produces a set of aspartic proteases that directly contributes to virulence properties such as adhesion, tissue invasion, and immune evasion. We show here that, in contrast to other secreted proteases, the cell surface-associated isoform Sap9 has a major impact on the recognition ofC. albicansby PMNs.SAP9is required for the induction of PMN chemotaxis towardC. albicansfilaments, an essential prerequisite of effective PMN activation. Furthermore, deletion ofSAP9leads to a mitigated release of reactive oxygen intermediates (ROI) in human PMNs and decreasesC. albicans-induced apoptosis triggered by ROI formation. In confrontation assays, killing of aSAP9deletion mutant is reduced in comparison to wild-typeC. albicans. These data clearly implicate Sap9 protease activity in the initiation of protective innate immunity and suggest novel molecular mechanisms inC. albicans-host interaction leading to neutrophil activation.
Regulated Delayed Expression of
rfaH
in an Attenuated
Salmonella
enterica
Serovar Typhimurium Vaccine Enhances Immunogenicity of Outer Membrane Proteins and a Heterologous Antigen
Authors: Kong Qingke , Liu Qing , Roland Kenneth L. , Curtiss Roy
Published: October 2009

RfaH is a transcriptional antiterminator that reduces the polarity of long operons encoding secreted and surface-associated cell components of
Salmonella enterica
serovar Typhimurium, including O antigen and lipopolysaccharide core sugars. A Δ
rfaH
mutant strain is attenuated in mice (50% lethal dose [LD
50
], >10
8
CFU). To examine the potential for using
rfaH
in conjunction with other attenuating mutations, we designed a series of strains in which we replaced the native
rfaH
promoter with the tightly regulated arabinose-dependent
araC
P
BAD
promoter so that
rfaH
expression was dependent on exogenously supplied arabinose provided during in vitro growth. Following colonization of host lymphoid tissues, where arabinose was not available, the P
BAD
promoter was no longer active and
rfaH
was not expressed. In the absence of RfaH, O antigen and core sugars were not synthesized. We constructed three mutant strains that expressed different levels of RfaH by altering the ribosome-binding sequence and start codon. One mutation, ΔP
rfaH178
, was introduced into the attenuated vaccine strain χ9241 (Δ
pabA
Δ
pabB
Δ
asdA
) expressing the pneumococcal surface protein PspA from an Asd
+
balanced-lethal plasmid. Mice immunized with this strain and boosted 4 weeks later induced higher levels of serum immunoglobulin G specific for PspA and for outer membrane proteins from other enteric bacteria than either an isogenic Δ
rfaH
derivative or the isogenic RfaH
+
parent. Eight weeks after primary oral immunization, mice were challenged with 200 LD
50
of virulent
S
treptococcus
pneumoniae
WU2. Immunization with ΔP
rfaH178
mutant strains led to increased levels of protection compared to that of the parent χ9241 and of a Δ
rfaH
derivative of χ9241.
A Family of Transcriptional Antitermination Factors Necessary for Synthesis of the Capsular Polysaccharides of
Bacteroides fragilis
Authors: Chatzidaki-Livanis Maria , Coyne Michael J. , Comstock Laurie E.
Published: October 2009

A single strain of
Bacteroides fragilis
synthesizes eight distinct capsular polysaccharides, designated PSA to PSH. These polysaccharides are synthesized by-products encoded by eight separate polysaccharide biosynthesis loci. The genetic architecture of each of these eight loci is similar, including the fact that the first gene of each locus is a paralog of the first gene of each of the other PS loci. These proteins are designated the UpxY family, where x is replaced by a to h, depending upon the polysaccharide locus from which it is produced. Mutational analysis of three separate
upxY
genes demonstrated that they are necessary and specific for transcription of their respective polysaccharide biosynthesis operon and that they function in
trans
. Transcriptional reporter constructs, reverse transcriptase PCR, and deletion analysis demonstrated that the UpxYs do not affect initiation of transcription, but rather prevent premature transcriptional termination within the 5′ untranslated region between the promoter and the
upxY
gene. The UpxYs have conserved motifs that are present in NusG and NusG-like proteins. Mutation of two conserved residues within the conserved KOW motif abrogated UpaY activity, further confirming that these proteins belong to the NusG-like (NusG
SP
) family. Alignment of highly similar UpxYs led to the identification of a small region of these proteins predicted to confer specificity for their respective loci. Construction of an
upaY-upeY
hybrid that produced a protein in which a 17-amino-acid segment of UpaY was changed to that of UpeY altered UpaY's specificity, as it was now able to function in transcriptional antitermination of the PSE biosynthesis operon.
Cag3 Is a Novel Essential Component of theHelicobacter pyloriCag Type IV Secretion System Outer Membrane Subcomplex
Authors: Pinto-Santini Delia M. , Salama Nina R.
Published: October 2009

Helicobacter pyloristrains harboring thecagpathogenicity island (PAI) have been associated with more severe gastric disease in infected humans. ThecagPAI encodes a type IV secretion (T4S) system required for CagA translocation into host cells as well as induction of proinflammatory cytokines, such as interleukin-8 (IL-8).cagPAI genes sharing sequence similarity with T4S components from other bacteria are essential for Cag T4S function. OthercagPAI-encoded genes are also essential for Cag T4S, but lack of sequence-based or structural similarity with genes in existing databases has precluded a functional assignment for the encoded proteins. We have studied the role of one such protein, Cag3 (HP0522), in Cag T4S and determined Cag3 subcellular localization and protein interactions. Cag3 is membrane associated and copurifies with predicted inner and outer membrane Cag T4S components that are essential for Cag T4S as well as putative accessory factors. Coimmunoprecipitation and cross-linking experiments revealed specific interactions with HpVirB7 and CagM, suggesting Cag3 is a new component of the Cag T4S outer membrane subcomplex. Finally, lack of Cag3 lowers HpVirB7 steady-state levels, further indicating Cag3 makes a subcomplex with this protein.
Activated by Different Signals, the PhoP/PhoQ Two-Component System Differentially Regulates Metal Uptake
Authors: Choi Eunna , Groisman Eduardo A. , Shin Dongwoo
Published: October 2009

The PhoP/PhoQ two-component system controls several physiological and virulence functions in
Salmonella enterica
. This system is activated by low Mg
2+
, acidic pH, and antimicrobial peptides, but the biological consequences resulting from sensing multiple signals are presently unclear. Here, we report that the PhoP/PhoQ system regulates different
Salmonella
genes depending on whether the inducing signal is acidic pH or low Mg
2+
. When
Salmonella
experiences acidic pH, the PhoP/PhoQ system promotes Fe
2+
uptake in a process that requires the response regulator RstA, activating transcription of the Fe
2+
transporter gene
feoB
. In contrast, the PhoP-induced RstA protein did not promote
feoB
expression at neutral pH with low Mg
2+
. The PhoP/PhoQ system promotes the expression of the Mg
2+
transporter
mgtA
gene only when activated in bacteria starved for Mg
2+
. This is because
mgtA
transcription promoted at high Mg
2+
concentrations by the acidic-pH-activated PhoP protein failed to reach the
mgtA
coding region due to the
mgtA
leader region functioning as a Mg
2+
sensor. Our results show that a single two-component regulatory system can regulate distinct sets of genes in response to different input signals.
Nitric Oxide Signaling inPseudomonas aeruginosaBiofilms Mediates Phosphodiesterase Activity, Decreased Cyclic Di-GMP Levels, and Enhanced Dispersal
Authors: Barraud Nicolas , Schleheck David , Klebensberger Janosch , Webb Jeremy S. , Hassett Daniel J. , Rice Scott A. , Kjelleberg Staffan
Published: October 2009

Bacteria in biofilms often undergo active dispersal events and revert to a free-swimming, planktonic state to complete the biofilm life cycle. The signaling molecule nitric oxide (NO) was previously found to trigger biofilm dispersal in the opportunistic pathogenPseudomonas aeruginosaat low, nontoxic concentrations (N. Barraud, D. J. Hassett, S. H. Hwang, S. A. Rice, S. Kjelleberg, and J. S. Webb, J. Bacteriol. 188:7344-7353, 2006). NO was further shown to increase cell motility and susceptibility to antimicrobials. Recently, numerous studies revealed that increased degradation of the secondary messenger cyclic di-GMP (c-di-GMP) by specific phosphodiesterases (PDEs) triggers a planktonic mode of growth in eubacteria. In this study, the potential link between NO and c-di-GMP signaling was investigated by performing (i) PDE inhibitor studies, (ii) enzymatic assays to measure PDE activity, and (iii) direct quantification of intracellular c-di-GMP levels. The results suggest a role for c-di-GMP signaling in triggering the biofilm dispersal event induced by NO, as dispersal requires PDE activity and addition of NO stimulates PDE and induces the concomitant decrease in intracellular c-di-GMP levels inP. aeruginosa. Furthermore, gene expression studies indicated global responses to low, nontoxic levels of NO inP. aeruginosabiofilms, including upregulation of genes involved in motility and energy metabolism and downregulation of adhesins and virulence factors. Finally, site-directed mutagenesis of candidate genes and physiological characterization of the corresponding mutant strains uncovered that the chemotaxis transducer BdlA is involved in the biofilm dispersal response induced by NO.
ScoC Regulates Bacilysin Production at the Transcription Level in
Bacillus subtilis
Authors: Inaoka Takashi , Wang Guojun , Ochi Kozo
Published: October 2009

Bacillus subtilis
mutants with high expression of the bacilysin operon
ywfBCDEFG
were isolated. Comparative genome sequencing analysis revealed that all of these mutants have a mutation in the
scoC
gene. The disruption of
scoC
by genetic engineering also resulted in increased expression of
ywfBCDEFG
. Primer extension and gel mobility shift analyses showed that the ScoC protein binds directly to the promoter region of
ywfBCDEFG
. Our results indicate that the transition state regulator ScoC, together with CodY and AbrB, negatively regulates bacilysin production in
B. subtilis
.
Contribution of arbuscular mycorrhizal symbiosis to in vitro root metal uptake: from trace to toxic metal conditionsThis paper is one of the papers presented at the 50th Annual Meeting of the Canadian Society of Plant Physiologists (CSPP) held at the University of Ottawa, Ontario, in June 2008. Other papers from this meeting are presented in the July 2009 Special Issue of Botany.
Authors: Audet Patrick , Charest Christiane
Published: October 2009

This in-vitro study investigated the role of arbuscular mycorrhizal (AM) symbiosis in root metal acquisition and stress tolerance from two experiments using a carrot root-organ culture system, and involving the essential micronutrient zinc as a typical metal contaminant. We demonstrated that the AM symbiosis plays a dual role in root metal acquisition by increasing nutrient uptake via mycorrhizal “enhanced uptake” at low (trace) metal concentrations in the growth medium, but then lessening the uptake through “metal-binding” processes at high (toxic) concentrations. Furthermore, we also observed the relative contribution of hyphal uptake and translocation to roots, which led us to suggest that the enhanced uptake and metal-binding processes likely occur simultaneously and (or) independently. Ultimately, symptoms of metal toxicity toward both the roots and AM fungi at the highest Zn exposure concentrations was observed. From this finding, a critical toxicity burden likely exists arising from conditions ranging from trace to toxic metal extremes.
Prey capture in the Venus flytrap: collection or selection?
Authors: Hutchens, John J. , Luken James O.
Published: October 2009

Charles Darwin first proposed that the Venus flytrap ( Dionaea muscipula Ellis) functions optimally by capturing and digesting large prey, the small prey escaping through openings at the trap margins. This hypothesis, although intuitively sound in the context of trap mechanics or plant allocation theory, has not been tested adequately with populations of plants growing in the field. Here, with traps collected in the endemic habitat over 9 months, we show that prey capture in the Venus flytrap is opportunistic rather than selective. While there was no effect of trap size on prey capture success, there was a significant but weak positive relationship between trap length and prey length. Prey sizes were well below the theoretical maximum holding capacities of traps and relatively small insects were represented across the range of trap sizes. Our results show that prey capture was not biased toward large invertebrates. Instead, we suggest that nonselective prey capture across the observed range of trap sizes is the best-fit explanation of trap function in the context of relatively limited ability to change allocation in response to sudden increases in resource availability.
EFFECT OF Ca-SUBSTITUTION ON THE OPTICAL BAND GAP AND URBACH ENERGY OF BaTi2O5 BULK GLASS
Authors: AHMAD JAVED , YU JIANDING , ARAI YASUTOMO
Published: October 2009

Optical transmittance of Ba 1-x Ca x Ti 2 O 5 (x=0, 0.01, 0.03) bulk glasses of ferroelectric BaTi 2 O 5 is measured at room temperature in the wavelength range 190–800 nm. The fundamental absorption edge located in the ultraviolet (UV) region tends to shift toward the longer wavelength region on increasing x. The optical band gap of 3.31 eV estimated for x=0 decreases on increasing x. The decrease in the optical band gap energy is related to the creation of non-bridging oxygen ions, which increase on Ca substitution. The observed increase in the Urbach energy with increasing x is associated with the possible increase of structural disorder in the ferroelectric BaTi 2 O 5-based bulk glass occurred by substituting Ca for Ba .
QUANTUM DIALOGUE BY USING THE TWO-QUTRIT ENTANGLED STATES
Authors: ZHANG LING-LING , ZHAN YOU-BANG
Published: October 2009

A protocol for quantum dialogue is proposed to exchange directly the communicators' secret messages by using the two-qutrit entangled state. In this protocol, the security of communication is ensured by the secret transmitting order of qutrits. It is shown that two legitimate users can directly transmit the secret messages by generalized Bell-basis measurement and classical communication.
MULTIUSER INTERFERENCE SUPPRESSION TECHNIQUES FOR DIRECT-SEQUENCE CDMA COMMUNICATION SYSTEMS
Authors: AZMI PAEIZ
Published: October 2009

In this paper, several techniques for multi-user interference suppression from power-controlled direct-sequence CDMA systems are proposed and the emphasis is on the one-shot structure. The proposed schemes arise from the optimum detector that takes into account the existence of power-controlled chip-synchronous multi-user interference and white Gaussian noise. Restricting the multi-user interference to the power-controlled chip-synchronous case strongly reduces the complexity of the optimum detector. For more reduction in the complexity, some approximations of the obtained techniques are also considered. It is shown that in asynchronous CDMA systems and in the presence of white Gaussian noise, the proposed detectors outperform the correlator with comparable complexity
QUANTUM WORMHOLE AS A RICCI FLOW
Authors: DZHUNUSHALIEV VLADIMIR
Published: October 2009

The idea is considered that a quantum wormhole in a spacetime foam can be described as a Ricci flow. In this interpretation, the Ricci flow is a statistical system and every metric in the Ricci flow is a microscopical state. The probability density of the microscopical state is connected with a Perelman's functional of a rescaled Ricci flow.
An Interview with Steven Weber
Authors: staff Ubiquity
Published: October 2009

Author Steven Weber looks beyond the hype on Open Source. More than a self-governing utopia, it's a practical, sustainable way of organizing and innovating. Its method may soon be applied successfully in other sectors. Plus, a "crazy" idea for Microsoft.
Reflections on the Limits of Artificial Intelligence
Authors: Tugui Alexandru
Published: October 2009

Nature is very simple and efficient in everything she makes, and is extremely obvious. We humans like to simulate in an extremely complicated manner what exists quite simply in nature, and what we succeed in simulating falls in the category of artificial intelligence. Artificial intelligence has limits of scope, but they fade away when compared with the performances of natural intelligence. In this study, we undertake to outline some limits of artificial intelligence compared to natural intelligence and some clear-cut differences that exist between the two.
Ken Sevcik on Performance Evaluation
Authors: Ubiquity staff
Published: October 2009

Ken Sevcik is Professor of Computer Science at the University of Toronto. He received his B.S. in 1966 from Stanford University and his PhD in 1971 from the University of Chicago. Sevcik joined the faculty at the University of Toronto in 1971, and was Chair of the Department from 1990 to 1992. He also served as Director of the Computer Systems Research Institute (CSRI). His research interests are in the use of analytic models for performance analysis of resource allocation, scheduling and file structures in computer systems, computer networks, and distributed data management systems.
Just right
Authors: Burns Mary
Published: October 2009

Instruction should go well beyond a skill focus to one that connects technology use with the actual aims of curriculum and learning outcomes
Reflections on challenges to the goal of invisible computing
Authors: Tripathi Arun Kumar
Published: October 2009

"Technology becomes subordinate to values through economics, government, or the professions. Our biggest problem is learning to recognize that we do have options, albeit often limited ones. Our tendency is to just create more technology rather than ask why." (Carl Mitcham, as he articulates the thesis of Albert Borgmann on the relationship between contemporary technologies and human values)
'Build or Buy' Your Next Porsche?
Authors: Meyer Rob
Published: October 2009

Rob Meyer, CEO of the Numerical Algorithms Group, wants you to be thinking clearly when you consider the component approach to development.
Software implemented fault tolerance through data error recovery
Authors: Saha Goutam Kumar
Published: October 2009

This paper examines how a new software-implemented data error recovery scheme can be so effective in comparison to conventional Error Correction Codes (ECC) during the execution time of an application. The proposed algorithm is three times faster than the conventional software-implemented ECC and application program designers can easily implement the proposed scheme because of its simplicity while designing their fault tolerant applications at no extra hardware cost. The proposed software-implemented scheme for execution-time data-error detection and correction relies on threefold replication of application data set as a basis for fault tolerance.
Software fault tolerance through run-time fault detection
Authors: Saha Goutam Kumar
Published: October 2009

Electrical transients often disrupt the proper functioning of a program. It causes the errors in program flow, data, program codes, or processor registers. The aim of this article is to detect transient faults as quickly as possible in order to prevent functions being performed wrongly or data being lost, during the execution of an application program. Recovery work is initiated immediately after the detection of errors for gaining high software fault tolerance and dependable computing. Transient errors are detected here, on tracing the presence of an odd processor status word (PSW) during the execution time of a computing application.
Corporate renewal engines
Authors: Delic Kemal A.
Published: October 2009

The great, long-living companies are able to adapt to tectonic market shifts and historical changes while crossing different technological epochs. Several books have captured historical and anecdotal evidence about such extraordinary businesses, while we have a few crisp and simple business models of these great companies.
Reflections on the philosophy of technology culture of technological reflection
Authors: Tripathi Arun Kumar
Published: October 2009

"Philosophers point out the liabilities, what happens when technology moves beyond lifting genuine burdens and starts freeing us from burdens that we should not want to be rid of." (Albert Borgmann)"The unintended consequences and dangers of technologization are real, and they deserve reflections and replies. Meanwhile the deeper danger of cultural and moral devastation goes unnoticed and is to some extent eclipsed by attention to the overt dangers (which, to repeat, need to be addressed forthwith)." (Albert Borgmann)
Software implemented fault tolerance
Authors: Saha Goutam Kumar
Published: October 2009

This short paper describes a low cost technique for gaining software implemented fault tolerance without using design diversity based N versions redundancy in both software and hardware. The proposed approach uses an enhanced single-version programming (ESVP) scheme for an application that executes on a single machine. ESVP employs triplicate application program along with multistage voting at inputs and outputs in order to tolerate single-point operational faults in input data, output data, an individual processing module and in an individual voting module through error masking. It is not aimed to tolerate software design bugs. This is a useful tool for designing a reliable low-cost application system.
VLSI Algorithms and architectures for JPEG2000
Authors: Acharya Tinku
Published: October 2009

In this paper, we presented VLSI algorithms and architectures for JPEG2000. JPEG2000 is the new standard for image compression. We briefly described the core algorithms for JPEG2000 standard and its several features desirable in many interactive multimedia applications. The core compression algorithm has three major components - discrete wavelet transform (DWT), fractional bit plane coding (BPC), and context adaptive binary arithmetic coding. DWT and BPC are very computationally, as well as memory expensive operations. As a result, special purpose VLSI implementations of these algorithms are desirable for many devices to compress large size images in real time. Traditionally, the DWT is realized by convolution based finite impulse response (FIR) filtering techniques. However, Lifting based implementation of DWT is found to be computationally efficient and suitable for VLSI implementations. The basic principle behind the lifting based scheme is to decompose the finite impulse response filters in wavelet transform into a finite sequence of simple filtering steps. Lifting based DWT implementation have been recommended in JPEG2000 standard. Consequently, this has become an area of active research and several architectures have been proposed in recent years. In this paper, we reviewed some of the key lifting architectures suitable for VLSI implementation. The embedded block coding with optimized truncation (EBCOT) algorithm has been adopted for computation of BPC in JPEG2000. This algorithm is complex and inefficient to implement in a general purpose machine. We have described a special purpose architecture suitable for VLSI implementation of EBCOT algorithm. We also reviewed some elegant architectures in the literature which exploit the underlying data and computational parallelism inherent in the EBCOT algorithms. We also presented a top-level systems architecture for VLSI implementation of the JPEG2000 standard.
Emerging issues of disinvesment in public enterprises (PEs)
Authors: Srivastava Vinay K.
Published: October 2009

There has been phenomenal and tremendous growth of PE's in India. They were established to attain the 'commanding heights' of the economy of the country and achieve rapid growth of industrialization and economic development. Some of these PEs later became 'white elephant' and started incurring losses. Several of them became chronically sick industries. The Govt. declared the disinvestment process, which began in 1991 with the sale of minority stakes in some PE's, shifted focus to strategic sales during 1999-2000 to 2003-04. The present UPA Govt. announced that, all disinvestment will be considered on a transparent and consultative case-by-case basis. The Govt. has approved the constitution of a "National Investment Fund" comprising of proceeds from disinvestment. The present paper is an attempt to discuss same important issues such as restructuring, valuation of equity, Mechanism of disinvestment, Application of disinvestment proceeds, Parliamentary approval and political issues.
Mobile IP
Authors: Hayat Bashir , Alam Saila
Published: October 2009

This review paper gives a brief insight about Mobile IP, its features and entities constituting Mobile IP environment. The paper explores the working and routing mechanism of Mobile IP with a deep insight about triangle routing in Mobile IP Version 4(MIPv4) and route optimization in Mobile IP Version 6(MIPv6). This paper discusses several security issues regarding Mobile IP implementation. This paper also highlights route optimization problems and focuses on the solution of those problems.
Is the GMO controversy relevant to computer ethics?
Authors: Thompson Paul B.
Published: October 2009

Computing and information technology professionals have exhibited high standards of engagement with ethical issues relating to privacy, information security and abuse of the technical capabilities they have been responsible for developing. But one can argue that computing capability is implicated in ethical controversies that receive relatively little discussion within the IT community. Stem cell research, nanotechnologies and other controversial areas of science would be impossible without the computational capacity of information processing. In many instances, the downstream applications of computer technology are deeply involved in the issues surrounding contested technologies.
End laptop serfdom
Authors: Andersen Espen
Published: October 2009

Time to end personal technology serfdom! I hate company-specific technology standards, at least those that specify technology in terms other than file formats, access protocols and application programming interfaces. In most companies I am in touch with, employees get a laptop and a cell phone and are required to use a set of standard capabilities of some sort. More often than not these are unnecessarily complicated, old-fashioned, expensive and singularly uninspiring. This is often for good reasons: The IT department wants to make things manageable for themselves and for the organization, and employees need to have a standard frame of reference and a compatible set of tools for work. The helpdesk can figure out which keys to press and the employees can see the same screens. Well and good, but the users are beginning to rebel at the lack of options especially those they have on their own or former computers.
Use of genetic algorithms for Indian music mixing
Authors: Gabrani Goldie , Bhargava Preeti , Bhawana Bhawana , Gill Gagandeep Singh
Published: October 2009

Music has changed and evolved through time and time tells that it has always been for the better. In our study, we have implemented Genetic Algorithms for the generation of music by music mixing to provide willing music lovers, the first step to personalize music to suit their liking. A music loop library, containing a list of all tentative loops which are to be used in the remix production alongwith the parameters which define them, is used for this purpose. A loop is an endless band of tape or music allowing continuous repetition. These loops cover all the major music instrument families with particular emphasis on Indian musical instruments as they have been extracted from Indian songs after careful observation using a sound editor. The combinations of different loops for the analysis is run through genetic algorithms. Some important parameters of a loop from the point of view of music mixing are: Depth, BPM (beats per minute), length of the loop and type of the instrument. A fitness function is calculated for the genetic algorithm to rank various combinations of loops for the next generation. The best loop combination can be selected out of the final set of population.
Interview with MIT's Robert Langer
Authors: staff ubiquity
Published: October 2009

Dr. Robert Langers work is at the interface of biotechnology and materials science. A major focus is the study and development of polymers to deliver drugs, particularly genetically engineered proteins, DNA and RNAi, continuously at controlled rates for prolonged periods of time.
Why visual aids need to be less visual
Authors: Yaffe Philip
Published: October 2009

I was recently invited to a presentation by an accomplished speaker. Needless to say, his speech was well structured, his manner relaxed and confident, his eye contact and body language excellent, etc. He normally spoke without slides, but this time he felt they would reinforce and illuminate his message. They didnt. In fact, they were more of a hindrance than a help.
Anticipating and resolving resource overloads
Authors: Clark Tom
Published: October 2009

The Concept of a Project Resource In the context of project management, a resource is any entity that contributes to the accomplishment of project activities. Most project resources perform work and include such entities as personnel, equipment and contractors. However, the concept of a resource (and the techniques of resource management presented in this paper) can also be applied to entities that do not perform work, but which must be available in order for work to be performed. Examples include materials, cash, and workspace. This paper focuses on the resource that is of greatest concern to most organizations personnel. In a project management system, personnel resources may be identified as individuals by name or as functional groups, such as computer programmers.
A fuzzy modeling approach to evaluate faculty performance
Authors: Neogi A. , Mondal A. C. , Mandal S. K.
Published: October 2009

Performance of a teacher is vital both for students and institution and must be measured and evaluated for positive reinforcement to teaching. This paper presents a mathematical model to evaluate faculty's teaching performance using fuzzy logic In this proposed evaluation the degree of satisfaction is defined in advance by experts with respect to levels of performance. Evaluator awards fuzzy marks into the fuzzy performance sheet according to each level of performance. From this, the degree of satisfaction of a subject topic is calculated and the result is calculated based on all the topics in the subject. The obtained results from the proposed approach are compared with the conventional non-fuzzy approach and the comparative results are presented.
Employee retention
Authors: Srivastava Vinay K. , Rastogi Shailesh
Published: October 2009

Loyalty is passé in the modern time and professionalism is the buzzword in the contemporary corporate world. The reasons of employee attrition are also changing. Now-a-days employee leaves an organization for many reasons. Some leave for growth, some leave for some family problems but majority of people switchover jobs due to only one reason that is DISSATISFACTION. Undoubtedly satisfaction and dissatisfaction sort of things have different meaning for different people but having majority of people satisfied is pretty germane for sustainable growth and high level of productivity in any organization. A threadbare analysis of attrition brings some major concerns like not having objectivity in job allocation, employee recognition and fairness in career advancements for consideration. They are also important causes of dissatisfaction for employees in organizations. This dissatisfaction finally gets a vent in the form of changing the job. This subjectivity in the issues of employee handling is the key for dissatisfaction. Management Control System is fully capable of bringing objectivity in the organization and managing this dissatisfaction which would finally be translated into high employee retention, and better productivity and better organizations.
Triple layer data security
Authors: Mukherjee Swarnendu , Bhattacharya Swarnendu , Chaudhury Amlan
Published: October 2009

The growth of high speed computer networks and that of Internet, in particular, has hiked the ease of Data Communication. But in the other hand this growth is also responsible for the snooping of Data at the same time. The ease, by which digital information can be duplicated and distributed, has led to the need for effective protection tools. Various encryption techniques like cryptography, digital watermarking, steganography etc have already been introduced in attempt to address these growing concerns. In this paper, an algorithmic approach is proposed in which along with the combination of cryptography and steganography (taken as security layers), an extra layer of security has been imposed in between them to obtain a completely secured data transmission scheme.