bluuebunny/crossref_metadata_2025 huggingface dataset:
Path Tracking of Parallel Manipulators in the Presence of Force Singularity
Authors: Kevin Jui C. K. , Sun Qiao
Published: November 2005

Parallel manipulators are uncontrollable at force singularities due to the infeasibly high actuator forces required. Existing remedies include the application of actuation redundancy and motion planning for singularity avoidance. While actuation redundancy increases cost and design complexity, singularity avoidance reduces the effective workspace of a parallel manipulator. This article presents a path tracking type of approach to operate parallel manipulators when passing through force singularities. We study motion feasibility in the neighborhood of singularity and conclude that a parallel manipulator may track a path through singular poses if its velocity and acceleration are properly constrained. Techniques for path verification and tracking are presented, and an inverse dynamics algorithm that takes actuator bounds into account is examined. Simulation results for a planar parallel manipulator are given to demonstrate the details of this approach.
Control of Flexible Structures Governed by the Wave Equation Using Infinite Dimensional Transfer Functions
Authors: Halevi Yoram
Published: November 2005

A method of noncollocated controller design for flexible structures, governed by the wave equation, is proposed. First an exact, infinite dimension, transfer function is derived and its properties are investigated. A key element in that part is the existence of time delays due to the wave motion. The controller design consists of two stages. The first one is an inner collocated rate loop. It is shown that there exists a controller that leads to a finite dimensional plus delay inner closed loop, which is the equivalent plant for the outer loop. In the second stage an outer noncollocated position loop is closed. It has the structure of an observer-predictor control scheme to compensate for the response delay. The resulting overall transfer function is second order, with arbitrarily assigned dynamics, plus delay.
Multi-Sensor Information Fusion Kalman Filter Weighted by Scalars for Systems with Colored Measurement Noises
Authors: Sun Shu-Li , Deng Zi-Li
Published: November 2005

An optimal information fusion criterion weighted by scalars is presented in the linear minimum variance sense. Based on this fusion criterion, a scalar weighting information fusion decentralized Kalman filter is given for discrete time-varying linear stochastic control systems measured by multiple sensors with colored measurement noises, which is equivalent to an information fusion Kalman predictor for systems with correlated noises. It has a two-layer fusion structure with fault tolerant and robust properties. Its precision is higher than that of each local filter. Compared with the fusion filter weighted by matrices and the centralized filter, it has lower precision when all sensors are faultless, but has reduced computational burden. Simulation researches show the effectiveness.
Power Scaling Bond Graph Approach to the Passification of Mechatronic Systems— with Application to Electrohydraulic Valves
Authors: Li P. Y. , Ngwompo R. F.
Published: November 2005

In many applications that require physical interaction with humans or other physical environments, passivity is a useful property to have in order to improve safety and ease of use. Many mechatronic applications (e.g., teleoperators, robots that interact with humans) fall into this category. In this paper, we develop an approach to design passifying control laws for mechatronic components from a bond graph perspective. Two new bond graph elements with power scaling properties are first introduced and the passivity properties of bond graphs containing these elements are investigated. These elements are used to better model mechatronic systems that have embedded energy sources. A procedure for passifying mechatronic systems is then developed using the four-way directional electrohydraulic flow control valve as an example. The passified valve is a two-port system that is passive with respect to the scaled power input at the command and hydraulic ports. This is achieved by representing the control valve in a suitable augmented bond graph, and then by replacing the signal bonds with power scaling elements. The procedure generalizes a previous passifying control law resulting in improved performance. Similar procedure can be applied to other mechatronic systems.
A CCCH Zinc Finger Conserved in a Replication Protein A Homolog Found in Diverse Euryarchaeotes
Authors: Lin Yuyen , Robbins Justin B. , Nyannor Ernest K. D. , Chen Yi-Hsing , Cann Isaac K. O.
Published: November 2005

We describe a CCCH type of zinc finger domain in a replication protein A (RPA) homolog found in members of different lineages of the
Euryarchaeota
, a subdomain of
Archaea
. The zinc finger is characterized by CX
2
CX
8
CX
2
H, where X is any amino acid. Using MacRPA3, a representative of this new group of RPA in
Methanosarcina acetivorans
, we made two deletion mutants: a C-terminal deletion mutant lacking the zinc finger and an N-terminal deletion mutant containing the zinc finger domain. Whereas the N-terminal deletion mutant contained zinc at a level comparable to the wild-type protein level, the C-terminal deletion mutant was devoid of zinc. We further created four different mutants of MacRPA3 by replacing each of the four invariable amino acids in the zinc finger with alanine. Each single mutation at an invariable position resulted in a protein containing less than 35% of the zinc found in the wild-type protein. Circular dichroism spectra suggested that although the mutation at the first cysteine resulted in minor perturbation of protein structure, mutations at the other invariable positions led to larger structural changes. All proteins harboring a mutation at one of the invariable positions bound to single-stranded DNA weakly, and this translated into reduced capacity to stimulate DNA synthesis by
M. acetivorans
DNA polymerase BI. By subjecting the protein and its mutants to oxidizing and reducing conditions, we demonstrated that ssDNA binding by MacRPA3 may be regulated by redox through the zinc finger. Thus, the zinc finger modules in euryarchaeal RPA proteins may serve as a means by which the function of these proteins is regulated in the cell.
Mutations That Activate the Silent
bgl
Operon of
Escherichia coli
Confer a Growth Advantage in Stationary Phase
Authors: Madan Ranjna , Kolter Roberto , Mahadevan S.
Published: November 2005

Wild-type strains of
Escherichia coli
are unable to utilize aromatic β-glucosides such as arbutin and salicin because the major genetic system that encodes the functions for their catabolism, the
bgl
operon, is silent and uninducible. We show that strains that carry an activated
bgl
operon exhibit a growth advantage over the wild type in stationary phase in the presence of the
rpoS819
allele that causes attenuated
rpoS
regulon expression. Our results indicate a possible evolutionary advantage in retaining the silent
bgl
operon by wild-type bacteria.
sinI- andexpR-Dependent Quorum Sensing inSinorhizobium meliloti
Authors: Gao Mengsheng , Chen Hancai , Eberhard Anatol , Gronquist Matthew R. , Robinson Jayne B. , Rolfe Barry G. , Bauer Wolfgang D.
Published: November 2005

Quorum sensing (QS) inSinorhizobium meliloti, the N-fixing bacterial symbiont ofMedicagohost plants, involves at least half a dozen differentN-acyl homoserine lactone (AHL) signals and perhaps an equal number of AHL receptors. The accumulation of 55 proteins was found to be dependent on SinI, the AHL synthase, and/or on ExpR, one of the AHL receptors. Gas chromatography-mass spectrometry and electrospray ionization tandem mass spectrometry identified 3-oxo-C14-homoserine lactone (3-oxo-C14-HSL), C16-HSL, 3-oxo-C16-HSL, C16:1-HSL, and 3-oxo-C16:1-HSL as thesinI-dependent AHL QS signals accumulated by the 8530expR+strain under the conditions used for proteome analysis. The 8530expR+strain secretes additional, unidentified QS-active compounds. Addition of 200 nM C14-HSL or C16:1-HSL, two of the known SinI AHLs, affected the levels of 75% of the proteins, confirming that their accumulation is QS regulated. A number of the QS-regulated proteins have functions plausibly related to symbiotic interactions with the host, including ExpE6, IdhA, MocB, Gor, PckA, LeuC, and AglE. Seven of 10 single-crossover β-glucuronidase (GUS) transcriptional reporters in genes corresponding to QS-regulated proteins showed significantly different activities in thesinIandexpRmutant backgrounds and in response to added SinI AHLs. ThesinImutant and several of the single-crossover strains were significantly delayed in the ability to initiate nodules on the primary root of the host plant,Medicago truncatula, indicating thatsinI-dependent QS regulation and QS-regulated proteins contribute importantly to the rate or efficiency of nodule initiation. ThesinIandexpRmutants were also defective in surface swarming motility. ThesinImutant was restored to normal swarming by 5 nM C16:1-HSL.
Enterobacterial Repetitive Intergenic Consensus Sequence Repeats in Yersiniae: Genomic Organization and Functional Properties
Authors: De Gregorio Eliana , Silvestro Giustina , Petrillo Mauro , Carlomagno Maria Stella , Di Nocera Pier Paolo
Published: November 2005

Genome-wide analyses carried out in silico revealed that the DNA repeats called enterobacterial repetitive intergenic consensus sequences (ERICs), which are present in severalEnterobacteriaceae, are overrepresented in yersiniae. From the alignment of DNA regions from the wholly sequencedYersinia enterocolitica8081 andYersinia pestisCO92 strains, we could establish that ERICs are miniature mobile elements whose insertion leads to duplication of the dinucleotide TA. ERICs feature long terminal inverted repeats (TIRs) and can fold as RNA into hairpin structures. The proximity to coding regions suggests that mostY. enterocoliticaERICs are cotranscribed with flanking genes. Elements which either overlap or are located next to stop codons are preferentially inserted in the same (or B) orientation. In contrast, ERICs located far apart from open reading frames are inserted in the opposite (or A) orientation. The expression of genes cotranscribed with A- and B-oriented ERICs has been monitored in vivo. In mRNAs spanning B-oriented ERICs, upstream gene transcripts accumulated at lower levels than downstream gene transcripts. This difference was abolished by treating cells with chloramphenicol. We hypothesize that folding of B-oriented elements is impeded by translating ribosomes. Consequently, upstream RNA degradation is triggered by the unmasking of a site for the RNase E located in the right-hand TIR of ERIC. A-oriented ERICs may act in contrast as upstream RNA stabilizers or may have other functions. The hypothesis that ERICs act as regulatory RNA elements is supported by analyses carried out inYersiniastrains which either lack ERIC sequences or carry alternatively oriented ERICs at specific loci.
The Alternative Sigma Factor AlgT RepressesPseudomonas aeruginosaFlagellum Biosynthesis by Inhibiting Expression offleQ
Authors: Tart Anne H. , Wolfgang Matthew C. , Wozniak Daniel J.
Published: November 2005

Pseudomonas aeruginosaposes a serious risk in individuals suffering from cystic fibrosis (CF). Strains colonizing the CF lung are generally motile but frequently convert to a nonmotile phenotype as the disease progresses. In many cases, this is coordinately regulated with the overproduction of the exopolysaccharide alginate. Both the expression of alginate (mucoidy) and the loss of flagellum synthesis may provide the bacterium with a selective advantage in the CF lung. Previously published data showed that the regulation of alginate production and flagellum biosynthesis in the CF isolate FRD1 is inversely controlled by the alternative sigma factor AlgT. In this study, we observed that in CF isolates, the mucoid and the nonmotile phenotypes occur predominantly together. Using microarrays, we compared the transcriptomes of isogenic AlgT+and AlgT−P. aeruginosaand discovered that AlgT significantly downregulated the majority of flagellar genes. A pronounced inhibitory effect was observed in several genes essential for proper flagellum expression, includingfleQ, which encodes an essential flagellar regulator. The microarray data were confirmed by reverse transcriptase PCR analysis and promoter fusion assays in isogenic AlgT+and AlgT−strains. Transmission electron microscopy, motility assays, and Western blots showed that ectopic expression of FleQ in mucoid, nonmotile CF isolates restored flagellum biosynthesis and motility. Together, these data show that AlgT mediates the negative control of flagellum expression by inhibiting the expression of the flagellar regulatorfleQ.
CheX Is a Phosphorylated CheY Phosphatase Essential forBorrelia burgdorferiChemotaxis
Authors: Motaleb M. A. , Miller Michael R. , Li Chunhao , Bakker Richard G. , Goldstein Stuart F. , Silversmith Ruth E. , Bourret Robert B. , Charon Nyles W.
Published: November 2005

Motility and chemotaxis are believed to be important in the pathogenesis of Lyme disease caused by the spirocheteBorrelia burgdorferi. Controlling the phosphorylation state of CheY, a response regulator protein, is essential for regulating bacterial chemotaxis and motility. Rapid dephosphorylation of phosphorylated CheY (CheY-P) is crucial for cells to respond to environmental changes. CheY-P dephosphorylation is accomplished by one or more phosphatases in different species, including CheZ, CheC, CheX, FliY, and/or FliY/N. Only acheXphosphatase homolog has been identified in theB. burgdorferigenome. However, a role forcheXin chemotaxis has not been established in any bacterial species. InactivatingB. burgdorferi cheXby inserting aflgB-kancassette resulted in cells (cheXmutant cells) with a distinct motility phenotype. While wild-type cells ran, paused (stopped or flexed), and reversed, thecheXmutant cells continuously flexed and were not able to run or reverse. Furthermore, swarm plate and capillary tube chemotaxis assays demonstrated thatcheXmutant cells were deficient in chemotaxis. Wild-type chemotaxis and motility were restored whencheXmutant cells were complemented with a shuttle vector expressing CheX. Furthermore, CheX dephosphorylated CheY3-P in vitro and eluted as a homodimer in gel filtration chromatography. These findings demonstrated thatB. burgdorferiCheX is a CheY-P phosphatase that is essential for chemotaxis and motility, which is consistent with CheX being the only CheY-P phosphatase in theB. burgdorferichemotaxis signal transduction pathway.
The
plmS
2
-Encoded Cytochrome P450 Monooxygenase Mediates Hydroxylation of Phoslactomycin B in
Streptomyces
sp. Strain HK803
Authors: Ghatge Mohini S. , Reynolds Kevin A.
Published: November 2005

Streptomyces
sp. strain HK803 produces six analogues of phoslactomycin (Plm A through Plm F). With the exception of Plm B, these analogues contain a C-18 hydroxyl substituent esterified with a range of short-alkyl-chain carboxylic acids. Deletion of the
plmS
2
open reading frame (ORF), showing high sequence similarity to bacterial cytochrome P450 monooxygenases (CYPs), from the Plm biosynthetic gene cluster has previously resulted in an NP1 mutant producing only Plm B (N. Palaniappan, B. S. Kim, Y. Sekiyama, H. Osada, and K. A. Reynolds, J. Biol. Chem.
278:
35552-35557, 2003). Herein, we report that a complementation experiment with an NP1 derivative (NP2), using a recombinant conjugative plasmid carrying the
plmS
2
ORF downstream of the
ermE*
constitutive promoter (pMSG1), restored production of Plm A and Plm C through Plm F. The 1.2-kbp
plmS
2
ORF was also expressed efficiently as an N-terminal polyhistidine-tagged protein in
Streptomyces coelicolor
. The recombinant PlmS
2
converted Plm B to C-18-hydroxy Plm B (Plm G). PlmS
2
was highly specific for Plm B and unable to process a series of derivatives in which either the lactone ring was hydrolyzed or the C-9 phosphate ester was converted to C-9/C-11 phosphorinane. This biochemical analysis and complementation experiment are consistent with a proposed Plm biosynthetic pathway in which the penultimate step is hydroxylation of the cyclohexanecarboxylic acid-derived side chain of Plm B by PlmS
2
(the resulting Plm G is then esterified to provide Plm A and Plm C through Plm F). Kinetic parameters for Plm B hydroxylation by PlmS
2
(

K
m

of 45.3 ± 9.0 μM and
k
cat
of 0.27 ± 0.04 s
−1
) are consistent with this step being a rate-limiting step in the biosynthetic pathway. The penultimate pathway intermediate Plm G has less antifungal activity than Plm A through Plm F and is not observed in fermentations of either the wild-type strain or NP2/pMSG1.
Demonstration of Cotranscription and 1-Methyl-3-Nitroso-Nitroguanidine Induction of a 30-Gene Operon ofBorrelia burgdorferi: Evidence that the 32-Kilobase Circular Plasmids Are Prophages
Authors: Zhang Hongming , Marconi Richard T.
Published: November 2005

TheBorreliagenome is comprised of linear and circular elements, including a group of 32-kb circular plasmids (cp32s). Earlier analyses identified a bacteriophage, φBB-1, that may package cp32s, suggesting that these plasmids are prophages. cp32-8, cp32-9, and cp32-1 (plasmids L, N, and P, respectively) encode virulence factors such as the factor H binding, OspE proteins (BBL39, BBN38, and BBP38). Here the expression patterns of cp32-8 open reading frames (ORFs) in in vitro-cultivated 1-methyl-3-nitroso-nitroguanidine (MNNG)-treated and untreated spirochetes and during infection were assessed. ORFs BBL42 through BBL28, which encode several bacteriophage protein homologs, were found to be cotranscribed and expression was upregulated by MNNG. Immunoblotting revealed that MNNG-induced transcription led to increased protein production. The expression of several genes that reside outside of the BBL42-BBL28 operon was not affected by MNNG. Some of these genes, including OspE (BBL39), appear to represent morons. Real-time reverse transcription-PCR of spirochetes in mouse tissue revealed that although the phage operon was not induced during infection, transcription of BBL23 (previously designated BlyA), a putative holin, was upregulated. This observation indicates that some genes within the operon can be independently transcribed from internal promoters. Additional transcriptional analyses of the operon identified multiple transcriptional start sites and provided evidence for the expression of a homologous operon from other cp32s. The data support the hypothesis put forth by C. Eggers and D. S. Samuels (J. Bacteriol. 181:7308-7313, 1999) that the cp32s are prophages, a finding with broad implications for our understanding ofBorreliapathogenesis andBorreliagenome evolution.
Growth Substrate- and Phase-Specific Expression of Biphenyl, Benzoate, and C
1
Metabolic Pathways in
Burkholderia xenovorans
LB400
Authors: Denef V. J. , Patrauchan M. A. , Florizone C. , Park J. , Tsoi T. V. , Verstraete W. , Tiedje J. M. , Eltis L. D.
Published: November 2005

Recent microarray experiments suggested that
Burkholderia xenovorans
LB400, a potent polychlorinated biphenyl (PCB)-degrading bacterium, utilizes up to three apparently redundant benzoate pathways and a C
1
metabolic pathway during biphenyl and benzoate metabolism. To better characterize the roles of these pathways, we performed quantitative proteome profiling of cells grown on succinate, benzoate, or biphenyl and harvested during either mid-logarithmic growth or the transition between the logarithmic and stationary growth phases. The Bph enzymes, catabolizing biphenyl, were ∼16-fold more abundant in biphenyl- versus succinate-grown cells. Moreover, the upper and lower
bph
pathways were independently regulated. Expression of each benzoate pathway depended on growth substrate and phase. Proteins specifying catabolism via benzoate dihydroxylation and catechol
ortho
-cleavage (
ben
-
cat
pathway) were approximately an order of magnitude more abundant in benzoate- versus biphenyl-grown cells at the same growth phase. The chromosomal copy of the benzoyl-coenzyme A (CoA) (
box
C
) pathway was also expressed during growth on biphenyl: Box
C
proteins were approximately twice as abundant as Ben and Cat proteins under these conditions. By contrast, proteins of the megaplasmid copy of the benzoyl-CoA (
box
M
) pathway were only detected in transition-phase benzoate-grown cells. Other proteins detected at increased levels in benzoate- and biphenyl-grown cells included general stress response proteins potentially induced by reactive oxygen species formed during aerobic aromatic catabolism. Finally, C
1
metabolic enzymes were present in biphenyl-grown cells during transition phase. This study provides insights into the physiological roles and integration of apparently redundant catabolic pathways in large-genome bacteria and establishes a basis for investigating the PCB-degrading abilities of this strain.
Decaprenylphosphoryl Arabinofuranose, the Donor of the
d
-Arabinofuranosyl Residues of Mycobacterial Arabinan, Is Formed via a Two-Step Epimerization of Decaprenylphosphoryl Ribose
Authors: Mikušová Katarína , Huang Hairong , Yagi Tetsuya , Holsters Marcelle , Vereecke Danny , D'Haeze Wim , Scherman Michael S. , Brennan Patrick J. , McNeil Michael R. , Crick Dean C.
Published: November 2005

The major cell wall polysaccharide of mycobacteria is a branched-chain arabinogalactan in which arabinan chains are attached to the 5 carbon of some of the 6-linked galactofuranose residues; these arabinan chains are composed exclusively of
d
-arabinofuranose (Ara
f
) residues. The immediate precursor of the polymerized Ara
f
is decaprenylphosphoryl-
d
-Ara
f
, which is derived from 5-phosphoribose 1-diphosphate (pRpp) in an undefined manner. On the basis of time course, feedback, and chemical reduction experiment results we propose that decaprenylphosphoryl-Ara
f
is synthesized by the following sequence of events. (i) pRpp is transferred to a decaprenyl-phosphate molecule to form decaprenylphosphoryl-β-
d
-5-phosphoribose. (ii) Decaprenylphosphoryl-β-
d
-5-phosphoribose is dephosphorylated to form decaprenylphosphoryl-β-
d
-ribose. (iii) The hydroxyl group at the 2 position of the ribose is oxidized and is likely to form decaprenylphosphoryl-2-keto-β-
d
-
erythro
-pentofuranose. (iv) Decaprenylphosphoryl-2-keto-β-
d
-
erythro
-pentofuranose is reduced to form decaprenylphosphoryl-β-
d
-Ara
f
. Thus, the epimerization of the ribosyl to an arabinosyl residue occurs at the lipid-linked level; this is the first report of an epimerase that utilizes a lipid-linked sugar as a substrate. On the basis of similarity to proteins implicated in the arabinosylation of the
Azorhizobium caulidans
nodulation factor, two genes were cloned from the
Mycobacterium tuberculosis
genome and expressed in a heterologous host, and the protein was purified. Together, these proteins (Rv3790 and Rv3791) are able to catalyze the epimerization, although neither protein individually is sufficient to support the activity.
Characterization of
Bacillus anthracis
Germinant Receptors In Vitro
Authors: Fisher Nathan , Hanna Philip
Published: November 2005

Bacillus anthracis
begins its infectious cycle as a metabolically dormant cell type, the endospore. Upon entry into a host, endospores rapidly differentiate into vegetative bacilli through the process of germination, thus initiating anthrax. Elucidation of the signals that trigger germination and the receptors that recognize them is critical to understanding the pathogenesis of
B. anthracis
. Individual mutants deficient in each of the seven putative germinant receptor-encoding loci were constructed via temperature-dependent, plasmid insertion mutagenesis and used to correlate these receptors with known germinant molecules. These analyses showed that the GerK and GerL receptors are jointly required for the alanine germination pathway and also are individually required for recognition of either proline and methionine (GerK) or serine and valine (GerL) as cogerminants in combination with inosine. The germinant specificity of GerS was refined from a previous study in a nonisogenic background since it was required only for germination in response to aromatic amino acid cogerminants. The
gerA
and
gerY
loci were found to be dispensable for recognition of all known germinant molecules. In addition, we show that the promoter of each putative germinant receptor operon, except that of the
gerA
locus, is active during sporulation. A current model of
B. anthracis
endospore germination is presented.
Involvement of SenC in Assembly of Cytochrome
c
Oxidase in
Rhodobacter capsulatus
Authors: Swem Danielle L. , Swem Lee R. , Setterdahl Aaron , Bauer Carl E.
Published: November 2005

SenC, a Sco1 homolog found in the purple photosynthetic bacteria, has been implicated in affecting photosynthesis and respiratory gene expression, as well as assembly of cytochrome
c
oxidase. In this study, we show that SenC from
Rhodobacter capsulatus
is involved in the assembly of a fully functional
cbb
3
-type cytochrome
c
oxidase, as revealed by decreased cytochrome
c
oxidase activity in a
senC
mutant. We also show that a putative copper-binding site in SenC is required for activity and that a SenC deletion phenotype can be rescued by the addition of exogenous copper to the growth medium. In addition, we demonstrate that a SenC mutation has an indirect effect on gene expression caused by a reduction in cytochrome
c
oxidase activity. A model is proposed whereby a reduction in cytochrome
c
oxidase activity impedes the flow of electrons through the respiratory pathway, thereby affecting the oxidation/reduction state of the ubiquinone pool, leading to alterations of photosystem and respiratory gene expression.
Identification of
Erwinia amylovora
Genes Induced during Infection of Immature Pear Tissue
Authors: Zhao Youfu , Blumer Sara E. , Sundin George W.
Published: November 2005

The enterobacterium
Erwinia amylovora
is a devastating plant pathogen causing necrotrophic fire blight disease of apple, pear, and other rosaceous plants. In this study, we used a modified in vivo expression technology system to identify
E. amylovora
genes that are activated during infection of immature pear tissue, a process that requires the major pathogenicity factors of this organism. We identified 394 unique pear fruit-induced (
pfi
) genes on the basis of sequence similarity to known genes and separated them into nine putative function groups including host-microbe interactions (3.8%), stress response (5.3%), regulation (11.9%), cell surface (8.9%), transport (13.5%), mobile elements (1.0%), metabolism (20.3%), nutrient acquisition and synthesis (15.5%), and unknown or hypothetical proteins (19.8%). Known virulence genes, including
hrp/hrc
components of the type III secretion system, the major effector gene
dspE
, type II secretion, levansucrase (
lsc
), and regulators of levansucrase and amylovoran biosynthesis, were upregulated during pear tissue infection. Known virulence factors previously identified in
E
. (
Pectobacterium
)
carotovora
and
Pseudomonas syringae
were identified for the first time in
E. amylovora
and included HecA hemagglutinin family adhesion, Peh polygalacturonase, new effector HopPtoC
EA
, and membrane-bound lytic murein transglycosylase MltE
EA
. An insertional mutation within
hopPtoC
EA
did not result in reduced virulence; however, an
mltE
EA
knockout mutant was reduced in virulence and growth in immature pears. This study suggests that
E. amylovora
utilizes a variety of strategies during plant infection and to overcome the stressful and poor nutritional environment of its plant hosts.
Genetic and Biochemical Analysis of the Twin-Arginine Translocation Pathway in Halophilic Archaea
Authors: Dilks Kieran , Giménez María Inés , Pohlschröder Mechthild
Published: November 2005

The twin-arginine translocation (Tat) pathway is present in a wide variety of prokaryotes and is capable of exporting partially or fully folded proteins from the cytoplasm. Although diverse classes of proteins are transported via the Tat pathway, in most organisms it facilitates the secretion of a relatively small number of substrates compared to the Sec pathway. However, computational evidence suggests that haloarchaea route nearly all secreted proteins to the Tat pathway. We have expanded previous computational analyses of the haloarchaeal Tat pathway and initiated in vivo characterization of the Tat machinery in a model haloarchaeon,
Haloferax volcanii
. Consistent with the predicted usage of the this pathway in the haloarchaea, we determined that three of the four identified
tat
genes in
Haloferax volcanii
are essential for viability when grown aerobically in complex medium. This represents the first report of an organism that requires the Tat pathway for viability when grown under such conditions. Deletion of the nonessential gene had no effect on the secretion of a verified substrate of the Tat pathway. The two TatA paralogs TatAo and TatAt were detected in both the membrane and cytoplasm and could be copurified from the latter fraction. Using size exclusion chromatography to further characterize cytoplasmic and membrane TatA proteins, we find these proteins present in high-molecular-weight complexes in both cellular fractions.
Biosynthesis of Hexahydroxyperylenequinone Melanin via Oxidative Aryl Coupling by Cytochrome P-450 in
Streptomyces griseus
Authors: Funa Nobutaka , Funabashi Masanori , Ohnishi Yasuo , Horinouchi Sueharu
Published: November 2005

Dihydroxyphenylalanine (DOPA) melanins formed from tyrosine by tyrosinases are found in microorganisms, plants, and animals. Most species in the soil-dwelling, gram-positive bacterial genus
Streptomyces
produce DOPA melanins and melanogenesis is one of the characteristics used for taxonomy. Here we report a novel melanin biosynthetic pathway involving a type III polyketide synthase (PKS), RppA, and a cytochrome P-450 enzyme, P-450mel, in
Streptomyces griseus
. In vitro reconstitution of the P-450mel catalyst with spinach ferredoxin-NADP
+
reductase/ferredoxin revealed that it catalyzed oxidative biaryl coupling of 1,3,6,8-tetrahydroxynaphthalene (THN), which was formed from five molecules of malonyl-coenzyme A by the action of RppA to yield 1,4,6,7,9,12-hexahydroxyperylene-3,10-quinone (HPQ). HPQ readily autopolymerized to generate HPQ melanin. Disruption of either the chromosomal
rppA
or
P-450mel
gene resulted in abolishment of the HPQ melanin synthesis in
S. griseus
and a decrease in the resistance of spores to UV-light irradiation. These findings show that THN-derived melanins are not exclusive in eukaryotic fungal genera but an analogous pathway is conserved in prokaryotic streptomycete species as well. A vivid contrast in THN melanin biosynthesis between streptomycetes and fungi is that the THN synthesized by the action of a type III PKS is used directly for condensation in the former, while the THN synthesized by the action of type I PKSs is first reduced and the resultant 1,8-dihydroxynaphthalene is then condensed in the latter.
Proteomic Characterization ofYersinia pestisVirulence
Authors: Chromy Brett A. , Choi Megan W. , Murphy Gloria A. , Gonzales Arlene D. , Corzett Chris H. , Chang Brian C. , Fitch J. Patrick , McCutchen-Maloney Sandra L.
Published: November 2005

TheYersinia pestisproteome was studied as a function of temperature and calcium by two-dimensional differential gel electrophoresis. Over 4,100 individual protein spots were detected, of which hundreds were differentially expressed. A total of 43 differentially expressed protein spots, representing 24 unique proteins, were identified by mass spectrometry. Differences in expression were observed for several virulence-associated factors, including catalase-peroxidase (KatY), murine toxin (Ymt), plasminogen activator (Pla), and F1 capsule antigen (Caf1), as well as several putative virulence factors and membrane-bound and metabolic proteins. Differentially expressed proteins not previously reported to contribute to virulence are candidates for more detailed mechanistic studies, representing potential new virulence determinants.
CspA Regulates Pigment Production in
Staphylococcus aureus
through a SigB-Dependent Mechanism
Authors: Katzif Samuel , Lee Eun-Hee , Law Anthony B. , Tzeng Yih-Ling , Shafer William M.
Published: November 2005

We report that the cold shock protein CspA of
Staphylococcus aureus
is required for maximal production of pigment. Results from transcriptional studies revealed that loss of CspA resulted in decreased expression of genes needed for the biosynthesis of 4,4′-diaponeurosporene and the alternative sigma factor SigB.
New Class of Competitive Inhibitor of Bacterial Histidine Kinases
Authors: Gilmour Raymond , Foster J. Estelle , Sheng Qin , McClain Jonathan R. , Riley Anna , Sun Pei-Ming , Ng Wai-Leung , Yan Dalai , Nicas Thalia I. , Henry Kenneth , Winkler Malcolm E.
Published: November 2005

Bacterial histidine kinases have been proposed as targets for the discovery of new antibiotics, yet few specific inhibitors of bacterial histidine kinases have been reported. We report here a novel thienopyridine (TEP) compound that inhibits bacterial histidine kinases competitively with respect to ATP but does not comparably inhibit mammalian serine/threonine kinases. Although it partitions into membranes and does not inhibit the growth of bacterial or mammalian cells, TEP could serve as a starting compound for a new class of histidine kinase inhibitors with antibacterial activity.
A Second Case of −1 Ribosomal Frameshifting Affecting a Major Virion Protein of the
Lactobacillus
Bacteriophage A2
Authors: Rodríguez Isabel , García Pilar , Suárez Juan E.
Published: November 2005

The bacteriophage A2 major tail protein gene utilizes a −1 translational frameshift to generate two structural polypeptides. Frameshifting is promoted by a slippery sequence and an RNA pseudoknot located 3′ of the gene. The major head gene presents a similar recoding ability. A2 is the only phage described with two −1 frameshifts.
Identification of Regions Involved in Enzymatic Stability of Peptide Deformylase ofMycobacterium tuberculosis
Authors: Saxena Rahul , Chakraborti Pradip K.
Published: November 2005

Sequence analysis of peptide deformylase ofMycobacterium tuberculosisrevealed the presence of insertions (residues 74 to 85) and an unusually long carboxy-terminal end (residues 182 to 197). Our results with deletion mutants indicated the contribution of these regions in maintaining enzymatic stability. Furthermore, we showed that the region spanning the insertions was responsible for maintaining resistance to oxidizing agents, like H2O2.
MORPHOLOGICAL STRUCTURE RECONSTRUCTION OF RETINAL VESSELS IN FUNDUS IMAGES
Authors: FANG BIN , YOU XINGE , TANG YUAN YAN , CHEN WEN SHENG
Published: November 2005

Vessels in retinal fundus images are useful in revealing the severity of eye-related diseases. In addition, they can act as landmarks for localizing lesions or the central vision area, and guide laser treatment of neovascularization. In this paper, we propose a two-stage scheme to extract vessels and reconstruct the morphological structure of vessels in retinal images. First, we employ mathematical morphology techniques to highlight large and small vessels with respect to their spatial properties. Different curvature response between vessel and noise patterns allows the use of curvature evaluation to remove enhanced vessel-like noise. A set of linear filters finalize the vessel map. However, the resulting vascular structure is incomplete of some important features in bifurcation points and central reflex. In order to rectify the pitfall, a reconstruction process is performed using dynamic local region growth to recover the morphological structure of vessels. Average performance of our method to extract vessels is 83.7% of TPR(True positive rate) and 3.8% of FPR(False positive rate) for 35 retinal images which include 21 abnormal images.
PERSONALIZED RECOMMENDATION BASED ON A MULTILEVEL CUSTOMER MODEL
Authors: JI JUNZHONG , LIU CHUNNIAN , SHA ZHIQIANG , ZHONG NING
Published: November 2005

Personalized recommendation needs powerful Web Intelligence (WI) technologies to manage, analyze and employ various business data on the Web for e-business intelligence. This paper presents a novel recommendation framework on the Web, which is based on a multilevel customer model comprising three submodels, namely, the customer shopping model (CSM), the customer preference model (CPM), and the customer consumption model (CCM). These models capture a customer's information from different aspects. After preprocessing of raw data, we first build the CSM based on Bayesian networks by mining from customer shopping transactions, and then find the CPM by analyzing customer shopping history. Furthermore, the customer purchasing power can be formalized as a linear CCM. By combining the CSM with the present customer shopping action, a recommendation algorithm based on Bayesian probability inference is used to generate an individual recommendation set of commodities. A personalized filter including customization of the CPM and orientation of the CCM is also used to realize a more personalized recommendation. Experimental evaluation on real world data shows that the proposed approach can achieve personalized commodities recommendation efficiently and effectively.
Determinants of Treasury-LIBOR Swap Spreads
Authors: Malhotra D. K. , Bhargava Vivek , Chaudhry Mukesh
Published: November 2005

Using data from the Treasury versus London Interbank Offer Swap Rates (LIBOR) for October 1987 to June 1998, this paper examines the determinants of swap spreads in the Treasury-LIBOR interest rate swap market. This study hypothesizes Treasury-LIBOR swap spreads as a function of the Treasury rate of comparable maturity, the slope of the yield curve, the volatility of short-term interest rates, a proxy for default risk, and liquidity in the swap market. The study finds that, in the long-run, swap spreads are negatively related to the yield curve slope and liquidity in the swap market. We also find that swap spreads are positively related to the short-term interest rate volatility. In the short-run, swap market's response to higher default risk seems to be higher spread between the bid and offer rates.
Korea's Post-Crisis Monetary Policy Reforms
Authors: Park Donghyun , Oh Junggun
Published: November 2005

Korea's financial crisis of 1997–1998 was brought about by the unsustainable combination of large capital inflows and an inefficient financial system. The Bank of Korea contributed to the crisis primarily through its failures as the regulator of the financial system rather than as the conductor of monetary policy. Our paper explores the role of the two major monetary policy reforms Korea has implemented in response to the crisis — the establishment of a new financial regulator and the adoption of inflation targeting — in Korea's efforts to build a stronger and more efficient financial system, thereby preventing crises in the future.
Corporate Governance, Cash Holdings, and Firm Value: Evidence from Japan
Authors: Luo Qi , Hachiya Toyohiko
Published: November 2005

This paper presents evidence on cash holdings for Japanese firms listed on the Tokyo Stock Exchange, focusing on the impact of corporate governance factors in cash holdings and the implication of cash holdings to firm value. We find that insider ownership and bank relations of firms play a significant role in determining cash holdings. Our results indicate that foreign stockholders select profitable firms to invest, and these firms have higher levels of cash. We document evidence that cash holdings lead to agency problems and impact firm value negatively, and governance characteristics affect the negative relation between cash holdings and firm value.
Response Asymmetries in Asian Stock Markets
Authors: Doong Shuh-Chyi , Yang Sheng-Yung , Chiang Thomas C.
Published: November 2005

This paper examines autocorrelation and cross-autocorrelation patterns for selected Asian stock returns. Special attention is given to examination of Asian stock returns and the impact on them of the past information. By employing a class of asymmetric specification of conditional mean and conditional variance models, we find the autocorrelation coefficient to be negative for the Japanese market and positive for the rest of the Asian markets studied. Our findings suggest that the Asian markets respond sensitively to the US market, especially on the down side. The asymmetric effects are found to be present in both mean and variance equations. The evidence is consistent with behavior in which investors in Asian markets tend to react more significantly to negative stock news originating from US sources than they do to positive news.
Challenges fuel excitement for work
Authors: Talbot Martin
Published: November 2005

Again this year, I am keeping a close eye on the Major League Baseball (MLB) playoffs. I watch a great pitch by Curt Schilling,crowds going wild on Carlos Beltran's homerun and some nice bounce light in Yankee Stadium. I am not watching this at home sitting on my couch but at work, trying to see the subtleties of the game. I am putting the final touches on Electronic Arts (EA)
MVP baseball 2005
, scheduled for release in early 2005. I have been working on EA's MVP Baseball franchise for the past two years as a Technical Art Director.
The beginning computer graphics course in computer science
Authors: Cunningham Steve , Hansmann Werner , Laxer Cary , Shi Jiaoying
Published: November 2005

A report from the working group on computer graphics in computer science 2004 SIGGRAPH/Eurographics Computer Graphics Education workshop, Zhejiang University, Hangzhou, China, June 2-6, 2004.
Teaching visualization
Authors: Ma Kwan-Liu
Published: November 2005

What draws students to computer graphics? For many it is video games and the movies. For many others it is the possibility of using visualization in their field of interest. For the last couple of years, I have been developing a course on visualization at Stanford.
Serious games...and less!
Authors: Blackman Sue
Published: November 2005

Many of us first heard the term "serious games" a couple of years ago at GDC (Game Developers Conference), the premier gathering place for game developers, publishers and industry hopefuls. As it happened, a colleague of mine thought he would take a peek into the room where a talk entitled "Serious Games" was being held. Expecting to see only a few people attending, he was amazed to find that it was standing room only! The use of game engines for non-game related applications had generated an inordinate amount of interest among a group of people normally known more for destroying grotesque aliens with absurdly proportioned weapons than reproducing mundane or real-life tasks in 3D.
Teaching 3D modeling and animation in the high schools
Authors: Cain Robin
Published: November 2005

Last week, a student wanted to know where I learned to teach computer animation. I hear this question a lot. In truth, when I graduated in the early 1980s with degrees in vocational education and industrial technology, teaching animation and visualization on a PC wasn't even in the picture.
Considerations in teaching a two quarter computer graphics sequence
Authors: Owen G. Scott
Published: November 2005

With the increasing emphasis on the use of Computer Graphics in Computer Science and other application areas, more schools are beginning to offer advanced courses in Computer Graphics, either at the undergraduate or the graduate level. Whereas there are many good textbooks for an introductory course the same is not true for an advanced course, The course content and external references for such a second course are in a state of rapid flux. The content of the second course also directly affects the content of the first course. Another issue is how many tools, in the sense of a graphics software support package, to provide for the students. This paper discusses the author's experiences in teaching both an introductory and a second Computer Graphics course for several years, how his courses have changed, and his recommendations both for course content and reference material.
An engineering graphics curriculum model with multidisciplinary implications
Authors: McGrath Michael B. , Bertoline Gary R. , Bowers Del , Pleck Michael H. , Sadowski Mary
Published: November 2005

This paper reports on a funded project to develop a conceptual model for an engineering graphics curriculum. The analysis lead to a framework that defined the body of knowledge appropriate for engineering graphics and and a model useful for multidisciplinary applications. It is based on the premise that computer tools available for design and research in visualization and creativity play important but not controlling roles in many visually based disciplines.
A workshop on computer graphics for undergraduate faculty
Authors: Owen G. Scott , Miller Valerie A.
Published: November 2005

A week long workshop in computer graphics, co-sponsored by Georgia State University (GSU) and the National Science Foundation (NSF grant No. USE-8954402 ) was held at GSU August 20-24,1990. The twenty four participants in the workshop were faculty from undergraduate institutions and the instructors were the authors of this paper. In the following we will describe the demographics of the faculty group, the subject areas covered, the format of the workshop, the developed course materials, and the results. This workshop can possibly be used as the prototype for future such workshops.
A survey of computer graphics image encoding and storage formats
Authors: Carlson Wayne E.
Published: November 2005

This paper is a survey of several storage formats used for computer generated or sampled images, both for purposes of archival storage and transmission (transfer from one location or platform to another). Various methodologies for the compression of such images are presented and discussed, Image storage standards and some of the more common commercial image storage techniques are presented in terms of the underlying compression algorithms they are based upon and the general internal data structures and formats.
Animation aerodynamics
Authors: Wejchert Jakub , Haumann David
Published: November 2005

Methods based on aerodynamics are developed to simulate and control the motion of objects in fluid flows. To simplify the physics for animation, the problem is broken down into two parts: a fluid flow regime and an object boundary regime. With this simplification one can approximate the realistic behaviour of objects moving in liquids or air. It also enables a simple way of designing and controlling animation sequences: from a set of flow primitives, an animator can design the spatial arrangement of flows, create flows around obstacles and direct flow timing. The approach is fast, simple, and is easily fitted into simulators that model objects governed by classical mechanics. The methods are applied to an animation that involves hundreds of flexible leaves being blown by wind currents.
Animated free-form deformation
Authors: Coquillart Sabine , Jancéne Pierre
Published: November 2005

Current research efforts focus on providing interactive techniques that make 3D concepts easy to use and accessible to large numbers of people. In this paper, a new interactive technique for animating deformable objects is presented. The technique allows easy specification and control of a class of deformations that cannot be produced by existing techniques without considerable human intervention.The methodology proposed relies on the Free-Form Deformation (FFD) technique. It makes use of a deformation tool that is animated like any other object.This approach provides a representation of the deformations independent of the surface geometry, and can be easily integrated into traditional hierarchical animation systems.