bluuebunny/crossref_metadata_2025 huggingface dataset:
Tissue-Associated “
Candidatus
Mycoplasma corallicola” and Filamentous Bacteria on the Cold-Water Coral
Lophelia pertusa
(Scleractinia)
Authors: Neulinger Sven C. , Gärtner Andrea , Järnegren Johanna , Ludvigsen Martin , Lochte Karin , Dullo Wolf-Christian
Published: December 2008

The cold-water coral
Lophelia pertusa
(Scleractinia, Caryophylliidae) is a key species in the formation of cold-water reefs, which are among the most diverse deep-sea ecosystems. It occurs in two color varieties: white and red. Bacterial communities associated with
Lophelia
have been investigated in recent years, but the role of the associated bacteria remains largely obscure. This study uses catalyzed reporter deposition fluorescence in situ hybridization to detect the in situ location of specific bacterial groups on coral specimens from the Trondheimsfjord (Norway). Two tissue-associated groups were identified: (i) bacteria on the host's tentacle ectoderm, “
Candidatus
Mycoplasma corallicola,” are flasklike, pointed cells and (ii) endoderm-associated bona fide TM7 bacteria form long filaments in the gastral cavity. These tissue-bound bacteria were found in all coral specimens from the Trondheimsfjord, indicating a closer relationship with the coral compared to bacterial assemblages present in coral mucus and gastric fluid.
Molecular Comparison of Bacterial Communities within Iron-Containing Flocculent Mats Associated with Submarine Volcanoes along the Kermadec Arc
Authors: Hodges Tyler W. , Olson Julie B.
Published: December 2008

Iron oxide sheaths and filaments are commonly found in hydrothermal environments and have been shown to have a biogenic origin. These structures were seen in the flocculent material associated with two submarine volcanoes along the Kermadec Arc north of New Zealand. Molecular characterization of the bacterial communities associated with the flocculent samples indicated that no known Fe-oxidizing bacteria dominated the recovered clone libraries. However, clones related to the recently described Fe-oxidizing bacterium
Mariprofundus ferrooxydans
were obtained from both the iron-containing flocculent (Fe-floc) and sediment samples, and peaks corresponding to
Mariprofundus ferrooxydans
, as well as the related clones, were observed in several of our terminal restriction fragment length polymorphism profiles. A large group of epsilonproteobacterial sequences, for which there is no cultured representative, dominated clones from the Fe-floc libraries and were less prevalent in the sediment sample. Phylogenetic analyses indicated that several operational taxonomic units appeared to be site specific, and statistical analyses of the clone libraries found that all samples were significantly different from each other. Thus, the bacterial communities in the Fe-floc samples were not more closely related to each other than to the sediment communities.
Oxidation of Lanthionines Renders the Lantibiotic Nisin Inactive
Authors: Wilson-Stanford Shawanda , Kalli Anastasia , Håkansson Kristina , Kastrantas James , Orugunty Ravi S. , Smith Leif
Published: December 2008

The peptide antibiotic nisin A belongs to the group of antibiotics called lantibiotics. They are classified as lantibiotics because they contain the structural group lanthionine. Lanthionines are composed of a single sulfur atom that is linked to the β-carbons of two alanine moieties. These sulfur atoms are vulnerable to environmental oxidation. A mild oxidation reaction was performed on nisin A to determine the relative effects it would have on bioactivity. High-mass-accuracy Fourier transform ion cyclotron resonance mass spectrometry data revealed the addition of seven, eight, and nine oxygens. These additions correspond to the five lanthionines, two methionines, and two histidines that would be susceptible to oxidation. Subsequent bioassays revealed that the oxidized form of nisin A had a complete loss of bactericidal activity. In a competition study, the oxidized nisin did not appear to have an antagonistic affect on the bioactivity of nisin A, since the addition of an equal molar concentration of the oxidized variant did not have an influence on the bactericidal activity of the native antibiotic. Electron microscopy data revealed that the oxidized forms were still capable of assembling into large circular complexes, demonstrating that oxidation does not disrupt the lateral assembly mechanism of the antibiotic. Affinity thin-layer chromatography and fluorescence microscopy experiments suggested that the loss of activity is due to the inability of the oxidized form of nisin to bind to the cell wall precursor lipid II. Given the loss of bioactivity following oxidation, oxidation should be an important factor to consider in future production, purification, pharmacokinetic, and pharmacodynamic studies.
Metabolism of Hydroxylated and Fluorinated Benzoates by
Syntrophus aciditrophicus
and Detection of a Fluorodiene Metabolite
Authors: Mouttaki Housna , Nanny Mark A. , McInerney Michael J.
Published: December 2008

Transformations of 2-hydroxybenzoate and fluorobenzoate isomers were investigated in the strictly anaerobic
Syntrophus aciditrophicus
to gain insight into the initial steps of the metabolism of aromatic acids. 2-Hydroxybenzoate was metabolized to methane and acetate by
S. aciditrophicus
and
Methanospirillum hungatei
cocultures and reduced to cyclohexane carboxylate by pure cultures of
S. aciditrophicus
when grown in the presence of crotonate. Under both conditions, transient accumulation of benzoate but not phenol was observed, indicating that dehydroxylation occurred prior to ring reduction. Pure cultures of
S. aciditrophicus
reductively dehalogenated 3-fluorobenzoate with the stoichiometric accumulation of benzoate and fluorine. 3-Fluorobenzoate-degrading cultures produced a metabolite that had a fragmentation pattern almost identical to that of the trimethylsilyl (TMS) derivative of 3-fluorobenzoate but with a mass increase of 2 units. When cells were incubated with deuterated water, this metabolite had a mass increase of 3 or 4 units relative to the TMS derivative of 3-fluorobenzoate.
19
F nuclear magnetic resonance spectroscopy (
19
F NMR) detected a metabolite in fluorobenzoate-degrading cultures with two double bonds, either 1-carboxyl-3-fluoro-2,6-cyclohexadiene or 1-carboxyl-3-fluoro-3,6-cyclohexadiene. The mass spectral and NMR data are consistent with the addition of two hydrogen or deuterium atoms to 3-fluorobenzoate, forming a 3-fluorocyclohexadiene metabolite. The production of a diene metabolite provides evidence that
S. aciditrophicus
contains dearomatizing reductase that uses two electrons to dearomatize the aromatic ring.
Construction of
Mycobacterium abscessus
Defined Glycopeptidolipid Mutants: Comparison of Genetic Tools
Authors: Medjahed Halima , Reyrat Jean-Marc
Published: December 2008

Mycobacterium abscessus
is a rapidly growing mycobacterial species that can be involved in pulmonary and disseminated infections in immunosuppressed or young cystic fibrosis patients. It is an emerging pathogen and has attracted recent attention due to the numerous cases of infection; furthermore, genomic tools have been developed for this species. Nevertheless, the study of this species has until now been limited to spontaneous variants. We report here a comparison of three different mutagenesis systems—the ts-
sacB
, the phage, and the recombineering systems—and show that there are important differences in their efficiency for the construction of allelic-exchange mutants. We show, using the
mmpL4b
gene of the glycopeptidolipid pathway as a target, that allelic-exchange mutants can be constructed with a reasonable efficiency (∼7%) using the recombineering system. These observations will facilitate genetic and cellular microbiology experiments involving the construction and use of well-defined mutants to study the virulence determinant of this emerging pathogen.
Cydia pomonella granulovirus
Genotypes Overcome Virus Resistance in the Codling Moth and Improve Virus Efficiency by Selection against Resistant Hosts
Authors: Berling Marie , Blachere-Lopez Christine , Soubabere Olivier , Lery Xavier , Bonhomme Antoine , Sauphanor Benoît , Lopez-Ferber Miguel
Published: December 2008

Cydia pomonella granulovirus
(CpGV) has been used for 15 years as a bioinsecticide in codling moth (
Cydia pomonella
) control. In 2004, some insect populations with low susceptibility to the virus were detected for the first time in southeast France. RGV, a laboratory colony of codling moths resistant to the CpGV-M isolate used in the field, was established with collection of resistant insects in the field followed by an introgression of the resistant trait into a susceptible colony (Sv). The resistance level (based on the 50% lethal concentrations [LC
50
s]) of the RGV colony to the CpGV-M isolate, the active ingredient in all commercial virus formulations in Europe, appeared to be over 60,000-fold compared to the Sv colony. The efficiency of CpGV isolates from various other regions was tested on RGV. Among them, two isolates (I12 and NPP-R1) presented an increased pathogenicity on RGV. I12 had already been identified as effective against a resistant
C. pomonella
colony in Germany and was observed to partially overcome the resistance in the RGV colony. The recently identified isolate NPP-R1 showed an even higher pathogenicity on RGV than other isolates, with an LC
50
of 166 occlusion bodies (OBs)/μl, compared to 1.36 × 10
6
OBs/μl for CpGV-M. Genetic characterization showed that NPP-R1 is a mixture of at least two genotypes, one of which is similar to CpGV-M. The 2016-r4 isolate obtained from four successive passages of NPP-R1 in RGV larvae had a sharply reduced proportion of the CpGV-M-like genotype and an increased pathogenicity against insects from the RGV colony.
The Plant Phenolic Compound
p
-Coumaric Acid Represses Gene Expression in the
Dickeya dadantii
Type III Secretion System
Authors: Li Yan , Peng Quan , Selimi Dija , Wang Qi , Charkowski Amy O. , Chen Xin , Yang Ching-Hong
Published: December 2008

The type III secretion system (T3SS) is a major virulence factor in many gram-negative bacterial pathogens. This secretion system translocates effectors directly into the cytosol of eukaryotic host cells, where the effector proteins facilitate bacterial pathogenesis by interfering with host cell signal transduction and other cellular processes. Plants defend themselves against bacterial pathogens by recognizing either the type 3 effectors or their actions and initiating a cascade of defense responses that often results in programmed cell death of the plant cell being attacked. Here we show that a plant phenolic compound,
p
-coumaric acid (PCA), represses the expression of T3SS genes of the plant pathogen
Dickeya dadantii
, suggesting that plants can also defend against bacterial pathogens by manipulating the expression of the T3SS. PCA repressed the expression of T3SS regulatory genes through the HrpX/Y two-component system, a core regulator of the T3SS, rather than through the global regulator GacS/A, which indirectly regulates the T3SS. A further analysis of several PCA analogs suggests that the
para
positioning of the hydroxyl group in the phenyl ring and the double bond of PCA may be important for its biological activity.
Hypovirus-Responsive Transcription Factor Gene
pro1
of the Chestnut Blight Fungus
Cryphonectria parasitica
Is Required for Female Fertility, Asexual Spore Development, and Stable Maintenance of Hypovirus Infection
Authors: Sun Qihong , Choi Gil H. , Nuss Donald L.
Published: December 2008

We report characterization of the gene encoding putative transcription factor PRO1, identified in transcriptional profiling studies as being downregulated in the chestnut blight fungus
Cryphonectria parasitica
in response to infection by virulence-attenuating hypoviruses. Sequence analysis confirmed that
pro1
encodes a Zn(II)
2
Cys
6
binuclear cluster DNA binding protein with significant sequence similarity to the
pro1
gene product that controls fruiting body development in
Sordaria macrospora
. Targeted disruption of the
C. parasitica pro1
gene resulted in two phenotypic changes that also accompany hypovirus infection, a significant reduction in asexual sporulation that could be reversed by exposure to high light intensity, and loss of female fertility. The
pro1
disruption mutant, however, retained full virulence. Although hypovirus CHV1-EP713 infection was established in the
pro1
disruption mutant, infected colonies continually produced virus-free sectors, suggesting that PRO1 is required for stable maintenance of hypovirus infection. These results complement the recent characterization of the hypovirus-responsive homologue of the
Saccharomyces cerevisiae
Ste12 C
2
H
2
zinc finger transcription factor gene,
cpst12
, which was shown to be required for
C. parasitica
female fertility and virulence.
A Strain-Specific Catalase Mutation and Mutation of the Metal-Binding Transporter Gene
mntC
Attenuate
Neisseria gonorrhoeae
In Vivo but Not by Increasing Susceptibility to Oxidative Killing by Phagocytes
Authors: Wu Hong , Soler-García Ángel A. , Jerse Ann E.
Published: December 2008

The hallmark of gonorrhea is an intense inflammatory response that is characterized by polymorphonuclear leukocytes (PMNs) with intracellular gonococci. A redundancy of defenses may protect
Neisseria gonorrhoeae
from phagocyte-derived reactive oxygen species. Here we showed that a gonococcal catalase (
kat
) mutant in strain MS11 was more sensitive to H
2
O
2
than mutants in cytochrome
c
peroxidase (
ccp
), methionine sulfoxide reductase (
msrA
), or the metal-binding protein (
mntC
) of the MntABC transporter.
kat ccp
and
kat ccp mntC
mutants were significantly more sensitive to H
2
O
2
than mutants in any single factor. None of the mutants showed increased susceptibility to murine PMNs. Recovery of the
mntC
and
kat ccp mntC
mutants from the lower genital tract of BALB/c mice, but not the
kat
or
kat ccp
mutants, was significantly reduced relative to wild-type bacteria. Interestingly, unlike the MS11
kat
mutant, a
kat
mutant of strain FA1090 was attenuated during competitive infection with wild-type FA1090 bacteria. The FA1090
kat
mutant and MS11
mntC
mutant were also attenuated in mice that are unable to generate a phagocytic respiratory burst. We conclude that inactivation of three well-characterized antioxidant genes (
kat
,
ccp
, and
mntC
) does not increase gonococcal susceptibility to the phagocytic respiratory burst during infection and that gonococcal catalase and the MntC protein confer an unidentified advantage in vivo. In the case of catalase, this advantage is strain specific. Finally, we also showed that an
msrA
mutant of strain MS11 demonstrated delayed attenuation in BALB/c but not C57BL/6 mice. Therefore, MsrA/B also appears to play a role in infection that is dependent on host genetic background.
Role of Complement in Protection againstCryptococcus gattiiInfection
Authors: Mershon Kileen L. , Vasuthasawat Alex , Lawson Gregory W. , Morrison Sherie L. , Beenhouwer David O.
Published: December 2008

Previous studies have shown that the alternative pathway of complement activation plays an important role in protection against infection withCryptococcus neoformans. Cryptococcus gattiidoes not activate the alternative pathway as well asC. neoformansin vitro. The role of complement inC. gattiiinfection in vivo has not been reported. In this study, we used mice deficient in complement components to investigate the role of complement in protection against aC. gattiiisolate from an ongoing outbreak in northwestern North America. While factor B-deficient mice showed an enhanced rate of death, complement component C3-deficient mice died even more rapidly, indicating that the alternative pathway was not the only complement pathway contributing to protection against disease. Both C3- and factor B-deficient mice had increased fungal burdens in comparison to wild-type mice. Histopathology revealed an overwhelming fungal burden in the lungs of these complement-deficient mice, which undoubtedly prevented efficient gas exchange, causing death. Following the fate of radiolabeled organisms showed that both factor B- and C3-deficient mice were less effective than wild-type mice in clearing organisms. However, opsonization ofC. gattiiwith complement components was not sufficient to prolong life in mice deficient in complement. Killing ofC. gattiiby macrophages in vitro was decreased in the presence of serum from factor B- and C3-deficient versus wild-type mice. In conclusion, we have demonstrated that complement activation is crucial for survival inC. gattiiinfection. Additionally, we have shown that the alternative pathway of complement activation is not the only complement pathway contributing to protection.
Efficacy of a Vaccine Based on Protective Antigen and Killed Spores against Experimental Inhalational Anthrax
Authors: Gauthier Yves P. , Tournier Jean-Nicolas , Paucod Jean-Charles , Corre Jean-Philippe , Mock Michèle , Goossens Pierre L. , Vidal Dominique R.
Published: December 2008

Protective antigen (PA)-based anthrax vaccines acting on toxins are less effective than live attenuated vaccines, suggesting that additional antigens may contribute to protective immunity. Several reports indicate that capsule or spore-associated antigens may enhance the protection afforded by PA. Addition of formaldehyde-inactivated spores (FIS) to PA (PA-FIS) elicits total protection against cutaneous anthrax. Nevertheless, vaccines that are effective against cutaneous anthrax may not be so against inhalational anthrax. The aim of this work was to optimize immunization with PA-FIS and to assess vaccine efficacy against inhalational anthrax. We assessed the immune response to recombinant anthrax PA from
Bacillus anthracis
(rPA)-FIS administered by various immunization protocols and the protection provided to mice and guinea pigs infected through the respiratory route with spores of a virulent strain of
B. anthracis
. Combined subcutaneous plus intranasal immunization of mice yielded a mucosal immunoglobulin G response to rPA that was more than 20 times higher than that in lung mucosal secretions after subcutaneous vaccination. The titers of toxin-neutralizing antibody and antispore antibody were also significantly higher: nine and eight times higher, respectively. The optimized immunization elicited total protection of mice intranasally infected with the virulent
B. anthracis
strain 17JB. Guinea pigs were fully protected, both against an intranasal challenge with 100 50% lethal doses (LD
50
) and against an aerosol with 75 LD
50
of spores of the highly virulent strain 9602. Conversely, immunization with PA alone did not elicit protection. These results demonstrate that the association of PA and spores is very much more effective than PA alone against experimental inhalational anthrax.
Immune Evasion ofLeptospiraSpecies by Acquisition of Human Complement Regulator C4BP
Authors: Barbosa Angela S. , Abreu Patricia A. E. , Vasconcellos Sílvio A. , Morais Zenaide M. , Gonçales Amane P. , Silva Aldacilene S. , Daha Mohamed R. , Isaac Lourdes
Published: December 2008

Leptospirosis is a spirochetal zoonotic disease of global distribution with a high incidence in tropical regions. In the last 15 years it has been recognized as an important emerging infectious disease due to the occurrence of large outbreaks in warm-climate countries and, occasionally, in temperate regions. Pathogenic leptospires efficiently colonize target organs after penetrating the host. Their invasiveness is attributed to the ability to multiply in blood, adhere to host cells, and penetrate into tissues. Therefore, they must be able to evade the innate host defense. The main purpose of the present study was to evaluate how severalLeptospirastrains evade the protective function of the complement system. The serum resistance of sixLeptospirastrains was analyzed. We demonstrate that the pathogenic strain isolated from infected hamsters avoids serum bactericidal activity more efficiently than the culture-attenuated or the nonpathogenicLeptospirastrains. Moreover, both the alternative and the classical pathways of complement seem to be responsible for the killing of leptospires. Serum-resistant and serum-intermediate strains are able to bind C4BP, whereas the serum-sensitive strain Patoc I is not. Surface-bound C4BP promotes factor I-mediated cleavage of C4b. Accordingly, we found that pathogenic strains displayed reduced deposition of the late complement components C5 to C9 upon exposure to serum. We conclude that binding of C4BP contributes to leptospiral serum resistance against host complement.
Functional Characterization of the Type III Secretion ATPase HrcN from the Plant Pathogen
Xanthomonas campestris
pv. vesicatoria
Authors: Lorenz Christian , Büttner Daniela
Published: December 2008

Many gram-negative plant and animal pathogenic bacteria employ a type III secretion (T3S) system to inject effector proteins into the cytosol of eukaryotic host cells. The membrane-spanning T3S apparatus is associated with an ATPase that presumably provides the energy for the secretion process. Here, we describe the role of the predicted ATPase HrcN from the plant pathogenic bacterium
Xanthomonas campestris
pathovar vesicatoria. We show that HrcN hydrolyzes ATP in vitro and is essential for T3S and bacterial pathogenicity. Stability of HrcN in
X. campestris
pv. vesicatoria depends on the conserved HrcL protein, which interacts with HrcN in vitro and in vivo. Both HrcN and HrcL bind to the inner membrane protein HrcU and specifically localize to the bacterial membranes under T3S-permissive conditions. Protein-protein interaction studies revealed that HrcN also interacts with the T3S substrate specificity switch protein HpaC and the global T3S chaperone HpaB, which promotes secretion of multiple effector proteins. Using an in vitro chaperone release assay, we demonstrate that HrcN dissociates a complex between HpaB and the effector protein XopF1 in an ATP-dependent manner, suggesting that HrcN is involved in the release of HpaB-bound effectors. Effector release depends on a conserved glycine residue in the HrcN phosphate-binding loop, which is crucial for enzymatic activity and protein function during T3S. There is no experimental evidence that T3S can occur in the absence of the ATPase, in contrast to recent findings reported for animal pathogenic bacteria.
The Cell Wall Regulator σISpecifically Suppresses the Lethal Phenotype ofmblMutants inBacillus subtilis
Authors: Schirner Kathrin , Errington Jeff
Published: December 2008

Bacterial actin homologues are thought to have a role in cell shape determination by positioning the cell wall synthetic machinery. They are also thought to control other functions, including cell polarity and chromosome segregation in various organisms.Bacillus subtilisand many other gram-positive bacteria have three actin isoforms, MreB, Mbl, and MreBH, which colocalize in helical structures that span the length of the cell, close to the inner surface of the cytoplasmic membrane. Deletion of themblgene has previously been reported to produce viable, although poorly growing, mutant cells. We now show that under normal conditionsΔmblcells are nonviable but suppressors allowing growth readily accumulate. In the presence of high concentrations of Mg2+, viable, nonsuppressed mutants can be obtained. A screen for suppressor mutations revealed that deletion ofrsgIrestores Mg2+-independent growth of themblmutant. Recent work has shown thatrsgIdeletion leads to upregulation of the alternative sigma factor σI. The basis of suppression is not yet clear, but it is independent of the Mg2+effect. We found that the construction of a triple mutant lacking all three actin homologues became possible in thersgIbackground. Triple mutant cells are spherical, but no significant defect in chromosome segregation was detected.
A Regulatory Network Controls Expression of the In Vivo-Expressed HreP Protease of
Yersinia enterocolitica
Authors: Wagner Karin , Schilling Jennifer , Fälker Stefan , Schmidt M. Alexander , Heusipp Gerhard
Published: December 2008

The human enteropathogen
Yersinia enterocolitica
survives and replicates in the lymphoid tissues of its host. Previous in vivo analyses of gene expression revealed that various chromosomal genes are expressed at this stage of infection, but not in vitro. One of these, termed
hreP
, encodes a protease that is necessary for full virulence of
Y. enterocolitica
. Using transposon mutagenesis, we identified three genes,
pypA
,
pypB
, and
pypC
, as positive regulators of
hreP
transcription. PypA is an inner membrane protein with no significant similarity to any known proteins; PypB is a ToxR-like transmembrane transcriptional regulator; and PypC is a cytoplasmic transcriptional regulator with an OmpR-like winged helix-turn-helix DNA binding motif. We show that all Pyp proteins are able to activate
hreP
independently of each other and that PypB and PypC interact directly with the
hreP
promoter region. Furthermore,
pypB
and
pypC
are autoregulated and regulate each other. Additional data indicate that transcription of
hreP
is repressed by the histone-like nucleoid-structuring protein H-NS in a temperature-dependent manner. Our data reveal a new regulatory network that might have implications for the controlled expression of further virulence-associated functions in
Yersinia
.
Relative Contributions of Recombination and Mutation to the Diversification of the
opa
Gene Repertoire of
Neisseria gonorrhoeae
Authors: Bilek Nicole , Ison Catherine A. , Spratt Brian G.
Published: December 2008

To understand the rates and mechanisms of
Neisseria gonorrhoeae opa
gene variation, the 11
opa
genes were amplified independently so that an
opa
allelic profile could be defined for any isolate from the sequences at each locus. The
opa
allelic profiles from 14 unrelated isolates were all different, with no
opa
alleles shared between isolates. Examination of very closely related isolates from sexual contacts and sexual networks showed that these typically shared most
opa
alleles, and the mechanisms by which recent changes occurred at individual
opa
loci could be determined. The great majority of changes were due to recombination among existing alleles that duplicated an
opa
allele present at another locus or resulted in a mosaic of existing
opa
alleles. Single nucleotide changes or insertion/deletion of a single codon also occurred, but few of these events were assigned to mutation, the majority being assigned to localized recombination. Introduction of novel
opa
genes from coinfecting strains was rare, and all but one were observed in the same sexual network. Changes at
opa
loci occurred at a greater rate than those at the porin locus, and the
opa11
locus changed more rapidly than other
opa
loci, almost always differing even between recent sexual contacts. Examination of the neighboring
pilE
gene showed that changes at
opa11
and
pilE
often occurred together, although this linkage may not be a causal one.
Positive Control of Ferric Siderophore Receptor Gene Expression by the Irr Protein inBradyrhizobium japonicum
Authors: Small Sandra K. , Puri Sumant , Sangwan Indu , O'Brian Mark R.
Published: December 2008

Ferric siderophore receptors are components of high-affinity iron-chelate transport systems in gram-negative bacteria. The genes encoding these receptors are generally regulated by repression. Here, we show that the ferrichrome receptor gene bll4920 and four additional putative ferric siderophore receptor genes inBradyrhizobium japonicumare positively controlled by the regulatory protein Irr, as observed by the low level of mRNA transcripts in anirrmutant in iron-limited cells. Potential Irr binding sites with iron control element (ICE)-like motifs were found upstream and distal to the transcription start sites of the five receptor genes. However, purified recombinant Irr bound only some of those elements. Nevertheless, dissection of the bll4920 promoter region showed that a component in extracts of wild-type cells grown in iron-limited media bound only in the ICE motif region of the promoter. This binding was not observed with extracts of cells from the parent strain grown under high-iron conditions or from anirrmutant strain. Furthermore, gel mobility supershift experiments identified Irr as the binding protein in cell extracts. Chromatin immunoprecipitation experiments demonstrated that Irr occupies the promoters of the five ferric iron transport genes in vivo. We conclude that Irr is a direct positive regulator of ferric iron transport inB. japonicum.
REVISITING HOCHSCHILD COHOMOLOGY FOR ALGEBRA BUNDLES
Authors: KIRANAGI B. S. , RAJENDRA R.
Published: December 2008

Hochschild cohomology of an associative algebra bundle with coefficients in a bimodule bundle has been defined and studied in earlier paper. Here, by using cohomological methods, we establish that an algebra bundle is a semidirect product of its radical bundle and a semisimple subalgebra bundle. Further we define multiplication algebra bundle of an algebra bundle and representation of an algebra bundle. We study special representations of an algebra bundle using Hochschild cohomology of an associative algebra bundle with coefficients in a bimodule bundle. We observe that if a representation of an algebra bundle is special then its obstruction is zero. Further we show that a subgroup H of H2(ξ, N) is faithfully represented as a transitive group of translations operating on the set of those equivalence classes of algebra bundle extensions of ξ which determine a given representation [φ, K].
n-RECOGNITION BY PRIME GRAPH OF THE SIMPLE GROUP PSL(2,q)
Authors: KHOSRAVI BEHROOZ
Published: December 2008

Let G be a finite group. The prime graph Γ(G) of G is defined as follows. The vertices of Γ(G) are the primes dividing the order of G and two distinct vertices p, q are joined by an edge if there is an element in G of order pq.

It is proved that if p > 11 and p ≢ 1 (mod 12), then PSL(2,p) is uniquely determined by its prime graph. Also it is proved that if p > 7 is a prime number and Γ(G) = Γ(PSL(2,p2)), then G ≅ PSL(2,p2) or G ≅ PSL(2,p2).2, the non-split extension of PSL(2,p2) by ℤ2. In this paper as the main result we determine finite groups G such that Γ(G) = Γ(PSL(2,q)), where q = pk. As a consequence of our results we prove that if q = pk, k > 1 is odd and p is an odd prime number, then PSL(2,q) is uniquely determined by its prime graph and so these groups are characterizable by their prime graph.
ON LIE–RINEHART–JACOBI ALGEBRAS
Authors: OKASSA EUGÈNE
Published: December 2008

We show that Jacobi algebras (Poisson algebras respectively) can be defined only as Lie–Rinehart–Jacobi algebras (as Lie–Rinehart–Poisson algebras respectively). Also we show that contact manifolds, locally conformal symplectic manifolds (symplectic manifolds respectively) can be defined only as symplectic Lie–Rinehart–Jacobi algebras (only as symplectic Lie–Rinehart–Poisson algebras respectively). We define symplectic Lie algebroids.
A PRUNING APPROACH TO PATTERN DISCOVERY
Authors: WANG HSIAO-FAN , CHAN ZU-WEN
Published: December 2008

In this study, we proposed a general pruning procedure to reduce the dimension of a large database so that the properties of the extracted subset can be well defined. Since learning functions have been widely applied, we take this group of functions as an example to demonstrate the proposed procedure. Based on the concept of Support Vector Machine (SVM), three major stages of preliminary pruning, fitting function, and refining are proposed to discover a subset that possess the characteristics of some learning function from the given large data set. Three models were used to illustrate and evaluate the proposed pruning procedure and the results have shown to be promising in application.
USE OF BAYESIAN METHOD FOR ASSESSING VESSEL TRAFFIC RISKS AT SEA
Authors: HU SHENPING , LI XUDONG , FANG QUANGEN , YANG ZAILI
Published: December 2008

Risks associated with a vessel traffic system at sea are analyzed according to the elements in this system and a new method is developed to ensure safe ship operation. Based on Bayes' point estimation and probability influence diagram to estimate the traffic accidents related to vessel traffic, an analysis model is established for the quantitative risk assessment (QRA) of the vessel traffic system at sea. After the analysis on occurrence likelihood of the accidents related to ship traffic, a structure on the basis of Bayesian networks is developed to obtain the QRA of their relative risks. QRA is also put forward after analyzing the features and situations of the vessel traffic system and identifying the corresponding hazards including characteristics of those hazards. The risk distributions of ship traffic are described and results are presented on QRA in relation to various features by using this risk assessment model. This method, verified in the cases of QRA, turns out to be feasible by the use of identified posterior probability.
ENTANGLEMENT SWAPPING AND QUANTUM COMMUNICATION IN CAVITY QED
Authors: SHAN CHUAN-JIA , LIU JI-BING , CHENG WEI-WEN , LIU TANG-KUN , HUANG YAN-XIA , LI HONG
Published: December 2008

We study entanglement swapping and quantum communication in the context of cavity QED. We first present an entanglement swapping scheme in cavities where two atoms without interacting previously can be entangled with the success probability unity. Then, conditioned on a novel property of entanglement swapping, we propose a secure direct communication protocol, in which two legitimate users can communicate deterministically.
INFLUENCE OF ENTANGLEMENT IN QUANTUM PARRONDO GAME
Authors: XU KUI , HUANG LIUSHENG , YANG WEI
Published: December 2008

Classical Parrondo game shows that the combination of two losing games can achieve a winning result. We investigate such an effect under quantum models, and make a complete research about the initial states that can be adapted. By the comparison of the payoffs which come from the GHZ class, W class and initial states without entanglement, we find out that entanglement plays an important role here. Moreover, we reveal that, particular initial state without entanglement can even provide us optimal payoff. Thorough discussion and exact results in this article will help us not only to make appropriate choices in quantum Parrondo game, but also have a deeper understanding about entanglement and quantum game.
Crowdsourcing for relevance evaluation
Authors: Alonso Omar , Rose Daniel E. , Stewart Benjamin
Published: December 2008

Relevance evaluation is an essential part of the development and maintenance of information retrieval systems. Yet traditional evaluation approaches have several limitations; in particular, conducting new editorial evaluations of a search system can be very expensive. We describe a new approach to evaluation called TERC, based on the crowdsourcing paradigm, in which many online users, drawn from a large community, each performs a small evaluation task.
The SIGIR 2008 workshop program
Authors: Anick Peter , Ng Hwee Tou
Published: December 2008

With the ever-expanding scope of the field of Information Retrieval, the SIGIR workshops program has grown into a vital component of the annual SIGIR conference. It provides an informal but structured setting for extended dialog and brainstorming. It allows scholars in budding areas to share ideas and set research agendas. It supports cross fertilization between existing communities and the development of new ones, often bringing together practitioners from industry and academia.
Spoken content retrieval
Authors: Kohler Joachim , Larson Martha , de Jong Franciska , Kraaij Wessel , Ordelman Roeland
Published: December 2008

The second workshop on Searching Spontaneous Conversational Speech (SSCS 2008) was held in Singapore on July 24, 2008 in conjunction with the 31st Annual International ACM SIGIR Conference. The goal of the workshop was to bring the speech community and the information retrieval community together. The forum was designed to be conducive to the close interaction and the intense discussion necessary to promote fusion of these fields into a single discipline with a concerted vision of spoken content retrieval. At the workshop, talks and posters were presented covering a wide range of topics including vocabulary independent search, spoken term detection, combination of models/indexes, use of speech recognition lattices for search, segmentation, temporal analysis, benchmarking, exploitation of prosody, speech surrogates for user interfaces and multi-language collections. Demonstrations of speech-based retrieval systems from a variety of application domains introduced a strong practical emphasis into the workshop program. The workshop concluded with a panel discussion, whose goal it was to identify future research directions for speech retrieval. Among the important challenges identified during the panel discussions were: dealing with large scale multimedia collections, representing audio/video content effectively in the user interface, focusing on perfecting the component technologies on which speech retrieval systems are based, and developing systems and approaches that will enable users (both content seekers and content providers) to actively create their own speech search applications or contribute to the indexability of their content.
Workshop on aggregated search
Authors: Murdock Vanessa , Lalmas Mounia
Published: December 2008

The Workshop on Aggregated seeks to define the research problems for aggregated search results, and to build a community of researchers working in this emerging area. Aggregated search addresses the issues of how to select and rank resources, how to present them to a user in such a way that information can be found efficiently and effectively. The aim of the workshop was to encourage discussion and the exchange of ideas about the directions for aggregated search. The workshop presented prototype systems, user studies of existing systems, as well as papers about component technologies.
Information access to cultural heritage
Authors: Larson Martha , Fernie Kate , Oomen Johan , Cigarran Recuero Juan Miguel
Published: December 2008

The workshop on Information Access to Cultural Heritage (IACH 2008) was held during the ECDL conference in Aarhus on the 18th September 2008. The workshop provided a venue to bring together academics carrying out research in the area of information access and practitioners working in the cultural heritage field. The aim was to encourage the exchange of ideas concerning the creation, curation, storage, retrieval and use of cultural heritage information. The day began with a keynote paper by Chris Batt, who looked to the future, challenging the audience to think of uses of technology to make sense of the landscape for users, shifting focus of information access to cultural heritage from
search
to
find
. The keynote was followed by a session on the European Digital Library with invited papers by Stefan Gradmann on the infrastructure of Europeana and by Rob Davies on work to develop the content of the Library in the EuropeanaLocal project. The proceedings continued with a series of papers on services being developed to provide access to cultural heritage collections and a wide range of media -- images, text, music and speech. A lively series of poster boasters followed and the day concluded with the poster session and a panel discussion on future directions. Given the attendance at the workshop and the good level of discussion throughout the day, we conclude that Information Access to Cultural Heritage is a growing area of research and promising area for exchange and collaboration between researchers and practitioners.
Automatic generation of lexical resources for opinion mining
Authors: Esuli Andrea
Published: December 2008

Opinion mining is a recent discipline at the crossroads of Information Retrieval and of Computational Linguistics which is concerned not with the topic a document is about, but with the opinion it expresses. It has a rich set of applications, ranging from tracking users' opinions about products or about political candidates as expressed in online forums, to customer relationship management.
Implementing domain-specific languages as the foundation of an honors intro CS course
Authors: Fisler Kathi
Published: December 2008

This position paper describes an honors introductory Computer Science course focused on designing and implementing domain-specific programming languages. The course presents programming language design as a fundamental tool for software engineering. Students build languages for prototypes of several nontrivial products (such as PowerPoint and TurboTax). The course aims to convey fundamental ideas behind programming languages in a form that mainstream Computer Science students can appreciate early in their careers. The paper includes descriptions of and links to assignments and course materials.
Addressing the disconnect between the good and the popular
Authors: Hind Michael
Published: December 2008

For several decades universities have taught programming languages as a fundamental part of their un-dergraduate curriculum. These courses cover the core topics used in the design of good programming languages. However, widely used commercial languages quite often seem to go against the conventional wisdom of good language design that is taught in these courses. This disconnect between what is taught as good language design and what languages are used in industry has put the programming language course in a bind. Specifically, as computer science departments feel the increased pressure to add new emerging topics, many departments are choosing to remove the programming language course from the core curriculum. In this position paper, we argue that the disconnect between good language design and industry practice is exactly why a programming language course should be a crucial ingredient in any undergraduate computer science education.
Teaching programming languages in a post-linnaean age
Authors: Krishnamurthi Shriram
Published: December 2008

Programming language "paradigms" are a moribund and tedious legacy of a bygone age. Modern language designers pay them no respect, so why do our courses slavishly adhere to them? This paper argues that we should abandon this method of teaching languages, offers an alternative, reconciles an important split in programming language education, and describes a textbook that explores these matters.
Use concurrent programming models to motivate teaching of programming languages
Authors: Leavens Gary T.
Published: December 2008

Undergraduate computer science students typically have only a limited understanding of their favorite languages and no inkling of other programming paradigms. Yet modern programmers typically work with several languages, and the availability of cheap concurrency is exposing fundamental problems in standard concurrent programming techniques (mutable objects and threads). This situation presents a great opportunity: by exploring nonstandard techniques for gaining intellectual control over concurrent programs, one can motivate and teach important semantic concepts (such as scoping) and important programming concepts (such as functional abstraction). Such a curriculum stimulates student interest in exploring new programming paradigms.
Rethinking pedagogy for teaching PL with more than PL concepts in mind
Authors: Pollock Lori
Published: December 2008

Individual department goals drive undergraduate computer science educators to teach with varying priorities on preparing students for continuing to graduate school or embarking on a career that leverages their education immediately after college. Programming languages play a key role in that education for both student profiles, even in curricula that include no core programming language concepts course. The "fattening" of our discipline into many subareas has prompted curricula reviews and rethinking of the undergraduate CS content, including programming language concepts (PL) and where they are taught in the curriculum. This paper proposes that we also rethink the pedagogy for teaching PL with diversity in mind.
Applying formal methods to gossiping networks with mCRL and groove
Authors: Crouzen Pepijn , van de Pol Jaco , Rensink Arend
Published: December 2008

In this paper we explore the practical possibilities of using formal methods to analyze gossiping networks. In particular, we use μCRL and Groove to model the peer sampling service, and analyze it through a series of model transformations to CTMCs and finally MRMs. Our tools compute the expected value of various network quality indicators, such as average path lengths, over all possible system runs. Both transient and steady state analysis are supported. We compare our results with the simulation and emulation results found in [10].
Analysis of a gossip protocol in PRISM
Authors: Kwiatkowska Marta , Norman Gethin , Parker David
Published: December 2008

Gossip protocols have been proposed as a robust and efficient method for disseminating information throughout dynamically changing networks. We present an analysis of a gossip protocol using probabilistic model checking and the tool PRISM. Since the behaviour of these protocols is both probabilistic and nondeterministic in nature, this provides a good example of the exhaustive, quantitative analysis that probabilistic model checking techniques can provide. In particular, we compute minimum and maximum values, representing the best- and worst-case performance of the protocol under any scheduling, and investigate both their relationship with the average values that would be obtained through simulation and the precise scheduling which achieve these values.
A view-probability-matrix approach to the modelling of gossiping protocols
Authors: Krieger Thomas , Riedl Martin , Schuster Johann , Siegle Markus
Published: December 2008

This paper addresses the quantitative analysis of gossiping protocols. In contrast to existing approaches which are entirely based on the simulation of the individual nodes' behaviours, we present a new approach based on summary stochastic models for the peer sampling service. Instead of an ordinary state- and transition-based model, a matrix-based approach is presented. Starting from a basic model with static node population and without ageing of neighbourhood information, refinements of the model are presented which enable the modelling of ageing and dynamic population. The paper also contains some experimental results for the different models introduced in the paper.