bluuebunny/crossref_metadata_2025 huggingface dataset:
Characterization of the osmotically inducible gene osmE of Escherichia coli K‐12
Authors: Gutierrez Claude , Gordia Sylvie , Bonnassie Sylvie
Published: October 2006

osmE, an osmotically inducible gene of Escherichia coli, was physically mapped on the bacterial chromosome, cloned and sequenced. osmE appeared to encode a 12 021 Da protein of unknown function, with a lipoprotein‐type signal sequence at the amino‐terminus. The osmE reading frame was confirmed by sequencing the junction of an osmE‐phoA gene fusion. osmE was demonstrated to be transcribed as a single cistron. A φ[osmEp–lac] operon fusion was constructed, and analysis of its expression demonstrated that osmE osmotic regulation probably occurs at the transcriptional level. The osmE promoter was identified by both S1 nuclease and primer extension mapping of the 5′ end of the osmE mRNA, by deletion analysis and by identification of a point mutation reducing its activity. Sequence information sufficient for expression and osmotic regulation is present on a DNA fragment extending from positions ‐37 to + 52 with respect to the osmE transcription start. Unin‐duced expression of the osmE‐lac fusion was increased in the presence of mutations in the hns and himA genes. The osmE promoter overlaps a promoter for a gene transcribed in the opposite direction, efg. Transcription from the efg promoter is only weakly affected by osmotic pressure and is independent of the presence of an intact OsmE protein.
Molecular cloning and characterization of the rfc gene of Pseudomonas aeruginosa (serotype O5)
Authors: de Kievit Teresa R. , Dasgupta Tapashi , Schweizer Herbert , Lam Joseph S.
Published: October 2006

Previous work from our laboratory has shown that cosmid clone pFVl00, containing a 26 kb insert, is able to restore O‐antigen synthesis in serotype O5 rough mutants of Pseudomonas aeruginosa. Mobilization of pFV100 into two P. aeruginosa semi‐rough (SR) mutants, AK14O1 and rd7513, resulted in O‐antigen expression, indicating that pFV100 may contain an O‐polymerase (rfc) gene. pFV.TK6, a subclone of pFVl00 that contains a 5.6 kb chromosomal insert, was able to complement O‐antigen expression in these SR mutants. Mutagenesis of pFV.TK6 using Tn1000 exposed a 1.5 kb region that was essential for complementing O‐antigen expression in AK14O1. A 2.0 kb Xhol‐HindIII fragment, containing this region, was cloned into vector pUCP26 and the resulting plasmid called pFV.TK8. In Southern analysis of the 20 P aeruginosa serotypes using a probe generated from the 1.5 kb Xhol fragment of pFV.TK8, the rfc probe hybridized to a common fragment of the cross‐reactive O2‐O5‐O16‐O18‐O20 serogroup, suggesting that these serotypes may share a common O‐polymerase gene. In functional studies of the rfc gene, the PAOl (serotype O5) chromosomal rfc was mutated using a gene‐replacement strategy. These knockout mutants expressed the SR lipopolysaccharide (LPS) phenotype, which indicated that they were no longer producing a functional O‐polymerase enzyme. Nucleotide sequence analysis of the insert DNA of pFV.TK8 revealed one open reading frame (ORF), designated ORF48.9, which could code for a 48.9 kDa protein. In comparisons of the P. aeruginosa rfc nucleotide and amino acid sequences with DNA and protein databases, no significant homology was found. However, the deduced structure of the P. aeruginosa Rfc protein indicated that it is very hydrophobic and contains 11 putative membrane‐spanning domains. Therefore, the predicted structure is similar to that of other reported Rfc proteins. Furthermore, comparison of the amino acid composition and codon usage of the P. aeruginosa Rfc with other Rfc proteins revealed significant similarity between them.
Purification of ArcA and analysis of is specific interaction with the pfl promoter‐regulatory region
Authors: Drapal Nikola , Sawers Gary
Published: October 2006

ArcA is one of several transcription factors required for optimal anaerobic induction of the pyruvate formatelyase (pfl) operon. To aid the study at the molecular level of the interaction of ArcA with the pfl promoter‐regulatory region we developed a procedure for the isolation of ArcA. The purification of ArcA involved chromatography in heparin agarose, hydroxylapatite and Mono‐Q matrices and delivered a protein that was >95% pure. Gel retardation assays demonstrated that ArcA bound specifically to the pfl regulatory region. Three distinct ArcA–DNA complexes could be resolved depending on the ArcA concentration used. This finding suggested that either multiple ArcA‐binding sites are present in the regulatory region or that ArcA can oligomerize at one or more sites. The DNA‐binding activity of ArcA could be increased an estimated 10‐fold by prior incubation of the protein with carbamoyl phosphate, suggesting that phosphorylation activates DNA binding or oligomerisation. DNase I footprint analyses identified four sites that were protected by ArcA from cleavage. Two of these sites spanned the transcription start site and —10 regions of promoters 6 and 7, while a third site partially overlapped the characterized binding site of integration host factor (IHF). ArcA exhibited the highest affinity for a stretch of DNA located between the IHF site and the transcription start site of promoter 7. These results are congruent with the hypothesis that a higher‐order nucleoprotein complex comprising several proteins, including ArcA, is required to activate transcription from the multiple promoters of the pfl operon.
Pro‐sequence‐assisted protein folding
Authors: Eder Jörg , Fersht Alan R.
Published: October 2006

Many proteins, including proteases and growth factors, are synthesized as precursors in the form of prepro‐proteins. Whereas the pre‐sequences usually act as signal peptides for transport, the pro‐sequences of an increasing number of these proteins have been found to be essential for the correct folding of their associated proteins. In contrast to the action of molecular chaperones, pro‐sequences appear to catalyse the protein‐folding reaction directly. The similarity between the pro‐sequence‐assisted folding mechanisms of different proteases supports the hypothesis that a common folding mechanism has developed through convergent evolution. Further, the frequent requirement of the pro‐sequences for both folding and intracellular transport or secretion suggests that these two functionalities are intimately related.
The bacterial ‘enigma’: cracking the code of cell–cell communication
Authors: Salmond G. P. C. , Bycroft B. W. , Stewart G. S. A. B. , Williams P.
Published: October 2006

In recent years it has become clear that the production of N‐acyl homoserine lactones (N‐AHLs) is widespread in Gram‐negative bacteria. These molecules act as diffusible chemical communication signals (bacterial pheromones) which regulate diverse physiological processes including bioluminescence, antibiotic production, piasmid conjugal transfer and synthesis of exoenzyme virulence factors in plant and animal pathogens. The paradigm for N‐AHL production is in the bioluminescence (lux) phenotype of Photobacterium fischeri (formerly classified as Vibrio fischeri) where the signalling molecule N‐(3‐oxohexanoyl)‐L‐homoserine lactone (OHHL) is synthesized by the action of the Luxl protein. OHHL is thought to bind to the LuxR protein, allowing it to act as a positive transcriptional activator in an autoinduction process that physiologically couples cell density (and growth phase) to the expression of the bioluminescence genes. Based on the growing information on Luxl and LuxR homologues in other N‐AHL‐producing bacterial species such as Erwinia carotovora, Pseudomonas aeruginosa, Yersinia enterocolitica, Agrobacterium tumefaciens and Rhizobium legumino‐sarum, it seems that analogues of the P. fischeri lux autoinducer sensing system are widely distributed in bacteria. The general physiological function of these simple chemical signalling systems appears to be the modulation of discrete and diverse metabolic processes in concert with cell density. In an evolutionary sense, the elaboration and action of these bacterial pheromones can be viewed as an example of multi‐cellularity in prokaryotic populations.
Tracheal colonization factor: a Bordetella pertussis secreted virulence determinant
Authors: Finn Theresa M. , Stevens Lisa A.
Published: October 2006

We report here the identification of a virulence‐associated factor, Tcf, (tracheal colonization factor), produced by strains of Bordetella pertussis but not Bordetella parapertussis or Bordetella bronchiseptica. This protein is encoded by the tcfA gene. When a strain of B. pertussis 18323 lacking this protein is used to infect mice with an aerosol challenge, the number of bacteria isolated from the tracheas is decreased 10‐foid when compared with the parent 18323. The derived amino acid sequence of tcfA predicts a 68 kDa RGD‐containing, proline‐rich protein, which after cleavage of a typical prokaryotic signal sequence would be 64 kDa. Amino acid sequence analysis demonstrates that the C‐terminal 30 kDa of this protein shows 50% identity to the 30 kDa C‐terminus of another Bordetella protein, the pertactin precursor. The N‐terminal 34 kDa region contains the three amino‐acid motif RGD and is 16.5% proline. Coupled in vitro transcription and translation analysis indicates that the tcfA gene product migrates as two bands of approximately 90 kDa. A fusion protein of the N‐terminal, 34 kDa portion of Tcf to maltose‐binding protein migrates, on SDS–PAGE, 30 kDa higher than expected from the combined molecular weights. Polyclonal antisera raised against the unique N‐terminal portion of Tcf recognizes 90 kDa and 60 kDa bands in immunoblots of whole‐cell lysates of strains of B. pertussis; it does not recognize any protein in whole‐cell lysates of B. bronchiseptica or B. parapertussis. Supernatants of cultures of B. pertussis 18323 contain the 60 kDa form of the protein. Southern blot analysis of chromosomal DNA from strains of B. bronchiseptica and B. parapertussis, using a probe derived from tcfA, shows strong hybridization only to B. pertussis DNA. Thus, Tcf appears to be a unique virulence factor of B. pertussis.
Organization of host‐inducible transcripts on the symbiotic plasmid of Rhizobium sp. NGR234
Authors: Fellay R. , Perret X. , Viprey V. , Broughton W. J. , Brenner S.
Published: October 2006

In a systematic approach to identify genes involved in the early steps of the legume—Rhizobium symbiosis, we studied transcription patterns of symbiotic plasmid‐borne loci. A competitive hybridization procedure was used to identify DNA restriction fragments carrying genes whose expression is enhanced by plant root exudates or by purified flavonoids. Fragments containing induced genes were then located on the physical map of the 500 kb pNGR234a. New inducible loci as well as previously described genes were identified and their time course of induction determined. After initial induction, transcription of loci such as nodABC and the host‐specificity genes nodSU decreased to undetectable levels 24 h after incubation with purified flavonoids. In contrast, expression of other loci is detectable only after several hours of induction. Surprisingly, many genes remained transcribed in the nodD1 mutant suggesting the presence of other flavonoid‐dependent activators in NGR234. The hsnl region, which is involved in host specificity, was shown to carry several inducible but independently regulated transcripts. Sequencing analysis revealed several open reading frames whose products, based on sequence similarities, may be involved in L‐fucose metabolism and its adjunction to the Nod factors.
Characterization of IS1221 from Mycoplasma hyorhinis: expression of its putative transposase in Escherichia coli incorporates a ribosomal frameshift mechanism
Authors: Zheng Jianhong , McIntosh Mark A.
Published: October 2006

Seven complete and two partial copies of IS1221 variants from Mycoplasma hyorhinis and Mycoplasma hyopneumoniae characterized to date have established a consensus IS1221 as a 1513 bp element with unique structural characteristics resembling the IS3 family of bacterial insertion sequences. Each IS1221 copy contains highly conserved 28 bp imperfect terminal inverted repeats and three distinctive internal inverted repeats (LIR, RIR and IIR). IIR is located within the coding region of the element and it is proposed that it plays a critical role in the regulation of putative transposase expression. Consensus IS1221 and one particular copy, G1135.2, contain a single long open reading frame (ORF). Two potential initiation codons are present at nucleotide 46 (AUG46) and nucleotide 397 (AUG397) and both are preceded by strong ribosome‐binding sites. Both initiation codons can be used efficiently in an Escherichia coli T7 expression system. The LIR has a negative regulatory effect on translation initiation from AUG46. A ‐1 translational frameshift event is shown to be involved in expression of the IS1221 ORF and results in the production of 20kDa and 6kDa truncated proteins from the respective upstream initiation codons of the IS1221 ORF. Base substitution and deletion mutations in sequences resembling characterized motifs in documented examples of translational frameshifting resulted in a significant increase in the full‐length products and a corresponding decrease in the truncated products from the IS1221 ORF. In contrast to the usual ‐1 frameshift regulatory event in the IS3 family, which produces a transframe fusion product as the active transposase, IS1221 may have evolved a high‐frequency ‐1 frameshift mechanism that produces a truncated product from the upstream coding domain and thereby results in the regulated low‐level production of the full‐length presumptive transposase.
Aminoacyl‐tRNA synthetase gene regulation in Bacillus subtilis: induction, repression and growth‐rate regulation
Authors: Putzer Harald , Laalami Soumaya , Brakhage Axel A. , Condon Ciarán , Grunberg‐Manago Marianne
Published: October 2006

The thrS gene in Bacillus subtilis is specifically induced by starvation for threonine and is, in addition, autorepressed by the overproduction of its own gene product, the threonyl‐tRNA synthetase. Both methods of regulation employ an antitermination mechanism at a factor‐independent transcription terminator that occurs just upstream of the start codon. The effector of the induction mechanism is thought to be the uncharged tRNAThr, which has been proposed to base pair in two places with the leader mRNA to induce antitermination. Here we show that the autoregulation by synthetase overproduction is likely to utilize a mechanism similar to that characterized for induction by amino acid starvation, that is by altering the levels of tRNA charging in the cell. We also demonstrate that the base pairing interaction at the two proposed contact points between the tRNA and the leader are necessary but not always sufficient for either form of regulation. Finally, we present evidence that the thrS gene is expressed in direct proportion to the growth rate. This method of regulation is also at the level of antitermination but is independent of the interaction of the tRNA with the leader region.
A family of modular type mannuronan C‐5‐epimerase genes controls alginate structure in Azotobacter vinelandii
Authors: Ertesvåg Helga , Høidal Hilde Kristin , Hals Ingrid Kathrin , Rian Anne , Doseth Berit , Valla Svein
Published: October 2006

The l‐guluronic acid residues in the Azotobacter vinelandii polysaccharide alginate originate from a post‐polymerization reaction catalysed by the enzyme mannuronan C‐5‐epimerase (ME). We have previously reported the cloning and expression of an A. vinelandii gene encoding this enzyme, and we show here that the organism encodes at least four other ME genes originating from a common ancestor gene by a complex rearrangement process. The biological function of the corresponding enzymes is probably to catalyse the formation of alginates with a variety of physical properties. This model may explain the origin of the structural variability found in alginates isolated both from prokaryotic and eukaryotic organisms. The A. vinelandii enzymes may also potentially be useful for certain medical and biotechnological applications of this commercially important polysaccharide.
Tracheal cytotoxin structural requirements for respiratory epithelial damage in pertussis
Authors: Luker Kathryn E. , Tyler Andrew N. , Marshall Garland R. , Goldman William E.
Published: October 2006

The respiratory epithelial pathology of pertussis (whooping cough) can be reproduced by tracheal cyto‐toxin (TCT), a disaccharide‐tetrapeptide released by Bordetella pertussis. TCT is a muramyl peptide, a class of peptidoglycan‐derived compounds which have many biological activities including adjuvanticity, somnogenicity, pyrogenicity, and cytotoxicity. The structural requirements for muramyl peptides to produce some of these biological effects have been partially characterized. Using in vitro assays with respiratory epithelial cells and tissue, we have previously determined that the disaccharide moiety of TCT is not involved in toxicity and that the side‐chain functional groups of diaminopimelic acid (A2pm) are crucial for toxicity. In this study, we determine the importance of every amino acid, functional group and chiral centre in the peptide portion of TCT. Although lactyl tetrapeptides are the most toxic of the TCT fragments, producing dose‐response curves identical to TCT, the smallest analogues of TCT which are active in our assay are of the form X‐γ‐(d)‐Glu‐meso‐A2pm, where X may be an amino acid or a blocking group. Within this active substructure, main‐chain chirality and all functional groups are essential for toxicity. This definition of the core region of TCT indicates that the TCT interaction site is unlike almost all other muramyl peptide interaction sites for which structure‐activity data are available.
Gene replacement by homologous recombination in Mycobacterium bovis BCG
Authors: Norman Elizabeth , Dellagostin Odir A. , McFadden Johnjoe , Dale Jeremy W.
Published: October 2006

Gene replacement by homologous recombination is a powerful tool for fundamental studies of gene function, as well as allowing specific attenuation of pathogens, but has proved difficult to achieve for Mycobacterium tuberculosis. We have used a plasmid‐based test system to demonstrate the occurrence of homologous recombination in the tuberculosis vaccine strain Mycobacterium bovis BCG, and we have successfully replaced a target gene in BCG by homologous recombination, using a shuttle plasmid. Specific inactivation of selected genes will facilitate study of virulence factors and drug resistance as well as allowing rational attenuation of M. tuberculosis for the production of new vaccines.
Cloning and expression of a murein hydrolase lipoprotein from Escherichia coli
Authors: Ehlert Kerstin , Höitje Joachim‐Volker , Templin Markus F.
Published: October 2006

On the basis of the published N‐terminal amino acid sequence of the soluble lytic transglycosylase 35 (Slt35) of Escherichia coli, an open reading frame (ORF) was cloned from the 60.8 min region of the E. coli chromosome. The nucleotide sequence of the ORF, containing a putative lipoprotein‐processing site, was shown by [3H]‐palmitate labelling to encode a lipoprotein with an apparent molecular mass of 36 kDa. A larger protein, presumably the prolipoprotein form, accumulated in the presence of globomycin. Over‐expression of the gene, designated mltB (for membrane‐bound lytic transglycosylase B), caused a 55‐fold increase in murein hydrolase activity in the membrane fraction and resulted in rapid cell lysis. After membrane fractionation by sucrose‐density‐gradient centrifugation, most of the induced enzyme activity was present in the outer and intermediate membrane fractions. Murein hydrolase activity in the soluble fraction of a homogenate of cells induced for MltB increased with time. This release of enzyme activity into the supernatant could be inhibited by the addition of the serine‐protease inhibitor phenylmethyl‐sulphonyl fluoride. It is concluded that the previously isolated Slt35 protein is a proteolytic degradation product of the murein hydrolase lipoprotein MltB. Surprisingly, a deletion in the mltB gene showed no obvious phenotype.
Characterization of heat‐shock response of the marine bacterium Vibrio harveyi
Authors: Klein Gracjana , Walczak Robert , Krasnowska Ewa , Blaszczak Adam , Lipińska Barbara
Published: October 2006

We have investigated heat‐shock response in a marine bacterium Vibrio harveyi. We have found that 39 C was the highest tempature at which V. harveyi was able to grow steadily. A shift from 30° C to 39° C caused increased synthesis of at least 10 proteins, as judged by SDS‐PAGE, with molecular masses of 90, 70, 58, 41, 31, 27, 22, 15, 14.5 and 14kDa. The 70, 58, 41 and 14.5 kDa proteins were immunologically homologous to DnaK, GroEL, DnaJ and GroES heat‐shock proteins of Escherichia coli, respectively. V. harveyi GroES protein had a lower molecular mass (14.5 kDa) than E. coli GroES, migrating in SDS‐PAGE as 15 kDa protein. We showed that a protein of ∼43 kDa, immunologically reactive with antiserum against E. coli sigma 32 subunit (σ32) of RNA polymerase, was induced by heat‐shock and co‐purified with V. harveyi RNA polymerase. These results suggest that the 43 kDa protein is a heat‐shock sigma protein of V. harveyi. Preparation containing the V. harveyi sigma 32 homologue, supplemented with core RNA polymerase of E. coli, was able to transcribe heat‐shock promoters of E. coli in vitro.
Negative regulation of defense responses in Arabidopsis by two NPR1 paralogs
Authors: Zhang Yuelin , Cheng Yu Ti , Qu Na , Zhao Qingguo , Bi Donglin , Li Xin
Published: October 2006

NPR1 is required for systemic acquired resistance, and there are five NPR1 paralogs in Arabidopsis. Here we report knockout analysis of two of these, NPR3 and NPR4. npr3 single mutants have elevated basal PR‐1 expression and the npr3 npr4 double mutant shows even higher expression. The double mutant plants also display enhanced resistance against virulent bacterial and oomycete pathogens. This enhanced disease resistance is partially dependent on NPR1, can be in part complemented by either wild‐type NPR3 or NPR4, and is not associated with an elevated level of salicylic acid. NPR3 and NPR4 interact with TGA2, TGA3, TGA5 and TGA6 in yeast two‐hybrid assays. Using bimolecular fluorescence complementation analysis, we show that NPR3 interacts with TGA2 in the nucleus of onion epidermal cells and Arabidopsis mesophyll protoplasts. Combined with our previous finding that basal PR‐1 levels are also elevated in the tga2 tga5 tga6 triple mutant, we propose that NPR3 and NPR4 negatively regulate PR gene expression and pathogen resistance through their association with TGA2 and its paralogs.
The gibberellin‐induced, cysteine‐rich protein GIP2 from Petunia hybrida exhibits in planta antioxidant activity
Authors: Wigoda Noa , Ben‐Nissan Gili , Granot David , Schwartz Amnon , Weiss David
Published: October 2006

Numerous GAST‐like genes have been identified in various plant species. All code for small proteins with a conserved C‐terminal region in which 12 cysteines are located in exactly the same positions. We have previously identified five gibberellin (GA)‐induced GAST1‐like genes in petunia, GIP1–5. GIP2 is expressed in elongating zones, and its suppression in transgenic petunia plants inhibits stem elongation, suggesting a role for the protein in GA‐induced cell growth. However, nothing is known about the biochemical activity of GIP2 or any other GAST‐like protein. As all contain putative catalytic disulfide bonds (putative redox‐active cysteines), we speculated that they might be involved in redox regulation. Expression analysis of GIP2, GIP4 and GIP5 revealed that they are induced by H2O2. To study whether GIP2 modulates H2O2 levels, we generated transgenic petunia plants expressing GIP2 under the regulation of the ubiquitous CaMV 35S promoter. The transgene reduced H2O2 levels in leaves following wounding. It also reduced the levels of H2O2 in guard cells following osmotic stress and ABA treatments, leading to the suppression of stomatal closure. In addition, the transgene promoted stem and corolla elongation. As reactive oxygen species (ROS) are involved in cell elongation, we suggest that GIP2 affects growth by regulating the levels of ROS. As all known GAST‐like proteins contain putative redox‐active cysteines, they may all act as antioxidants.
In vivo confocal microscopy in recurrent granular dystrophy in corneal graft after penetrating keratoplasty
Authors: Traversi Claudio , Martone Gianluca , Malandrini Alex , Tosi Gian Marco , Caporossi Aldo
Published: October 2006

Abstract

Two case reports of recurrent granular dystrophy in corneal grafts after penetrating keratoplasty are presented. Slit‐lamp examination and confocal microscopy (HRT II) were performed in two patients with recurrent granular dystrophy. All confocal microscopic findings of granular dystrophy were evaluated in the graft. Dystrophic lesions of the donor cornea presented the same confocal microscopic aspects in both eyes, and were similar to granular dystrophy lesions. Confocal microscopy is an imaging method that may provide new information on corneal microanatomy in dystrophies. It may be particularly useful in improving the early diagnosis of dystrophic lesions in corneal grafts.
The risk of malignant hyperthermia in children undergoing muscle biopsy for suspected neuromuscular disorder
Authors: FLICK RANDALL P. , GLEICH STEPHEN J. , HERR MOLLY M. H. , WEDEL DENISE J.
Published: October 2006

Background:  It is assumed that those children with known or suspected neuromuscular disorders (NMD) are at increased risk for malignant hyperthermia (MH). Despite the lack of conclusive data, most of these children are managed with a nontriggering anesthetic. This study examined the risk of MH in children exposed to a triggering anesthetic while undergoing muscle biopsy for suspected NMD.

Methods:  Between 1992 and 2005, the medical records of 351 children under 21 years of age were identified as having undergone muscle biopsy for suspected NMD. Of these, only 274 received a volatile anesthetic agent or succinylcholine and were included for study. Records were examined for evidence of MH or rhabdomyolysis.

Results:  No patient exhibited signs or symptoms suggestive of MH. One patient was found, by muscle biopsy, to have evidence of rhabdomyolysis prior to exposure to a volatile anesthetic. Of 274 patients, only three received succinylcholine. None developed MH or rhabdomyolysis. The estimated risk of a patient with suspected NMD developing MH as a result of exposure to volatile anesthetic agents during muscle biopsy is 1.09% or less.

Conclusion:  The estimated risk of MH or rhabdomyolysis is 1.09% or less in a diverse population of children with suspected NMD.
When insects help to resolve plant phylogeny: evidence for a paraphyletic genus Acacia from the systematics and host‐plant range of their seed‐predators
Authors: Kergoat Gaël J. , Silvain Jean‐François , Buranapanichpan Sawai , Tuda Midori
Published: October 2006

In this study we use an indirect method to address the issue of the systematics of the large and economically important genus Acacia (Leguminosae, Mimosoideae, Acacieae). We propose the use of host‐preference data in closely related insect species as a potentially useful tool to investigate host systematic issues, especially when other approaches yield inconsistent results. We have examined the evolution of host‐plant use of a highly specialized group of seed‐feeders who predate Acacia— the seed‐beetles (Coleoptera, Chrysomelidae, Bruchinae). First, the evolution of host‐plant preferences in a large clade of Bruchidius species was investigated using molecular phylogenetics and character optimization methods. Second, the scope of our study was enlarged by critically reviewing the host‐plant records of all bruchine genera associated with Acacia. Both morphological and molecular data were used to define relevant insect clades, for which comparisons of host‐plant range were performed. Interestingly, the analyses of host‐plant preferences from 163 seed‐beetle species recovered similar patterns of host‐plant associations in the distinct clades which develop within Acacia seeds. Our results clearly support the hypothesis of Acacia being a paraphyletic genus and provide useful insights with reference to the systematics of the whole subfamily as well. This study should also be of interest to those involved in the numerous biological control programs which either already use or aim to use seed‐beetles as auxiliary species to limit the propagation of several invasive legume tree species.
PREDICTION AND PREDICATION
Authors: Hyman John
Published: October 2006

Nelson Goodman's own solution to his new riddle of induction turns on the degree to which predicates are entrenched in our use of language. However, this solution requires that judgements concerning the degree to which a predicate is entrenched can be made independently of any canon of perceptible similarity. I argue that this requirement cannot be met.

The riddle itself depends upon the claim that since ‘green’ can be defined positionally in terms of ‘grue’ and ‘bleen’, ‘grue’ and ‘bleen’ are symmetrically related to ‘green’ and ‘blue’, and positionality is therefore ‘an entirely relative matter’. However, in order to establish that positionality is an entirely relative matter, we would need to provide a non‐positional definition of ‘grue’, rather than a positional definition of ‘green’.

We therefore need to decide whether ‘grue’ can be defined ostensively by means of a single sample, as ‘green’ can. I argue that any attempt to provide such a definition is bound to fail, and hence the new riddle of induction does not reveal that ‘the roots of inductive validity are to be found in our use of language’.
THE INCOMPATIBILITY OF THE VIRTUES
Authors: Walker A. D. M.
Published: October 2006

The paper examines a single, apparently simple argument for the existence of incompatibilities between the virtues as traits of character. This argument appeals not to empirical truths about human psychology or human nature but to the possibility of conflict between the exercise of different virtues in action. There are, for example, situations in which we can exercise the virtue of truthfulness only at the expense of not exercising the virtue of tact, as when we are asked a question to which the straightforward answer will pain our questioner. The person who in these situations would give a straightforward answer possesses the virtue of truthfulness to a higher degree than the person who would respond more evasively, whereas the latter person possesses the virtue of tact to a higher degree than the former. But since the two responses are mutually exclusive, it follows that the degree to which we possess the virtue of truthfulness must, at least in some measure, correlate inversely with the degree to which we possess the virtue of tact. And similarly for many other pairs of virtues. My paper focusses on the two cardinal assumptions of this argument, viz., (i) that sometimes the exercise of one virtue can conflict with the exercise of another, and (ii) that the degree to which a person possesses a virtue correlates directly with the extent of its exercise, and defends both assumptions against a variety of objections which allege that, in different ways, they are insensitive to the complexity of the virtues.
PUNISHMENT ‐ A TALE OF TWO ISLANDS
Authors: Walker Mark Thomas
Published: October 2006

An imaginary desert island scenario provides the setting for a story which is designed to expose the shortcomings of deterrence, reform and restitution theories of punishment, and to emphasize the intuitive appeal of Kant's strong retributivist insistence that there is a positive obligation to punish offenders just qua offenders, and not merely an automatic right to do so (weak retributivism). Nevertheless, it is urged that though the fact that an offence has been committed can in itself suffice to establish that punishment is in some sense required, this requirement at most supports a position that is intermediate between Kantian retributivism and weak retributivism.
THE NUMBERING SYSTEM OF THE TRACTATUS
Authors: Mayer Verena
Published: October 2006

The significance of the complicated numbering of the propositions in the Tractatus has occasioned much speculation. Wittgenstein's own explanation has, following Stenius, been generally regarded as misleading. But an examination of the Prototractatus reveals that the numbering system was for Wittgenstein principally an aid in the composition of his work. It allowed him to mark out certain propositions which required further work or supplementation, without disturbing the basic structure of the treatise. But the reworking of the Prototractatus to form the Tractatus considerably changed the original order in which the ideas were connected, and thus made it more difficult to understand the Tractatus. Several specific examples make it clear that it is essential to look back at the context of the Prototractatus in order to achieve a correct interpretation of many of the propositions in the Tractatus.
DIRECTED ACTION AND ANIMAL COMMUNICATION
Authors: Radner Daisie
Published: October 2006

Human action theory, with its emphasis on intentions and reasons, does little to enhance our understanding of the actions of nonhuman animals. Many animal (and human) actions are directed to objects in the world, including other animals. The notion of directedness can be analysed without attributing intentions or reasons to the agent. An action is directed to object X if and only if: (1) the agent singles out X, either by orientation or by selective performance of the action in the presence of X; (2) the agent recognizes X as a suitable object; and (3) the goal of the action is that X should be in a certain relation to the agent or to some other object. The goal of an action is not necessarily attributable to the agent as the agent's goal in acting. Moreover, an agent can have a goal in acting without understanding how the action achieves the goal. The usefulness of the concept of directed action in the study of animal communication is illustrated with examples from the recent ethological literature.
HUMANISM AND THE MEANING OF LIFE
Authors: Teichman Jenny
Published: October 2006

This paper addresses two related questions: 1. Does human life have a purpose? and 2. Is human life intrinsically valuable?

Clearly human beings have personal, communal and common purposes, but we cannot know whether there is an external transcendent purpose in addition to these. However the argument that mundane purposes are meaningless without transcendent purposes, though valid, rests on false premises. There are four ways of explaining the intrinsic value of life. The first (pantheism) is the idea that human life is sacred because everything is sacred. A second is that life is intrinsically valuable because something else is valuable and indeed sacred – the idea, for instance, that mankind is made in the image of God. The third is that human life lacks value because of its contrast with the sanctity of the gods. The humanistic explanation is that human life as such has intrinsic value.

There are (at least) six reasons for holding that human life is intrinsically valuable; these reasons are given.
DO I HAVE TO BE HERE NOW?
Authors: Williams C. J. F.
Published: October 2006

Kaplan claims that (1) ‘I am here now’, though analytic, is not a necessary truth. But this sentence is not a proposition, in a sense of proposition in which some, but not all, sentences are propositions. Since it is not a proposition, it is not true, and consequently not analytic. It is in fact a fragment of a proposition, the same fragment as ‘he was there then’ in (2) ‘CJFW said in Oxford on 23 September 1991 that he was there then’. Sentences containing indexicals in general owe their sense to the corresponding fragments of sentences containing ‘quasi‐indexicals’(‘then’, for example, is the quasi‐indexical to ‘now’ as indexical). Someone uttering (1) assertively will thereby make a proposition like (2) true. (2) entails (3) ‘CJFW said in Oxford on 23 September 1993 that CJFW was in Oxford on 23 September 1991′. So by uttering (1) in the appropriate circumstances I made it true that I had asserted the proposition (4) ‘CJFW was in Oxford on 23 September 1991′. What is analytic and necessarily true is the proposition ‘If (3) then (4)’.
SCEPTICISM AND THE FRAMEWORK‐RELATIVITY OF ENQUIRY
Authors: Daukas Nancy
Published: October 2006

Many argue that sceptical enquiry is incoherent insofar as it requires a detachment from and assessment of the framework judgements that constitute our practice of enquiry. This paper accepts that enquiry is relative to a framework, but argues that the Cartesian sceptical enquiry is consistent with that relativity. Part I presents Marie McGinn's Wittgen‐steinian anti‐sceptical argument, comparing its view of enquiry to Carnap's. Part II clarifies the sense in which Wittgenstein's ‘Moore‐type’ framework judgements could be unquestionable, and argues that McGinn's antisceptical argument fails. Part III shows that the sceptical enquiry finds all our beliefs to lack justification by suspending our normal non‐sceptical framework judgement regarding perception in a way that is consistent with the framework‐relativity of enquiry, and encouraged by normal standards. The paper closes by recommending a view of scepticism as a stimulus for enquiry.1
TRUTH, PERMANENCE, AND THE REGULATION OF BELIEF: LOEB'S CARTESIAN ARGUMENT1
Authors: Miller Alexander
Published: October 2006

In this paper I outline an argument which Louis Loeb attributes to Descartes, which attempts to ground the epistemic priority of reason over sense‐perception in the brute psychological irresistibility of the former. I claim that the position thus ascribed to Descartes collapses into a crude form of idealism, and attempt to pinpoint precisely the flaw in the argument which gives rise to this collapse. I finish by suggesting that the same flaw might be apparent in Philip Pettit's recent development of the notion of response‐dependent concepts.
RATIONAL CHOICE: EXTENSIONS AND REVISION
Authors: Nida‐Rümelin Julian
Published: October 2006

The rational choice paradigm has proved to be a fruitful means of analysis and explanation in various disciplines concerned with questions of practical rationality, but in various attempts to extend its fields of application the deficiencies of the original account of rational choice have become evident. This paper tries to give a systematic overview of ways in which the rational choice paradigm can be extended and modified.
FORTUNATE MISFORTUNE
Authors: Smilansky Saul
Published: October 2006

Sometimes people are unfortunate in ways which facilitate their success ‐ and happiness. This creates the perplexity whether someone can be said to have been unfortunate, if an apparent misfortune has been, overall, beneficial to his or her life. I argue that whether something is a misfortune cannot be determined in itself, even in seemingly obvious cases. It depends also upon what one makes of it, what it makes of one. In short, it depends upon what happens later. People cannot claim to have suffered a misfortune for which they are to be pitied or compensated, when this ‘misfortune’ is crucial in having made them what they are, what they are happy to be. Hard determinism aside, the notion of ‘fortunate misfortune’ lacks, however, an easy parallel in ‘unfortunate good‐fortune’.
SUPERVENIENT DUALISM
Authors: Granger Herbert
Published: October 2006

The topic under examination is the idea of ‘supervenient dualism’, which Christopher Shields first put forward in his study of Aristotle's theory of psychology. Shields takes supervenient dualism to be a form of ‘substance supervenience’, in which an immaterial substance supervenes upon a material or physical substance. Shields, however, does not develop a convincing version of supervenient dualism because he fails to develop a convincing version of substance supervenience. A plausible version of substance supervenience can be developed in the light of Jaegwon Kim's idea of ‘multiple‐domain supervenience’, although this version of substance supervenience is not able to provide the basis for an adequate formulation of supervenient dualism. The nature of this version of substance supervenience depends upon a relation of coordination between the substances, and there does not seem to be any relation of coordination that yields a form of substance supervenience that also counts as a form of supervenient dualism.
GAME THEORY AND KNOWLEDGE BY SIMULATION
Authors: Morton Adam
Published: October 2006

This paper makes a connection between some developments in game theory and issues about everyday psychological knowledge. I argue that there are two‐person situations in which agents will do badly if they use a particular simple theory of rationality to predict one another's actions. If we assume that our everyday techniques for anticipating one another's actions will get better results than this, it follows that these techniques do not consist in applying a theory like this one. One alternative is that when we anticipate actions we supplement whatever theories we have with a capacity to imagine the other person's motivation. I sketch a way of modelling this capacity.1
MENTAL ARITHMETIC
Authors: Squires Roger
Published: October 2006

The popular idea that mental calculation involves covert operations as counterparts to the scribblings, sayings or manipulations involved in classroom calculation is rejected by familiar arguments in Section I. Philosophers do not readily agree on an alternative account. Section II considers reasons why they are puzzled, reasons which encourage a return to the discredited position. The currently fashionable Causal or Functionalist view is criticised in Section III. Section IV reconsiders the stubborn fact that when someone calculates in their head they do something at the time which explains their arithmetical successes or failures. Some dispositional descriptions are rejected as inadequate. Though a restrained dispositionalism is finally supported, it does not have the implication that nothing was going on in the silence.
SCEPTICISM AND THE JUSTIFICATION OF TRANSCENDENTAL IDEALISM
Authors: Bermúdez José Luis
Published: October 2006

In this paper I explore a justification for transcendental idealism that emerges from the dialogue with philosophical scepticism in which Kant is on and off engaged throughout the Critique of Pure Reason.1 Many commentators, most prominently Strawson, have claimed that transcend‐ ental idealism is an unfortunate addition to the Critique, one that can profitably be excised in the interests of clarity and coherence.2 Against this general picture I urge that transcendental idealism is in fact a very natural consequence of some of the central doctrines of the Critical Philosophy. It is in the context of Kant's debate with scepticism that this emerges most clearly. Nonetheless, I argue that Kant's employment of transcendental idealism against the sceptic is seriously compromised by his postulating the existence of unknowable things‐in‐themselves. As long as he maintains that there are unknowable things‐in‐themselves which are responsible for our having the experience that we do have, his position seems to collapse into sceptical idealism. In the final section of the paper I suggest that the only possible escape from this difficulty would be to rule out the possibility of affirming that unknowable things‐in‐themselves exist. I also suggest that an argument to this effect exists in the Critique and that Kant's position would be more consistent had he adhered to it.
POLITICAL OBLIGATION, FAIRNESS, AND INDEPENDENCE
Authors: Wolff Jonathan
Published: October 2006

In the first section the problem of political obligation is motivated, and in Section 2 the core structure of the problem is laid bare. A recognition of this structure prompts reflection that the problem will appear very different to different thinkers, depending on their moral theories. It also invites the speculation that the problem will be incapable of solution on some moral theories while trivial on others. This polarity does reflect the state of much of the literature until fairly recently. However this picture is seen to be too crude, and in the third section it is shown how an interesting solution has been proposed by advocates of the ‘theory of fairness’. In Section 4 this theory is evaluated, concentrating particularly on George Klosko's version, which is, in part, rejected. However it is argued that no version of the theory is able to guarantee universal political obligations. In Section 5 it is argued that this is an unnoticed advantage of the theory, for it may well be that, morally at least, we should allow those who do not benefit from the existence of the state to escape political obligations. The consequences of this view are examined and found not to be as threatening as they might first have appeared.
MORAL RELEVANCE AND CETERIS PARIBUS PRINCIPLES
Authors: Frazier Robert L.
Published: October 2006

My goal in this paper is twofold: to provide an account of what makes properties morally relevant, and to indicate the role such properties have in our moral thinking.

I suppose that a property is morally relevant just in case it must, ceteris paribus, determine the moral status (the rightness or wrongness) of actions having it. The main part of the paper concerns the conditions under which the ceteris paribus caveat is satisfied, that is, when other things are equal. I argue that the caveat is satisfied when, with respect to a proposed set of morally relevant properties, an act differs from its alternatives at most in the degree to which it has one of those properties.

Since other things are seldom equal, it is natural to wonder why what is true when they are equal should be important when they are not. That is, why is moral relevance, as I characterize it, a useful moral notion? I suggest that it is only by recognizing the moral relevance of properties that we are able to engage in useful moral thinking about the future.
FUNCTIONAL EXPLANATIONS AND NATURAL NORMS
Authors: Price Carolyn
Published: October 2006

In this paper, I try to develop an account of functions which might be of use to a biologist engaged in classifying and explaining natural phenomena. The most pressing difficulty facing such an account is the need to reconcile the normativity of function statements with their explanatory force. I consider two familiar accounts of function statements, offered by Andrew Woodfield (an ‘Actual Capacity Theorist’) and Larry Wright (a ‘Historical Theorist’). I examine both accounts in search of the strongest possible formulation of each type of theory. I fail to find a formulation of the ACT which is completely immune from counterexamples, but I do find a satisfactory formulation of the HT. In particular, I argue that the HT should incorporate a point central to the ACT that functions involve a means/end relationship between two devices. I then consider functional explanations: I argue that an ACT which holds that function statements are intrinsically explanatory cannot offer a satisfactory account. The account offered by Woodfield, who rejects this assumption, is adequate, though less attractive than the account suggested by the HT. I conclude by considering how the HT can account for functional norms.
ON ULTIMATE EPISTEMIC FOUNDATIONS1
Authors: van Woudenberg René
Published: October 2006

This paper is a contribution to the debate on epistemic foundationalism. Section I expounds and criticises Hans Albert's critical rationalist antifoundationalism position. Section I1 discusses Karl‐Otto Apel's ‘transcendental pragmatic’ argument for ultimate epistemic foundations. Section III suggests how the latter argument can be restated so as to avoid ambiguity and yield a plausible case for epistemic foundationalism.