bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

SummarySeven 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

SummaryThe 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

SummaryThe 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

SummaryThe 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

SummaryGene 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

SummaryOn 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

SummaryWe 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

SummaryNPR1 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

SummaryNumerous 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

AbstractTwo 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

SummaryBackground:  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.
PREDICTION AND PREDICATION
Authors: Hyman John 
Published: October 2006

AbstractNelson 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

AbstractThe 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

AbstractAn 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

AbstractThe 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

AbstractHuman 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

AbstractThis 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

AbstractKaplan 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)’.