Proinflammatory activity of cell-wall constituents from gram-positive bacteria.

Innate immunity reacts to conserved bacterial molecules. The outermost lipopolysaccharide (LPS) of Gram-negative organisms is highly inflammatory. It activates responsive cells via specific CD14 and toll-like receptor-4 (TLR4) surface receptor and co-receptors. Gram-positive bacteria do not contain LPS, but carry surface teichoic acids, lipoteichoic acids and peptidoglycan instead. Among these, the thick peptidoglycan is the most conserved. It also triggers cytokine release via CD14, but uses the TLR2 co-receptor instead of TLR4 used by LPS. Moreover, whole peptidoglycan is 1000-fold less active than LPS in a weight-to-weight ratio. This suggests either that it is not important for inflammation, or that only part of it is reactive while the rest acts as ballast. Biochemical dissection of Staphylococcus aureus and Streptococcus pneumoniae cell walls indicates that the second assumption is correct. Long, soluble peptidoglycan chains (approximately 125 kDa) are poorly active. Hydrolysing these chains to their minimal unit (2 sugars and a stem peptide) completely abrogates inflammation. Enzymatic dissection of the pneumococcal wall generated a mixture of highly active fragments, constituted of trimeric stem peptides, and poorly active fragments, constituted of simple monomers and dimers or highly polymerized structures. Hence, the optimal constraint for activation might be 3 cross-linked stem peptides. The importance of structural constraint was demonstrated in additional studies. For example, replacing the first L-alanine in the stem peptide with a D-alanine totally abrogated inflammation in experimental meningitis. Likewise, modifying the D-alanine decorations of lipoteichoic acids with L-alanine, or deacylating them from their diacylglycerol lipid anchor also decreased the inflammatory response. Thus, although considered as a broad-spectrum pattern-recognizing system, innate immunity can detect very subtle differences in Gram-positive walls. This high specificity underlines the importance of using well-characterized microbial material in investigating the system.

Modulation of plant HMG-CoA reductase by protein phosphatase 2A: Positive and negative control at a key node of metabolism

The enzyme HMG-CoA reductase (HMGR) has a key regulatory role in the mevalonate pathway for isoprenoid biosynthesis, critical not only for normal plant development, but also for the adaptation to demanding environmental conditions. Consistent with this notion, plant HMGR is modulated by many diverse endogenous signals and external stimuli. Protein phosphatase 2A (PP2A) is involved in auxin, abscisic acid, ethylene and brassinosteroid signaling and now emerges as a positive and negative multilevel regulator of plant HMGR, both during normal growth and in response to a variety of stress conditions. The interaction with HMGR is mediated by B" regulatory subunits of PP2A, which are also calcium binding proteins. The new discoveries uncover the potential of PP2A to integrate developmental and calcium-mediated environmental signals in the control of plant HMGR.

The effect of positive airway pressure during pre-oxygenation and induction of anaesthesia upon duration of non-hypoxic apnoea

Résumé de l'étude. L'application d'une pression positive (PEEP) pendant la phase d'induction d'une anesthésie générale peut prévenir la formation d'atélectasies pulmonaires. Ceci pourrait permettre d'accroître la durée d'apnée non hypoxique par l'augmentation de la capacité pulmonaire résiduelle fonctionnelle (CRF). Nous avons étudié le bénéfice de l'application d'une PEEP durant la phase d'induction d'une anesthésie générale sur la durée d'apnée avant que la saturation périphérique en oxygène atteigne 90%. Quarante patients ASA I-II ont été randomisés en deux groupes distincts. - Dans le groupe PEEP (n=20), les patients ont été pré-oxygénés durant 5 minutes avec une Fi02 à l00% par l'intermédiaire d'un appareil de CPAP (6cmH2O). Après induction de l'anesthésie, les patients furent ventilés mécaniquement (PEEP 6cmH2O) durant 5 minutes supplémentaires. - Dans le groupe ZEEP (n=20), aucune pression positive (ni CPAP, ni PEEP) ne fut utilisée. La durée d'apnée pour atteindre une saturation périphérique de 90% fut mesurée. La durée d'apnée non hypoxique était plus longue dans le groupe PEEP par rapport au groupe ZEEP (599 +/- 135 s vs 470 +/- 150 s, p= 0,007). Nous concluons que l'application d'une pression positive durant la phase d'induction d'une anesthésie générale chez l'adulte prolonge la durée d'apnée non hypoxique de plus de 2 minutes.

Cooccurrence of predominant Panton-Valentine leukocidin-positive sequence type (ST) 152 and multidrug-resistant ST 241 Staphylococcus aureus clones in Nigerian hospitals.

Ninety-six clinical isolates of Staphylococcus aureus from Nigeria were characterized phenotypically and genetically. Twelve multidrug-resistant methicillin (meticillin)-resistant S. aureus (MRSA) isolates carrying a new staphylococcal cassette chromosome mec element and a high proportion of Panton-Valentine leukocidin (PVL)-positive methicillin-susceptible S. aureus (MSSA) isolates were observed. The cooccurrence of multidrug-resistant MRSA and PVL-positive MSSA isolates entails the risk of emergence of a multidrug-resistant PVL-positive MRSA clone.

Methionine-321 in the C-terminal alpha-helix of catabolic ornithine carbamoyltransferase from Pseudomonas aeruginosa is important for positive homotropic cooperativity.

Pseudomonas aeruginosa has a pair of distinct ornithine carbamoyltransferases. The anabolic ornithine carbamoyltransferase encoded by the argF gene catalyzes the formation of citrulline from ornithine and carbamoylphosphate. The catabolic ornithine carbamoyltransferase encoded by the arcB gene promotes the reverse reaction in vivo; although this enzyme can be assayed in vitro for citrulline synthesis, its unidirectionality in vivo is determined by its high concentration at half maximum velocity for carbamoylphosphate ([S]0.5) and high cooperativity toward this substrate. We have isolated mutant forms of catabolic ornithine carbamoyltransferase catalyzing the anabolic reaction in vivo. The corresponding arcB mutant alleles on a multicopy plasmid specifically suppressed an argF mutation of P. aeruginosa. Two new mutant enzymes were obtained. When methionine 321 was replaced by isoleucine, the mutant enzyme showed loss of homotropic cooperativity at physiological carbamoylphosphate concentrations. Substitution of glutamate 105 by lysine resulted in a partial loss of the sigmoidal response to increasing carbamoylphosphate concentrations. However, both mutant enzymes were still sensitive to the allosteric activator AMP and to the inhibitor spermidine. These results indicate that at least two residues of catabolic ornithine carbamoyltransferase are critically involved in positive carbamoylphosphate cooperativity: glutamate 105 (previously known to be important) and methionine 321. Mutational changes in either amino acid will affect the geometry of helix H2, which contains several residues required for carbamoylphosphate binding.

Optimization strategies for fast detection of positive selection on phylogenetic trees.

MOTIVATION: The detection of positive selection is widely used to study gene and genome evolution, but its application remains limited by the high computational cost of existing implementations. We present a series of computational optimizations for more efficient estimation of the likelihood function on large-scale phylogenetic problems. We illustrate our approach using the branch-site model of codon evolution. RESULTS: We introduce novel optimization techniques that substantially outperform both CodeML from the PAML package and our previously optimized sequential version SlimCodeML. These techniques can also be applied to other likelihood-based phylogeny software. Our implementation scales well for large numbers of codons and/or species. It can therefore analyse substantially larger datasets than CodeML. We evaluated FastCodeML on different platforms and measured average sequential speedups of FastCodeML (single-threaded) versus CodeML of up to 5.8, average speedups of FastCodeML (multi-threaded) versus CodeML on a single node (shared memory) of up to 36.9 for 12 CPU cores, and average speedups of the distributed FastCodeML versus CodeML of up to 170.9 on eight nodes (96 CPU cores in total).Availability and implementation: ftp://ftp.vital-it.ch/tools/FastCodeML/. CONTACT: selectome@unil.ch or nicolas.salamin@unil.ch.

Interrogating eleven fast-evolving genes for signatures of recent positive selection in worldwide human populations

Different signatures of natural selection persist over varying time scales in our genome, revealing possible episodes of adaptative evolution during human history. Here, we identify genes showing signatures of ancestral positive selection in the human lineage and investigate whether some of those genes have been evolving adaptatively in extant human populations. Specifically, we compared more than 11,000 human genes with their orthologs inchimpanzee, mouse, rat and dog and applied a branch-site likelihood method to test for positive selection on the human lineage. Among the significant cases, a robust set of 11 genes were then further explored for signatures of recent positive selection using SNP data. We genotyped 223 SNPs in 39 worldwide populations from the HGDP Diversity panel and supplemented this information with available genotypes for up to 4,814 SNPs distributed along 2 Mb centered on each gene. After exploring the allele frequency spectrum, population differentiation and the maintainance of long unbroken haplotypes, we found signals of recent adaptative phenomena in only one of the 11 candidate gene regions. However, the signal ofrecent selection in this region may come from a different, neighbouring gene (CD5) ratherthan from the candidate gene itself (VPS37C). For this set of positively-selected genes in thehuman lineage, we find no indication that these genes maintained their rapid evolutionarypace among human populations. Based on these data, it therefore appears that adaptation forhuman-specific and for population-specific traits may have involved different genes.

Dissection of hormone-responsive plasma membrane to nucleus signaling of Bravis Radix : its role in vascular differentiation and root meristem growth

AbstractPlants continuously grow during their complete life span and understanding the mechanisms that qualitatively regulate their traits remains a challenging topic in biology. The hormone auxin has been identified as a crucial molecule for shaping plant growth, as it has a role in most developmental processes. In the root, the directional, so-called polar transport of auxin generates a peak of concentration that specifies and maintains the stem cell niche and a subsequent gradient of decreasing concentration that also regulates cell proliferation and differentiation. For these reasons, auxin is considered the main morphogen of the root, as it is fundamental for its organization and maintenance. Recently, in Arabidopsis thaliana, a natural variation screen allowed the discovery of BREVIS RADIX (BRX) gene as a limiting factor for auxin responsive gene expression and thus for root growth.In this study, we discovered that BRX is a direct target of auxin that positively feeds back on auxin signaling, as a transcriptional co-regulator, through interaction with the Auxin Response Factor (ARF) MONOPTEROS (MP), modulating the auxin gene response magnitude during the transition between division and differentiation in the root meristem. Moreover, we provide evidence that BRX is activated at the plasma membrane level as an associated protein before moving into the nucleus to modulate cellular growth.To investigate the discrepancy between the auxin concentration and the expression pattern of its downstream targets, we combined experimental and computational approaches. Expression profiles deviating from the auxin gradient could only be modeled after intersection of auxin activity with the observed differential endocytosis pattern and with positive auto- regulatory feedback through plasma- membrane-to-nucleus transfer of BRX. Because BRX is required for expression of certain auxin response factor targets, our data suggest a cell-type-specific endocytosis-dependent input into transcriptional auxin perception. This input sustains expression of a subset of auxin-responsive genes across the root meristem's division and transition zones and is essential for meristem growth. Thus, the endocytosis pattern provides specific positional information to modulate auxin response. RésuméLes plantes croissent continuellement tout au long de leur cycle de vie. Comprendre et expliquer les mécanismes impliqués dans ce phénomène reste à l'heure actuelle, un défi. L'hormone auxine a été identifiée comme une molécule essentielle à la régulation de la croissance des plantes, car impliquée dans la plupart des processus développementaux. Dans la racine, le transport polaire de l'auxine, par la génération d'un pic de concentration, spécifie et maintient la niche de cellules souches, et par la génération d'un gradient de concentration, contrôle la prolifération et la différentiation cellulaire. Puisque l'auxine est essentielle pour l'organisation et la maintenance du système racinaire, il est considéré comme son principal morphogène. Récemment, dans la plante modèle, Arabidopsis thalinana, un criblage des variations génétique a permis d'identifier le gène Brevis radix (BRX) comme facteur limitant l'expression des gènes de réponse à l'auxine et par là même, la croissance de la racine.Dans ce travail, nous avons découvert que BRX est une cible direct de l'auxine qui rétroactive positivement le signalement de l'hormone, agissant ainsi comme un régulateur transcriptionnel à travers l'interaction avec la protéine Monopteros (MP) de la famille des facteurs de réponse à l'auxine (Auxin Responsive Factor, ARF), et modulant ainsi la magnitude de la réponse des gènes reliés à l'auxine durant la division et la différentiation cellulaire dans le méristème de la racine. De plus, nous fournissons des preuves que BRX est activées au niveau de la membrane plasmique, tel une protéine associée se déplaçant à l'intérieur du noyau et modulant la croissance cellulaire.Pour mener à bien l'investigation des divergences entre la concentration de l'auxine et les schémas d'expression de ses propres gènes cibles, nous avons combiné les approches expérimentales et computationnelles. Les profiles d'expressions déviant du gradient d'auxine pourraient seulement être modéliser après intersection de l'activité de l'auxine avec les schémas différentiels d'endocytose observés et les boucles de rétroaction positives et autorégulatrices par le transfert de BRX de la membrane plasmique au noyau. Puisque BRX est requis pour l'expression de certains gènes cibles des facteurs de réponse à l'auxine, nos données suggèrent une contribution dépendante d'une endocytose spécifique au type de cellule dans la perception transcriptionnelle à l'auxine Cette contribution soutient l'expression d'un sous-set de gène de réponse à l'auxine dans la division du méristème racinaire et la zone de transition, et par conséquent, est essentielle pour la croissance méristematique. Ainsi, le schéma d'endocytose fournit des informations positionnelles spécifiques à la modulation de la réponse à l'auxine.

Distribution of events of positive selection and population differentiation in a metabolic pathway: the case of asparagine N-glycosylation

Asparagine N-Glycosylation is one of the most important forms of protein post-translational modification in eukaryotes. This metabolic pathway can be subdivided into two parts: an upstream sub-pathway required for achieving proper folding for most of the proteins synthesized in the secretory pathway, and a downstream sub-pathway required to give variability to trans-membrane proteins, and involved in adaptation to the environment and innate immunity. Here we analyze the nucleotide variability of the genes of this pathway in human populations, identifying which genes show greater population differentiation and which genes show signatures of recent positive selection. We also compare how these signals are distributed between the upstream and the downstream parts of the pathway, with the aim of exploring how forces of population differentiation and positive selection vary among genes involved in the same metabolic pathway but subject to different functional constraints. Our results show that genes in the downstream part of the pathway are more likely to show a signature of population differentiation, while events of positive selection are equally distributed among the two parts of the pathway. Moreover, events of positive selection are frequent on genes that are known to be at bifurcation points, and that are identified as being in key position by a network-level analysis such as MGAT3 and GCS1. These findings indicate that the upstream part of the Asparagine N-Glycosylation pathway has lower diversity among populations, while the downstream part is freer to tolerate diversity among populations. Moreover, the distribution of signatures of population differentiation and positive selection can change between parts of a pathway, especially between parts that are exposed to different functional constraints. Our results support the hypothesis that genes involved in constitutive processes can be expected to show lower population differentiation, while genes involved in traits related to the environment should show higher variability. Taken together, this work broadens our knowledge on how events of population differentiation and of positive selection are distributed among different parts of a metabolic pathway.

Recognition of Gram-positive Intestinal Bacteria by Hybridoma- and Colostrum-derived Secretory Immunoglobulin A Is Mediated by Carbohydrates.

Humans live in symbiosis with 10(14) commensal bacteria among which >99% resides in their gastrointestinal tract. The molecular bases pertaining to the interaction between mucosal secretory IgA (SIgA) and bacteria residing in the intestine are not known. Previous studies have demonstrated that commensals are naturally coated by SIgA in the gut lumen. Thus, understanding how natural SIgA interacts with commensal bacteria can provide new clues on its multiple functions at mucosal surfaces. Using fluorescently labeled, nonspecific SIgA or secretory component (SC), we visualized by confocal microscopy the interaction with various commensal bacteria, including Lactobacillus, Bifidobacteria, Escherichia coli, and Bacteroides strains. These experiments revealed that the interaction between SIgA and commensal bacteria involves Fab- and Fc-independent structural motifs, featuring SC as a crucial partner. Removal of glycans present on free SC or bound in SIgA resulted in a drastic drop in the interaction with Gram-positive bacteria, indicating the essential role of carbohydrates in the process. In contrast, poor binding of Gram-positive bacteria by control IgG was observed. The interaction with Gram-negative bacteria was preserved whatever the molecular form of protein partner used, suggesting the involvement of different binding motifs. Purified SIgA and SC from either mouse hybridoma cells or human colostrum exhibited identical patterns of recognition for Gram-positive bacteria, emphasizing conserved plasticity between species. Thus, sugar-mediated binding of commensals by SIgA highlights the currently underappreciated role of glycans in mediating the interaction between a highly diverse microbiota and the mucosal immune system.

Role of CLOCK and circadian rhythms in calcium homeostasis

Le maintien d'une concentration sanguine constante de calcium est d'une importance cruciale et trois organes participent à la balance calcique normale : les reins, les intestins et les os. La concentration plasmatique de calcium est strictement régulée par l'hormone parathyroïdienne (PTH) et par la vitamine D. Des variations circadiennes de la PTH, de la vitamine D ainsi que du calcium plasmatique ont été décrites précédemment chez l'humain ainsi que chez le rat. Ces rythmes de PTH dans le sérum sont importants pour la régulation du remodelage de l'os. En effet, il a été montré chez les souris C57BL/6J que des injections de PTH une fois par jour mènent à une augmentation de la densité minérale de l'os alors que l'infusion en continu de PTH est associée à une diminution de cette densité. La vitamine D joue également un rôle fondamental dans la physiologie osseuse, car un déficit en vitamine D peut conduire à une ostéomalacie. Cependant la fonction des oscillations de vitamine D au niveau de l'homéostasie osseuse reste inconnue. L'horloge circadienne est un système interne de contrôle biologique du temps générant des rythmes de 24 heures dans l'expression des gènes, ainsi que dans la physiologie et le comportement. Ce contrôle s'opère par des boucles rétroactives positives et négatives de l'expression de gènes circadiens tels que CLOCK, BMAL1, CRY1 et 2 ou PERI et 2. Dans ce travail, nous avons émis l'hypothèse que l'homéostasie calcique est sous le contrôle de l'horloge circadienne. Dans un premier temps, nous avons montré chez les souris C57BL/6J des variations journalières des concentrations de calcium, de PTH et de vitamine D dans le sang, ainsi que de calcium dans les urines. Nous avons également démontré des changements au niveau de l'expression rénale des gènes importants dans l'homéostasie du calcium, tant au niveau de l'ARN messager que des protéines. Ensuite, pour analyser le rôle du système de l'horloge circadienne dans l'homéostasie du calcium, nous avons étudié des souris dans lesquelles a été supprimé le gène CLOCK crucial pour la fonction de l'horloge et nous avons comparé ces souris à des souris de type sauvage de même portée. Les souris CLOCK-I- étaient hypercalciuriques à chaque moment de la journée. Cependant le rythme circadien de l'excrétion de calcium était préservé. Le taux de calcium plasmatique ne différait pas entre les génotypes, mais les souris CLOCK -/- ne montraient pas de variations journalières de ce paramètre. Une perte du rythme journalier était également observée pour les niveaux de vitamine D, perte qui pourrait être une cause de l'altération de la micro-architecture osseuse révélée chez les souris CLOCK-/-. En effet, ces souris montrent une diminution du nombre de trabécules, de leur volume ainsi que de leur surface, ce qui suggère la présence d'ostéoporose. Nous avons également trouvé que le rythme de l'expression de l'ARN messager de CYP27B1 était aboli dans les reins des souris CLOCK -/-, ce qui peut expliquer l'altération du rythme de la vitamine D. Les taux sanguins de PTH étaient comparables entre les souris CLOCK -/- et de type sauvage. Dans les reins, une augmentation de l'expression de l'ARN messager de TRPV5 et NCX1 a été constatée, ce qui suggérerait une augmentation de la réabsorption de calcium dans le tubule convoluté distal et dans le tubule connecteur. Dans les intestins, la réabsorption calcique était diminuée, chez les souris CLOCK-I-, fait confirmé par une diminution des niveaux d'ARN messager de TRPV6 et PMCAL. En résumé, la suppression du gène CLOCK chez les souris a conduit à une hypercalciurie, une altération du rythme des taux plasmatiques de calcium et de vitamine D et à une détérioration de l'architecture osseuse. Pour conclure, ces résultats montrent que l'horloge circadienne est essentielle à l'homéostasie calcique ainsi qu'à la physiologie des os. - L'ostéoporose affecte environ 22 millions de femmes et 5.5 millions d'hommes en Europe, réduisant significativement leur qualité de vie et a causé 3.5 millions de nouvelles fractures en 2010. Les dépenses totales liées à ces fractures ont atteint 37 milliards d'euro et ce coût devrait augmenter de 25% d'ici à 2025. Le nombre de nouvelles fractures dues à l'ostéoporose à travers le monde est estimé à environ 1000 par heure. Parmi les causes de l'ostéoporose, le déficit én calcium et/ou en vitamine D joue un rôle important, mais il existe également des causes génétiques ou liées à des facteurs comme les hormones sexuelles (estrogènes, testostérone), l'âge, le tabac, le poids corporel, certains médicaments,... La vie est rythmique : ceci est dû à l'alternance naturelle du jour et de la nuit et de ses effets sur le corps. La prise alimentaire, par exemple, est un processus qui a lieu pendant la phase active, qui est prévisible (il se produit toujours au même moment) et qui peut être anticipé par le corps. Pour cela, une horloge interne est présente dans chaque cellule du corps et est synchronisée par la lumière du jour, entre autres stimuli. Cette horloge indique la phase du jour et régule l'expression de gènes impliqués dans les différents processus qui nécessitent une anticipation. Pendant mon travail de thèse, je me suis demandé si des îythmes circadiens (c'est-à-dire d'une durée d'environ 24 heures et indépendants des stimuli externes) étaient observables'pour les gènes régulant les flux de calcium dans le corps et si l'interruption de ces rythmes pouvait mener à des altérations de la qualité de l'os. J'ai d'abord travaillé avec des souris normales et j'ai pu montrer la présence de rythmes au niveau du calcium sanguin et urinaire, mais également au niveau des hormones et gènes qui contrôlent le métabolisme du calcium dans le corps, comme la vitamine D et l'hormone parathyroidienne. De manière intéressante, j'ai observé que la plupart de ces gènes ont un rythme synchronisé. J'ai ensuite utilisé un modèle de souris dans lequel l'horloge interne a été génétiquement invalidée et j'ai montré que ces souris présentent une augmentation de leur excrétion urinaire de calcium et un rythme circadien altéré de la vitamine D dans le sang. Ces souris absorbent aussi moins bien le calcium intestinal et présentent une ostéoporose marquée. Ce travail montre donc que l'horloge interne est nécessaire pour établir un rythme circadiens de certains facteurs influant les flux de calcium dans l'organisme, comme la vitamine D, et que la perturbation de ces rythmes mène à une dérégulation du métabolisme osseux. Ainsi, la perturbation de l'horloge interne peut causer une ostéoporose et une hypercalciurie qui pourraient aboutir à la formation de fractures et de calculs rénaux. L'extrapolation de ces observations chez l'homme ou à des changements plus subtiles des rythmes circadiens, comme le décalage horaire, restent à montrer. Cette recherche a démontré que les rythmes circadiens des mécanismes de régulation des flux de calcium dans l'organisme sont essentiels au maintien d'un squelette normal et suggère que les perturbations des rythmes circadiens pourraient être une nouvelle cause de l'ostéoporose. - Maintaining constant calcium concentration in the plasma is of a crucial importance and three organs participate in normal calcium balance - kidney, gut and bone. Plasma calcium concentration is strictly regulated by parathyroid hormone (PTH) and vitamin D. Circadian variations of PTH, vitamin D and plasma calcium were previously described in humans, as well as in rats. Rhythms in serum PTH are important for balanced bone remodelling. Indeed in C57BL/6J mice, PTH injection once per day leads to an increase in bone mineral density (BMD), whilst continuous infusion is associated with decreased BMD. Vitamin D also plays a crucial role in bone physiology, since the deficiency in vitamin D can lead to rickets/osteomalacia. However, the role of vitamin D rhythms in bone homeostasis remains unknown. The circadian clock is an. internal time-keeping system generating rhythms in gene expression with 24h periodicity, in physiology and in behaviour. It is operated by positive- and negative-feedback loops of circadian genes, such as CLOCK, BMAL1, CRY1 and 2 or PERI and 2. In this work, we hypothesized, that calcium homeostasis is under the control of the circadian clock. First, we showed daily variations in urinary calcium and serum calcium, PTH and l,25(OH)2 vitamin D, together with renal mRNA and protein levels of genes involved in calcium homeostasis in C57BL/6J mice. Second, and to investigate the role of the circadian clock system in calcium handling, we studied mice lacking the gene CLOCK crucial for fonction of the clock system and compared them to the WT littermates. CLOCK-/- mice were hypercalciuric at all timepoints of the day. However, the circadian rhythm of calcium excretion was preserved. Serum calcium levels did not differ between the genotypes, but CLOCK-/- mice did not exhibit daily variation for this parameter. Loss of rhythm was observed also for serum l,25(OH)2 vitamin D levels, which may be one of the causes of altered bone microarchitecture that was revealed in CLOCK-/- mice. They displayed increased trabecular separation and decreased trabecular number, trabecular bone volume and trabecular bone surface, suggestive of osteoporosis. We found that the rhythm of the mRNA expression of CYP27B1 was abolished in the kidney of CLOCK-/- mice, which could induce the altered rhythm of l,25(OH)2 vitamin. Serum PTH levels were comparable between CLOCK-/- and WT mice. In the kidney, increased mRNA expression of TRPV5 and NCX1 suggests increased calcium reabsorption in the distal convoluted and connecting tubule. In the gut, intestinal calcium absorption was decreased in CLOCK¬/- mice, confirmed by decreased mRNA levels of TRPV6 and PMCA1. In summary, deletion of the CLOCK gene in mice conducts to hypercalciuria, alteration of the rhythm in serum calcium and l,25(OH)2D levels, and impainnent of their bone microarchitecture. In conclusion, these data show that the circadian clock system is essential in calcium homeostasis and bone physiology.

Interpreting Breast International Group (BIG) 1-98: a randomized, double-blind, phase III trial comparing letrozole and tamoxifen as adjuvant endocrine therapy for postmenopausal women with hormone receptor-positive, early breast cancer.

The Breast International Group (BIG) 1-98 study is a four-arm trial comparing 5 years of monotherapy with tamoxifen or with letrozole or with sequences of 2 years of one followed by 3 years of the other for postmenopausal women with endocrine-responsive early invasive breast cancer. From 1998 to 2003, BIG -98 enrolled 8,010 women. The enhanced design f the trial enabled two complementary analyses of efficacy and safety. Collection of tumor specimens further enabled treatment comparisons based on tumor biology. Reports of BIG 1-98 should be interpreted in relation to each individual patient as she weighs the costs and benefits of available treatments. Clinicaltrials.gov ID: NCT00004205.

Tapping the innovation potential of corporate engagement with stakeholders

Summary This dissertation explores how stakeholder dialogue influences corporate processes, and speculates about the potential of this phenomenon - particularly with actors, like non-governmental organizations (NGOs) and other representatives of civil society, which have received growing attention against a backdrop of increasing globalisation and which have often been cast in an adversarial light by firms - as a source of teaming and a spark for innovation in the firm. The study is set within the context of the introduction of genetically-modified organisms (GMOs) in Europe. Its significance lies in the fact that scientific developments and new technologies are being generated at an unprecedented rate in an era where civil society is becoming more informed, more reflexive, and more active in facilitating or blocking such new developments, which could have the potential to trigger widespread changes in economies, attitudes, and lifestyles, and address global problems like poverty, hunger, climate change, and environmental degradation. In the 1990s, companies using biotechnology to develop and offer novel products began to experience increasing pressure from civil society to disclose information about the risks associated with the use of biotechnology and GMOs, in particular. Although no harmful effects for humans or the environment have been factually demonstrated even to date (2008), this technology remains highly-contested and its introduction in Europe catalysed major companies to invest significant financial and human resources in stakeholder dialogue. A relatively new phenomenon at the time, with little theoretical backing, dialogue was seen to reflect a move towards greater engagement with stakeholders, commonly defined as those "individuals or groups with which. business interacts who have a 'stake', or vested interest in the firm" (Carroll, 1993:22) with whom firms are seen to be inextricably embedded (Andriof & Waddock, 2002). Regarding the organisation of this dissertation, Chapter 1 (Introduction) describes the context of the study, elaborates its significance for academics and business practitioners as an empirical work embedded in a sector at the heart of the debate on corporate social responsibility (CSR). Chapter 2 (Literature Review) traces the roots and evolution of CSR, drawing on Stakeholder Theory, Institutional Theory, Resource Dependence Theory, and Organisational Learning to establish what has already been developed in the literature regarding the stakeholder concept, motivations for engagement with stakeholders, the corporate response to external constituencies, and outcomes for the firm in terms of organisational learning and change. I used this review of the literature to guide my inquiry and to develop the key constructs through which I viewed the empirical data that was gathered. In this respect, concepts related to how the firm views itself (as a victim, follower, leader), how stakeholders are viewed (as a source of pressure and/or threat; as an asset: current and future), corporate responses (in the form of buffering, bridging, boundary redefinition), and types of organisational teaming (single-loop, double-loop, triple-loop) and change (first order, second order, third order) were particularly important in building the key constructs of the conceptual model that emerged from the analysis of the data. Chapter 3 (Methodology) describes the methodology that was used to conduct the study, affirms the appropriateness of the case study method in addressing the research question, and describes the procedures for collecting and analysing the data. Data collection took place in two phases -extending from August 1999 to October 2000, and from May to December 2001, which functioned as `snapshots' in time of the three companies under study. The data was systematically analysed and coded using ATLAS/ti, a qualitative data analysis tool, which enabled me to sort, organise, and reduce the data into a manageable form. Chapter 4 (Data Analysis) contains the three cases that were developed (anonymised as Pioneer, Helvetica, and Viking). Each case is presented in its entirety (constituting a `within case' analysis), followed by a 'cross-case' analysis, backed up by extensive verbatim evidence. Chapter 5 presents the research findings, outlines the study's limitations, describes managerial implications, and offers suggestions for where more research could elaborate the conceptual model developed through this study, as well as suggestions for additional research in areas where managerial implications were outlined. References and Appendices are included at the end. This dissertation results in the construction and description of a conceptual model, grounded in the empirical data and tied to existing literature, which portrays a set of elements and relationships deemed important for understanding the impact of stakeholder engagement for firms in terms of organisational learning and change. This model suggests that corporate perceptions about the nature of stakeholder influence the perceived value of stakeholder contributions. When stakeholders are primarily viewed as a source of pressure or threat, firms tend to adopt a reactive/defensive posture in an effort to manage stakeholders and protect the firm from sources of outside pressure -behaviour consistent with Resource Dependence Theory, which suggests that firms try to get control over extemal threats by focussing on the relevant stakeholders on whom they depend for critical resources, and try to reverse the control potentially exerted by extemal constituencies by trying to influence and manipulate these valuable stakeholders. In situations where stakeholders are viewed as a current strategic asset, firms tend to adopt a proactive/offensive posture in an effort to tap stakeholder contributions and connect the organisation to its environment - behaviour consistent with Institutional Theory, which suggests that firms try to ensure the continuing license to operate by internalising external expectations. In instances where stakeholders are viewed as a source of future value, firms tend to adopt an interactive/innovative posture in an effort to reduce or widen the embedded system and bring stakeholders into systems of innovation and feedback -behaviour consistent with the literature on Organisational Learning, which suggests that firms can learn how to optimize their performance as they develop systems and structures that are more adaptable and responsive to change The conceptual model moreover suggests that the perceived value of stakeholder contribution drives corporate aims for engagement, which can be usefully categorised as dialogue intentions spanning a continuum running from low-level to high-level to very-high level. This study suggests that activities aimed at disarming critical stakeholders (`manipulation') providing guidance and correcting misinformation (`education'), being transparent about corporate activities and policies (`information'), alleviating stakeholder concerns (`placation'), and accessing stakeholder opinion ('consultation') represent low-level dialogue intentions and are experienced by stakeholders as asymmetrical, persuasive, compliance-gaining activities that are not in line with `true' dialogue. This study also finds evidence that activities aimed at redistributing power ('partnership'), involving stakeholders in internal corporate processes (`participation'), and demonstrating corporate responsibility (`stewardship') reflect high-level dialogue intentions. This study additionally finds evidence that building and sustaining high-quality, trusted relationships which can meaningfully influence organisational policies incline a firm towards the type of interactive, proactive processes that underpin the development of sustainable corporate strategies. Dialogue intentions are related to type of corporate response: low-level intentions can lead to buffering strategies; high-level intentions can underpin bridging strategies; very high-level intentions can incline a firm towards boundary redefinition. The nature of corporate response (which encapsulates a firm's posture towards stakeholders, demonstrated by the level of dialogue intention and the firm's strategy for dealing with stakeholders) favours the type of learning and change experienced by the organisation. This study indicates that buffering strategies, where the firm attempts to protect itself against external influences and cant' out its existing strategy, typically lead to single-loop learning, whereby the firm teams how to perform better within its existing paradigm and at most, improves the performance of the established system - an outcome associated with first-order change. Bridging responses, where the firm adapts organisational activities to meet external expectations, typically leads a firm to acquire new behavioural capacities characteristic of double-loop learning, whereby insights and understanding are uncovered that are fundamentally different from existing knowledge and where stakeholders are brought into problem-solving conversations that enable them to influence corporate decision-making to address shortcomings in the system - an outcome associated with second-order change. Boundary redefinition suggests that the firm engages in triple-loop learning, where the firm changes relations with stakeholders in profound ways, considers problems from a whole-system perspective, examining the deep structures that sustain the system, producing innovation to address chronic problems and develop new opportunities - an outcome associated with third-order change. This study supports earlier theoretical and empirical studies {e.g. Weick's (1979, 1985) work on self-enactment; Maitlis & Lawrence's (2007) and Maitlis' (2005) work and Weick et al's (2005) work on sensegiving and sensemaking in organisations; Brickson's (2005, 2007) and Scott & Lane's (2000) work on organisational identity orientation}, which indicate that corporate self-perception is a key underlying factor driving the dynamics of organisational teaming and change. Such theorizing has important implications for managerial practice; namely, that a company which perceives itself as a 'victim' may be highly inclined to view stakeholders as a source of negative influence, and would therefore be potentially unable to benefit from the positive influence of engagement. Such a selfperception can blind the firm from seeing stakeholders in a more positive, contributing light, which suggests that such firms may not be inclined to embrace external sources of innovation and teaming, as they are focussed on protecting the firm against disturbing environmental influences (through buffering), and remain more likely to perform better within an existing paradigm (single-loop teaming). By contrast, a company that perceives itself as a 'leader' may be highly inclined to view stakeholders as a source of positive influence. On the downside, such a firm might have difficulty distinguishing when stakeholder contributions are less pertinent as it is deliberately more open to elements in operating environment (including stakeholders) as potential sources of learning and change, as the firm is oriented towards creating space for fundamental change (through boundary redefinition), opening issues to entirely new ways of thinking and addressing issues from whole-system perspective. A significant implication of this study is that potentially only those companies who see themselves as a leader are ultimately able to tap the innovation potential of stakeholder dialogue.

The complete genome sequence of the gram-positive bacterium Bacillus subtilis.

Bacillus subtilis is the best-characterized member of the Gram-positive bacteria. Its genome of 4,214,810 base pairs comprises 4,100 protein-coding genes. Of these protein-coding genes, 53% are represented once, while a quarter of the genome corresponds to several gene families that have been greatly expanded by gene duplication, the largest family containing 77 putative ATP-binding transport proteins. In addition, a large proportion of the genetic capacity is devoted to the utilization of a variety of carbon sources, including many plant-derived molecules. The identification of five signal peptidase genes, as well as several genes for components of the secretion apparatus, is important given the capacity of Bacillus strains to secrete large amounts of industrially important enzymes. Many of the genes are involved in the synthesis of secondary metabolites, including antibiotics, that are more typically associated with Streptomyces species. The genome contains at least ten prophages or remnants of prophages, indicating that bacteriophage infection has played an important evolutionary role in horizontal gene transfer, in particular in the propagation of bacterial pathogenesis.