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Developing a predictive understanding of subsurface flow and transport is complicated by the disparity of scales across which controlling hydrological properties and processes span. Conventional techniques for characterizing hydrogeological properties (such as pumping, slug, and flowmeter tests) typically rely on borehole access to the subsurface. Because their spatial extent is commonly limited to the vicinity near the wellbores, these methods often cannot provide sufficient information to describe key controls on subsurface flow and transport. The field of hydrogeophysics has evolved in recent years to explore the potential that geophysical methods hold for improving the quantification of subsurface properties and processes relevant for hydrological investigations. This chapter is intended to familiarize hydrogeologists and water-resource professionals with the state of the art as well as existing challenges associated with hydrogeophysics. We provide a review of the key components of hydrogeophysical studies, which include: geophysical methods commonly used for shallow subsurface characterization; petrophysical relationships used to link the geophysical properties to hydrological properties and state variables; and estimation or inversion methods used to integrate hydrological and geophysical measurements in a consistent manner. We demonstrate the use of these different geophysical methods, petrophysical relationships, and estimation approaches through several field-scale case studies. Among other applications, the case studies illustrate the use of hydrogeophysical approaches to quantify subsurface architecture that influence flow (such as hydrostratigraphy and preferential pathways); delineate anomalous subsurface fluid bodies (such as contaminant plumes); monitor hydrological processes (such as infiltration, freshwater-seawater interface dynamics, and flow through fractures); and estimate hydrological properties (such as hydraulic conductivity) and state variables (such as water content). The case studies have been chosen to illustrate how hydrogeophysical approaches can yield insights about complex subsurface hydrological processes, provide input that improves flow and transport predictions, and provide quantitative information over field-relevant spatial scales. The chapter concludes by describing existing hydrogeophysical challenges and associated research needs. In particular, we identify the area of quantitative watershed hydrogeophysics as a frontier area, where significant effort is required to advance the estimation of hydrological properties and processes (and their uncertainties) over spatial scales relevant to the management of water resources and contaminants.

Age, Life-satisfaction, and Relative Income – Insights from the UK and Germany

We first confirm previous results with the German Socio-Economic Panel by Layard et al. (2010), and obtain strong negative effects of comparison income. However, when we split the sample by age, we find quite different results for reference income. The effects on lifesatisfaction are positive and significant for those under 45, consistent with Hirschman’s (1973) ‘tunnel effect’, and only negative (and larger than in the full sample) for those over 45, when relative deprivation dominates. Thus for young respondents, reference income’s signalling role, indicating potential future prospects, can outweigh relative deprivation effects. Own-income effects are also larger for the older sample, and of greater magnitude than the comparison income effect. In East Germany the reference income effects are insignificant for all. With data from the British Household Panel Survey, we confirm standard results when encompassing all ages, but reference income loses significance in both age groups, and most surprisingly, even own income becomes insignificant for those over 45, while education has significant negative effects.

Evolutionary genomics and HIV restriction factors.

PURPOSE OF REVIEW: To provide updated insights into innate antiviral immunity and highlight prototypical evolutionary features of well characterized HIV restriction factors. RECENT FINDINGS: Recently, a new HIV restriction factor, Myxovirus resistance 2, has been discovered and the region/residue responsible for its activity identified using an evolutionary approach. Furthermore, IFI16, an innate immunity protein known to sense several viruses, has been shown to contribute to the defense to HIV-1 by causing cell death upon sensing HIV-1 DNA. SUMMARY: Restriction factors against HIV show characteristic signatures of positive selection. Different patterns of accelerated sequence evolution can distinguish antiviral strategies--offense or defence--as well as the level of specificity of the antiviral properties. Sequence analysis of primate orthologs of restriction factors serves to localize functional domains and sites responsible for antiviral action. We use recent discoveries to illustrate how evolutionary genomic analyses help identify new antiviral genes and their mechanisms of action.

New insights into the phylogenetics and biogeography of Arum (Araceae): unravelling its evolutionary history

The heat- and odour-producing genus Arum (Araceae) has interested scientists for centuries. This long-term interest has allowed a deep knowledge of some complex processes, such as the physiology and dynamics of its characteristic lure-and-trap pollination system, to be built up. However, mainly because of its large distributional range and high degree of morphological variation, species' limits and relationships are still under discussion. Today, the genus comprises 28 species subdivided into two subgenera, two sections and six subsections. In this study, the phylogeny of the genus is inferred on the basis of four plastid regions, and the evolution of several morphological characters is investigated. Our phylogenetic hypothesis is not in agreement with the current infrageneric classification of the genus and challenges the monophyly of several species. This demonstrates the need for a new infrageneric classification based on characters reflecting the evolution of this enigmatic genus. To investigate the biogeography of Arum deeply, further spatiotemporal analyses were performed, addressing the importance of the Mediterranean basin in the diversification of Arum. Our results suggest that its centre of origin was the European-Aegean region, and that major diversification happened during the last 10 Myr.

Chemical genetic analysis of cdc2p : new insights into the regulation of cytokinesis in "Schizosaccharomyces pombe"

RÉSUMÉ La protéine kinase cyciine-cdc2p (Cdk) joue un rôle fondamental dans la progression du cycle cellulaire dans la levure de fission Schizosaccharomyces pombe. Nous avons étudié le rôle de cdc2p dans la régulation de la cascade de septation ou SIN (septation initiation network) en mitose et en méiose. Le SIN contrôle l'initiation de la cytokinèse à la fin de la mitose, et est supposé être négativement régulé par cdc2p. Nous avons mutagénéisé le site actif de cdc2p afin qu'il puisse lier un analogue de l'ATP (PP1) qui agit comme inhibiteur. Cet analogue ne peut pas lier la kinase de type sauvage. Cette approche dite «chemical genetics» permet une meilleure résolution temporelle comparée à l'approche classique utilisant les mutants sensibles à une température élevée. Nous avons montré que ce mutant cdc2-as (analogue sensitive) est fonctionnel et que, in vitro, l'activité kinase est inhibée en présence de l'analogue. Les cellules portant cette mutation, contrairement aux cellules de type sauvage s'arrêtent de manière irréversible soit en G2 soit en G1 et G2, suivant la concentration de l'inhibiteur. L'inactivation de cdc2p-as dans des cellules arrêtées en métaphase conduit au recrutement asymétrique des protéines du SIN sur le pôle du fuseau mitotique et au recrutement des composants du SIN, ainsi que de la ß-(1,3)glucan synthase à l'anneau contractile. De plus, nos résultats montrent que l'orthologue de la phosphatase cdc14p dans S. pombe, fip1p/clp1p, joue un rôle dans la régulation de la localisation des protéines du SIN suite à l'inactivation de cdc2p. Finalement, l'activité de cdc2p est requise pour maintenir la polo-like kinase plo1p sur les pôles du fuseau mitotique dans les premiers stages de la mitose. C'est pourquoi nous concluons que l'inactivation de cdc2p est suffisante pour activer le SIN et promouvoir la cytokinèse. Dans une étude séparée, nous avons caractérisé des potentiellement nouveaux composants ou régulateurs du SIN qui ont été isolés dans deux criblages génétiques visant à isoler des mutants atténuants la signalisation du SIN. Summary : The cyclin dependent protein kinase (Cdk) cdc2p plays a central role in the cell cycle progression of fission yeast Schizosaccharomyces pombe. We have studied the role of cdc2p in regulating the septation initiation network (SIN) in mitosis and meiosis. The SIN regulates the initiation of cytokinesis at the end of mitosis and is thought to be inhibited by cdc2p. We have mutated the active site of cdc2p to permit binding of an inhibitory ATP analogue (PP1), which is unable to bind unmodified kinases. This "chemical genetic" approach provides a much higher temporal resolution than it can be achieved with classical temperature-sensitive mutants. We demonstrate that cdc2-as (analogue sensitive) is functional and that addition of PP1 inhibits cdc2p kinase activity in vitro. Cells carrying the cdc2-as allele, but not cdc2+, undergo reversible cell cycle arrest following addition of PP1 either in G2, or at both major commitment points in the cell cycle (G1 and G2), depending upon the concentration of PP1. Inactivation of cdc2p-as in cells arrested in early mitosis promotes both the asymmetric recruitment of SIN proteins to the spindle pole bodies (SPBs), and the recruitment of the most downstream SIN components and ß-(1,3)-glucan synthase to the contractile ring. Furthermore, our results indicate that the S. pombe orthologue of Cdc14p, flp1p/clp1p, plays a role in regulating the relocalisation of SIN proteins following inactivation of cdc2p, and that cdc2p activity is required to retain the polo like kinase plot p on the SPBs in early mitosis. Thus, we conclude that inactivation of cdc2p is sufficient to activate the SIN and to promote cytokinesis. In a separate study, we have initially characterised potential novel components or regulators of the SIN pathway identified by two genetic screens for mutants attenuating SIN signaling.

Theoretical study on receptor-G protein recognition: new insights into the mechanisms of the alpha1b-adrenergic recptor activation

This work compares the structural/dynamics features of the wild-type alb-adrenergic receptor (AR) with those of the D142A active mutant and the agonist-bound state. The two active receptor forms were compared in their isolated states as well as in their ability to form homodimers and to recognize the G alpha q beta 1 gamma 2 heterotrimer. The analysis of the isolated structures revealed that, although the mutation- and agonist-induced active states of the alpha 1b-AR are different, they, however, share several structural peculiarities including (a) the release of some constraining interactions found in the wild-type receptor and (b) the opening of a cytosolic crevice formed by the second and third intracellular loops and the cytosolic extensions of helices 5 and 6. Accordingly, also their tendency to form homodimers shows commonalties and differences. In fact, in both the active receptor forms, helix 6 plays a crucial role in mediating homodimerization. However, the homodimeric models result from different interhelical assemblies. On the same line of evidence, in both of the active receptor forms, the cytosolic opened crevice recognizes similar domains on the G protein. However, the docking solutions are differently populated and the receptor-G protein preorientation models suggest that the final complexes should be characterized by different interaction patterns.

Human GnRH deficiency: a unique disease model to unravel the ontogeny of GnRH neurons.

Evolutionary survival of a species is largely a function of its reproductive fitness. In mammals, a sparsely populated and widely dispersed network of hypothalamic neurons, the gonadotropin-releasing hormone (GnRH) neurons, serve as the pilot light of reproduction via coordinated secretion of GnRH. Since it first description, human GnRH deficiency has been recognized both clinically and genetically as a heterogeneous disease. A spectrum of different reproductive phenotypes comprised of congenital GnRH deficiency with anosmia (Kallmann syndrome), congenital GnRH deficiency with normal olfaction (normosmic idiopathic hypogonadotropic hypogonadism), and adult-onset hypogonadotropic hypogonadism has been described. In the last two decades, several genes and pathways which govern GnRH ontogeny have been discovered by studying humans with GnRH deficiency. More importantly, detailed study of these patients has highlighted the emerging theme of oligogenicity and genotypic synergism, and also expanded the phenotypic diversity with the documentation of reversal of GnRH deficiency later in adulthood in some patients. The underlying genetic defect has also helped understand the associated nonreproductive phenotypes seen in some of these patients. These insights now provide practicing clinicians with targeted genetic diagnostic strategies and also impact on clinical management.

Developments in the scientific and clinical understanding of gout.

Gout is the most common form of inflammatory arthritis in the elderly. In the last two decades, both hyperuricemia and gout have increased markedly and similar trends in the epidemiology of the metabolic syndrome have been observed. Recent studies provide new insights into the transporters that handle uric acid in the kidney as well as possible links between these transporters, hyperuricemia, and hypertension. The treatment of established hyperuricemia has also seen new developments. Febuxostat and PEG-uricase are two novel treatments that have been evaluated and shown to be highly effective in the management of hyperuricemia, thus enlarging the therapeutic options available to lower uric acid levels. Monosodium urate (MSU) crystals are potent inducers of inflammation. Within the joint, they trigger a local inflammatory reaction, neutrophil recruitment, and the production of pro-inflammatory cytokines as well as other inflammatory mediators. Experimentally, the uptake of MSU crystals by monocytes involves interactions with components of the innate immune system, namely Toll-like receptor (TLR)-2, TLR-4, and CD14. Intracellularly, MSU crystals activate multiple processes that lead to the formation of the NALP-3 (NACHT, LRR, and pyrin domain-containing-3) inflammasome complex that in turn processes pro-interleukin (IL)-1 to yield mature IL-1 beta, which is then secreted. The inflammatory effects of MSU are IL-1-dependent and can be blocked by IL-1 inhibitors. These advances in the understanding of hyperuricemia and gout provide new therapeutic targets for the future.

Angiotensin II receptor blockade prevents acute renal sodium retention induced by low levels of orthostatic stress.

BACKGROUND: Depending on its magnitude, lower body negative pressure (LBNP) has been shown to induce a progressive activation of neurohormonal, renal tubular, and renal hemodynamic responses, thereby mimicking the renal responses observed in clinical conditions characterized by a low effective arterial volume such as congestive heart failure. Our objective was to evaluate the impact of angiotensin II receptor blockade with candesartan on the renal hemodynamic and urinary excretory responses to a progressive orthostatic stress in normal subjects. METHODS: Twenty healthy men were submitted to three levels of LBNP (0, -10, and -20 mbar or 0, -7.5, and -15 mm Hg) for 1 hour according to a crossover design with a minimum of 2 days between each level of LBNP. Ten subjects were randomly allocated to receive a placebo and ten others were treated with candesartan 16 mg orally for 10 days before and during the three levels of LBNP. Systemic and renal hemodynamics, renal sodium excretions, and the hormonal response were measured hourly before, during, and for 2 hours after LBNP. RESULTS: During placebo, LBNP induced no change in systemic and renal hemodynamics, but sodium excretion decreased dose dependently with higher levels of LBNP. At -20 mbar, cumulative 3-hour sodium balance was negative at -2.3 +/- 2.3 mmol (mean +/- SEM). With candesartan, mean blood pressure decreased (76 +/- 1 mm Hg vs. 83 +/- 3 mm Hg, candesartan vs. placebo, P < 0.05) and renal plasma flow increased (858 +/- 52 mL/min vs. 639 +/- 36 mL/min, candesartan vs. placebo, P < 0.05). Glomerular filtration rate (GFR) was not significantly higher with candesartan (127 +/- 7 mL/min in placebo vs. 144 +/- 12 mL/min in candesartan). No significant decrease in sodium and water excretion was found during LBNP in candesartan-treated subjects. At -20 mbar, the 3-hour cumulative sodium excretion was + 4.6 +/- 1.4 mmol in the candesartan group (P= 0.02 vs. placebo). CONCLUSION: Selective blockade of angiotensin II type 1 (AT1) receptors with candesartan increases renal blood flow and prevents the antinatriuresis during sustained lower body negative pressure despite a modest decrease in blood pressure. These results thus provide interesting insights into potential benefits of AT1 receptor blockade in sodium-retaining states such as congestive heart failure.

The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis

Mycorrhizal symbioses--the union of roots and soil fungi--are universal in terrestrial ecosystems and may have been fundamental to land colonization by plants. Boreal, temperate and montane forests all depend on ectomycorrhizae. Identification of the primary factors that regulate symbiotic development and metabolic activity will therefore open the door to understanding the role of ectomycorrhizae in plant development and physiology, allowing the full ecological significance of this symbiosis to be explored. Here we report the genome sequence of the ectomycorrhizal basidiomycete Laccaria bicolor (Fig. 1) and highlight gene sets involved in rhizosphere colonization and symbiosis. This 65-megabase genome assembly contains approximately 20,000 predicted protein-encoding genes and a very large number of transposons and repeated sequences. We detected unexpected genomic features, most notably a battery of effector-type small secreted proteins (SSPs) with unknown function, several of which are only expressed in symbiotic tissues. The most highly expressed SSP accumulates in the proliferating hyphae colonizing the host root. The ectomycorrhizae-specific SSPs probably have a decisive role in the establishment of the symbiosis. The unexpected observation that the genome of L. bicolor lacks carbohydrate-active enzymes involved in degradation of plant cell walls, but maintains the ability to degrade non-plant cell wall polysaccharides, reveals the dual saprotrophic and biotrophic lifestyle of the mycorrhizal fungus that enables it to grow within both soil and living plant roots. The predicted gene inventory of the L. bicolor genome, therefore, points to previously unknown mechanisms of symbiosis operating in biotrophic mycorrhizal fungi. The availability of this genome provides an unparalleled opportunity to develop a deeper understanding of the processes by which symbionts interact with plants within their ecosystem to perform vital functions in the carbon and nitrogen cycles that are fundamental to sustainable plant productivity.

Organizational configurations of strategic choices and strategic management accounting

This is the first study to adopt a configurational paradigm in an investigation of strategic management accounting (SMA) adoption. The study examines the alignment and effectiveness of strategic choice and strategic management accounting (SMA) system design configurations. Six configurations were derived empirically by deploying a cluster analysis of data collected from a sample of 193 large Slovenian companies. The first four clusters appear to provide some support for the central configurational proposition that higher levels of vertical and horizontal configurational alignments are associated with higher levels of performance. Evidence that contradicts the theory is also apparent, however, as the remaining two clusters exhibit high degrees of SMA vertical and horizontal alignment, but low performance levels. A particular contribution of the paper concerns its demonstration of the way that the configurational paradigm can be operationalised to examine management accounting phenomena and the nature of management accounting insights that can derive from applying the approach.

Insights into the regulation of two caspase-activating platforms, the inflammasome and the PIDDosome

Résumé: Les organismes multicellulaires ont adopté diverses stratégies pour répondre aux stress auxquels ils sont exposés. Cette étude a exploré deux de ces stratégies l'inflammation en réponse à une invasion par un pathogène, et l'apoptose ou la survie en réponse aux dommages à l'ADN. L'interleukine-lß (IL-lß) est une importante cytokine inflammatoire. Elle est synthétisée sous forme d'un précurseur inactif et nécessite un clivage par la caspase-1 pour être activée. La caspase-1 elle-même est activée dans un complexe appelé inflammasome. Certains NLRs (Nod-like receptors), IPAF et les NALPs, sont capables de former des inflammasomes fonctionnels. Cette étude s'est intéressée au rôle d'un autre NLR structurellement proche, la protéine NAIP, dans la régulation de la caspase-1 et la maturation de l'IL-1 ß. NAIP est incorporé à l'inflammasome contenant NALP3 et est capable d'inhiber l'activation de la caspase-1 et la maturation de l'IL-lß. Cette fonction inhibitrice dépend des ses domaines BIR et est inhibée par ses LRRs. Le mécanisme exact d'inhibition reste à définir et la régulation de l'activation de NAIP est discutée. La deuxième partie de cette étude concerne la protéine PIDD. Cette protéine est impliquée avec RAIDD dans l'activation de la caspase-2, et est aussi capable, avec l'aide de RIP et de NEMO, d'activer NF-κB en réponse aux dommages à l'ADN. Deux isoformes de PIDD ont déjà été décrites dans la littérature, PIDD (isoforme 1) et LRDD (isoforme 2) et une troisième isoforme est rapportée ici. L'étude de l'expression de ces isoformes a montré qu'elles sont exprimées différemment dans les tissus et dans les lignées cellulaires, et que l'isoforme 3 est induite en réponse à un stress génotoxique. La caractérisation fonctionnelle a établi que les trois isoformes sont capables d'activer NF-κB, donc la survie, mais que seule l'isoforme 1 peut interagir avec RAIDD pour activer la caspase-2 et sensibiliser les cellules à la mort induite par un stress génotoxique. Le domaine intermédiaire de PIDD, situé entre le deuxième ZU5 et le DD est essentiel pour l'interaction entre PIDD et RAIDD et l'activation de la caspase-2 qui en découle. En conclusion, l'épissage différentiel de l'ARNm de PIDD permet la production d'au moins trois protéines possédant des fonctions agonistes ou antagonistes et qui peuvent participer au choix cellulaire entre survie et apoptose en réponse aux dommages à l'ADN. Summary: Multicellular organisms have evolved several strategies to cope with the stresses they encounter. The present study has explored two of these strategies: inflammation in response to a pathogenic invasion, and apoptosis or repair/survival in response to DNA damage. Interleukin-lß (IL-lß) is a key mediator of inflammation. It is synthesized as an inactive precursor and requires cleavage by caspase-1 to be activated. caspase-1 itself is activated in molecular platforms called inflammasomes, which can be formed by members of the NOD-like receptors (NLR) family, like IPAF and NALPs. This study has investigated the role of another NLR, the structurally related protein NAIP, in the regulation of caspase-1 activation and IL-lß maturation. An inhibitory role of NAIP on caspase-1 activation and IL-lß maturation was demonstrated, as well as NAIP incorporation in the NALP3 inflammasome. This inhibitory property relies on NAIP BIR domains and is inhibited by NAIP LRRs. The exact mechanism of NAIP-mediated caspase-1 activation remains to be elucidated and the regulation of NAIP activation is discussed. The second part of this study focused on the caspase-2 activating protein PIDD. This protein is known to mediate caspase-2 activation via RAIDD and to signal NF-κB via RIP and NEMO in response to DNA damage. Two isoforms of PIDD, PIDD (isoform 1) and LRDD (isoform 2), have already been reported and a third isoform is described here. Investigation of the expressional regulation of these isoforms indicated that they are differentially expressed in tissues and cell lines, and that isoform 3 mRNA levels are upregulated in response to genotoxic stress. Functional studies demonstrated that all three isoforms can activate NF-κB in response to DNA damage, but only isoform 1 is able to interact with RAIDD and activate caspase-2, sensitizing cells to genotoxic stress-induced cell death. The intermediate domain located between the second ZUS and the DD is essential for the interaction of PIDD and RAIDD and the subsequent caspase-2 activation. Thus the differential splicing of PIDD mRNA leads to the formation of at least thrée proteins with antagonizing/agonizing functions that could participate in determining cell fate in response to DNA damage.

Global transcriptome sequencing identifies chlamydospore specific markers in Candida albicans and Candida dubliniensis.

Candida albicans and Candida dubliniensis are pathogenic fungi that are highly related but differ in virulence and in some phenotypic traits. During in vitro growth on certain nutrient-poor media, C. albicans and C. dubliniensis are the only yeast species which are able to produce chlamydospores, large thick-walled cells of unknown function. Interestingly, only C. dubliniensis forms pseudohyphae with abundant chlamydospores when grown on Staib medium, while C. albicans grows exclusively as a budding yeast. In order to further our understanding of chlamydospore development and assembly, we compared the global transcriptional profile of both species during growth in liquid Staib medium by RNA sequencing. We also included a C. albicans mutant in our study which lacks the morphogenetic transcriptional repressor Nrg1. This strain, which is characterized by its constitutive pseudohyphal growth, specifically produces masses of chlamydospores in Staib medium, similar to C. dubliniensis. This comparative approach identified a set of putatively chlamydospore-related genes. Two of the homologous C. albicans and C. dubliniensis genes (CSP1 and CSP2) which were most strongly upregulated during chlamydospore development were analysed in more detail. By use of the green fluorescent protein as a reporter, the encoded putative cell wall related proteins were found to exclusively localize to C. albicans and C. dubliniensis chlamydospores. Our findings uncover the first chlamydospore specific markers in Candida species and provide novel insights in the complex morphogenetic development of these important fungal pathogens.