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Selected AbstractsDecoding epithelial signals: critical role for the epidermal growth factor receptor in controlling intestinal transport functionACTA PHYSIOLOGICA, Issue 1 2009D. F. McCole Abstract The intestinal epithelium engages in bidirectional transport of fluid and electrolytes to subserve the physiological processes of nutrient digestion and absorption, as well as the elimination of wastes, without excessive losses of bodily fluids that would lead to dehydration. The overall processes of intestinal ion transport, which in turn drive the secretion or absorption of water, are accordingly carefully regulated. We and others have identified the epidermal growth factor receptor (EGFr) as a critical regulator of mammalian intestinal ion transport. In this article, we focus on our studies that have uncovered the intricate signalling mechanisms downstream of EGFr that regulate both chloride secretion and sodium absorption by colonocytes. Emphasis will be placed on the EGFr-associated regulatory pathways that dictate the precise outcome to receptor activation in response to signals that may seem, on their face, to be quite similar if not identical. The concepts to be discussed underlie the ability of the intestinal epithelium to utilize a limited set of signalling effectors to produce a variety of outcomes suitable for varying physiological and pathophysiological demands. Our findings therefore are relevant not only to basic biological principles, but also may ultimately point to new therapeutic targets in intestinal diseases where ion transport is abnormal. [source] The Impacts of Supermarket Procurement on Farming Communities in India: Evidence from Rural KarnatakaDEVELOPMENT POLICY REVIEW, Issue 4 2010Bill Pritchard The rapid expansion of supermarket retailing, with its impact on farmer communities, represents a contentious part of India's recent economic development. This article reports on three districts of Karnataka, where a survey of 78 farmers supplying fruits and vegetables to Reliance Fresh, a leading supermarket chain, reveals low levels of vertical co-ordination, a lack of written contracts, and highly competitive environments, with the quality parameters used by supermarkets specifying only a limited set of conditions. These findings suggest that supermarket-led restructuring in India has not yet reached a stable institutional situation. [source] Phylogeny of the teashirt-related zinc finger (tshz) gene family and analysis of the developmental expression of tshz2 and tshz3b in the zebrafishDEVELOPMENTAL DYNAMICS, Issue 3 2010Joana S. Santos Abstract The tshz genes comprise a family of evolutionarily conserved transcription factors. However, despite the major role played by Drosophila tsh during the development of the fruit fly, the expression and function of other tshz genes have been analyzed in a very limited set of organisms and, therefore, our current knowledge of these genes is still fragmentary. In this study, we perform detailed phylogenetic analyses of the tshz genes, identify the members of this gene family in zebrafish and describe the developmental expressions of two of them, tshz2 and tshz3b, and compare them with meis1, meis2.1, meis2.2, pax6a, and pax6b expression patterns. The expression patterns of these genes define a complex set of coexpression domains in the developing zebrafish brain where their gene products have the potential to interact. Developmental Dynamics 239:1010,1018, 2010. © 2010 Wiley-Liss, Inc. [source] Identification of Lmo1 as part of a Hox-dependent regulatory network for hindbrain patterningDEVELOPMENTAL DYNAMICS, Issue 9 2007Christelle Matis Abstract The embryonic functions of Hox proteins have been extensively investigated in several animal phyla. These transcription factors act as selectors of developmental programmes, to govern the morphogenesis of multiple structures and organs. However, despite the variety of morphogenetic processes Hox proteins are involved in, only a limited set of their target genes has been identified so far. To find additional targets, we used a strategy based upon the simultaneous overexpression of Hoxa2 and its cofactors Pbx1 and Prep in a cellular model. Among genes whose expression was upregulated, we identified LMO1, which codes for an intertwining LIM-only factor involved in protein,DNA oligomeric complexes. By analysing its expression in Hox knockout mice, we show that Lmo1 is differentially regulated by Hoxa2 and Hoxb2, in specific columns of hindbrain neuronal progenitors. These results suggest that Lmo1 takes part in a Hox paralogue 2,dependent network regulating anteroposterior and dorsoventral hindbrain patterning. Developmental Dynamics 236:2675,2684, 2007. © 2007 Wiley-Liss, Inc. [source] Connecting patient needs with treatment managementACTA PSYCHIATRICA SCANDINAVICA, Issue 2009R. Kerwin Objective:, To propose ideas for the development of a core strategy for monitoring patients with schizophrenia to ensure physical health and optimal treatment provision. Method:, A panel of European experts in the field of schizophrenia met in Bordeaux in June 2006 to discuss, ,Patient management optimisation through improved treatment monitoring.' Results:, Key consensus from the discussion deemed that weight gain, oral health and ECG parameters were core baseline parameters to be monitored in all patients with schizophrenia. Further, an identification of a patient's own barriers to treatment alongside local health service strategies might comprise elements of an individualised management strategy which would contribute to optimisation of treatment. Any monitoring strategy should be kept simple to encourage physician compliance. Conclusion:, A practical solution to the difficulties of providing holistic patient care would be to suggest a limited set of physical parameters to be monitored by physicians on a regular basis. [source] To what extent can management variables explain species assemblages?ECOGRAPHY, Issue 6 2004A study of carabid beetles in forests Studies concerning the influence of forest management on invertebrate communities often focus on a limited set of chosen variables and rarely quantify the importance of management as opposed to other influences. We aimed at: 1) comparing the importance for species assemblages of habitat variables defined by management with those independent of it; 2) understanding the ecological significance of the variation remaining when both management and non-management variables are used. We caught carabid beetles according to a stratified pitfall sampling based on forest structure, tree composition and stand age. Forty-nine habitat variables were measured using three spatial scales. We decomposed the variation of species assemblages with successive constrained ordinations based on sets of variables, and studied the life traits of the species least and best explained by the model including all of the variables. Forest structure, composition and stand age showed important effects but explained a relatively small part of the overall variation in species assemblages. Management accounted for ca 30% of the variation, but non-management variables had a significant impact and the interaction between management and non-management sets resulted in significant influences. Most species for which the variation was highly explained by the model were generally large and with inefficient wings, while the least explained species were small. Our study suggests that: 1) even with highly controlled samples, the influence of management on species assemblages should not be studied by a limited set of categorical variables; 2) management variables may interact with factors outside of the manager's control; 3) a significant part of the variation cannot be explained by habitat variables and needs taking ecological processes into account; 4) rules to optimise constrained ordination techniques applied to species-habitat studies can be proposed. [source] A general framework for neutral models of community dynamicsECOLOGY LETTERS, Issue 12 2009Omri Allouche Abstract Neutral models of community dynamics are a powerful tool for ecological research, but their applications are currently limited to unrealistically simple types of dynamics and ignore much of the complexity that characterize natural ecosystems. Here, we present a new analytical framework for neutral models that unifies existing models of neutral communities and extends the applicability of existing models to a much wider spectrum of ecological phenomena. The new framework extends the concept of neutrality to fitness equivalence and in spite of its simplicity explains a wide spectrum of empirical patterns of species diversity including positive, negative and unimodal productivity,diversity relationships; gradual and highly delayed declines in species diversity with habitat loss; and positive and negative responses of species diversity to habitat heterogeneity. Surprisingly, the abundance distribution in all of these cases is given by the dispersal limited multinomial (DLM), the abundance distribution in Hubbell's zero-sum model, showing DLM's robustness and demonstrating that it cannot be used to infer the underlying community dynamics. These results support the hypothesis that ecological communities are regulated by a limited set of fundamental mechanisms much simpler than could be expected from their immense complexity. Ecology Letters (2009) 12: 1287,1297 [source] Dilemmas of an Economic TheoristECONOMETRICA, Issue 4 2006Ariel Rubinstein What on earth are economic theorists like me trying to accomplish? This paper discusses four dilemmas encountered by an economic theorist: The dilemma of absurd conclusions: Should we abandon a model if it produces absurd conclusions or should we regard a model as a very limited set of assumptions that will inevitably fail in some contexts? The dilemma of responding to evidence: Should our models be judged according to experimental results? The dilemma of modelless regularities: Should models provide the hypothesis for testing or are they simply exercises in logic that have no use in identifying regularities? The dilemma of relevance: Do we have the right to offer advice or to make statements that are intended to influence the real world? [source] Geography and the Immigrant Division of LaborECONOMIC GEOGRAPHY, Issue 3 2007Mark Ellis Abstract: Immigrants concentrate in particular lines of work. Most investigations of such employment niching have accented either the demand for labor in a limited set of mostly low-wage industries or the efficiency of immigrant networks in supplying that labor; space has taken a backseat or has been ignored. In contrast, this article's account of immigrant employment niching modulates insights built on social network theories with understandings derived from relative location. We do so by altering the thinking about employment niches as being metropolitan wide to considering them as local phenomena. Specifically, the analysis examines the intraurban variation in niching by Mexican, Salvadoran, Chinese, and Vietnamese men and women in four industries in Los Angeles. Niching is uneven; in some parts of the metropolitan area, these groups niche at high rates in these industries, whereas in others, there is no unusual concentration. We show how a group's propensity to niche in an industry is generally higher when the industry is located close to the group's residential neighborhoods and demonstrate the ways in which the proximity of competing groups dampens this geographic advantage. The study speaks to debates on immigrant niching and connects with research on minority access to employment and accounts of the agglomeration of firms. More generally, it links the geographies of home and work in a new way, relating patterns of immigrant residential segregation to those of immigrant employment niches. [source] Homeostatic sleep regulation is preserved in mPer1 and mPer2 mutant miceEUROPEAN JOURNAL OF NEUROSCIENCE, Issue 6 2002Caroline Kopp Abstract A limited set of genes, Clock, Bmal1, mPer1, mPer2, mCry1 and mCry2, has been shown to be essential for the generation of circadian rhythms in mammals. It has been recently suggested that circadian genes might be involved in sleep regulation. We investigated the role of mPer1 and mPer2 genes in the homeostatic regulation of sleep by comparing sleep of mice lacking mPER1 (mPer1 mutants) or a functional mPER2 (mPer2 mutants), and wild-type controls (WT) after 6 h of sleep deprivation (SD). Our main result showed that after SD, all mice displayed the typical increase of slow-wave activity (SWA; EEG power density between 0.75 and 4 Hz) in nonREM sleep, reflecting the homeostatic response to SD. This increase was more prominent over the frontal cortex as compared to the occipital cortex. The genotypes did not differ in the effect of SD on the occipital EEG, while the effect on the frontal EEG was initially diminished in both mPer mutants. Differences between the genotypes were seen in the 24-h distribution of sleep, reflecting especially the phase advance of motor activity onset observed in mPer2 mutants. While the daily distribution of sleep was modulated by mPer1 and mPer2 genes, sleep homeostasis reflected by the SWA increase after 6-h SD was preserved in the mPer mutants. The results provide further evidence for the independence of the circadian and the homeostatic components underlying sleep regulation. [source] Identification of the maximum acceptable frequencies of upper-extremity motions in the sagittal planeHUMAN FACTORS AND ERGONOMICS IN MANUFACTURING & SERVICE INDUSTRIES, Issue 3 2009Ochae Kwon The present study examined the maximum acceptable frequencies (MAFs; motions/min) of upper-extremity motions in the sagittal plane at different forces. A dumbbell of 9.8 or 39.2 N was rotated by the arm about the shoulder, the forearm about the elbow, and the hand about the wrist; a dynamometer was pressed to 2.45 or 9.8 N by the index finger. Seventeen right-handed Korean men in their 20s without any history of musculoskeletal disorders received 1 hour of individual training and conducted each upper-extremity task for 30 minutes a day, assuming they were on an incentive basis. The participants determined their MAFs for 8 hours of work by the self-adjustment method, and work pulse (change in heart rate; beats per minute [bpm]) and rating of perceived exertion (RPE) were measured. For a limited set of conditions, the reproducibility of the MAF experimental protocol was found satisfactory (r = 0.97; interclass correlation coefficient > 0.95). The average MAFs of arm, forearm, hand, and index finger motions were 24, 45, 56, and 128 at their low force level and 9, 20, 30, and 66 at their high force level. The average work pulses of arm, forearm, and hand motions were 3.0, 2.1, and 1.5 times that of index finger motion (4.2 bpm at their low force level and 5.7 bpm at their high force level). The maximum average RPEs at the upper-extremity regions ranged from 2.1 (weak) to 3.1 (moderate) in Borg's CR-10 scale. © 2009 Wiley Periodicals, Inc. [source] Kinetics of the gas-phase reaction of n -C6,C10 aldehydes with the nitrate radicalINTERNATIONAL JOURNAL OF CHEMICAL KINETICS, Issue 3 2003Jun Noda Rate coefficients for gas-phase reaction between nitrate radicals and the n -C6,C10 aldehydes have been determined by a relative rate technique. All experiments were carried out at 297 ± 2 K, 1020 ± 10 mbar and using synthetic air or nitrogen as the bath gas. The experiments were made with a collapsible sampling bag as reaction chamber, employing solid-phase micro extraction for sampling and gas chromatography/flame ionization detection for analysis of the reaction mixtures. One limited set of experiments was carried out using a glass reactor and long-path FTIR spectroscopy. The results show good agreement between the different techniques and conditions employed as well as with previous studies (where available). With butanal as reference compound, the determined values (in units of 10,14 cm3 molecule,1 s,1) for each of the aldehydes were as follows: hexanal, 1.7 ± 0.1; heptanal, 2.1 ± 0.3; octanal, 1.5 ± 0.2; nonanal, 1.8 ± 0.2; and decanal, 2.2 ± 0.4. With propene as reference compound, the determined rate coefficients were as follows: heptanal, 1.9 ± 0.2; octanal, 2.0 ± 0.3; and nonanal, 2.2 ± 0.3. With 1-butene as reference compound, the rate coefficients for hexanal and heptanal were 1.6 ± 0.2 and 1.8 ± 0.1, respectively. © 2002 Wiley Periodicals, Inc. Int J Chem Kinet 35: 120,129, 2003 [source] The SAXS/WAXS software system of the DUBBLE CRG beamline at the ESRFJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 4 2001E. Homan The small/wide-angle X-ray scattering (SAXS/WAXS) system on the DUBBLE CRG beamline at the ESRF is used for both static and time-resolved measurements. The integrated system developed for control and data reduction deals effectively with the high rates of incoming data from the different detector systems, as well as the presentation of results for the user. To ensure that the data may be used directly by a wide range of packages, they may be recorded in a number of output formats, thus serving as a practical test bed where developing standards may be compared and contrasted. The software system implements proposals raised at the canSAS meetings to promote a limited set of standard data formats for small-angle scattering studies. The system presented can cope with a volume of results in excess of 10,Gbytes of data per experiment and shows the advantages achieved by minimizing the dependence on raw-data formats. [source] In Silico Modeling and Simulation of Bone Biology: A ProposalJOURNAL OF BONE AND MINERAL RESEARCH, Issue 7 2005Nadine A Defranoux Abstract Contemporary, computer-based mathematical modeling techniques make it possible to represent complex biological mechanisms in a manner that permits hypothesis testing in silico. This perspective shows how such approaches might be applied to bone remodeling and therapeutic research. Currently, the dominant conceptual model applied in bone research involves the dynamic balance between the continual build-up and breakdown of bone matrix by two cell types, the osteoblasts and osteoclasts, acting together as a coordinated, remodeling unit. This conceptualization has served extraordinarily well as a focal point for understanding how mutations, chemical mediators, and mechanical force, as well as external influences (e.g., drugs, diet) affect bone structure and function. However, the need remains to better understand and predict the consequences of manipulating any single factor, or combination of factors, within the context of this complex system's multiple interacting pathways. Mathematical models are a natural extension of conceptual models, providing dynamic, quantitative descriptions of the relationships among interacting components. This formalization creates the ability to simulate the natural behavior of a system, as well as its modulation by therapeutic or dietetic interventions. A number of mathematical models have been developed to study complex bone functions, but most include only a limited set of biological components needed to address a few specific questions. However, it is possible to develop larger, multiscale models that capture the dynamic interactions of many biological components and relate them to important physiological or pathological outcomes that allow broader study. Examples of such models include Entelos' PhysioLab platforms. These models simulate the dynamic, quantitative interactions among a biological system's biochemicals, cells, tissues, and organs and how they give rise to key physiologic and pathophysiologic outcomes. We propose that a similar predictive, dynamical, multiscale mathematical model of bone remodeling and metabolism would provide a better understanding of the mechanisms governing these phenomena as well as serve as an in silico platform for testing pharmaceutical and clinical interventions on metabolic bone disease. [source] A new GROMOS force field for hexopyranose-based carbohydratesJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 13 2005Roberto D. Lins Abstract A new parameter set (referred to as 45A4) is developed for the explicit-solvent simulation of hexopyranose-based carbohydrates. This set is compatible with the most recent version of the GROMOS force field for proteins, nucleic acids, and lipids, and the SPC water model. The parametrization procedure relies on: (1) reassigning the atomic partial charges based on a fit to the quantum-mechanical electrostatic potential around a trisaccharide; (2) refining the torsional potential parameters associated with the rotations of the hydroxymethyl, hydroxyl, and anomeric alkoxy groups by fitting to corresponding quantum-mechanical profiles for hexopyranosides; (3) adapting the torsional potential parameters determining the ring conformation so as to stabilize the (experimentally predominant) 4C1 chair conformation. The other (van der Waals and nontorsional covalent) parameters and the rules for third and excluded neighbors are taken directly from the most recent version of the GROMOS force field (except for one additional exclusion). The new set is general enough to define parameters for any (unbranched) hexopyranose-based mono-, di-, oligo- or polysaccharide. In the present article, this force field is validated for a limited set of monosaccharides (,- and ,-D-glucose, ,- and ,-D-galactose) and disaccharides (trehalose, maltose, and cellobiose) in solution, by comparing the results of simulations to available experimental data. More extensive validation will be the scope of a forthcoming article. © 2005 Wiley Periodicals, Inc. J Comput Chem 26: 1400,1412, 2005 [source] The mismeasurement of sexual selectionJOURNAL OF EVOLUTIONARY BIOLOGY, Issue 3 2010H. KLUG Abstract Sexual selection can explain major micro- and macro-evolutionary patterns. Much of current theory predicts that the strength of sexual selection (i) is driven by the relative abundance of males and females prepared to mate (i.e. the operational sex ratio, OSR) and (ii) can be generally estimated by calculating intra-sexual variation in mating success (e.g. the opportunity for sexual selection, Is). Here, we demonstrate the problematic nature of these predictions. The OSR and Is only accurately predict sexual selection under a limited set of circumstances, and more specifically, only when mate monopolization is extremely strong. If mate monopolization is not strong, using OSR or Is as proxies or measures of sexual selection is expected to produce spurious results that lead to the false conclusion that sexual selection is strong when it is actually weak. These findings call into question the validity of empirical conclusions based on these measures of sexual selection. [source] "Short Fried-Rice-Eating Chinese MCs" and "Good-Hair-Havin Uncle Tom Niggas": Performing Race and Ethnicity in Freestyle Rap BattlesJOURNAL OF LINGUISTIC ANTHROPOLOGY, Issue 1 2010H. Samy Alim This article shows how emcees create local meanings of race and ethnicity in freestyle rap battles. We demonstrate how performers attach new social meanings to race and ethnicity in verbal duels, even as they also reproduce normative meanings around gender and sexuality. Further, we suggest that the construction of local, alternative meanings around race and ethnicity might actually help support dominant racial hierarchies by relegating "blackness" suitable for only a limited set of domains. Despite the enduring nature of these broader racial hierarchies, we conclude that performances are activities in which individuals contest and negotiate the social meanings of identities.,[performance, style, race/ethnicity, verbal duels, freestyle rap] [source] A two-phase analysis of solute partitioning into the stratum corneumJOURNAL OF PHARMACEUTICAL SCIENCES, Issue 3 2006Johannes M. Nitsche Abstract An analysis is presented of partition coefficients KSC/w describing solute distribution into fully hydrated stratum corneum (SC) from dilute aqueous solution (w). A comprehensive database is compiled from the experimental literature covering more than eight decades in the octanol/water partition coefficient Ko/w. It is analyzed according to a two-phase model following that of Anderson, Raykar, and coworkers (1988, 1989), which accounts for uptake by intercellular lipid and corneocyte (keratin plus water) phases having inherently different lipophilicities, as characterized by an SC lipid/water partition coefficient Klip/w and a partition coefficient PCpro/w quantifying cornoeocyte-phase binding. Regression of 72 data points yields useful best-fit recalibrations of power laws (or linear free energy relationships) giving Klip/w and PCpro/w as functions of Ko/w. The specific conclusions of the analysis are as follows: (i) The two-phase model offers substantial improvements over previously proposed analytical representations of KSC/w, yielding an rms error in log10KSC/w of 0.30 limited by the scatter in the data. (ii) The best-fit description of the lipid phase is given by the power law Klip/w,=,0.43 (Ko/w)0.81, suggesting about half the absolute value of Klip/w relative to previous estimates. (iii) The best-fit description of corneocyte-phase binding differs negligibly from the correlation found by Anderson, Raykar, and coworkers for the more limited set of compounds studied by them. Explicit consideration of the two-phase nature of the SC also furnishes a rational basis for predicting the effects of varying hydration state upon KSC/w. © 2006 Wiley-Liss, Inc. and the American Pharmacists Association J Pharm Sci 95:649,666, 2006 [source] 15 Phylogeny of the chlorophyta: inferences from 18S and 26S rDNAJOURNAL OF PHYCOLOGY, Issue 2003M. A. Buchheim Recent studies of the Chlorophyceae using 18S and 26S rDNA data in meta-analysis have demonstrated the power of combining these two sets of rDNA data. Furthermore, the 26S rDNA data complement the more conserved 18S gene for many chlorophycean lineages. Consequently, this data approach was pursued in an expanded taxon-sampling scheme for the Chlorophyta, with special reference to the classes Chlorophyceae and Trebouxiophyceae. Results of these new phylogenetic analyses identify Microspora sp. (UTEX LB 472) and Radiofilum transversale (UTEX LB 1252) as sister taxa which, in turn, form a basal clade in the Cylindrocapsa alliance (Treubaria, Trochiscia, Elakatothrix). The relative position of the "Cylindrocapsa" clade within the Chlorophyceae remains uncertain. The enhanced taxon-sampling has not resolved the relative positions of the Oedogoniales, Chaetophorales or Chaetopeltidales. Furthermore, the Sphaeropleaceae are supported as members of the Sphaeropleales in only some analyses, raising concerns about the status of the order. Although based on a limited set of taxa (currently <10), a combined data approach reveals support for a monophyletic Trebouxiophyceae that includes the distinctive organisms, Geminella and Eremosphaera. The goal of a well-resolved phylogeny for the Chlorophyta remains just that, a goal. Achieving that goal obviously will require additional taxon sampling in the Prasinophyceae and Ulvophyceae, as well as, the Trebouxiophyceae. Moreover, it is clear that other genes (e.g., cp-atpB, cp-rbcL, cp-16S, mt-nad5) will be needed to help address problems of resolution based on the rDNA data alone. Supported by NSF DEB 9726588 and DEB 0129030. [source] Phylogeography of ninespine sticklebacks (Pungitius pungitius) in North America: glacial refugia and the origins of adaptive traitsMOLECULAR ECOLOGY, Issue 18 2010JACLYN T. ALDENHOVEN Abstract The current geographical distribution of the ninespine stickleback (Pungitius pungitius) was shaped in large part by the glaciation events of the Pleistocene epoch (2.6 Mya,10 Kya). Previous efforts to elucidate the phylogeographical history of the ninespine stickleback in North America have focused on a limited set of morphological traits, some of which are likely subject to widespread convergent evolution, thereby potentially obscuring relationships among populations. In this study, we used genetic information from both mitochondrial DNA (mtDNA) sequences and nuclear microsatellite markers to determine the phylogenetic relationships among ninespine stickleback populations. We found that ninespine sticklebacks in North America probably dispersed from at least three glacial refugia,the Mississippi, Bering, and Atlantic refugia,not two as previously thought. However, by applying a molecular clock to our mtDNA data, we found that these three groups diverged long before the most recent glacial period. Our new phylogeny serves as a critical framework for examining the evolution of derived traits in this species, including adaptive phenotypes that evolved multiple times in different lineages. In particular, we inferred that loss of the pelvic (hind fin) skeleton probably evolved independently in populations descended from each of the three putative North American refugia. [source] Time-resolved structural studies of protein reaction dynamics: a smorgasbord of X-ray approachesACTA CRYSTALLOGRAPHICA SECTION A, Issue 2 2010Sebastian Westenhoff Proteins undergo conformational changes during their biological function. As such, a high-resolution structure of a protein's resting conformation provides a starting point for elucidating its reaction mechanism, but provides no direct information concerning the protein's conformational dynamics. Several X-ray methods have been developed to elucidate those conformational changes that occur during a protein's reaction, including time-resolved Laue diffraction and intermediate trapping studies on three-dimensional protein crystals, and time-resolved wide-angle X-ray scattering and X-ray absorption studies on proteins in the solution phase. This review emphasizes the scope and limitations of these complementary experimental approaches when seeking to understand protein conformational dynamics. These methods are illustrated using a limited set of examples including myoglobin and haemoglobin in complex with carbon monoxide, the simple light-driven proton pump bacteriorhodopsin, and the superoxide scavenger superoxide reductase. In conclusion, likely future developments of these methods at synchrotron X-ray sources and the potential impact of emerging X-ray free-electron laser facilities are speculated upon. [source] Multi-scale phenotyping of leaf expansion in response to environmental changes: the whole is more than the sum of partsPLANT CELL & ENVIRONMENT, Issue 9 2009CHRISTINE GRANIER ABSTRACT The leaf is a multi-scale dynamic unit that is determined by mechanisms at different organizational scales (cell, tissue, whole leaf and whole plant) and affected by both internal (genotype) and external (environmental) determinisms. The recent development of phenotyping platforms and imaging techniques provides new insights into the temporal and spatial patterns of leaf growth as affected by those determinisms. Conclusions about the overriding mechanisms often depend on the considered organizational scale and of time resolution which varies from minutes to several weeks. Analyses of leaf growth responses to environmental conditions have revealed robust emerging properties at whole plant or whole leaf scales. They have highlighted that the control of individual leaf expansion is more complex than merely the sum of cellular processes, and the control at the whole plant level is more complex than the sum of individual leaf expansions. However, in many cases, the integrated leaf-growth variable can be simplified to a limited set of underlying variables to be measured for comparative analyses of leaf growth or modelling purposes. [source] CLUMSY SOLUTIONS FOR A COMPLEX WORLD: THE CASE OF CLIMATE CHANGEPUBLIC ADMINISTRATION, Issue 4 2006MARCO VERWEIJ Successful solutions to pressing social ills tend to consist of innovative combinations of a limited set of alternative ways of perceiving and resolving the issues. These contending policy perspectives justify, represent and stem from four different ways of organizing social relations: hierarchy, individualism, egalitarianism and fatalism. Each of these perspectives: (1) distils certain elements of experience and wisdom that are missed by the others; (2) provides a clear expression of the way in which a significant portion of the populace feels we should live with one another and with nature; and (3) needs all of the others in order to be sustainable. ,Clumsy solutions', policies that creatively combine all opposing perspectives on what the problems are and how they should be resolved , are therefore called for. We illustrate these claims for the issue of global warming. [source] Top-down proteomics with a quadrupole time-of-flight mass spectrometer and collision-induced dissociationRAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 5 2009Andrea Armirotti With slight modifications of the instrumental parameters, we demonstrate that satisfactory top-down data can be obtained with collision-induced dissociation (CID) tandem mass spectrometry on a quadrupole time-of-flight (qTOF) instrument not originally designed for this purpose. Protein identification is achieved with both N- and C-terminal sequence tags and BLAST database searches. The accurate mass measurement of multiply charged fragment ions (mostly y and b-type) supplements the limited set of cleavage sites and provides a high degree of sequence coverage (90,100%). Post-translational modification issues can be addressed too. This approach might help those mass spectrometry (MS) core facilities that are not able to afford very high-resolution instruments, thus expanding the benefits of top-down protein analysis over the worldwide MS community. Copyright © 2009 John Wiley & Sons, Ltd. [source] Can 4D-Var use dynamical information from targeted observations of a baroclinic structure?THE QUARTERLY JOURNAL OF THE ROYAL METEOROLOGICAL SOCIETY, Issue 651 2010E. A. Irvine Abstract Targeted observations are generally taken in regions of high baroclinicity, but often show little impact. One plausible explanation is that important dynamical information, such as upshear tilt, is not extracted from the targeted observations by the data assimilation scheme and used to correct initial condition error. This is investigated by generating pseudo targeted observations which contain a singular vector (SV) structure that is not present in the background field or routine observations, i.e. assuming that the background has an initial condition error with tilted growing structure. Experiments were performed for a single case-study with varying numbers of pseudo targeted observations. These were assimilated by the Met Office four-dimensional variational (4D-Var) data assimilation scheme, which uses a 6 h window for observations and background-error covariances calculated using the National Meteorological Centre (NMC) method. The forecasts were run using the operational Met Office Unified Model on a 24 km grid. The results presented clearly demonstrate that a 6 h window 4D-Var system is capable of extracting baroclinic information from a limited set of observations and using it to correct initial condition error. To capture the SV structure well (projection of 0.72 in total energy), 50 sondes over an area of 1×106 km2 were required. When the SV was represented by only eight sondes along an example targeting flight track covering a smaller area, the projection onto the SV structure was lower; the resulting forecast perturbations showed an SV structure with increased tilt and reduced initial energy. The total energy contained in the perturbations decreased as the SV structure was less well described by the set of observations (i.e. as fewer pseudo observations were assimilated). The assimilated perturbation had lower energy than the SV unless the pseudo observations were assimilated with the dropsonde observation errors halved from operational values. Copyright © 2010 Royal Meteorological Society [source] Controlling International Joint Ventures: An Investigation of Australian Parent PartnersAUSTRALIAN ACCOUNTING REVIEW, Issue 2 2009Francesco Giacobbe International joint ventures (IJVs) are an important modern organisational form, with their complexity presenting significant management and control issues. Our research uses a cross-sectional survey of Australian parent partners of IJVs to provide insights into the characteristics of Australian companies and their IJVs, performance outcomes and choices of parent partners management control systems (MCS) design in terms of operational areas they seek to control (focus), the extent to which they exercise control (extent) and the mechanisms of control used (formal and informal). Australian parent partners of IJVs generally are, partnering in countries close to Australia in the Asia-Pacific, in activities similar to those they undertake in Australia, contributing a significant amount of resources, but overall have only limited IJV experience. Australian parent partners focus on a limited set of controls, often with tighter formalised control structures. Finally, overall they are satisfied with the performance of their IJVs, with higher satisfaction for organisational learning and product/customer dimensions than financial performance. [source] Ab Initio Group Contribution Method for Activation Energies of Hydrogen Abstraction ReactionsCHEMPHYSCHEM, Issue 1 2006Mark Saeys Prof. Abstract The group contribution method for activation energies is applied to hydrogen abstraction reactions. To this end an ab initio database was constructed, which consisted of activation energies calculated with the ab initio CBS-QB3 method for a limited set of well-chosen homologous reactions. CBS-QB3 is shown to predict reaction rate coefficients within a factor of 2,4 and Arrhenius activation energies within 3,5 kJ,mol,1of experimental data. Activation energies in the set of homologous reactions vary over 156 kJ,mol,1with the structure of the abstracting radical and over 94 kJ,mol,1with the structure of the abstracted hydrocarbon. The parameters required for the group contribution method, the so-called standard activation group additivity values, were determined from this database. To test the accuracy of the group contribution method, a large set of 88 additional activation energies were calculated from first principles and compared with the predictions from the group contribution method. It was found that the group contribution method yields accurate activation energies for hydrogen-transfer reactions between hydrogen molecules, alkylic hydrocarbons, and vinylic hydrocarbons, with the largest deviations being less than 6 kJ,mol,1. For reactions between allylic and propargylic hydrocarbons, the transition state is believed to be stabilized by resonance effects, thus requiring the introduction of an appropriate correction term to obtain a reliable prediction of the activation energy for this subclass of hydrogen abstraction reactions. [source] Life, information, entropy, and time: Vehicles for semantic inheritanceCOMPLEXITY, Issue 1 2007Antony R. Crofts Abstract Attempts to understand how information content can be included in an accounting of the energy flux of the biosphere have led to the conclusion that, in information transmission, one component, the semantic content, or "the meaning of the message," adds no thermodynamic burden over and above costs arising from coding, transmission and translation. In biology, semantic content has two major roles. For all life forms, the message of the genotype encoded in DNA specifies the phenotype, and hence the organism that is tested against the real world through the mechanisms of Darwinian evolution. For human beings, communication through language and similar abstractions provides an additional supra-phenotypic vehicle for semantic inheritance, which supports the cultural heritages around which civilizations revolve. The following three postulates provide the basis for discussion of a number of themes that demonstrate some important consequences. (i) Information transmission through either pathway has thermodynamic components associated with data storage and transmission. (ii) The semantic content adds no additional thermodynamic cost. (iii) For all semantic exchange, meaning is accessible only through translation and interpretation, and has a value only in context. (1) For both pathways of semantic inheritance, translational and copying machineries are imperfect. As a consequence both pathways are subject to mutation and to evolutionary pressure by selection. Recognition of semantic content as a common component allows an understanding of the relationship between genes and memes, and a reformulation of Universal Darwinism. (2) The emergent properties of life are dependent on a processing of semantic content. The translational steps allow amplification in complexity through combinatorial possibilities in space and time. Amplification depends on the increased potential for complexity opened by 3D interaction specificity of proteins, and on the selection of useful variants by evolution. The initial interpretational steps include protein synthesis, molecular recognition, and catalytic potential that facilitate structural and functional roles. Combinatorial possibilities are extended through interactions of increasing complexity in the temporal dimension. (3) All living things show a behavior that indicates awareness of time, or chronognosis. The ,4 billion years of biological evolution have given rise to forms with increasing sophistication in sensory adaptation. This has been linked to the development of an increasing chronognostic range, and an associated increase in combinatorial complexity. (4) Development of a modern human phenotype and the ability to communicate through language, led to the development of archival storage, and invention of the basic skills, institutions and mechanisms that allowed the evolution of modern civilizations. Combinatorial amplification at the supra-phenotypical level arose from the invention of syntax, grammar, numbers, and the subsequent developments of abstraction in writing, algorithms, etc. The translational machineries of the human mind, the "mutation" of ideas therein, and the "conversations" of our social intercourse, have allowed a limited set of symbolic descriptors to evolve into an exponentially expanding semantic heritage. (5) The three postulates above open interesting epistemological questions. An understanding of topics such dualism, the élan vital, the status of hypothesis in science, memetics, the nature of consciousness, the role of semantic processing in the survival of societies, and Popper's three worlds, require recognition of an insubstantial component. By recognizing a necessary linkage between semantic content and a physical machinery, we can bring these perennial problems into the framework of a realistic philosophy. It is suggested, following Popper, that the ,4 billion years of evolution of the biosphere represents an exploration of the nature of reality at the physicochemical level, which, together with the conscious extension of this exploration through science and culture, provides a firm epistemological underpinning for such a philosophy. © 2007 Wiley Periodicals, Inc. Complexity, 2007 [source] | ||||||||||||||||||||||||||||||||||