Living to die and dying to live: the survival strategy behind leaf senescence

Senescence represents the final developmental act of the leaf, during which the leaf cell is dismantled in a coordinated manner to remobilize nutrients and to secure reproductive success. The process of senescence provides the plant with phenotypic plasticity to help it adapt to adverse environmental conditions. Here, we provide a comprehensive overview of the factors and mechanisms that control the onset of senescence. We explain how the competence to senesce is established during leaf development, as depicted by the senescence window model. We also discuss the mechanisms by which phytohormones and environmental stresses control senescence, as well as the impact of source-sink relationships on plant yield and stress tolerance. In addition, we discuss the role of senescence as a strategy for stress adaptation and how crop production and food quality could benefit from engineering or breeding crops with altered onset of senescence.

Theoretical insight into diagnosing observation error correlations using observation-minus-background and observation-minus-analysis statistics

To improve the quantity and impact of observations used in data assimilation it is necessary to take into account the full, potentially correlated, observation error statistics. A number of methods for estimating correlated observation errors exist, but a popular method is a diagnostic that makes use of statistical averages of observation-minus-background and observation-minus-analysis residuals. The accuracy of the results it yields is unknown as the diagnostic is sensitive to the difference between the exact background and exact observation error covariances and those that are chosen for use within the assimilation. It has often been stated in the literature that the results using this diagnostic are only valid when the background and observation error correlation length scales are well separated. Here we develop new theory relating to the diagnostic. For observations on a 1D periodic domain we are able to the show the effect of changes in the assumed error statistics used in the assimilation on the estimated observation error covariance matrix. We also provide bounds for the estimated observation error variance and eigenvalues of the estimated observation error correlation matrix. We demonstrate that it is still possible to obtain useful results from the diagnostic when the background and observation error length scales are similar. In general, our results suggest that when correlated observation errors are treated as uncorrelated in the assimilation, the diagnostic will underestimate the correlation length scale. We support our theoretical results with simple illustrative examples. These results have potential use for interpreting the derived covariances estimated using an operational system.

Diagnosing observation error correlations for Doppler radar radial winds in the Met Office UKV model using observation-minus-background and observation-minus-analysis statistics

With the development of convection-permitting numerical weather prediction the efficient use of high resolution observations in data assimilation is becoming increasingly important. The operational assimilation of these observations, such as Dopplerradar radial winds, is now common, though to avoid violating the assumption of un- correlated observation errors the observation density is severely reduced. To improve the quantity of observations used and the impact that they have on the forecast will require the introduction of the full, potentially correlated, error statistics. In this work, observation error statistics are calculated for the Doppler radar radial winds that are assimilated into the Met Office high resolution UK model using a diagnostic that makes use of statistical averages of observation-minus-background and observation-minus-analysis residuals. This is the first in-depth study using the diagnostic to estimate both horizontal and along-beam correlated observation errors. By considering the new results obtained it is found that the Doppler radar radial wind error standard deviations are similar to those used operationally and increase as the observation height increases. Surprisingly the estimated observation error correlation length scales are longer than the operational thinning distance. They are dependent on both the height of the observation and on the distance of the observation away from the radar. Further tests show that the long correlations cannot be attributed to the use of superobservations or the background error covariance matrix used in the assimilation. The large horizontal correlation length scales are, however, in part, a result of using a simplified observation operator.

Direct observation by time-resolved infrared spectroscopy of the bright and the dark excited states of the [Ru(phen)2(dppz)]2+ light-switch compound in solution and when bound to DNA

The [Ru(phen)2(dppz)]2+ complex (1) is non-emissive in water but is highly luminescent in organic solvents or when bound to DNA, making it a useful probe for DNA binding. To date, a complete mechanistic explanation for this “light-switch” effect is still lacking. With this in mind we have undertaken an ultrafast time resolved infrared (TRIR) study of 1 and directly observe marker bands between 1280–1450 cm-1, which characterise both the emissive “bright” and the non-emissive “dark” excited states of the complex, in CD3CN and D2O respectively. These characteristic spectral features are present in the [Ru(dppz)3]2+ solvent light-switch complex but absent in [Ru(phen)3]2+, which is luminescent in both solvents. DFT calculations show that the vibrational modes responsible for these characteristic bands are predominantly localised on the dppz ligand. Moreover, they reveal that certain vibrational modes of the “dark” excited state couple with vibrational modes of two coordinating water molecules, and through these to the bulk solvent, thus providing a new insight into the mechanism of the light-switch effect. We also demonstrate that the marker bands for the “bright” state are observed for both L- and D enantiomers of 1 when bound to DNA and that photo-excitation of the complex induces perturbation of the guanine and cytosine carbonyl bands. This perturbation is shown to be stronger for the L enantiomer, demonstrating the different binding site properties of the two enantiomers and the ability of this technique to determine the identity and nature of the binding site of such intercalators.

Selecting algorithms for Earth observation of climate within the European Space Agency Climate Change initiative: introduction to a special issue

This special issue is focused on the assessment of algorithms for the observation of Earth’s climate from environ- mental satellites. Climate data records derived by remote sensing are increasingly a key source of insight into the workings of and changes in Earth’s climate system. Producers of data sets must devote considerable effort and expertise to maximise the true climate signals in their products and minimise effects of data processing choices and changing sensors. A key choice is the selection of algorithm(s) for classification and/or retrieval of the climate variable. Within the European Space Agency Climate Change Initiative, science teams undertook systematic assessment of algorithms for a range of essential climate variables. The papers in the special issue report some of these exercises (for ocean colour, aerosol, ozone, greenhouse gases, clouds, soil moisture, sea surface temper- ature and glaciers). The contributions show that assessment exercises must be designed with care, considering issues such as the relative importance of different aspects of data quality (accuracy, precision, stability, sensitivity, coverage, etc.), the availability and degree of independence of validation data and the limitations of validation in characterising some important aspects of data (such as long-term stability or spatial coherence). As well as re- quiring a significant investment of expertise and effort, systematic comparisons are found to be highly valuable. They reveal the relative strengths and weaknesses of different algorithmic approaches under different observa- tional contexts, and help ensure that scientific conclusions drawn from climate data records are not influenced by observational artifacts, but are robust.

Evaluating and optimizing oral formulations of live bacterial vaccines using a gastro-small intestine model

Gastrointestinal (GI) models that mimic physiological conditions in vitro are important tools for developing and optimizing biopharmaceutical formulations. Oral administration of live attenuated bacterial vaccines (LBV) can safely and effectively promote mucosal immunity but new formulations are required that provide controlled release of optimal numbers of viable bacterial cells, which must survive gastrointestinal transit overcoming various antimicrobial barriers. Here, we use a gastro-small intestine gut model of human GI conditions to study the survival and release kinetics of two oral LBV formulations: the licensed typhoid fever vaccine Vivotif comprising enteric coated capsules; and an experimental formulation of the model vaccine Salmonella Typhimurium SL3261 dried directly onto cast enteric polymer films and laminated to form a polymer film laminate (PFL). Neither formulation released significant numbers of viable cells when tested in the complete gastro-small intestine model. The poor performance in delivering viable cells could be attributed to a combination of acid and bile toxicity plus incomplete release of cells for Vivotif capsules, and to bile toxicity alone for PFL. To achieve effective protection from intestinal bile in addition to effective acid resistance, bile adsorbent resins were incorporated into the PFL to produce a new formulation, termed BR-PFL. Efficient and complete release of 4.4x107 live cells per dose was achieved from BR-PFL at distal intestinal pH, with release kinetics controlled by the composition of the enteric polymer film, and no loss in viability observed in any stage of the GI model. Use of this in vitro GI model thereby allowed rational design of an oral LBV formulation to maximize viable cell release.

Could in-home sensors surpass human observation of people with Parkinson’s at high risk of falling? An ethnographic study

Self-report underpins our understanding of falls among people with Parkinson’s (PwP) as they largely happen unwitnessed at home. In this qualitative study, we used an ethnographic approach to investigate which in-home sensors, in which locations, could gather useful data about fall risk. Over six weeks, we observed five independently mobile PwP at high risk of falling, at home. We made field notes about falls (prior events and concerns) and recorded movement with video, Kinect, and wearable sensors. The three women and two men (aged 71 to 79 years) having moderate or severe Parkinson’s were dependent on others and highly sedentary. We most commonly noted balance protection, loss, and restoration during chair transfers, walks across open spaces and through gaps, turns, steps up and down, and tasks in standing (all evident walking between chair and stairs, e.g.). Our unobtrusive sensors were acceptable to participants: they could detect instability during everyday activity at home and potentially guide intervention. Monitoring the route between chair and stairs is likely to give information without invading the privacy of people at high risk of falling, with very limited mobility, who spend most of the day in their sitting rooms.

Regional representativity of AERONET observation sites during the biomass burning season in South America determined by correlation studies with MODIS Aerosol Optical Depth

This paper presents an analysis of ground-based Aerosol Optical Depth (AOD) observations by the Aerosol Robotic Network (AERONET) in South America from 2001 to 2007 in comparison with the satellite AOD product of Moderate Resolution Imaging Spectroradiometer (MODIS), aboard TERRA and AQUA satellites. Data of 12 observation sites were used with primary interest in AERONET sites located in or downwind of areas with high biomass burning activity and with measurements available for the full time range. Fires cause the predominant carbonaceous aerosol emission signal during the dry season in South America and are therefore a special focus of this study. Interannual and seasonal behavior of the observed AOD at different sites were investigated, showing clear differences between purely fire and urban influenced sites. An intercomparison of AERONET and MODIS AOD annual correlations revealed that neither an interannual long-term trend may be observed nor that correlations differ significantly owing to different overpass times of TERRA and AQUA. Individual anisotropic representativity areas for each AERONET site were derived by correlating daily AOD of each site for all years with available individual MODIS AOD pixels gridded to 1 degrees x 1 degrees. Results showed that for many sites a good AOD correlation (R(2) > 0.5) persists for large, often strongly anisotropic, areas. The climatological areas of common regional aerosol regimes often extend over several hundreds of kilometers, sometimes far across national boundaries. As a practical application, these strongly inhomogeneous and anisotropic areas of influence are being implemented in the tropospheric aerosol data assimilation system of the Coupled Chemistry-Aerosol-Tracer Transport Model coupled to the Brazilian Regional Atmospheric Modeling System (CCATT-BRAMS) at the Brazilian National Institute for Space Research (INPE). This new information promises an improved exploitation of local site sampling and, thus, chemical weather forecast.

Acquisition of Pavlovian Fear Conditioning Using beta-Adrenoceptor Activation of the Dorsal Premammillary Nucleus as an Unconditioned Stimulus to Mimic Live Predator-Threat Exposure

In the present work, we sought to mimic the internal state changes in response to a predator threat by pharmacologically stimulating the brain circuit involved in mediating predator fear responses, and explored whether this stimulation would be a valuable unconditioned stimulus (US) in an olfactory fear conditioning paradigm (OFC). The dorsal premammillary nucleus (PMd) is a key brain structure in the neural processing of anti-predatory defensive behavior and has also been shown to mediate the acquisition and expression of anti-predatory contextual conditioning fear responses. Rats were conditioned by pairing the US, which was an intra-PMd microinjection of isoproterenol (ISO; beta-adrenoceptor agonist), with amyl acetate odor-the conditioned stimulus (CS). ISO (10 and 40 nmol) induced the acquisition of the OFC and the second-order association by activation of beta-1 receptors in the PMd. Furthermore, similar to what had been found for contextual conditioning to a predator threat, atenolol (beta-1 receptor antagonist) in the PMd also impaired the acquisition and expression of OFC promoted by ISO. Considering the strong glutamatergic projections from the PMd to the dorsal periaqueductal gray (dPAG), we tested how the glutamatergic blockade of the dPAG would interfere with the OFC induced by ISO. Accordingly, microinjections of NMDA receptor antagonist (AP5, 6 nmol) into the dPAG were able to block both the acquisition, and partially, the expression of the OFC. In conclusion, we have found that PMd beta-1 adrenergic stimulation is a good model to mimic predatory threat-induced internal state changes, and works as a US able to mobilize the same systems involved in the acquisition and expression of predator-related contextual conditioning. Neuropsychopharmacology (2011) 36, 926-939; doi:10.1038/npp.2010.231; published online 5 January 2011

AMYGDALAR ROLES DURING EXPOSURE TO A LIVE PREDATOR AND TO A PREDATOR-ASSOCIATED CONTEXT

The amygdala plays a critical role in determining the emotional significance of sensory stimuli and the production of fear-related responses. Large amygdalar lesions have been shown to practically abolish innate defensiveness to a predator; however, it is not clear how the different amygdalar systems participate in the defensive response to a live predator. Our first aim was to provide a comprehensive analysis of the amygdalar activation pattern during exposure to a live cat and to a predator-associated context. Accordingly, exposure to a live predator up-regulated Fos expression in the medial amygdalar nucleus (MEA) and in the lateral and posterior basomedial nuclei, the former responding to predator-related pheromonal information and the latter two nuclei likely to integrate a wider array of predatory sensory information, ranging from olfactory to non-olfactory ones, such as visual and auditory sensory inputs. Next, we tested how the amygdalar nuclei most responsive to predator exposure (i.e. the medial, posterior basomedial and lateral amygdalar nuclei) and the central amygdalar nucleus (CEA) influence both unconditioned and contextual conditioned anti-predatory defensive behavior. Medial amygdalar nucleus lesions practically abolished defensive responses during cat exposure, whereas lesions of the posterior basomedial or lateral amygdalar nuclei reduced freezing and increased risk assessment displays (i.e. crouch sniff and stretch postures), a pattern of responses compatible with decreased defensiveness to predator stimuli. Moreover, the present findings suggest a role for the posterior basomedial and lateral amygdalar nuclei in the conditioning responses to a predator-related context. We have further shown that the CEA does not seem to be involved in either unconditioned or contextual conditioned anti-predatory responses. Overall, the present results help to clarify the amygdalar systems involved in processing predator-related sensory stimuli and how they influence the expression of unconditioned and contextual conditioned anti-predatory responses. (C) 2011 IBRO. Published by Elsevier Ltd. All rights reserved.

CD8(+) T cell adjuvant effects of Salmonella FliCd flagellin in live vaccine vectors or as purified protein

Salmonella flagellin, the flagellum structural subunit, has received particular interest as a vaccine adjuvant conferring enhanced immunogenity to soluble proteins or peptides, both for activation of antibody and cellular immune responses. In the present study, we evaluated the Salmonella enterica FliCd flagellin as a T cell vaccine adjuvant using as model the 9-mer (SYVPSAEQI) synthetic H2(d)-restricted CD8(+) T cell-specific epitope (CS(280-288)) derived from the Plasmodium yoelii circumsporozoite (G) protein. The FliCd adjuvant effects were determined under two different conditions: (i) as recombinant flagella, expressed by orally delivered live S. Dublin vaccine strains expressing the target CS(280-288) peptide fused at the central hypervariable domain, and (ii) as purified protein in acellular vaccines in which flagellin was administered to mice either as a recombinant protein fused or admixed with the target CS(280-288) peptide. The results showed that CS(280-288)-specific cytotoxic CD8(+) T cells were primed when BALB/c mice were orally inoculated with the expressing the CS280-288 epitope S. Dublin vaccine strain. In contrast, mice immunized with purified FliCd admixed with the CS280-288 peptide and, to a lesser extent, fused with the target peptide developed specific cytotoxic CD8(+) T cell responses without the need of a heterologous booster immunization. The CD8(+) T cell adjuvant effects of flagellin, either fused or not with the target peptide, correlated with the in vivo activation of CD11c(+) dendritic cells. Taken together, the present results demonstrate that Salmonella flagellins are flexible adjuvant and induce adaptative immune responses when administered by different routes or vaccine formulations. (C) 2009 Elsevier Ltd. All rights reserved.

On modeling and evaluating multicomputer transcoding architectures for live-video streams

The pervasive and ubiquitous computing has motivated researches on multimedia adaptation which aims at matching the video quality to the user needs and device restrictions. This technique has a high computational cost which needs to be studied and estimated when designing architectures and applications. This paper presents an analytical model to quantify these video transcoding costs in a hardware independent way. The model was used to analyze the impact of transcoding delays in end-to-end live-video transmissions over LANs, MANs and WANs. Experiments confirm that the proposed model helps to define the best transcoding architecture for different scenarios.

Automatically linking live experiences captured with a ubiquitous infrastructure

Ubiquitous computing aims at providing services to users in everyday environments such as the home. One research theme in this area is that of building capture and access applications which support information to be recorded ( captured) during a live experience toward automatically producing documents for review (accessed). The recording demands instrumented environments with devices such as microphones, cameras, sensors and electronic whiteboards. Since each experience is usually related to many others ( e. g. several meetings of a project), there is a demand for mechanisms supporting the automatic linking among documents relative to different experiences. In this paper we present original results relative to the integration of our previous efforts in the Infrastructure for Capturing, Accessing, Linking, Storing and Presenting information (CALiSP). Ubiquitous computing aims at providing services to users in everyday environments such as the home. One research theme in this area is that of building capture and access applications which support information to be recorded (captured) during a live experience toward automatically producing documents for review (accessed). The recording demands instrumented environments with devices such as microphones, cameras, sensors and electronic whiteboards. Since each experience is usually related to many others (e.g. several meetings of a project), there is a demand for mechanisms supporting the automatic linking among documents relative to different experiences. In this paper we present original results relative to the integration of our previous efforts in the Infrastructure for Capturing, Accessing, Linking, Storing and Presenting information (CALiSP).

Direct Observation of Tetragonal Distortion in Epitaxial Structures through Secondary Peak Split in a Synchrotron Radiation Renninger Scan

This paper reports a direct observation of an interesting split of the (022)(022) four-beam secondary peak into two (022) and (022) three-beam peaks, in a synchrotron radiation Renninger scan (phi-scan), as an evidence of the layer tetragonal distortion in two InGaP/GaAs (001) epitaxial structures with different thicknesses. The thickness, composition, (a perpendicular to) perpendicular lattice parameter, and (01) in-plane lattice parameter of the two epitaxial ternary layers were obtained from rocking curves (omega-scan) as well as from the simulation of the (022)(022) split, and then, it allowed for the determination of the perpendicular and parallel (in-plane) strains. Furthermore, (022)(022) omega:phi mappings were measured in order to exhibit the multiple diffraction condition of this four-beam case with their split measurement.