Mass spectrometry imaging of glucosinolates in arabidopsis flowers and siliques

Glucosinolates are multi-functional plant secondary metabolites which play a vital role in plant defence and are, as dietary compounds, important to human health and livestock well-being. Knowledge of the tissue-specific regulation of their biosynthesis and accumulation is essential for plant breeding programs. Here, we report that in Arabidopsis thaliana, glucosinolates are accumulated differentially in specific cells of reproductive organs. Using matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI), distribution patterns of three selected compounds, 4-methylsulfinylbutyl (glucoraphanin), indol-3-ylmethyl (glucobrassicin), and 4-benzoyloxybutyl glucosinolates, were mapped in the tissues of whole flower buds, sepals and siliques. The results show that tissue localization patterns of aliphatic glucosinolate glucoraphanin and 4-benzoyloxybutyl glucosinolate were similar, but indole glucosinolate glucobrassicin had different localisation, indicating a possible difference in function. The high resolution images obtained by a complementary approach, cryo-SEM Energy Dispersive X-ray analysis (cryo-SEM-EDX), confirmed increased concentration of sulphur in areas with elevated amounts of glucosinolates, and allowed identifying the cell types implicated in accumulation of glucosinolates. High concentration of sulphur was found in S-cells adjacent to the phloem in pedicels and siliques, indicating the presence of glucosinolates. Moreover, both MALDI MSI and cryo-SEM-EDX analyses indicated accumulation of glucosinolates in cells on the outer surface of the sepals, suggesting that a layer of glucosinolate-accumulating epidermal cells protects the whole of the developing flower, in addition to the S-cells, which protect the phloem. This research demonstrates the high potential of MALDI MSI for understanding the cell-specific compartmentation of plant metabolites and its regulation.

Application of DIGE and mass spectrometry in the study of type 2 Diabetes Mellitus (T2DM) mouse models

Knowledge of the differences between the amounts and types of protein that are expressed in diseased compared to healthy subjects may give an understanding of the biological pathways that cause disease. This is the reasoning behind the presented protocol, which uses difference gel electrophoresis to discover up‐ or down‐regulated proteins between mice of different genotypes, or of those fed on different diets, that may thus be prone to develop diabetes‐like phenotypes. Subsequent analysis of these proteins by tandem mass spectrometry typically facilitates their identification with a high degree of confidence.

Liquid AP-UV-MALDI enables stable ion yields of multiply charged peptide and protein ions for sensitive analysis by mass spectrometry

In biological mass spectrometry (MS), two ionization techniques are predominantly employed for the analysis of larger biomolecules, such as polypeptides. These are nano-electrospray ionization [1, 2] (nanoESI) and matrix-assisted laser desorption/ionization [3, 4] (MALDI). Both techniques are considered to be “soft”, allowing the desorption and ionization of intact molecular analyte species and thus their successful mass-spectrometric analysis. One of the main differences between these two ionization techniques lies in their ability to produce multiply charged ions. MALDI typically generates singly charged peptide ions whereas nanoESI easily provides multiply charged ions, even for peptides as low as 1000 Da in mass. The production of highly charged ions is desirable as this allows the use of mass analyzers, such as ion traps (including orbitraps) and hybrid quadrupole instruments, which typically offer only a limited m/z range (< 2000–4000). It also enables more informative fragmentation spectra using techniques such as collisioninduced dissociation (CID) and electron capture/transfer dissociation (ECD/ETD) in combination with tandem MS (MS/MS). [5, 6] Thus, there is a clear advantage of using ESI in research areas where peptide sequencing, or in general, the structural elucidation of biomolecules by MS/MS is required. Nonetheless, MALDI with its higher tolerance to contaminants and additives, ease-of-operation, potential for highspeed and automated sample preparation and analysis as well as its MS imaging capabilities makes it an ionization technique that can cover bioanalytical areas for which ESI is less suitable. [7, 8] If these strengths could be combined with the analytical power of multiply charged ions, new instrumental configurations and large-scale proteomic analyses based on MALDI MS(/MS) would become feasible.

Associating spontaneous with evoked activity in a neural mass model of cat visual cortex

Spontaneous activity of the brain at rest frequently has been considered a mere backdrop to the salient activity evoked by external stimuli or tasks. However, the resting state of the brain consumes most of its energy budget, which suggests a far more important role. An intriguing hint comes from experimental observations of spontaneous activity patterns, which closely resemble those evoked by visual stimulation with oriented gratings, except that cortex appeared to cycle between different orientation maps. Moreover, patterns similar to those evoked by the behaviorally most relevant horizontal and vertical orientations occurred more often than those corresponding to oblique angles. We hypothesize that this kind of spontaneous activity develops at least to some degree autonomously, providing a dynamical reservoir of cortical states, which are then associated with visual stimuli through learning. To test this hypothesis, we use a biologically inspired neural mass model to simulate a patch of cat visual cortex. Spontaneous transitions between orientation states were induced by modest modifications of the neural connectivity, establishing a stable heteroclinic channel. Significantly, the experimentally observed greater frequency of states representing the behaviorally important horizontal and vertical orientations emerged spontaneously from these simulations. We then applied bar-shaped inputs to the model cortex and used Hebbian learning rules to modify the corresponding synaptic strengths. After unsupervised learning, different bar inputs reliably and exclusively evoked their associated orientation state; whereas in the absence of input, the model cortex resumed its spontaneous cycling. We conclude that the experimentally observed similarities between spontaneous and evoked activity in visual cortex can be explained as the outcome of a learning process that associates external stimuli with a preexisting reservoir of autonomous neural activity states. Our findings hence demonstrate how cortical connectivity can link the maintenance of spontaneous activity in the brain mechanistically to its core cognitive functions.

Large-scale surface mass balance of ice sheets from a comprehensive atmospheric model

The surface mass balance for Greenland and Antarctica has been calculated using model data from an AMIP-type experiment for the period 1979–2001 using the ECHAM5 spectral transform model at different triangular truncations. There is a significant reduction in the calculated ablation for the highest model resolution, T319 with an equivalent grid distance of ca 40 km. As a consequence the T319 model has a positive surface mass balance for both ice sheets during the period. For Greenland, the models at lower resolution, T106 and T63, on the other hand, have a much stronger ablation leading to a negative surface mass balance. Calculations have also been undertaken for a climate change experiment using the IPCC scenario A1B, with a T213 resolution (corresponding to a grid distance of some 60 km) and comparing two 30-year periods from the end of the twentieth century and the end of the twenty-first century, respectively. For Greenland there is change of 495 km3/year, going from a positive to a negative surface mass balance corresponding to a sea level rise of 1.4 mm/year. For Antarctica there is an increase in the positive surface mass balance of 285 km3/year corresponding to a sea level fall by 0.8 mm/year. The surface mass balance changes of the two ice sheets lead to a sea level rise of 7 cm at the end of this century compared to end of the twentieth century. Other possible mass losses such as due to changes in the calving of icebergs are not considered. It appears that such changes must increase significantly, and several times more than the surface mass balance changes, if the ice sheets are to make a major contribution to sea level rise this century. The model calculations indicate large inter-annual variations in all relevant parameters making it impossible to identify robust trends from the examined periods at the end of the twentieth century. The calculated inter-annual variations are similar in magnitude to observations. The 30-year trend in SMB at the end of the twenty-first century is significant. The increase in precipitation on the ice sheets follows closely the Clausius-Clapeyron relation and is the main reason for the increase in the surface mass balance of Antarctica. On Greenland precipitation in the form of snow is gradually starting to decrease and cannot compensate for the increase in ablation. Another factor is the proportionally higher temperature increase on Greenland leading to a larger ablation. It follows that a modest increase in temperature will not be sufficient to compensate for the increase in accumulation, but this will change when temperature increases go beyond any critical limit. Calculations show that such a limit for Greenland might well be passed during this century. For Antarctica this will take much longer and probably well into following centuries.

Midlatitude Forcing Mechanisms for Glacier Mass Balance Investigated Using General Circulation Models

A process-oriented modeling approach is applied in order to simulate glacier mass balance for individual glaciers using statistically downscaled general circulation models (GCMs). Glacier-specific seasonal sensitivity characteristics based on a mass balance model of intermediate complexity are used to simulate mass balances of Nigardsbreen (Norway) and Rhonegletscher (Switzerland). Simulations using reanalyses (ECMWF) for the period 1979–93 are in good agreement with in situ mass balance measurements for Nigardsbreen. The method is applied to multicentury integrations of coupled (ECHAM4/OPYC) and mixed-layer (ECHAM4/MLO) GCMs excluding external forcing. A high correlation between decadal variations in the North Atlantic oscillation (NAO) and mass balance of the glaciers is found. The dominant factor for this relationship is the strong impact of winter precipitation associated with the NAO. A high NAO phase means enhanced (reduced) winter precipitation for Nigardsbreen (Rhonegletscher), typically leading to a higher (lower) than normal annual mass balance. This mechanism, entirely due to internal variations in the climate system, can explain observed strong positive mass balances for Nigardsbreen and other maritime Norwegian glaciers within the period 1980–95. It can also partly be responsible for recent strong negative mass balances of Alpine glaciers.

A Possible Change in Mass Balance of Greenland and Antarctic Ice Sheets in the Coming Century

A high-resolution GCM is found to simulate precipitation and surface energy balance of high latitudes with high accuracy. This opens new possibilities to investigate the future mass balance of polar glaciers and its effect on sea level. The surface mass balance of the Greenland and the Antarctic ice sheets is simulated using the ECHAM3 GCM with TI06 horizontal resolution. With this model, two 5-year integrations for the present and doubled carbon dioxide conditions based on the boundary conditions provided by the ECHAM1/T21 transient experiment have been conducted. A comparison of the two experiments over Greenland and Antarctica shows to what extent the effect of climate change on the mass balance on the two largest glaciers of the world can differ. On Greenland one sees a slight decrease in accumulation and a substantial increase in melt, while on Antarctica a large increase in accumulation without melt is projected. Translating the mass balances into terms of sea-level equivalent. the Greenland discharge causes a sea level rise of 1.1 mm yr−1, while the accumulation on Antarctica tends to lower it by 0.9 mm yr−1. The change in the combined mass balance of the two continents is almost zero. The sea level change of the next century can be affected more effectively by the thermal expansion of seawater and the mass balance of smaller glaciers outside of Greenland and Antarctica.

A Lagrangian model of air-mass photochemistry and mixing using a trajectory ensemble: the Cambridge Tropospheric Trajectory model of Chemistry And Transport (CiTTyCAT) version 4.2

A Lagrangian model of photochemistry and mixing is described (CiTTyCAT, stemming from the Cambridge Tropospheric Trajectory model of Chemistry And Transport), which is suitable for transport and chemistry studies throughout the troposphere. Over the last five years, the model has been developed in parallel at several different institutions and here those developments have been incorporated into one "community" model and documented for the first time. The key photochemical developments include a new scheme for biogenic volatile organic compounds and updated emissions schemes. The key physical development is to evolve composition following an ensemble of trajectories within neighbouring air-masses, including a simple scheme for mixing between them via an evolving "background profile", both within the boundary layer and free troposphere. The model runs along trajectories pre-calculated using winds and temperature from meteorological analyses. In addition, boundary layer height and precipitation rates, output from the analysis model, are interpolated to trajectory points and used as inputs to the mixing and wet deposition schemes. The model is most suitable in regimes when the effects of small-scale turbulent mixing are slow relative to advection by the resolved winds so that coherent air-masses form with distinct composition and strong gradients between them. Such air-masses can persist for many days while stretching, folding and thinning. Lagrangian models offer a useful framework for picking apart the processes of air-mass evolution over inter-continental distances, without being hindered by the numerical diffusion inherent to global Eulerian models. The model, including different box and trajectory modes, is described and some output for each of the modes is presented for evaluation. The model is available for download from a Subversion-controlled repository by contacting the corresponding authors.

Fractal spatialities

This paper argues for the use of ‘fractals’ in theorising sociospatial relations. From a realist position, a nonmathematical but nonmetaphoric and descriptive view of ‘fractals’ is advanced. Insights from the natural sciences are combined with insights on the position of the observer from Luhmann and notions of assemblages and repetitions from Deleuze. It is argued that the notion of ‘fractals’ can augment current understanding of sociospatialities in three ways. First, it can pose questions about the scalar position of the observer or the grain of observation; second, as a signifier of particular attributes, it prompts observation and description of particular structuring processes; and third, the epistemic access afforded by the concept can open up possibilities for transformative interventions and thereby inform the same. The theoretical usefulness of the concept is demonstrated by discussing the territory, place, scale, and networks (TPSN) model for theorising sociospatial relations advanced by B Jessop, N Brenner, and M Jones in their 2008 paper “Theorizing sociospatial relations”, published in this journal (volume 26, pages 389–401). It is suggested that a heuristic arising from a ‘fractal’ ontology can contribute to a polymorphous, as opposed to polyvalent, understanding of sociospatial relations.

Fractal spaces in planning and governance

This paper discusses concepts of space within the planning literature, the issues they give rise to and the gaps they reveal. It then introduces the notion of 'fractals' borrowed from complexity theory and illustrates how it unconsciously appears in planning practice. It then moves on to abstract the core dynamics through which fractals can be consciously applied and illustrates their working through a reinterpretation of the People's Planning Campaign of Kerala, India. Finally it highlights the key contribution of the fractal concept and the advantages that this conceptualisation brings to planning.

The Greenland Ice Sheet's surface mass balance in a seasonally sea-ice free Arctic

General circulation models predict a rapid decrease in sea ice extent with concurrent increases in near surface air temperature and precipitation in the Arctic over the 21st century. This has led to suggestions that some Arctic land ice masses may experience an increase in accumulation due to enhanced evaporation from a seasonally sea ice free Arctic Ocean. To investigate the impact of this phenomenon on Greenland ice sheet climate and surface mass balance (SMB) a regional climate model, HadRM3, was used to force an insolation-temperature melt SMB model. A set of experiments designed to investigate the role of sea ice independently from sea surface temperature (SST) forcing are described. In the warmer and wetter SI + SST simulation Greenland experiences a 23% increase in winter SMB but 65% reduced summer SMB, resulting in a net decrease in the annual value. This study shows that sea ice decline contributes to the increased winter balance, causing 25% of the increase in winter accumulation; this is largest in eastern Greenland as the result of increased evaporation in the Greenland Sea. These results indicate that the seasonal cycle of Greenland's SMB will increase dramatically as global temperatures increase, with the largest changes in temperature and precipitation occurring in winter. This demonstrates that the accurate prediction of changes in sea ice cover is important for predicting Greenland SMB and ice sheet evolution.

Understanding the spatial mass transfer behaviour of a pulsating jet HMV system: vortex generation and characterisation

The flow patterns generated by a pulsating jet used to study hydrodynamic modulated voltammetry (HMV) are investigated. It is shown that the pronounced edge effect reported previously is the result of the generation of a vortex ring from the pulsating jet. This vortex behaviour of the pulsating jet system is imaged using a number of visualisation techniques. These include a dye system and an electrochemically generated bubble stream. In each case a toroidal vortex ring was observed. Image analysis revealed that the velocity of this motion was of the order of 250 mm s−1 with a corresponding Reynolds number of the order of 1200. This motion, in conjunction with the electrode structure, is used to explain the strong ‘ring and halo’ features detected by electrochemical mapping of the system reported previously.