Global vegetation models: incorporating transient changes to structure and composition

Abstract. We describe an approach for developing a Dynamic Global Vegetation Model (DGVM) that accounts for transient changes in vegetation distribution over a decadal time scale. The DGVM structure is based on a linkage between an equilibrium global vegetation model and smaller scale ecosystem dynamics modules that simulate the rate of vegetation change. Vegetation change is classified into four basic types, based largely on the projected change in above-ground biomass of the vegetation. These four types of change are: (1) dieback of forest, shrubland or grassland; (2) successional replacement within forest, shrubland or grassland; (3) invasion of forest, shrubland or grassland; (4) change in tree/grass ratio. We then propose an approach in which the appropriate ecosystem dynamics module for each type of change is applied and the grid cells of the global model updated accordingly. An approach for accounting for fire, as an example of a disturbance which may strongly influence the rate and spatial pattern of forest dieback, is incorporated. We also discuss data needs for the development, calibration and validation of the model.     

Effects of large Saduria entomon (Isopoda) on spatial distribution of their small S. entomon and Monoporeia affinis (Amphipoda) prey

We performed laboratory experiments to investigate the effects of predator avoidance and numerical effects of predation on spatial distribution of small Saduria entomon (Isopoda) and Monoporeia affinis (Amphipoda), with large S. entomon as predators. The horizontal distribution and mortality of the prey species, separately and together, were studied in aquaria with a spatial horizontal refuge. We also estimated effects of refuge on mortality of small S. entomon and M. affinis by experiments without the refuge net. In addition, we investigated whether predation risk from large S. entomon influenced the swimming activity of M. affinis, to clarify the mechanisms behind the spatial distribution. Both small S. entomon and M. affinis avoided large S. entomon. The avoidance behaviour of M. fffinis contributed about 10 times more to the high proportion in the refuge than numerical effects of predation. Due to the low mortality of small S. entomon the avoidance behaviour of this species was even more important for the spatial distribution. The combined effect of avoidance behaviour and predation in both species was aggregation, producting a positive correlation between the species in density. M. affinis showed two types of avoidance behaviour. In the activity experiments they reduced activity by 36% and buried themselves in the sediment. In the refuge experiments we also observed avoidance behaviour with the emigration rate from the predator compartment being twice the immigration rate. The refuge did not lower predation mortality in M. affinis, probably due to the small scale of the experimental units in relation to the mobility of the species. Predation mortality in small S. entomon was higher in absence of a refuge and especially high in absence of M. affinis.     

Self-organization of an oscillatory neural system

Hebbian dynamics is used to derive the differential equations for the synaptic strengths in the neural circuitry of the locomotive oscillator. Initially, neural connection are random. Under a specified arborization hypothesis relating to the density of neural connections, the differential equations are shown to model the self-organization and the stability of the oscillator.     

Long timestep dynamics of peptides by the dynamics driver approach

Previous experience with the Langevin/implicit-Euler scheme for dynamics (“LI”) on model systems (butane, water) has shown that LI is numerically stable for timesteps in the 5–20 fs range but quenches high-frequency modes. To explore applications to polypeptides, we apply LI to model systems (several dipeptides, a tetrapeptide, and a 13-residue oligoalanine) and also develop a new dynamics driver approach (“DA”). The DA scheme, based on LI, addresses the important issue of proper sampling, which is unlikely to be solved by small-time step integration methods or implicit methods with intrinsic damping at room temperature, such as LI. Equilibrium averages, time-dependent molecular properties, and sampling trends at room temperature are reported for both LI and DA dynamics simulations, which are then compared to those generated by a standard explicit discretization of the Langevin equation with a 1 fs timestep. We find that LI's quenching effects are severe on both the fast and slow (due to vibrational coupling) frequency modes of all-atom polypeptides and lead to more restricted dynamics at moderate timesteps (40 fs). The DA approach empirically counteracts these damping effects by adding random atomic perturbations to the coordinates at each step (before the minimization of a dynamics function). By restricting the energetic fluctuations and controlling the kinetic energy, we are able with a 60 fs timestep to generate continuous trajectories that sample more of the relevant conformational space and also reproduce reasonably Boltzmann statistics. Although the timescale for transition may be accelerated by the DA approach, the transitional. information obtained for the alanine dipeptide and the tetrapeptide is consistent with that obtained by several other theoretical approaches that focus specifically on the determination of pathways. While the trajectory for oligoalanine by the explicit scheme over the nanosecond timeframe remains in the vicinity of the full α_R-helix starting structure, and a high-temperature (6000°K) MD trajectory departs slowly from the a helical structure, the DA-generated trajectory for the same CPU time exhibits unfolding and refolding and reveals a range of conformations with an intermediate helix content. Significantly, this range of states is more consistent with spectroscopic experiments on small peptides, as well as the cooperative two-state model for helix–coil transition. The good, near-Boltzmann statistics reported for the smaller systems above, in combination with the interesting oligoalanine results, suggest that DA is a promising tool for efficiently exploring conformational spaces of biomolecules and exploring folding/unfolding processes of polypeptides. © 1995 Wiley-Liss, Inc.     

Dynamic properties of some β-chain mutant hemoglobins

The thermal behavior of the Soret band relative to the carbonmonoxy derivatives of some β-chain mutant hemoglobins is studied in the temperature range 300–10 K and compared to that of wild-type carbonmonoxy hemoglobin. The band profile at various temperatures is modeled as a Voigt function that accounts for homogeneous broadening and for the coupling with high- and low-frequency vibrational modes, while inhomogeneous broadening is taken into account with a gaussian distribution of purely electronic transition frequencies. The various contributions to the overall bandwidth are singled out With this analysis and their temperature dependence, in turn, gives information on structural and dynamic properties of the system studied. In the wildtype and mutant hemoglobins, the values of homogeneous bandwidth and of the coupling constants to high-frequency vibrational modes are not modified with respect to natural human hemoglobin, thus indicating that the local electronic and vibrational properties of the heme–CO complex are not altered by the recombinant procedures. On the contrary, differences in the protein dynamic behavior are observed. The most relevant are those relative to the “polar isosteric” βVal-67(Ell) →Thr substitution, localized in the heme pocket, which results in decreased coupling with low-frequency modes and increased anharmonic motions. Mutations involving residue βLys-144(HC1) at the C-terminal and residue βCys-112(G14) at the α₁β₁ interface have a smaller effect consisting in an increased coupling with low-frequency modes. Mutations at the β-N-terminal and at the α₁β₂ interface have no effect on the dynamic properties of the heme pocket. © 1995 Wiley-Liss, Inc.     

Shoot regeneration after fire or freezing temperatures and its relation to plant life-form for some heathland species

Shoot regeneration after prescribed burning or following the freezing temperatures of winter was monitored for nineteen heathland species present in an Arctostaphyleto-Callunetum community in northeast Scotland. Species whose renewal buds were near the surface of the ground started to grow earlier in the spring than species with renewal buds above the surface, but grouping species according to the position of their renewal bud (i.e. their life-form) did not account for all of the interspecific variation apparent. In the case of shoot regeneration after fire, species whose renewal buds were destroyed by fire because they were above-ground started to regenerate about the same time as species with belowground buds, protected from fire, but reached their maximum frequency of occurrence later. Grouping species by life-form was of limited value as a means of interpreting this interspecific variation in the timing of shoot regeneration after fire. It would be unwise to use plant life-form as the sole basis for interpreting or predicting a species' response to temperature stress when extreme temperatures occur regularly, as they do in heathland. The possible use of other plant traits to interpret and predict interspecific variation in the regeneration rate of heathland plants is discussed.Nomenclature follows Tutin et al. (1964–1980) for vascular plants. Acknowledgements. The Nature Conservancy Council and Mr J. J. Humphries kindly allowed Dinnet Moor to be used for the work presented here. One of us (RJR) received financial support for field work from the Natural Sciences and Engineering Research Council of Canada.     

Organization and dynamics of lipids in bovine brain coated and uncoated vesicles

Three characteristics have been demonstrated by the chemical analysis of bovine brain coated vesicles following removal of the coat proteins: a high protein content, a high cholesterol/lipid ratio and a high percentage of phosphatidylethanolamine amongst the phospholipids.The study of lipid bilayer organization and dynamics has been performed using the fluorescent probes pyrene and parinaric acid (cis and trans). This has allowed the study of both lateral mobility and rotational motion in the lipid bilayer of the coated and uncoated vesicles.Lateral mobility in the fluid phase of the lipid is slightly reduced by the presence of the clathrin coat, as indicated by the lower diffusion coefficient of pyrene in coated compared with uncoated vesicles.At all temperatures from 6° to 30°C, solid-phase domains, probed by trans parinaric acid, coexist with fluid-phase domains in the lipid bilayer. The temperature dependence of the parinaric acid lifetimes and of their amplitudes strongly suggests that the solid phase domains decrease in size with temperature, both in coated and uncoated vesicles.However, the difference in the value of the anisotropy at long times (r ), between coated and uncoated vesicles (a difference which is more pronounced for cis than for trans parinaric acid), indicates that the presence of the clathrin coat introduces disorder in the surrounding lipids, thus suggesting a possible role of the clathrin in the formation of the pits on the plasma membrane.Abbreviations CVs coated vesicles - UVs uncoated vesicles - TLC thin layer chromatography - DMSO dimethylsulfoxide - DPPC dipalmitoylphosphatidylcholine - cis Pna cis parinaric acid - (9,11,13,15-cis-trans-trans-cis) octadecatetraenoic acid - Trans Pna Trans parinaric acid - (9,11,13,15-all-trans) octadecatetraenoic acid     

Mutant hemoglobin stability depends upon location and nature of single point mutation

The temperature dependence of the rates of heme release from the beta subunits of methemoglobin A and 5 beta mutant methemoglobins has been determined. The rates were largest for two hemoglobins with mutations distal to heme, previously known to be unstable. The other 3 mutants also released heme faster than A. These hemoglobins, with single point mutations at the alpha 1/beta 2 interface, were previously thought to be stable. The low reported yields of the 5 mutant proteins covaries with the relative rates of heme release from the met species.     

Species turnover in deciduous forest vegetation

Summary Permanent quadrats were marked out in two areas of hardwood forest vegetation in 1969, and listings of their vascular plant species were taken on several occasions over the snow-free seasons of 1969, 1970, 1971 and 1976. Over the period of study, mean numbers of species per m² remained virtually constant, but variations in the species compositions of individual quadrats were such that mean turnover ratios of 0.115 and 0.085, respectively, were computed for the two stands. Between 1969 and 1976 averages of 20% and 14%, respectively, of the species found in individual quadrats were replaced. This was not accomplished by qualitative changes in the floras of the two stands. Rather, it reflects the operation of a system of continuous rearrangements of species in the small quadrats of both sample areas.Taxonomical nomenclature and life-form system used in this study are according to Gleason & Cronquist (1963).William Phillips, Ian Sutherland and Sheila Thompson helped in the field; Professor Keith Wade commented on the material; Abal Sen drafted the diagram; and the research is part of that funded by the National Research Council of Canada.     

Änderungen in der Stickstoffversorgung auf Dauerflächen im Brachland

Summary Starting in 1968 plant succession and nitrogen status in the top soil of an old field was investigated. The soil is a calcareous loam which was sterilized by heating. In the absence of human influence distinct successional stages with characteristic floristical and physiognomical features were observed. During the first six years vegetational development was characterized by competition between therophytes and hemicryptophytes. Agricultural treatments such as annual ploughing (spring, summer) and cutting (autumn) were found to change the trend of the succession.Five years after starting the experiment total nitrogen content in the top soil of the control area had increased slightly, while the ploughed plots persisted in their low values. A comparison of the nitrogen mineralisation between 1970 and 1974 showed decreasing amounts of mineral nitrogen in the later stage (1970: 67 kg N_min/ha/30 weeks; 33 kg N_min/ha/30 weeks). On the other hand, mineral nitrogen supply on the ploughed plots was not significantly different after the five-years-period. It is suggested that in old-field vegetation the external nitrogen cycle of the early therophyte stage changed to an internal one when long-lived hemicryptophytes, rhizome- and root-budding geophytes became dominant.Tables 1 to 4 show the vegetation development under different treatments; the figures represent average cover values per vegetation season using Londo's (1975) scale. Table 5 contains the total nitrogen concentration values in the uppermost of 10 cm of mineral soil, and Table 6 lists the values for soil volume, mean soil temperatures, average water content, and mineral nitrogen supplies for 1970 and 1974.

Contribution to the Symposium of the Working Group for Succession Research on Permanent Plots, held at Yerseke, the Netherlands, October 1975.