CENTRAL MOMENTS AND PROBABILITY DISTRIBUTION OF COLLESS'S COEFFICIENT OF TREE IMBALANCE

The great increase in the number of phylogenetic studies of a wide variety of organisms in recent decades has focused considerable attention on the balance of phylogenetic trees—the degree to which sister clades within a tree tend to be of equal size—for at least two reasons: (1) the degree of balance of a tree may affect the accuracy of estimates of it; (2) the degree of balance, or imbalance, of a tree may reveal something about the macroevolutionary processes that produced it. In particular, variation among lineages in rates of speciation or extinction is expected to produce trees that are less balanced than those that result from phylogenetic evolution in which each extant species of a group has the same probability of speciation or extinction. Several coefficients for measuring the balance or imbalance of phylogenetic trees have been proposed. I focused on Colless's coefficient of imbalance (7) for its mathematical tractability and ease of interpretation. Earlier work on this statistic produced exact methods only for calculating the expected value. In those studies, the variance and confidence limits, which are necessary for testing the departure of observed values of I from the expected, were estimated by Monte Carlo simulation. I developed recursion equations that allow exact calculation of the mean, variance, skewness, and complete probability distribution of I for two different probability-generating models for bifurcating tree shapes. The Equal-Rates Markov (ERM) model assumes that trees grow by the random speciation and extinction of extant species, with all species that are extant at a given time having the same probability of speciation or extinction. The Equal Probability (EP) model assumes that all possible labeled trees for a given number of terminal taxa have the same probability of occurring. Examples illustrate how these theoretically derived probabilities and parameters may be used to test whether the evolution of a monophyletic group or set of monophyletic groups has proceeded according to a Markov model with equal rates of speciation and extinction among species, that is, whether there has been significant variation among lineages in expected rates of speciation or extinction.     

Energy metabolism of Chironomus anthracinus (Diptera: Chironomidae) from the profundal zone of Lake Esrom,Denmark, as a function of body size,temperature and oxygen concentration

The profundal zone of Lake Esrom, Denmark has a dense population of Chironomus anthracinus, which survives 2–4 months of oxygen depletion each summer during stratification. The metabolism of 3rd and 4th instar larvae was examined in regard to variation in biomass and temperature. Respiration at air saturation was described by a curvilinear multiple regression relating oxygen consumption to individual AFDW and temperature. At 10 °C and varying oxygen regimes the O₂ consumption and CO₂ production of 4th instar larvae were almost unaltered from saturation to about 3 mg O₂ l^–1, but decreased steeply below this level. The respiratory quotient increased from 0.82 at saturation to about 3.4 at oxygen concentrations near 0.5 mg O₂ l^–1. This implied a shift from aerobic to partially anaerobic metabolism. At 0.5 mg O₂ l^–1 the total energy production equalled 20% of the rate at saturation of which more than one third was accounted for by anaerobic degradation of glycogen. This corresponded to a daily loss of 12 µg mg AFDW^–1 or approximately 5% of the body reserves. At unchanged metabolic rate the glycogen store would last three weeks, but long term oxygen deficiency causes a further suppression of the energy metabolism in C. anthracinus.     

Predicting responses of photosynthesis and root fraction to elevated [CO2]a: interactions among carbon,nitrogen, and growth*

At elevated atmospheric CO₂ concentrations ([CO₂]_a), photosynthetic capacity (A_max) and root fraction (η_R, the ratio of root to plant dry mass) increased in some studies and decreased in others. Here, we have explored possible causes of this, focusing on the relative magnitudes of the effects of elevated [CO₂]_a on specific leaf (n_m) and plant (n_p) nitrogen concentrations, leaf mass per unit area (h), and plant nitrogen productivity (α). In our survey of 39 studies with 35 species, we found that elevated [CO₂]_a led to decreased n_m and n_p in all the studies and to increased h and α in most of the studies. The magnitudes of these changes varied with species and with experimental conditions. Based on a model that integrated [CO₂]_a-induced changes in leaf nitrogen into a biochemically based model of leaf photosynthesis, we predicted that, to a first approximation, photosynthesis will be upregulated (A_max will increase) when growth at increased [CO₂]_a leads to increases in h that are larger than decreases in n_m. Photosynthesis will be downregulated (A_max will decrease) when increases in h are smaller than decreases in n_m. The model suggests that photosynthetic capacity increases at elevated [CO₂]_a only when additional leaf mesophyll more than compensates the effects of nitrogen dilution. We considered two kinds of regulatory paradigms that could lead to varying responses of η_R to elevated [CO₂]_a, and compared the predictions of each with the data. A simple static model based on the functional balance concept predicts that η_R should increase when neither n_p nor h is very responsive to elevated [CO₂]_a. The quantitative and qualitative agreement of the predictions with data from the literature, however, is poor. A model that predicts η_R from the relative sensitivities of photosynthesis and relative growth rate to elevated [CO₂]_a corresponds much more closely to the observations. In general, root fraction increases if the response of photosynthesis to [CO₂]_a is greater than that of relative growth rate.     

Dynamic approaches to the mechanism of photosynthesis

An account of the author's life and scientific research is presented. Two main lines of research have been pursued: (1) Studies on the physiological aspect of photosynthesis started from experiments with crops under field conditions and then extended to the study of photosynthesis in nature; and (2) studies on the mechanism of photophosphorylation and related problems which began with the measurement of quantum requirement of photophosphorylation. This work led to the discovery of the high energy state of phosphorylation and many other interesting findings. In recent years, efforts have been made to study the operation and regulation of photosynthetic apparatus with a view to link the above-mentioned lines of research together.Written at the invitation of Govindjee.     

Selective disruption of energy flow from phycobilisomes to Photosystem I

Efficient production of ATP and NADPH by the light reactions of oxygen-evolving photosynthesis demands continuous adjustment of transfer of absorbed light energy from antenna complexes to Photosystem I (PS I) and II (PS II) reaction center complexes in response to changes in light quality. Treatment of intact cyanobacterial cells with N-ethylmaleimide appears to disrupt energy transfer from phycobilisomes to Photosystem I (PS I). Energy transfer from phycobilisomes to Photosystem II (PS II) is unperturbed. Spectroscopic analysis indicates that the individual complexes (phycobilisomes, PS II, PS I) remain functionally intact under these conditions. The results are consistent with the presence of connections between phycobiliproteins and both PS II and PS I, but they do not support the existence of direct contacts between the two photosystems.Abbreviations Chl chlorophyll - EPR electron paramagnetic resonance - NEM N-ethylmaleimide - PBS phycobilisome - PS photosystem     

Woody-tissue respiration for Simarouba amara and Minquartia guianensis,two tropical wet forest trees with different growth habits

We measured CO₂ efflux from stems of two tropical wet forest trees, both found in the canopy, but with very different growth habits. The species were Simarouba amara, a fast-growing species associated with gaps in old-growth forest and abundant in secondary forest, and Minquartia guianensis, a slow-growing species tolerant of low-light conditions in old-growth forest. Per unit of bole surface, CO₂ efflux averaged 1.24 mol m^–2 s^–1 for Simarouba and 0.83 mol m^–2s^–1 for Minquartia. CO₂ efflux was highly correlated with annual wood production (r ²=0.65), but only weakly correlated with stem diameter (r ²=0.22). We also partitioned the CO₂ efflux into the functional components of construction and maintenance respiration. Construction respiration was estimated from annual stem dry matter production and maintenance respiration by subtracting construction respiration from the instantaneous CO₂ flux. Estimated maintenance respiration was linearly related to sapwood volume (39.6 mol m^–3s^–1 at 24.6° C, r ²=0.58), with no difference in the rate for the two species. Maintenance respiration per unit of sapwood volume for these tropical wet forest trees was roughly twice that of temperate conifers. A model combining construction and maintenance respiration estimated CO₂ very well for these species (r ²=0.85). For our sample, maintenance respiration was 54% of the total CO₂ efflux for Simarouba and 82% for Minquartia. For our sample, sapwood volume averaged 23% of stem volume when weighted by tree size, or 40% with no size weighting. Using these fractions, and a published estimate of aboveground dry-matter production, we estimate the annual cost of woody tissue respiration for primary forest at La Selva to be 220 or 350 g C m^–2 year^–1, depending on the assumed sapwood volume. These costs are estimated to be less than 13% of the gross production for the forest.     

Transpiration measurements on apple trees with an improved stem heat balance method

Since the late eighties a handy and user-friendly sap flow meter (Dynagage®) is on the market which can quantify 0205 the sap flow through intact plant stems, based on the stem heat balance method. The documentation about its accuracy and reliability, however, is still too limited to use it as a standard method in field experiments with apple trees. We therefore tested this commercial system on potted apple trees (Malus domestica L.; cv. Red Elstar and Jonagold; on rootstock M9 vf) with stem diameters of 1.8 to 4 cm. The measured sap flow was compared with mass loss measured by an automated balance, supposing the total mass loss of the trees was equal to the water loss by transpiration. The results revealed three major problems:

The Wageningen Rhizolab — a facility to study soil-root-shoot-atmosphere interactions in crops

A research facility is described for the integrated study of soil-root-shoot-atmosphere relationships in crops. The Wageningen Rhizolab has been in use since 1990, and consists of two rows, each with eight below-ground compartments aligned along a corridor. A rain shelter automatically covers the experimental area at the start of rainfall. Compartments are 125 cm × 125 cm and 200 cm deep. Each compartment has a separate drip irrigation system. Crop canopy photosynthesis, respiration, and transpiration can be measured simultaneously and continuously on four out of eight compartments at a time. Each compartment can be filled with a selected soil material (repacked soil) and is accessible from the corridor over its full depth. Multiple sensors for measuring soil moisture status, electrical conductivity, temperature, soil respiration, trace gases and oxygen are installed in spatial patterns in accordance with the requirements of the experiments. Sensors are connected to control and data-acquisition devices. Likewise, provisions have been made to sample manually the soil solution and soil atmosphere. Root observation tubes (minirhizotrons) are installed horizontally at depth intervals ranging from 5 cm (upper soil layers) to 25 cm (below 1 m). The facility is at present in use to study growth and development of vegetation (crops) in relation to drought, nutrient status, soil-borne diseases, and underground root competition. One important application is the study of elevated CO₂ concentration and climate change and the way they affect crops and their carbon economy. Growth and development of field grown vegetables and winter cover crops are also evaluated. The common aspect of those studies is to gain a better understanding of crop growth under varying environmental conditions, and to collect datasets that may help to improve mechanistic crop growth simulation models that can address suboptimal growth conditions.     

Optimization of the electrostatic interactions in proteins of different functional and folding type

The 3-dimensional optimization of the electrostatic interactions between the charged amino acid residues was studied by Monte Carlo simulations on an extended representative set of 141 protein structures with known atomic coordinates. The proteins were classified by different functional and structural criteria, and the optimization of the electrostatic interactions was analyzed. The optimization parameters were obtained by comparison of the contribution of charge-charge interactions to the free energy of the native protein structures and for a large number of randomly distributed charge constellations obtained by the Monte Carlo technique. On the basis of the results obtained, one can conclude that the charge-charge interactions are better optimized in the enzymes than in the proteins without enzymatic functions. Proteins that belong to the mixed αβ folding type are electrostatically better optimized than pure α-helical or β-strand structures. Proteins that are stabilized by disulfide bonds show a lower degree of electrostatic optimization. The electrostatic interactions in a native protein are effectively optimized by rejection of the conformers that lead to repulsive charge-charge interactions. Particularly, the rejection of the repulsive contacts seems to be a major goal in the protein folding process. The dependence of the optimization parameters on the choice of the potential function was tested. The majority of the potential functions gave practically identical results.     

Is there an energy conservation “system” in brain that protects against the consequences of energy depletion?

A poorly understood marked decrease (circa 50% of control) in local cerebral glucose utilization is caused by sublethal doses of NaCN. The decrease is global, occurring in essentially all brain regions and is entirely reversible within hours, leaving no obvious pathology. This event is not unique to NaCN in so far as a strikingly similar pattern of decreased glucose utilization occus with some other toxins. Nor can it be attributed to a direct action of NaCN since local application by microdialysis to the striatum produces a global depression. These results imply that some widely distributed system or substance is involved. We speculate the existence of a system possibly related to the reticular activating system that senses a fall in energy production and acts globally to make cells quiescent and thus would give some protection from excitotoxic driven damage.Special issue dedicated to Dr. Sidney Ochs.