The posterior probability distribution of alignments and its application to parameter estimation of evolutionary trees and to optimization of multiple alignments

How to sample alignments from their posterior probability distribution given two strings is shown. This is extended to sampling alignments of more than two strings. The result is first applied to the estimation of the edges of a given evolutionary tree over several strings. Second, when used in conjunction with simulated annealing, it gives a stochastic search method for an optimal multiple alignment.Correspondence to: L. Allison     

EFFECTS OF FLOWING WATER ON NITROGEN- AND PHOSPHORUS-LIMITED PHOTOSYNTHESIS AND OPTIMUM N:P RATIOS BY SPIROGYRA FLUVIATILIS (CHAROPHYCEAE)1,2

The effects of flowing water on net photosynthesis, dark respiration, specific growth rate, and optimum N:P ratios by Spirogyra fluviatilis Hilse were assessed. The alga was cultivated under nitrogen or phosphorus limitation in laboratory streams at three flow velocities: 3, 12, and 30 cm·s^?1. The Droop equation adequately described respiration and photosynthesis (PS_net) as a function of N or P cell quota (Q^N or Q^p). The data show that for N- or P-limited Spirogyra fluviatilis, flowing water is physiologically costly. Generally, flowing water had little effect on respiration rates; however, the proportion of gross photosynthesis devoted to dark respiration did increase with flow velocity. For photosynthesis, the minimum N and P cell quotas increased with velocity, and the theoretical PS_net maxima for N and P both appeared greatest at 12 cm·s^?1. The Droop models showed that for any given Q^N or Q^p, PS_net, was reduced by the 30-cm·s^?1 treatment. Consistent with this finding, independent estimates of specific growth rates for P-limited S. fluviatilis in the laboratory streams were inversely related to flow velocity when ambient PO₄^?3 was undetectable. However, growth was not diminished at the fastest velocity when PO₄^?3 was available for uptake. Thus, the increase in cellular phosphorus demand can be offset by flow-enhanced P uptake when conditions permit; otherwise, growth will be impaired. The optimum N:P ratios for S. fluviatilis at 3, 12, and 30 cm·s^?1 were 50, 58, and 52 by atoms, respectively, when calculated for PS_net= 0. The optimum ratios were inversely related to PS_net and decreased to approximately 20 when PS_net was near maximum. The potential for flowing water to mediate nutrient partitioning among lotic algae by altering growth rates and optimum nutrient ratios is discussed.     

Distribution of two congeneric charrs in streams of Hokkaido Island,Japan: considering multiple factors across scales

Salvelinus leucomaenis (white-spotted charr) and S. malma (Dolly Varden) are distributed throughout Hokkaido Island, Japan, but sites where they occur in sympatry are rare. In general, S. malma inhabit upstream reaches and S. leucomaenis extend downstream to the ocean. Factors influencing their distribution were analyzed at four spatial scales ranging from the whole island to individual stream pools. At the island scale, S. leucomaenis were found in the warmer south-west region and at lower altitudes elsewhere, whereas S. malma were found in the colder north-east and at higher altitudes. At a regional scale, the downstream limit of S. malma and upstream limit of S. leucomaenis shifted to lower altitude from south-west to north-east across the island, coincident with the decrease in temperature. Further analysis showed that transition points from S. leucomaenis or sympatry to S. malma in individual watersheds were closely related to an index of cumulative mean monthly temperatures exceeding 5°C. However, at the scale of a single watershed, the transition occurred at different altitudes, gradients, and temperatures in two tributaries, apparently because stream discharge, habitat, and disturbances from floods interacted with these abiotic factors to limit distribution. The two charr species developed interspecific dominance hierarchies in individual pools, and there was strong complementary density compensation among stream pools that could be explained by interspecific competition but not by differences in habitat. However, patterns at watershed and regional scales suggested that interspecific competition interacts with temperature in complex ways. We conclude that the importance of various abiotic and biotic factors in shaping Hokkaido charr distributions depends on the scale at which they are viewed.     

Do salt bridges stabilize proteins? A continuum electrostatic analysis

The electrostatic contribution to the free energy of folding was calculated for 21 salt bridges in 9 protein X-ray crystal structures using a continuum electrostatic approach with the DELPHI computer-program package. The majority (17) were found to be electrostatically destabilizing; the average free energy change, which is analogous to mutation of salt bridging side chains to hydrophobic isosteres, was calculated to be 3.5 kcal/mol. This is fundamentally different from stability measurements using pKa shifts, which effectively measure the strength of a salt bridge relative to 1 or more charged hydrogen bonds. The calculated effect was due to a large, unfavorable desolvation contribution that was not fully compensated by favorable interactions within the salt bridge and between salt-bridge partners and other polar and charged groups in the folded protein. Some of the salt bridges were studied in further detail to determine the effect of the choice of values for atomic radii, internal protein dielectric constant, and ionic strength used in the calculations. Increased ionic strength resulted in little or no change in calculated stability for 3 of 4 salt bridges over a range of 0.1-0.9 M. The results suggest that mutation of salt bridges, particularly those that are buried, to "hydrophobic bridges" (that pack at least as well as wild type) can result in proteins with increased stability. Due to the large penalty for burying uncompensated ionizable groups, salt bridges could help to limit the number of low free energy conformations of a molecule or complex and thus play a role in determining specificity (i.e., the uniqueness of a protein fold or protein-ligand binding geometry).     

Determination of the size of the Azotobacter vinelandii chromosome

The chromosome of Azotobacter vinelandii UW was digested separately with the rape cutter restriction endonucleases Swal (5-ATTTAAAT), PmeI (5GTTTAAAC) and Pacl (5-TTAATTAA) and the products were separated by pulsed-field gel electrophoresis. The size of the chromosome was determined to be approximately 4.5 megabase pairs (Mb) based on the sum of the sizes of the restriction fragments. This is almost the same as the size of the chromosome of Escherichia coli. The inability of the undigested DNA to enter the gel has led us to infer that the chromosome is circular.     

The effect of pulsed microwaves on passive electrical properties and interspike intervals of snail neurons

The effects of pulsed microwaves (2.45 GHz, 10 μs, 100 pps, SAR: 81.5 kW/kg peak, 81.5 W/kg average) on membrane input resistance and action potential (AP) interval statistics were studied in spontaneously active ganglion neurons of land snails (Helix aspersa), at strictly constant temperature (20.8±.07°C worst case). Statistical comparison with sham-irradiated neurons revealed a significant increase in the mean input resistance of neurons exposed to pulsed microwaves (P ? .05 ). Pulsed microwaves had no visible effect on mean AP firing rate; this observation was confirmed by analysis of interspike intervals (ISIs). Using an integrator model for spontaneously active neurons, we found the net input current to be more variable in neurons exposed to pulsed microwaves. The mean input current was not affected. The standard deviation of ISIs and the autocorrelation of the input current were marginally affected, but these changes were not consistent across neurons. Although the observed effects were less obvious than those reported in other studies, they represent evidence of a direct interaction between neurons and pulsed microwaves, in the absence of macroscopic temperature changes. The data do not suggest a single, specific mechanism for such interaction. © 1993 Wiley-Liss, Inc.     

Intracellular aminopeptidases inStreptomyces lividans 66

Summary We have investigated the aminopeptidase activities present inStreptomyces lividans strains. The majority of these activities proved to be intracellular with multiple active species. Two aminopeptidase P genes were identified to be responsible for the ability to hydrolyze amino terminal peptide bonds adjacent to proline residues. Two other broad spectrum aminopeptidases were found to display homology at both the DNA and protein levels. One showed significant homology to PepN proteins, particularly around the putative zinc-binding residues which are important for catalysis. The second broad spectrum activity was not analyzed in detail but showed a different spectrum of substrate specificity to that of PepN.     

日本落叶松引种区林地棕壤肥力的多变量分析

本研究从日本落叶松引种区林地棕壤9个主要理化性状及与之配套的17株优势木材料入手,采用多变量分析方法筛选出影响该地区日本落叶松生长的主要肥力因子为氮及磷,並据此将该林地棕壤划分为9个肥力类型。在进行聚类分析时,本研究的创新在于以任意二样本点在各主成份上的坐标值为变量,以各主成份的贡献率为权重,重新定义欧氏距离公式,对主成份坐标值聚类,使其更为合理、直观。同时采用回归分析拟合出理化性状间的多个回归方程。此研究为该林地科学施肥、速生丰产、永续利用提供了可靠的数量依据。     

一端受外力的交联振荡器链中的内部传输

本文研究了二类一端受外力的交联振荡器链：最邻近多相位交联振荡器链,以及多重交联振荡器链,讨论了它们产生内部传输,即各振荡器与外力具有相同频率的现象。文中近似相位差方程、指数二分性理论和中心流形理论被应用于系统的渐近近似。研究。本文得到了更符合于实际情况的神经网络CPG链动态特性分析结论。     

Experimental evaluation of realized niche models for predicting responses of plant species to a change in environmental conditions

Abstract. We estimated, using logistic regression techniques, the realized niches of the four dominant species in an experimental marsh complex located in the Delta Marsh, Manitoba, Canada. These models were then used to predict the probability of occurrence of these species in selected elevation ranges when water levels were raised in 1985 either 0, 30 or 60 cm above the long-term normal water level. These realized-niche models were calculated using elevation and species data collected in 1980. After having been eliminated by two years of deep flooding, the emergent vegetation in this complex had been re-established during a drawdown beginning in either 1983 or 1984. Our hypothesis was that from 1985 to 1989 the frequencies of occurrence of species in selected elevation ranges would converge to their probabilities predicted from the 1980 logistic models. This was not borne out by our results. Actual frequencies and predicted probabilities of occurrence of a species were similar at best less than 40% and then mostly in the control (0 cm) treatment. The realized-niche models were not adequate to predict the distribution of emergents after an increase in water level in the short term because the emergent species did not migrate upslope. Emergent species in the medium and high treatments either (1) died out - Scolochloa festucacea and Scirpus lacustris - after 3 yr because they could not survive permanent flooding, (2) stayed where they were - Phragmites australis - because they were unable to move upslope through clonal growth, or (3) became more widespread - Typha glauca only because of the expansion of small local populations already established in 1985 in areas dominated formerly by other species.