AnO(N 2 logN) restriction map comparison and search algorithm

We present anO(R logP) time,O(M+P ² ) space algorithm for searching a restriction map withM sites for the best matches to a shorter map withP sites, whereR, the number of matching site pairs, is bounded byMP. As first proposed by Watermanet al. (1984,Nucl. Acids Res. 12, 237–242) the objective function used to score matches is additive in the number of unaligned sites and the discrepancies in the distances between adjacent aligned sites. Our algorithm is basically a sparse dynamic programming computation in which “candidate lists” are used to model the future contribution of all previously computed entries to those yet to be computed. A simple modification to the algorithm computes the distance between two restriction maps withM andN sites, respectively, inO(MN(logM+logN)) time. This author’s work was supported in part by National Library of Medicine Grant R01-LM4960. This author’s work was supported in part by National Library of Medicine Grant R01-LM5110.     

Constrained sequence alignment

This paper presents a dynamic programming algorithm for aligning two sequeces when the alignment is constrained to lie between two arbitrary boundary lines in the dynamic programming matrix. For affine gap penalties, the algorithm requires onlyO(F) computation time andO(M+N) space, whereF is the area of the feasible region andM andN are the sequence lengths. The result extends to concave gap penalties, with somewhat increased time and space bounds. K.-M. C. and W. M. were supported in part by grant R01 LM05110 from the National Library of Medicine. R. C. H. was supported by PHS grant R01 DK27635.     

Hydrophobicity of biosurfaces as shown by chemoreceptive Thresholds inTetrahymena,Physarum andNitella

Summary Responses (chemotaxis and changes in membrane potential) ofTetrahymena, Physarum, andNitella against aqueous solution of homologous series ofn-alcohols,n-aldehydes andn-fatty acids were studied for clarifying the hydrophobic character of chemoreceptive membranes. Results were: (1) All organisms studied responded to homologous compounds examined when the concentration of these chemicals exceeded their respective threshold,C _th , and the response,R, were expressed approximately asR= log (C/C _th ) forC>C _th , (2) Increase of the length of hydrocarbon chain in homologues decreasedC _th . Plots of logC _th against the number of carbon atoms,n, inn-alcohols,n-aldehydes andn-fatty acids showed linear relationships as represented by logC _th =–An+B. A andB are positive constants for respective functional end groups of the chemicals and biological membranes used. The above empirical equation was interpreted in terms of the partition equilibrium of methylene groups between bulk solution and membrane phase. ParameterA was shown to be a measure of hydrophobicity of the membrane, andB represented the sensitivity of chemoreception of the membrane. (3) Thresholds,C _th , for various hydrophobic reagents were compared with those of human olfactory reception,T. Plots of logT against logC _th fell on straight lines for respective organisms with different slopes which were proportional to parameterA.     

Trade-off relationships between some reproductive characteristics in plants with special reference to life history stragegy

Several reproductive triats in plants were studied in more than 200 populations of 61 wild species from diverse ecological conditions. As a result, it was found that there occur three distinct types of plants in the energy allocation patterns to reproductive structures (RA) and the propagule output per plant (P_N), i.e. (1) the number of propagules per plant increases in response to the increase in RA (Type I), (2) the number of propagules decreases in response to the increase in RA (Type II), and (3) the RA remains constant despite the great differences in the propagule number per plant. A conspicuous trade-off relationship was also discovered to occur between the RA to a single propagule (R_A) and the propagule output per plant (P_N), such that log R_A=logC−blot P_N, or R_A=C/P_N ^b =CP_N ^−b , where C is a constant. The three different ranges ofb-values were recognized, i.e.b<1.0,b>1.0, andb=1.0, which correspond to Type I, Type II, and Type III, respectively. Related problems to the concept ofr- andK-strategy are also discussed.     

Optimal sequence alignment allowing for long gaps

A new algorithm for optimal sequence alignment allowing for long insertions and deletions is developed. The algorithm requires O((L+C)MN) computational steps, O(LN) primary memory and O(MN) secondary memory storage, whereM andN(M≥N) are sequence lengths,L (typicallyL≤3) is the number of segment specifying the gap weighting function, andC is a constant. We have also modified our earlier traceback algorithm so that it finds all and only the optimal alignments in a compact form of a directed graph. The current versions accept a set of aligned sequences as input, which facilitates multiple sequence alignment by some iterative procedures. Dedicated to Professor Akiyoshi Wada on the occasion of his 60th birthday.     

13C-N.M.R.-spectral study of the pH behavior of reductively [13C]methylated,glycophorin a glyco-octapeptides and a related glycopentapeptide

The pH dependence of the labeled-carbon resonances of reductively [¹³C] methylated compounds tri-l-Ser, glyco-octapeptide A^M, asialoglyco-octapeptide A^M, glyco-octapeptide A^N, asialoglyco-octapeptide A^N, and a glycopentapeptide was investigated. The results are discussed relative to those previously observed for reductively [¹³C]methylated, intact glycophorins A^M and A^N, and in terms of the mode of display of the MN blood-group specificities by these related glycoproteins. The results indicated that the α-d-NeuAc groups appear to affect the pH-titration results of glyco-octapeptides A^M and A^N. Moreover, comparison of the pH-titration results for reductively [¹³C]methylated glyco-octapeptide A^M and reductively [¹³C]methylated asialoglyco-octapeptide A^M with those of a reductively [¹³C]methylated glycopentapeptide and reductively [¹³C]methylated tri-l-Ser indicated that the other carbohydrate residues present (α-d-GalNAc and β-d-Gal) may also affect the pH-titration results. The reductive-methylation modification appears to affect the chemical shifts of the carbohydrate and peptide carbon atoms of the glycopentapeptide minimally.     

Telomere Length Distribution and Southern Blot Analysis

Southern blot analysis of terminal restriction fragments (TRFs) is the standard method for quantitative examination of telomere length distributions. Since TRFs contain a subtelomeric component, central parameters of the TRF distributionn(L) such as the arithmetic mean (M) or the median (Me) cannot be derived directly from Southern blot data, i.e. from the optical density distributionOD(L). Several estimates have been applied instead; the seeming arithmetic meanA, the “center of mass”C, and the positions of maximal (P) and half-maximal optical density (P). We show thatC>A>Mfor any non-truncated distributionsn(L), andP>M>P1/2 for any symmetrical unimodaln(L).Symmetric appearance on a Southern blot, however, suggests positive skewness ofn(L). Thus, alognormalform ofn(L) may be considered. Then,C>A>M>P=Me>P. Alternatively, aWeibulldistribution may be assumed. The latter is compatible with negative feedback-regulation of the telomere lengths. Using the maximum likelihood method we compare these distributions with FISH-data on telomere lengths in different cell types. The fit of the lognormal distribution is clearly superior. Lognormal genesis may relate to telomere breakage and recombination.Truncation of the upper end of the TRF distribution is possible due to Southern blot artifacts. Thereby, the order of the estimates may change toP>C>A. Having minimal sensitivity to truncation,Pseems to be the optimal choice. however, the variability ofPis high since peakedness ofOD(L) and DNA length resolution are inversely related.     

Measurement of the chlorophyll fluorescence induction kinetics with a 10 µs time resolution and its application in the forest decline research

Summary Measurement methods are described which determine the initial phase of the fluorescence induction kinetics with a maximum time resolution of 10 µs simultaneously for the two fluorescence componentsF ₆₈₅(t) andF ₁₃₀(t) selected by filters at the wavelengths 685 nm and 730 nm, respectively. The excitation light provided by a He-Ne laser (632.8 nm) is switched on within 0.3 µs (maximum intensityI _e=12 mW/cm²).F _o,F _p, andF _s, the initial-, peak-, and steady-state intensity and the initial valueR _o of the ratioR(t)=F ₇₃₀(t)/F ₆₈₅(t) can accurately be determined as well as the initial time derivativeF _o ^* of the fluorescence intensity.F _o andF _o ^* are related to the quantum yield _a of the antenna and to the photochemical quantum yield _pc, respectively. Spruce, oak, birch, poplar, and soy bean show a decline ofR(t) fromR _o to a first minimumR _b at some 10 ms which has a similar value as the second minimumR _p in the time range of seconds. Furthermore, the initial valueR _o and the steady-state valueR _S ofR(t) are also very similar. Measurements on spruce with water deficiency and with varying excitation light intensityI _e show effects on the initial phase of the fluorescence induction kinetics. Further measurements on spruce of different damage classes indicate that for the current year's needles the ratioF _p/F_o, is the most sensitive parameter to differentiate between the damage classes and thatF _o/F_s andR _o/R_b are also affected. As demonstrated by measurements on leaves of soy beans, the initial decrease ofR(t) fromR _o toR _b originates from a change of the fluorescence spectrum because no change of the leaf transmission can be observed in the time range between 10 µs and 1 ms.     

Synthesis and binding studies of 2-O- and 11-O-substituted N-alkylnoraporphines

We synthesized several novel 2-O- or 11-O-substituted N-alkylnoraporphines and assessed their affinities at dopamine D₁ and D₂, and serotonin 5-HT_1A receptors in rat forebrain tissue. Tested compounds displayed moderate to high affinities to D₂ receptors but low affinities to D₁ and 5HT_1A receptors. The findings accord with previous evidence of a lipophilic cavity on the surface of the D₂ receptor to accommodate N-alkyl moieties of aporphines. The most D₂-potent (K_i = 97 nM) and selective novel agent (>100-fold vs. D₁ and 5-HT_1A sites) was R(−)-2-(2-hydroxyethoxy)-11-hydroxy-N-n-propylnoraporphine (compound 11).     

Differential recruitment of bivalve species in the northern Wadden Sea after the severe winter of 1995/96 and of subsequent milder winters

High recruitment of the bivalves Cerastoderma edule, Mytilus edulis, Macoma balthica and Mya arenaria in summer after severe winters is an often reported phenomenon in the Wadden Sea. After the severe winter of 1995/96 however, only Cerastoderma and Mytilus followed this pattern in the Sylt-R?m? Bight. Repeated sampling of Cerastoderma, Macoma and Mya following a severe (1995/96), a moderate (1996/97), and a mild winter (1997/98) revealed that early recruitment was highest after the mild winter. In Cerastoderma the eventual high recruitment at the end of summer 1996 was caused by reduced benthic mortality. Low recruitment of Macoma and Mya after the severe winter may have been caused by a higher susceptibility to epibenthic predation and/or a higher susceptibility to passive re-suspension than in Cerastoderma and Mytilus. In all cases, post-settlement processes were decisive for reproductive success. Received in revised form: 7 May 2001 Electronic Publication     

A model separating leaf structural and physiological effects on carbon gain along light gradients for the shade-tolerant species Acer saccharum

A process-based leaf gas exchange model for C₃ plants was developed which specifically describes the effects observed along light gradients of shifting nitrogen investment in carboxylation and bioenergetics and modified leaf thickness due to altered stacking of photosynthetic units. The model was parametrized for the late-successional, shade-tolerant deciduous species Acer saccharum Marsh. The specific activity of ribulose-1,5-bisphosphate carboxylase (Rubisco) and the maximum photosynthetic electron transport rate per unit cytochrome f (cyt f) were used as indices that vary proportionally with nitrogen investment in the capacities for carboxylation and electron transport. Rubisco and cyt f per unit leaf area are related in the model to leaf dry mass per area (M_A), leaf nitrogen content per unit leaf dry mass (N_m), and partitioning coefficients for leaf nitrogen in Rubisco (P_R) and in bioenergetics (P_B). These partitioning coefficients are estimated from characteristic response curves of photosynthesis along with information on lear structure and composition. While P_R and P_B determine the light-saturated value of photosynthesis, the fraction of leaf nitrogen in thylakoid light-harvesting components (P_L) and the ratio of leaf chlorophyll to leaf nitrogen invested in light harvesting (C_B), which is dependent on thylakoid stoichiometry, determine the initial photosynthetic light utilization efficiency in the model. Carbon loss due to mitochondrial respiration, which also changes along light gradients, was considered to vary in proportion with carboxylation capacity. Key model parameters - N_m, P_R, P_B, P_LC_B and stomatal sensitivity with respect to changes in net photosynthesis (G_r) – were examined as a function of M_A, which is linearly related to irradiance during growth of the leaves. The results of the analysis applied to A. saccharum indicate that P_B and P_R increase, and G_f, P_L and C_B decrease with increasing M_A. As a result of these effects of irradiaiice on nitrogen partitioning, the slope of the light-saturated net photosynthesis rate per unit leaf dry mass (A^m_max) versus N_m relationship increased with increasing growth irradiance in mid-season. Furthermore, the nitrogen partitioning coefficients as well as the slopes of A^m_max versus N_m were independent of season, except during development of the leaf photosynthetic apparatus. Simulations revealed that the acclimation to high light increased A^m_max by 40% with respect to the low light regime. However, light-saturated photosynthesis per leaf area (A^a_max) varied 3-fold between these habitats, suggesting that the acclimation to high light was dominated by adjustments in leaf anatomy (A^a_max=A^m_maxM_A) rather than in foliar biochemistry. This differed from adaptation to low light, where the alterations in foliar biochemistry were predicted to be at least as important as anatomical modifications. Due to the light-related accumulation of photosynthetic mass per unit area, A^a_max depended on M_A and leaf nitrogen per unit area (N_a). However, N_a conceals the variation in both M_A and N_m (N_a=N_mM_A), and prevents clear separation of anatomical adjustments in foliage structure and biochemical modifications in foliar composition. Given the large seasonal and site nutrient availability-related variation in N_m, and the influences of growth irradiance on nitrogen partitioning, the relationship between A^a_max and N_a is universal neither in time nor in space and in natural canopies at mid-season is mostly driven by variability in M_A. Thus, we conclude that analyses of the effects of nitrogen investments on potential carbon acquisition should use mass-based rather than area-based expressions.     

Allozyme diversity and systematics inAnnonaceae—a pilot project

Five species ofAnnona and one species fromArtabotrys, Cananga, Polyalthia, andRollinia were investigated in regard to 11 different allozyme loci. Preliminary studies on small population samples ofAnnona suggest genetic uniformity in three species and variability within and between populations in two other species. The allotetraploid origin ofA. glabra is clearly shown by its hybrid enzyme bands. The genetic distance between fiveAnnona species partly corresponds with their morphological relationships; onlyA. muricata appears more separated than is suggested by morphology. A comparison of the five genera demonstrates close relationship betweenAnnona andRollinia. Two enzyme loci are identical within all taxa investigated and possibly may serve as a genetic marker for the family.     

Evidence for a folded conformation of the cell wall protein fromAcetabularia (Polyphysa) cliftonii

Summary The cell wall protein fromAcetabularia has a non-random structure in aqueous solution at pH 5.3, as determined on the basis of intrinsic viscosity, sedimentation velocity and small angle X-ray scattering experiments. This non-random structure is stable in a pH range of 4.5–6.8, as observed on the basis of circular dichroism and viscosity measurements, supporting that the cell wall protein has a specific folded structure. All hydrodynamic measurements, including small angle X-ray scattering in solution, in this pH range are consistent with a prolate ellipsoid model for the shape of this protein, with overall dimensions ofc=86.0 Å,b=7.0 Å, anda=7.5 Å, and with a radius of gyration ofR=39.5 Å. The possibility of a coiled shape was investigated using a worm-like chain model, but it was inconsistent with the experimental data. Instead, a filled particle with uniform density which is equivalent in the scattering behavior is proposed. By a comparison of the observed radius of gyration, R_g=39.5 Å, and the radius of gyration of the cross section,R _c =7.5 Å, we were able to describe the cell wall protein in terms of a prolate ellipsoid of revolution. Comparisons of the experimental scattering curve, plotted as logl (h) versus logh, with the corresponding plots of normalized intensities, calculated for particles of particular shape and various axial ratios indicate a very asymmetric shape for the cell wall protein fromAcetabularia.This research was supported by a grant of the Deutsche Forschungsgemeinschaft.     

Abstract biological systems as sequential machines: III. Some algebraic aspects

Using the relationship between (M,R) and sequential machines developed in previous work, it is shown that the totality of (M,R) which can be formed over a given categoryA itself forms a category in a natural fashion.     

常绿阔叶林8种乔灌木叶片氮含量及其分配与光合能力的关系

以浙江天童国家森林公园常绿阔叶林为研究对象,采用空间代替时间的方法,研究了5个不同演替阶段常见的4种乔木以及4种灌木叶片的光饱和速率(Pmax)、光合氮素利用效率(PNUE)及其与叶片氮含量(NL)、叶片氮素在细胞壁的分配比例(细胞壁N/叶片总N,NCW/NL)、氮素在光合酶中的分配比例(NR/NL)、单位面积叶干重(LMA)的相互关系。结果表明:(1)演替系列4种乔木和4种灌木各种间指标除NL外均表现出显著差异,前期种较后期种具有更高的NR/NL、PNUE、Pmax,而后期种LMA、NCW/NL、MCW/ML(细胞壁干重/叶片总干重)更大,NL在乔木各种间差异不明显,在灌木种间则差异显著;乔木种较灌木种具有更大的LMA、NCW/NL、MCW/ML,而NR/NL则较灌木小;8种植物的Pmax与NL以杨梅为最高,连蕊茶最低;苦槠具有最高的PNUE,而栲树最低。(2)随着演替的进行,前期种的NR/NL、PNUE、Pmax有减小趋势,而LMA、NCW/NL、MCW/ML逐渐增大,后期种则表现出相反的趋势。(3)NR/NL与Pmax、PNUE之间呈显著正相关关系,而LMA、NCW/NL、MCW/ML则与Pmax、PNUE、NR/NL显著负相关。研究认为,NR/NL与NCW/NL之间的负相关性及其对PNUE的影响可以在一定程度上解释树木在光合与维持两方面的权衡关系以及演替的生理机制。     

Regulation of biosynthesis of pesticidal metabolic complexes inStreptomyces griseus

The complex of pesticidal metabolites produced byStreptomyces griseus LKS-1 consists of a peptide antibiotic (A), nonactic acids (B), macrotetrolides (C), pyrrolizines (D), and of cycloheximide. The latter unwanted phytotoxic compound was eliminated by treatment with mutagens. Combined approaches, including both genetic and physiological manipulations, resulted in the following alterations in the biosynthetic capacity: (1) A more than 80-fold increase in the production of C under a substantial decrease in the yields ofA, B andD, the ratio of the components ofC being steered toward the required more active ones; (2) a more than 300-fold increase in the production ofB under suppression of the formation ofA andC: (3) a 10-fold increase in the yields ofD under suppression ofA andC; (4 a significant increase in the yields ofA with eliminatingB, C andD. The level of inorganic phosphate in fermentation media and the sensitivity of the organism to carbon catabolite repression were important factors participating in the regulation of the above biosynthetic processes.     

Stress-strain behavior for curved exponential strips

For the two-parameter (A, α) exponentially-stiffening constituitive relation, typical of many biological materials, it is shown that the uniaxial stress-strain behavior of an initially curved strip is significantly changed by the residual bending stresses. Closedform theoretical results depend on the thickness to radius ratio (h/R) and the relative strain level ε(h/R). The bending stresses tend to obscure accurate measurement ofA and α unless care is taken. However, it is shown that by changing co-ordinates to (dℝ/d∈, ℝ)-space, bothA and α can be recovered from the high stress data, and α alone can be recovered from the low stress data. This has practical application to the mechanics of cornea, sclera, and heart muscle.     

Additive genetic variance within populations derived by single-seed descent and pod-bulk descent

Summary Breeders of self-pollinated legumes commonly use single-seed descent (SSD) or pod-bulk descent (PBD) to produce segregating populations of highly inbred individuals. We presented equations for the expected value of the additive genetic variance within populations derived by SSD (E(V _A)_SSD) and PBD (E(V _A)_PBD) in terms of the initial population size (N ₀), the number of seed harvested per pod (M), the probability of survival of an individual (), and the generation at which the population is evaluated (S _t). Differences between (E(V _A)_SSD) and (E(V _A)_PBD) are due to differences in the expected amount of random drift which occurs with the two methods after the S ₀ generation. With both methods, random drift occurs when progeny are sampled from heterozygous parents. An additional component of random drift occurs when sampled progeny fail to survive during SSD, or when sampling occurs amoung families during PBD. For values of N ₀, M, , and S _t that are typical of soybean (Glycine max (L.) Merr.) breeding programs, (E(V _A)_SSD) will be greater than (E(V _A)_PBD). The ratio of (E(V _A)_SSD) to (E(V _A)_PBD) will: (1) increase as M and increase; (2) approach a value of 1.00 as N ₀ increases; and (3) be a curvilinear function of S _t. Plant breeders should compare SSD and PBD based upon values of (E(V _A)_SSD) and (E(V _A)_PBD) and the expected cost of carrying out the two methods.Contribution No. 2910 of the South Carolina Agricultural Experiment Station, Clemson University     

Within-canopy variation in the rate of development of photosynthetic capacity is proportional to integrated quantum flux density in temperate deciduous trees

The present study was undertaken to test for the hypothesis that the rate of development in the capacity for photosynthetic electron transport per unit area (J_max;A), and maximum carboxylase activity of Rubisco (V_cmax;A) is proportional to average integrated daily quantum flux density (Q_int) in a mixed deciduous forest dominated by the shade‐intolerant species Populus tremula L., and the shade‐tolerant species Tilia cordata Mill. We distinguished between the age‐dependent changes in net assimilation rates due to modifications in leaf dry mass per unit area (M_A), foliar nitrogen content per unit dry mass (N_M), and fractional partitioning of foliar nitrogen in the proteins of photosynthetic electron transport (F_B), Rubisco (F_R) and in light‐harvesting chlorophyll‐protein complexes (V_cmax;A ∝ M_AN_MF_R; J_max;A ∝ M_AN_MF_B). In both species, increases in J_max;A and V_cmax;A during leaf development were primarily determined by nitrogen allocation to growing leaves, increases in leaf nitrogen partitioning in photosynthetic machinery, and increases in M_A. Canopy differences in the rate of development of leaf photosynthetic capacity were mainly controlled by the rate of change in M_A. There was only small within‐canopy variation in the initial rate of biomass accumulation per unit Q_int (slope of M_A versus leaf age relationship per unit Q_int), suggesting that canopy differences in the rate of development of J_max;A and V_cmax;A are directly proportional to Q_int. Nevertheless, M_A, nitrogen, J_max;A and V_cmax;A of mature leaves were not proportional to Q_int because of a finite M_A in leaves immediately after bud‐burst (light‐independent component of M_A). M_A, leaf chlorophyll contents and chlorophyll : N ratio of mature leaves were best correlated with the integrated average quantum flux density during leaf development, suggesting that foliar photosynthetic apparatus, once developed, is not affected by day‐to‐day fluctuations in Q_int. However, for the upper canopy leaves of P. tremula and for the entire canopy of T. cordata, there was a continuous decline in N contents per unit dry mass in mature non‐senescent leaves on the order of 15–20% for a change of leaf age from 40 to 120 d, possibly manifesting nitrogen reallocation to bud formation. The decline in N contents led to similar decreases in leaf photosynthetic capacity and foliar chlorophyll contents. These data demonstrate that light‐dependent variation in the rate of developmental changes in M_A determines canopy differences in photosynthetic capacity, whereas foliar photosynthetic apparatus is essentially constant in fully developed leaves.     

Selective distortion of the planar group CαC'(O)O to a chiral flat tetrahedron in the amino acid alanine

Based on a Cambridge Structural Database (CSD) search, a meta‐analysis of 116 structures of alanine H₃NC_αH(CH₃)C′(O)O and its derivatives H₃NC_αH(CH₃)C′(O)O(H/R/M), protonated, esterified, or coordinated at the carboxylic group, shows that in the first step of a chirality chain, the L configuration at C_α induces (M) and (P) conformations with respect to rotation around the central C′─C_α bond. In the second step, the (M) and (P) conformations selectively distort the planar carboxylic group C_αC'(O_cis)O_trans to asymmetric flat (R) and (S) tetrahedra. High diastereoselectivities are caused by the two players attraction N…O_cis and repulsion O_trans…C_Me, which work together in (L,M,R) configurations but against each other in (L,P,S) configurations.