A rapid computer technique for analysing molecular interactions

A rapid method for analysing enzyme — substrate interactionsusing a discriminant analysis program is described. This technqueidentifies the structural features of substrate molecules whichare important in determining metabolic activity. Two model systems,nucleoside diphosphatase activity of Golgi membranes and theinteraction of yeast hexokinase with a range of D-sugars, areused as illustrations of the technique. The conclusions fromboth models are consistent with those previously obtained fromanalytical techniques. Received on January 21, 1986; accepted on April 1, 1986     

Spatial and temporal variations in the composition and density of crustacean plankton in the five basins of Lake Kariba, Zambia-Zimbabwe

Lake Kariba is a man-made reservoir which is now over 30 yearsold. The reservoir was built on the Zambezi river on the borderbetween Zambia and Zimbabwe. The crustacean zooplankton of thisman-made lake were studied over 3 years from March 1986 to February1988. This period included three seasons — (i) warm, rainyseason, (ii) cool, dry season and (iii) warm, dry season —which have a major influence on the limnology of the lake. Crustaceanplankton species composition and abundance varied among thefive basins. The most upstream basin had the highest numberof species and highest densities at all the sampling times overthe period of this study. There was both spatial and temporalheterogeneity in species composition and abundance along thelong axis of the lake. ¹Present address: Department of Biological Science, Universityof Botswana, P. Bag 0022, Gaborone, Botswana     

Water Stress and --SH-Dependent Physiological Activities in Young Maize Plants

In young maize plants, water stress affects the —SH-dependentactivities: photosynthesis and dark respiration are reducedto about 60% at the wilting point; protein synthesis is inhibitedeven by moderate stress; and nitrate reductase activity is immediatelyinhibited also, prior to significant changes in the water statusof the plant As protoplasmatic protein denaturation occurs,protein —SS—increases at the expense of —SH,with consequent decrease of the —SH/—SS— ratio.The linear correlation between —SH/—SS— ratioand —SH-dependent activities suggests a strict dependencebetween them. A moderate increment both in rhodanese activityand labile sulphide content has been also demonstrated at thebeginning of the stress.     

Interfacing similarity search software with the sequence retrieval system ACNUC

A method of interfacing sequence similarity search softwarewith the fast sequence retrieval system ACNUC is described.The method is written in FORTRAN 77 and is straightforward toimplement because no textprocessing code is required —a minimum of 12 extra lines of FORTRAN provided the interfacefor most applications. The method is also efficient, since sequencesare located by simple indexing techniques, with no linear searchesof large database files necessary. Received on November 20, 1986; accepted on January 8, 1987     

A demonstration of pharmacokinetics and physiological modelling using a microcomputer for data capture and analysis

We describe a simple and inexpensive demonstration of mass transportand exchange using dye clearance from a hydro-dynamic model.A microcomputer was used for data acquisition and storage, non-linearleast squares curve fitting, compartmental analysis and parameterestimation. The system is useful for demonstrating the indicator— dilution technique for fluid volume measurement andcompartmental analysis in pharmacokinetics. Received on August 8, 1986; accepted on September 25, 1986     

Metabolism of (--)-kaurene-3H and (--)-kaurenol-3H during the photoperiodic floral induction in Pharbitis nil

(—)-Kaurene-U-³H was metabolized in seedlings of Pharbitisnil, a short-day plant, to labeled ( — )-kaurenol, ( —)-kaurenal, ( — )-kaurenoic acid, and unidentified polarsubstances, in this sequence. No significant effect of photoperiodicfloral induction upon the metabolism of ( — )-kaurene-U-³Hor ( — )-kaurenol-U-³H was observed, which suggests that( — )-kaurene metabolism is not involved in photoperiodicfloral induction ¹This work was supported in part by grants from the Ministryof Education. (Received September 24, 1970; )     

Day/night temperature environment affects cell elongation but not division in Lilium longiflorum Thunb

Lilium tongiflorum Thunb. cv. ‘Nellie White’ plantswere grown in different day/night temperature (DT/NT) environmentsto determine the anatomical basis for differential responsesof stem elongation to DT and NT. Lilium plants were forced in1986 and 1987 under 25 and 12 different DT/NT environments,respectively, with temperatures ranging from 14 to 30 °C.Parenchyma and epidermal cell length and width were measuredin stem tissue (1987) and epidermal cell length and width weremeasured in leaf tissue (1986). Total cell number per internodeand vertical cell number per internode were calculated. Stemparenchyma and stem and leaf epidermal cell length increasedlinearly as the difference (DIF) between DT and NT increased(DIF = DT —- NT), i.e. as DT increased relative to NT.DIF had no effect on stem parenchyma width, stem and leaf epidermalcell width, or cell number per internode. Data suggested thatstem elongation responses to DIF are elicited primarily througheffects on cell elongation and not division. Key words: Thermoperiodism, thermomorphogenesis, stem elongation, DIF, cell division, cell elongation, leaf expansion     

Isocitrate Lyase from Germinating Soybean Cotyledons: Purification and Characterization

Ruchti, M. and Widmer, F. 1986. Isocitrate lyase from germinatingsoybean cotyledons: purification and characterization.—J.exp. Bot. 37: 1685–1690. Isocitrate lyase (E.C. 4.1.3.1 [EC] ) was purified from the cotyledonsof 7-d-old soybean seedlings. Three molecular forms were detectedwith pi values of 6·46, 6·25 and 6·0. Themain form (pl = 6·46) had an approximate Mr of 130000,a pH optimum of 8·0, a K_m (isocitrate) close to 2·0mol m^–3 and a molecular activity of 615 min ^–1 at25 °C. The purified enzyme is not a glycoprotein and isheat labile. Key words: Isocitrate lyase, soybean     

Grazing of echinoderm larvae (Paracentrotus lividus and Arbacia lixula) on naturally occurring particulate matter

Larvae (72 hr old) of P. lividus and A. lixula grazed on varioussuspensions of natural particulate matter with a size rangeof 2 to 30 microns, and on two species of algae (Phaeodactylumtricor-nutum and Nitzschia sp.) — Larvae graze most in the size range where the particleconcentration is highest. — If larvae deplete certain size categories of particlesthey then graze other size ranges in which the concentrationis still high. — The grazing rate of the two species varied between 988and 91.949 µm³ per pluteus per hour. — For A. lixula larvae the grazing rate increases withincreasing temperature to a maximum at 22°C.     

Dynamics of dolphin porpoising revisited

Porpoising is the popular name for the high-speed surface piercingmotion of dolphins and other species, in which long, ballisticjumps are alternated with sections of swimming close to thesurface. The first analysis of this behavior (Au and Weihs,1980) showed that above a certain "crossover" speed this behavioris energetically advantageous, as the reduction in drag dueto movement in the air becomes greater than the added cost ofleaping. Since that publication several studies documented porpoisingbehavior at high speeds. The observations indicated that thebehavior was more complex than previously assumed. The leapswere interspersed with relatively long swimming bouts, of abouttwice the leap length. In the present paper, the possibilityof dolphins using a combination of leaping and burst and coastswimming is examined. A three-phase model is proposed, in whichthe dolphin leaps out of the water at a speed U_f, which is thefinal speed obtained at the end of the burst phase of burstand coast swimming. The leap is at constant speed and so theanimal returns to the water at U_f, goes to a shallow depth andstarts horizontal coasting while losing speed, till it reachesU_i. At that point it starts active swimming, accelerating toU_f. It then starts the next leap. Ranges of speeds for whichthis three-stage swimming is advantageous are calculated asa function of animal and physical parameters. Notation C—Constant defined in equation (12) C_D—Coasting drag coefficient D—Drag g—Gravitational acceleration H—Height of jump J—Energy required for jump k—Ratio of swim length to jump length l—Distance L—Total distance (eq. 28) m—Added mass M—Animal mass M₁—Total mass r—Coefficient defined in eq. (22) R—Ratio of energies, for three-phase swimming R₂—Ratio of energies, for burst and coast swimming t—Time T—Thrust U—Speed V—Body volume W—Weight     

The Mode of Action of Benzoic Acid and Some Related Compounds on Flowering in Lemna paucicostata

Benzoic acid (BA) (10 µM) added to the medium during onlythe first 24 h of culture induced flowering in Lemna paucicostata151 even under continuous light at 24.5?C when 1/10 M medium(pH 4.0) containing 1 µM benzyladenine (BAd) was usedas the basic medium. Flower buds were produced on the 4th–5thday and almost all the fronds that developed during the subsequent3–4 days had flower buds. Even a 4-h treatment with BA(50 µM) followed by culture in the basic medium inducedflowering. This suggests that the effect of BA is inductive.A similar effect of BA was observed in strain 381, a sensitiveshort-day plant, but not in strain 441 or 6746. Even in the absence of BAd in the medium, a 24-h treatment withBA induced flowering, but the induced state disappeared rapidlyafter the 5th-6th day. BAd was effective when given after theBA treatment and had no significant effect when added duringthe BA treatment. BA given after a single inductive dark periodalso promoted flowering in strains 441 and 381. BAd seems towork to sustain the induced state or to promote the developmentof flower buds rather than inducing flowering. A short-term treatment with nicotinic acid (NA) at 200–500µM was as effective as 10µM BA, but that with salicylicacid (SA) was ineffective at all concentrations tested. 5-C1-SAand EDDHA were also effective, although not as effective asBA. (Received April 10, 1986; Accepted July 12, 1986)     

Dorsiventrality in Photosynthetic Light Response Curves of a Leaf

Terashima, I. 1986. Dorsiventrality in photosynthetic lightresponse curves of a leaf.—J. cxp. Bot. 37 399–405 The photosynthetic light response curve of a leaf of Glycinemax (L.) Merrill obtained by illuminating the adaxial side layabove that obtained by illuminating the abaxial side. However,after inverting the leaf for 11 d, the curve obtained by illuminatingthe abax.ial side came to lie slightly above that obtained byilluminating the adaxial side. The difference in the shape oflight response curves is satisfactorily explained only whenthe intra-leaf heterogeneities in light absorption and in photosyntheticactivity are taken into account. Key words: Photosynthetic rate, direction of illumination     

Graphics of RNA secondary structure; towards an object-oriented algorithm

We present a new algorithm for the display of RNA secondarystructure. The principle of the algorithm is entirely differentfrom those currently in use in that our algorithm is ‘objectoriented’ while currrent algorithms are ‘procedural’.The circular RNA molecule of chrysanthemum stunt viroid wasused as input data for demonstrating the operation of the program.The major interest of this method will be found in its potentialuse in simulation graphics of RNA folding processes. Received on October 9, 1986; accepted on February 17, 1987     

Whole Plant Studies using Radioactive 13-Nitrogen: IV. A COMPARTMENTAL MODEL FOR THE UPTAKE AND TRANSPORT OF AMMONIUM IONS BY ZEA MAYS

Presland, M. R. and McNaughton, G. S. 1986. Whole plant studiesusing radioactive 13-nitrogen IV. A compartmental model forthe uptake and transport of ammonium ions by Zea mays.—Jexp. Bot. 37: 1619–1632 Ammonium ion uptake by roots of hydroponically grown maize seedlingsand the transport of ammonium-sourced nitrogen to the shootwere measured using the short-lived isotope 13-nitrogen. Theyare shown to be described by a five compartment model—ammoniumin the root bathing solution, ammonium entering the root, nitrogenbound in the root, nitrogen outside the load region but stillwithin the root, and nitrogen in the shoot. Once taken intothe root symplasm, ammonium-sourced nitrogen was not exchangedwith the external solution. Activity-time profiles for nitrogentransported both basally and apically from the load region ofthe root implied the existence of large well-mixed pools inthe transport path, though the capacity of the pools inferredfrom modelling the profiles was greater than found by dissectingroots following loading with labelled ammonium. Key words: Ammonium uptake, Zea mays, compartmental model, 13-nitrogen     

Hyperbolic regression analysis for kinetics, electrophoresis, ELISA, RIA, Bradford, Lowry, and other applications

Hyperbolic regression analysis is an effective method for fittingexperimental data points obtained from a variety of experimentsin molecular biology, including enzyme kinetics, agarose gelelectrophoresis of DNA fragments, SDS—polyacrylamide gelelectrophoresis of proteins, enzyme–linked immunosorbentassays (ELISA), radioimmunoassays (RIA), Bradford protein quantitationassays, Lowry protein assays, and other applications. Hyperbolicregression yields excellent fitted curves without the biasesthat are introduced by carrying out linear regression on doublereciprocal coordinates, and it produces one simple equation,encompassing all the data points, that can be used easily ina pocket calculator to estimate the values of unknown samplesfrom the known standards. Received on February 9, 1986; accepted on April 11, 1986     

Dielectric-Gravimetric Measurements on Fucus vesiculosus and Ascophyllum nodosum During Dehydration

Careri, G., Giansanti, A. and Fensom, D. 1986. Dielectnc-gravimetricmeasurements on Fucus vesiculosus and Ascophyllum nodosum duringdehydration.—J. exp. Bot. 37: 375–378. Samples of the marine algae Fucus vesiculosus and Ascophyllumnodosum were dehydrated between plates of a condenser so thatsimultaneous measurements of dielectric properties and rateof water loss could be made. During the desiccation process,both the evaporation rate and the dielectric properties becomezero at a critical hydration H_c, indicating that for H <H_c,the residual water must be in a tightly bound state. The absolutevalues of H_c, depend on the nature of the sample, but they arein the range 0·1–0·3, well above the hydrationlimit for active ion uptake (H=0·02). It is concludedthat, in these fucoids, living cells are maintained in the hydrationregion where water is in the bound state only. Key words: Fucus, Ascophyllwn, dielectric, dehydration     

Flower-Promoting Effects of Iron and EDDHA in Lemna paucicostata 151

Lemna paucicostata 151 cultured in 1/10 strength M medium containing50 µM FeCl₃ easily flowered in response to short days,although it scarcely flowered under any photoperiod when themedium contained the standard amount of iron (2 µM FeCl₃).The flowering response was accomparied by an increase in theiron content of the plants, which was maximal at pH 5.0. Instandard M medium containing 50 µM FeCl³, this plant didnot flower even though it had a high iron content. Ethylenediamine-di (o-hydroxyphenylacetic acid) (EDDHA) inducedflowering of this strain under continuous light even in theabsence of iron and copper, and its effect was slightly loweredby the presence of iron in the medium. Thus the flower-inducingactivity of EDDHA could not be attributed to the action of ironor copper. EDTA inhibited both the iron uptake and floweringin Fe-rich medium under short-day conditions. (Received May 16, 1986; Accepted July 25, 1986)     

Pressure Effects on Membrane Potentials of Mesophyll Cell Protoplasts and Epidermal Cell Protoplasts of Commelina communis L.

Pantoja, O. and Willmer, C. M. 1986. Pressure effects on membranepotentials of mesophyll cell protoplasts and epidermal cellprotoplasts of Commelina communis L.—J. exp. Bot. 37:315–320. Membrane potentials of epidermal cell protoplasts and mesophyllcell protopiasts of Comnelina communis were measured when theprotoplasts were immobilized in a suction micropipette. Whenzero suction was employed, membrane potentials of both protoplasttypes were near to zero. As suction pressure was increased,membrane potentials became increasingly more negative with gradientsof 14·3 mV/kPa and 10·5 mV/kPa for mesophyll cellprotoplasts and epidermal cell protoplasts, respectively. Theplasma membrane is stretched when suction pressure is appliedto protoplasts and it is considered that this simulates cellturgor pressure which is associated with negative membrane potentialsof intact cells. The results help to explain why some investigatorsobtain positive membrane potentials for protoplasts while othersobtain negative values. The results also indicate that considerablecaution is needed in the interpretation of ion flux data whenprotoplasts are used. Key words: Commelina communis, membrane potentials, pressure, protoplasts     

A simple method for predicting the secondary structure of globular proteins: implications and accuracy

A method is presented for predicting the secondary structureof globular proteins from their amino acid sequence. It is basedon a rigorous statistical exploitation of the well-known biologicalfact that the amino acid compositions of each secondary structureare different. We also propose an evaluation process that allowsus to estimate the capacity of a method to predict the secondarystructure of a new protein which does not have any homologousproteins whose structure is already known. This evaluation processshows that our method has a prediction accuracy of 58.7% overthree states for the 62 proteins of the Kabsch and Sander (1983a)data bank. This result is better than that obtained by the mostwidely used methods—Lim (1974), Chou and Fasman (1978)and Garnier et al. (1978)—and also than that obtainedby a recent method based on local homologies (Levin et al.,1986). Our prediction method is very simple and may be implementedon any microcomputer and even on programmable pocket calculators.A simple Pascal implementation of the method prediction algorithmis given. The interpretation of our results in terms of proteinfolding and directions for further work are discussed. Received on December 15, 1987; accepted on April 12, 1988     

Simulation of the Structural Development of Warm-Temperate Rain Forest Stands

The change in all-sized dbh distribution with stand age wassimulated using data from secondary stands of different agesafter clear-felling in warm-temperate rain forests in YakushimaIsland, southern Japan. The cumulative basal area [cm² m^–2]of all trees larger than a given dbh x [cm] was used as an indexof onesided density effect, which primarily regulates the growthrate and mortality of the tree at x. The relative growth ratein dbh was expressed by a negative linear function of both thecumulative basal area and logarithmic dbh, irrespective of standage. Mortality was found to be positively related to the cumulativebasal area. From these empirical relations, the change in dbhdistribution during the course not only of stand developmentafter clear-felling, but also of gap regeneration within primaryforests, was successfully simulated using the continuity equation,eliminating ‘stand age factors’ from the model.Results of the simulation satisfied the —3/2 power lawof self-thinning. Competition, continuity equation, cumulative basal area, simulation, size distribution, stand dynamics, —3/2 power law, warm-temperate rain forest, Yakushima Island