A program for the graphic representation and manipulation of DNA sequences

We have developed a program for the graphic representation andmanipulation of DNA sequences. The program (named CARTE fromthe French for ‘map’) is intended as a tool in theplanning and analysis of recombinant DNA experiments. DNA sequencesare represented as standard restriction maps, using any desiredcombination of restriction enzymes. Features of interest, suchas promoters or coding sequences, can be highlighted. The sequencecan be manipulated to mimic cloning, using deletions, insertionsor replacements at specified sites. This process is facilitatedby the simultaneous display of a graphic map of the entire sequence,a detailed picture of the work in progress, and a menu of functions. Received on November 17, 1986; accepted on March 12, 1987     

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     

Factors determining Petal Colour of Baccara Roses III: EFFECT OF THE RATIO BETWEEN CYANIN AND PELARGONIN

The changes in colour and in the pigment concentration of thetwo sides of Baccara rose petals which occur when plants aregrown under various temperature regimes, were examined. Theinner side of the petal is redder and the predominant pigmentis pelargonin whereas the outer petal surface tends to ‘blue’,and, the predominant pigment on this side is cyanin. The cyanin:pelargonin ratio on the outer side of petals increased three-foldunder the influence of low temperatures. The outer surface of petals growing for a long period underlow tempertaures was ‘blue’ when compared with thered petals which had been subjected to low temperatures fora short period. The cyanin: pelargonin ratio of ‘blue’petals was higher than that of red petals. Total pigment contentwas similar in both types of petal. Flowers grown under hightemperatures ‘blued’ without a concomitant fallin the cyaninpel: argonin ratio. Examination of colour solutions in which the ratio between cyaninand pelargonin was varied revealed that the colour of the solutionbecame bluer as this ratio increased. We suggest that the ‘blueing’ of Baccara rose petalsis caused primarily by a dilution of the cyanin content, butwhen the ratio between cyaniri and pelargonin increases sharply,‘blueing’ may also occur in dark flowers in whichthe total pigment content did not diminish.     

Confusion in the use of the taste adjectives 'sour' and 'bitter'

Subjects from Britain and America were tested on their skillat applying the taste adjectives ‘sweet’, ‘sour’,‘salty’, and ‘bitter’ to clearly distinguishablesolutions of sucrose, citric acid, NaCl and quinine sulphate,respectively. The main error that occurred was calling citricacid ‘bitter’ while the tendency to call quininesulphate ‘sour’ was not so common; this is the wellknown sour-bitter confusion. A sour-salty confusion was alsonoted as well as a tendency to call citric acid ‘sweet’.All these confusions were rectified by mere definition usingstandards. Skill at applying taste adjectives was not alwaysfound to be consistent over time. More errors occurred at lowersolution concentrations, even though stimuli were clearly distinguishable;indistinguishability of stimuli may account for some confusionsin other studies. ^*Present address: Department of Psychology, University of Bristol,Bristol BS8 1HH, England.     

A program for predicting significant RNA secondary structures

We describe a program for the analysis of RNA secondary structure.There are two new features in this program. (i) To get vectorspeeds on a vector pipeline machine (such as Cray X-MP/24) wehave vectorized the secondary structure dynamic algorithm. (ii)The statistical significance of a locally ‘optimal’secondary structure is assessed by a Monte Carlo method. Theresults can be depicted graphically including profiles of thestability of local secondary structures and the distributionof the potentially significant secondary structures in the RNAmolecules. Interesting regions where both the potentially significantsecondary structures and ‘open’ structures (single-strandedcoils) occur can be identified by the plots mentioned above.Furthermore, the speed of the vectorized code allows repeatedMonte Carlo simulations with different overlapping window sizes.Thus, the optimal size of the significant secondary structureoccurring in the interesting region can be assessed by repeatingthe Monte Carlo simulation. The power of the program is demonstratedin the analysis of local secondary structures of human T-celllymphotrophic virus type III (HIV). Received on August 17, 1987; accepted on January 5, 1988     

A program for drawing evolutionary trees

From the measures of evolutionary distance between pairs ofsequences in a set, it is possible to infer the genetic treeor trees which best fit these known data. DENDRON is a new program,written in FORTRAN 66, which computes an initial tree from thebottom-up, then searches among increasingly divergent treesfor a better fit. As a check on the consistency of the measures,the program tests all triplets for the triangle inequality.DENDRON also calculates a single ‘top-down’ tree,progressing from the trunk to the twigs, for comparison withthe ‘bottom-up’ trees. Received on August 17, 1987; accepted on June 1, 1988     

RNA secondary structures: comparison and determination of frequently recurring substructures by consensus

A method for assessing the preserved stem - loops of RNA secondarystructures is presented. Frequently recurring helical stemsin a set of secondary structures resulting from the simulatedfolding process of a given RNA are assessed and consensus structuralmotifs can then be selected to construct a secondary structureof the RNA. Alternatively, it can be applied to a series of‘optimal’ and ‘suboptimal’ secondarystructures computed using the dynamic program developed by Williamsand Tinoco. To demonstrate the power and the usefulness of theprogram we give examples of this procedure. Received on October 28, 1987; accepted on April 2, 1989     

The Sensitivity of Light Modulation of Enzyme Activity to Arsenite and Sulphite and of Photosynthetic Induction toArsenite is Determined by a Cytoplasmic Gene

Muschinek, G., Alscher, R. and Anderson, L. E. 1987. The sensitivityof light modulation of enzyme activity to arsenite and sulphiteand of photosynthetic induction to arsenite is determined bya cytoplasmic gene—J. exp. Bot. 38: 1069–1075. The membrane component of the light modulation system was moresensitive to arsenite and to sulphite in the Pisum cultivar‘Nugget’ than in the cultivar ‘Progress No.9’. Likewise, the induction phase of CO₂ fixation wasmore arsenite sensitive in chloroplasts isolated from ‘Nugget’plants. Sensitivity was controlled by a cytoplasmic gene. Key words: Induction, light modulation, arsenite sensitivity     

Recognition of characteristic patterns in sets of functionally equivalent DNA sequences

An algorithm has been developed for the identification of unknownpatterns which are distinctive for a set of short DNA sequencesbelieved to be functionally equivalent. A pattern is definedas being a string, containing fully or partially specified nucleotidesat each position of the string. The advantage of this ‘vague’definition of the pattern is that it imposes minimum constraintson the characterization of patterns. A new feature of the approachdeveloped here is that it allows a ‘fair’ simultaneoustesting of patterns of all degrees of degeneracy. This analysisis based on an evaluation of inhomogeneity in the empiricaloccurrence distribution of any such pattern within a set ofsequences. The use of the nonparametric kernel density estimationof Parzen allows one to assess small disturbances among thesequence alignments. The method also makes it possible to identifysequence subsets with different characteristic patterns. Thisalgorithm was implemented in the analysis of patterns characteristicof sets of promoters, terminators and splice junction sequences.The results are compared with those obtained by other methods. Received on November 17, 1986; accepted on June 15, 1987     

Immunological Identification of a Putative Precursor of the Insoluble Glycoprotein Framework of the Chlamydomonas Cell Wall

To identify precursors of the insoluble glycoprotein frameworkof the Chlamydomonas cell wall, a polyclonal antibody was raisedagainst the mixture of polypeptides released from the insolublewall fraction by chemical deglycosylation. This antibody preferentiallycross-reacted with a ‘150 kDa’ salt-soluble cellwall glycoprotein. The conclusion that this ‘150 kDa’glycoprotein is a putative precursor of the insoluble cell wallfraction was corroborated by the results of pulse-chase experimentsand by experiments with antibodies raised against the ‘150kDa’ salt-soluble glycoprotein and against its 100 kDadeglycosylation product, respectively. Whereas the antibodyagainst the ‘150 kDa’ glycoprotein preferentiallyrecognized carbohydrate side chains, the antibody against its100 kDa deglycosylation product was found to have essentiallythe same specificity towards glycosylated and deglycosylatedcell wall components as the antibody against the deglycosylationproducts of the insoluble wall fraction. Furthermore, the antibodyagainst the deglycosylated, insoluble wall fraction recognizedalmost the same set of peptide fragments derived by V8 proteasetreatment from the ‘150 kDa’ salt-soluble cell wallglycoprotein and its 100 kDa deglycosylation product, respectively,as the antibody against the 100 kDa deglycosylated cell wallpolypeptide. (Received April 22, 1994; Accepted November 21, 1995)     

Errors between sites in restriction site mapping

Restriction site mapping programs construct maps by generatingpermutations of fragments and checking for consistency. Unfortunatelymany consistent maps often are obtained within the experimentalerror bounds, even though there is only one actual map. A particularlyefficient algorithm is presented that aims to minimize errorbounds between restriction sites. The method is generalizedfor linear and circular maps. The time complexity is derivedand execution times are given for multiple enzymes and a rangeof error bounds. Received on July 17, 1987; accepted on November 3, 1987     

Temperature Effects on Phenological Development and Yield of Muskmelon

Our goal was to construct a simple muskmelon phenology modelthat could be run with easily obtainable weather station dataand used by growers to quantify phenological development andaid in projecting harvest dates. A growth chamber experimentwas conducted with two cultivars of muskmelon (‘Gold Rush’and ‘Mission’) to determine how main vine leaf appearancerates responded to temperature. We identified three cardinaltemperatures for leaf appearance rate: the base temperature(10 °C) at which leaf appearance rate was zero; an optimumtemperature (34 °C) at which the rate of leaf appearancewas maximal; and an upper threshold temperature (45 °C)at which leaf appearance rate returned to zero. Using thesethree cardinal temperatures, we constructed a simplified thermalunit accumulator for hourly measurements of air temperature.Main vine plastochron interval (PI), thermal time to harvest,and final yield were determined for three cultivars of muskmelon(‘Explorer’, ‘Gold Rush’ and ‘Mission’)grown in the field at Overton, TX, USA, over six transplantingdates from March to June 1998. PI was calculated for each cultivarx transplanting date combination as the reciprocal of the slopeof main vine node number vs. accumulated hourly thermal units(     

'Callose' in the Impermeable Seed Coat of Sesbania punicea

Dry legumes of Sesbania punicea (Cav.) Benth. contain impermeableseeds which are either beige-greenish or reddish. When keptin water for over one year they do not swell. Quick imbibitionwas induced by a deep cut, abrasion with coarse abrasive paper,immersion in concentrated sulphuric acid, in boiling water andin boiling KOH solutions. Neither lipid solvents (acetone, chloroform,cyclohexane, diethyl ether, ethanol, xylene), nor, at room temperature,KOH solutions up to 50% per cent, permeabilized the seeds. Astrong barrier to water entry appeared to be located in thepalisade layer which showed ‘light points’ in places,and which seemed to be transversal thickenings. In the testa,‘ callose’, which may play a role in the impermeabilityof the Sesbania punicea seed, was detected. Sesbania punicea, germination, seed dormancy, seed coat impermeability, ‘callose’     

Effect of large- and of small-bodied zooplankton on phytoplankton in a eutrophic oxbow

Macrozooplankton and microzooplankton effects on the phytoplanktonwere measured in situ in a eutrophic lake. Indigenous phytoplanktonwere incubated for 5 days in 301 mesocosms with either the macro-and microzooplankton (complete), microzooplankton only (micro)or no zooplankton (none). Changes in phytoplankton biovolumewere investigated. Rotifer densities became significantly higherin the ‘micro’ treatment than in the ‘complete’and ‘none’ treatments. Total algal biovolume changedlittle in the ‘complete’ and ‘none’treatments, but increased significantly in the ‘micro’treatment. The results suggest that macrozooplankton (Daphniamagna) suppressed it and microzooplankton (Keratella cochlearis)enhanced it. They had opposite net effects on the phytoplankton.Suppression of microzooplankton by Daphnia probably had an indirectnegative effect on the phytoplankton.     

Plant Morphology: The Historic Concepts of Wilhelm Troll, Walter Zimmermann and Agnes Arber

Recent molecular systematic and developmental genetic findingshave drawn attention to plant morphology as a discipline dealingwith the phenotypic appearance of plant forms. However, sincedifferent terms and conceptual frameworks have evolved overa period of more than 200 years, it is reasonable to surveythe history of plant morphology; this is the first of two paperswith this aim. The present paper deals with the historic conceptsof Troll, Zimmermann and Arber, which are based on Goethe'smorphology. Included are contrasting views of ‘unity anddiversity’, ‘position and process’, and ‘morphologyand phylogeny’, which, in part, are basic views of currentplant morphology, phylogenetic systematics and developmentalgenetics. Wilhelm Troll established the ‘type concept’and the ‘principle of variable proportions’. Hehas provided the most comprehensive overview of the positionalrelations of plant forms. Agnes Arber started from the universaldynamics of life and attempted to describe all structures asprocesses. She paid attention to ‘repetitive branching’,‘differential growth’, and ‘parallelism’.As a result she has recently been rediscovered by developmentalbotanists. Walter Zimmermann rejected any metaphysical influenceon plant form and instead called for objective procedures. Hewas mainly interested in phylogenetic ‘character transformation’and the ‘reconstruction of genealogical lines’.Guided by the example of flower-like inflorescences, a futurepaper will deal with functional and developmental constraintsinfluencing plant forms. Recent morphological concepts (‘trialectical’,‘continuum’/‘fuzzy’, ‘processmorphology’) will be discussed and related to currentmorphological and developmental genetic research. Copyright2001 Annals of Botany Company Plant form, plant morphology, natural philosophy, homology, phylogeny, Goethe, Troll, Arber, Zimmermann, typology, character transformation, differential growth, complementarity     

Diurnal Phototropism in Leaves of Lavatera cretica L. under Conditions of Simulated Solar-Tracking

Diurnal laminar reorientation was followed in solar-trackingleaves of Lavatera cretica L. under simulated conditions. Asimulated ‘sun’ was moved over the lamina in a 180?arc in the vertical plane of the mid-vein, at an angular velocityof 15? h^–1 in a regime of 12-h photoperiods. In one groupof plants the petioles of the experimental leaves were arrangedto face ‘sunrise’, while in the other they werearranged to face ‘sunset’. At ‘sunrise’,the laminae in both groups, which were inclined towards theanticipated direction of ‘sunrise’, changed theirelevation towards the rising ‘sun’, resulting inprogressive reduction in the angle of incidence (AI) of lighton the laminar surface (AI= differential between laminar and‘solar’ elevation). As a result, laminar and ‘solar’elevation converged, and laminar reorientation gradually ceased,until the ‘solar’ elevation had passed the normalto the laminar surface (AI=0?). laminar reorientation was thenresumed, but its direction was reversed to follow the directionof ‘solar’ reorientation. During most of the remaining‘day’, laminar elevation (LE) trailed that of the‘sun’ by an average of 11?-14?. Laminar reorientationthen anticipated ‘sunset’ by starting to slow down60 to 90min in advance. During the 12-h dark period, the laminareoriented towards the anticipated direction of the subsequent‘sunrise’. The time-course of nocturnal reorientationwas qualitatively different in the two groups of experimentalplants. The time-course of diurnal phototropism under naturaland simulated conditions is analysed and compared and differencesand similarities between them are discussed. Key words: Diurnal phototropism, solar-tracking, vectorial excitation     

Effects of Flooding and Drainage and their Alternation on the Growth and Uptake of Nutrients by Rice (Oryza sativa L., indica, var. IR-8)

Continuous flooding of the soil (‘flooded’ treatment)gave best growth of IR-8 variety of rice whereas soil drainedfor 4 weeks and then flooded for 8 (‘drained and flooded’treatment) resulted in poorest growth and chlorotic plants.Plants grown in the continuously drained soil (‘drained’treatment) and those in the soil flooded for 4 weeks and thendrained for 8 (‘flooded and drained’ treatment)showed intermediate growth. There were no differences in therelative water content of plants growing in the various treatments.Analyses of plant tissues showed that a consideration of therelative concentration of Fe, Mn, and P in the shoots is mostclosely related to the performance of rice under various culturalconditions. An increase in the concentration of Fe in the planttissues following flooding was correlated with the best growth(‘flooded’ treatment) unless it was accompaniedby high level of Mn (as in the ‘drained and flooded’treatment) which may have proved toxic, e.g. by interferencewith Fe metabolism as was evidenced by chlorosis. Measurementsof oxidation-reduction potentials, oxygen diffusion rates, andthe concentration of exchangeable and soluble Fe and Mn in thesoils have shown that the ‘drained and flooded’treatment caused the most extreme reducing conditions. Floodingaccompanied by the development of extreme reducing conditionsled to a greater accumulation of Mn in the shoots (‘drainedand flooded’ treatment) whereas flooding accompanied bythe maintenance of oxidizing conditions (‘flooded’treatment) resulted in a lower uptake of Mn. Growth of riceplants for 4 weeks in the drained soil did not fit them forthe reduced conditions which developed during subsequent flooding(‘drained and flooded’ treatment).     

The Influence of the Plant Growth-regulator, 2-Methyl-4-Chlorophenoxyacetic Acid, on the Metabolism of Carbohydrate, Nitrogen and Minerals in Solanum lycopersicum (Tomato)

The effects of the foliar application of phytocidal concentrationsof 2-methyl-4-chlorophenoxyacetic acid (MCPA) on change in totaldry weight, and in ‘available carbohydrate’ (starch,‘total’ and ‘reducing’ sugars), totalnitrogen, phosphorus, potassium, calcium, and magnesium of ‘tops’and roots of tomato plants have been followed over a periodof 14 days following spraying. There were two main treatments—‘nutrient’(nutrient supply to roots continued after spraying) and ‘water’(distilled water only supplied to roots after spraying) and‘water’ (distilled water only supplied to rootsafter spraying)—the sub-treatments consisting of ‘MCPA’versus ‘no-MCPA’ for each of the main treatments.Twelve different times of sampling were used. In analysing the present data, the quantity ‘residualdry weight’ (total dry weight less ‘available carbohydrate’),which was originally introduced by Mason and Maskell as a basisof reference for analyses of plant organs in short-period experimentsnot involving appreciable growth, has been used as an estimateof the permanent structure of plant growth. This new use ofthe ‘residual dry weight’ basis has brought outimportant features which were obscured when the data were leftin their primary form (as percentages of total dry weight oramounts per plant). Growth, as measured by increase in ‘residual dry weight’,was greatly inhibited by 2-methyl-4-chlorophenoxyacetic acidshortly after spraying, in both the presence and the absenceof nutrient. In the presence of 2-methyl-4-chlorophenoxyacetic acid, netassimilation rate (estimated as rate of increase in total dryweight per gram ‘residual dry weight’ of the ‘tops’)was greatly diminished while uptake of total nitrogen and ofP₂O₅ (estimated as increase in total nitrogen or of P₂O₅ ofthe whole plant per day per 1 g. ‘residual dry weight’of the roots) appeared to undergo a similar but much smallerdiminution. It seemed probable, however, that in the presenceof MCPA a larger proportion of the carbohydrate actually formedwas utilized for synthesis of aminoacids and protein. In the plant as a whole there was no evidence of actual depletionof ‘available carbohydrate’ as a result of MCPAtreatment, this fraction showing a steady increase in all treatmentsthroughout the experiment. The rate of increase was, however,much reduced by MCPA treatment. The ‘tops’ presentedmuch the same picture as the whole plant, but for the rootsthe situation was quite different. While the roots of the ‘no-MCPA’plants and also of the ‘MCPA-water’ plants showeda steady increase in available carbohydrate, those of the ‘MCPA-nutrient’plants rose only very slightly (from the initial value of 8mg. per plant to about 10 mg.) during the first 2 days, andthen in the next 2 days declined to a value (about 6 mg.) belowthe initial and remained at this low level for the rest of theexperiment. It is suggested that the phytocidal effect of 2-methyl-4-chlorophenoxyaceticacid in the presence of nutrient may be due to depletion ofthe ‘available carbohydrate’ supplies in the roots,which is shown to be brought about, in part, by reduced transportfrom the tops, and partly by the relatively greater utilizationof the carbohydrate present. These results offer an explanationfor the facts that plants showing vigorous growth are more easilykilled by MCPA and that perennial plants, particularly thosewith storage tissues in their roots, are more resistant. Further,they suggest the useful practical application that MCPA treatmentshould be given when the carbohydrate reserves of the rootsare at a minimum. For perennial plants, conditions might beexpected to be optimal for the application of MCPA in late spring,at a time when the first ‘flush’ of growth is slowingdown and before any appreciable new reserves of carbohydratehave been accumulated. It was also shown that 2-methyl-4-chlorophenoxyacetic acid preventedthe net synthesis of starch, but still permitted an appreciablenet formation of sucrose. 2-methyl-4-chlorophenoxyacetic acid appeared to have no effecton the uptake of potassium, calcium, or of magnesium. The lackof effect on potassium is contrasted with the previous observationby Rhodes, Templeman, and Thruston (1950) that sub-lethal concentrationsof MCPA, applied over a relatively long period to the rootsof tomato plants, specifically depressed the uptake of potassium.     

The Extraction, Solubility, and Characterization of Two Groups of Barley Storage Polypeptides

This paper reports further studies on the characteristics ofthe storage protein fraction (hordein) of barley. Hordein consistsof two groups of polypeptides (termed ‘B’ and ‘C’)coded by two separate but linked loci. Whereas the ‘C’polypeptides are readily soluble and extracted in 60% (v/v)ethanol at room temperature, the ‘B’ group is moresoluble in, and therefore more efficiently extracted by, 50%(v/v) propan-1-ol or 45% (v/v) propan-2-ol at elevated temperaturesand in the presence of 2-mercaptoethanol. However, the mostefficient conditions for hordein extraction (50% propan-1-ol+ 2% (v/v) 2-mercaptoethanol at 60 °C) also extract somecontaminating non-hordein polypeptides resulting in an apparentlyincreased lysine content of the hordein fraction. Amino acid analysis of the purified ‘B’ and ‘C’hordein groups shows that, whereas ‘C’ hordein containsmore glutamate + glutamine, proline, and phenylalanine than‘B’ hordein, it contains only traces of lysine andsulphur amino acids in contrast to ‘B’ hordein whichcontains 0·5% lysine 0·6% methionine, and 2·5%cysteine. Equilibrium sedimentation analyses carried out on the purified‘B’ and ‘C’ groups indicates that thepreparations were reasonably monodisperse with molecular weightsof approximately 32 000 and 52 000 respectively. These valuesare considerably lower than those previously determined by SDS-PAGE.