Pattern recognition in DNA sequences and its application to consensus foot-printing

We consider the problem of comparing several nucleic acid sequencesto identify words occurring imperfectly (patterns with no gap)with unusual frequency. Methods for computing, representing,and inspecting interactively the structure of such repeatingmotifs in nucleic acids and more generally any text are described.Multiple sequences are treated as one large concatenate. Ina preprocessing step, a lexical index is created to providerapid string matching for the enumeration of the words matchinga pattern. For given word features (word length, minimal frequency),a sequence profile is displayed. The profile can be inspectedinteractively with on-line algorithms. Applications to the identificationof regulatory elements in DNA regions involved in the controlof gene expression are presented. Our program (‘DNA-Lexemics’)runs on the Macintosh.     

The growing outer epidermal wall: design and physiological role of a composite structure

Background: The cells of growing plant organs secrete an extracellular fibrouscomposite (the primary wall) that allows the turgid protoplaststo expand irreversibly via wall-yielding events, which are regulatedby processes within the cytoplasm. The role of the epidermisin the control of stem elongation is described with specialreference to the outer epidermal wall (OEW), which forms a ‘tensileskin’. Novel Facts: The OEW is much thicker and less extensible than the walls ofthe inner tissues. Moreover, in the OEW the amount of celluloseper unit wall mass is considerably greater than in the innertissues. Ultrastructural studies have shown that the expandingOEW is composed of a highly ordered internal and a diffuse outerhalf, with helicoidally organized cellulose microfibrils inthe inner (load-bearing) region of this tension-stressed organwall. The structural and mechanical backbone of the wall consistsof helicoids, i.e. layers of parallel, inextensible cellulosemicrofibrils. These ‘plywood laminates’ containcrystalline ‘cables’ orientated in all directionswith respect to the axis of elongation (isotropic material).Cessation of cell elongation is accompanied by a loss of order,i.e. the OEW is a dynamic structure. Helicoidally arranged extracellularpolymers have also been found in certain bacteria, algae, fungiand animals. In the insect cuticle crystalline cutin nanofibrilsform characteristic ‘OEW-like’ herringbone patterns. Conclusions: Theoretical considerations, in vitro studies and computer simulationssuggest that extracellular biological helicoids form by directedself-assembly of the crystalline biopolymers. This spontaneousgeneration of complex design ‘without an intelligent designer’evolved independently in the protective ‘skin’ ofplants, animals and many other organisms.     

A system for pattern matching applications on biosequences

ANREP is a system for finding matches to patterns composed of(i) spacing constraints called ‘spacers’, and (ii)approximate matches to ‘motifs’ that are, recursively,patterns composed of ‘atomic’ symbols. A user specifiessuch patterns via a declarative, free-format and strongly typedlanguage called A that is presented here in a tutorial stylethrough a series of progressively more complex examples. Thesample patterns are for protein and DNA sequences, the applicationdomain for which ANREP wos specifically created. ANREP providesa unified framework for almost all previously proposed biosequencepatterns and extends them by providing approximate matching,a feature heretofore unavailable except for the limited caseof individual sequences. The pemformance of ANREP is discussedand an appendix gives concise specification of syntax and semantics.A portable C softwore package implementing ANREP is availablevia anonymous remote file transfer.     

Morphology and Anatomy of Stems and Pedicels of Spring Flush Shoots Associated with Citrus Fruit Set

Flowering and vegetative shoots of ‘Shamouti’ orange[Citrus sinensis (L.) Osbeck] and ‘Marsh’ seedlessgrapefruit (Citrus paradisi Macf.) were examined for correlationof their morphology and anatomy with fruit set. Fruit set isfavoured on leafy inflorescences whereas abortion is nearlycomplete on leafless inflorescences. Leafless inflorescencesof ‘Shamouti’ with one flower were found to havea very thin stem which contained few vascular bundles, whereasthose with three flowers had better-developed vascular systems.The vascular system of leafy inflorescences is significantlydifferent from that of leafless ones and contains a distinctcentral xylem cylinder. The vascular area of leafless inflorescencesis only about one-quarter of that of the leafy ones. The vascularsystem of grapefruit resembles that of the ‘Shamouti’orange. This study emphasizes the importance of the dimensionof the vascular system for fruit set and provides a possibleexplanation for the better fruit set on both leafy and leaflessinflorescences with several flowers compared with single-floweredinflorescences. Anatomy; citrus; fruit set; leafless inflorescence; leafy inflorescence; pedicel; vascular system; vegetative shoot     

A method for delineating structurally homogeneous regions in protein sequences

A homogeneous region in a protein sequence is a set of contiguousresidues that share common features, concerning physsico-chemical,structural and mutational information. This paper presents amethod for identifying such homogeneous regions. From a profiledescribing a given type of biological information along thesequence, the algorithm allows the segmentation of the sequenceby optimizing a criterion characterized by two user-definedcontrol parameters: the ‘homogenizing degree’ ofthe regions and the ‘site neighbourhood’ size. Weapply the method to the envelope proteins of the human immunodeficiencyvirus HIV-1, for the identification of homogeneous regions ina hydrophobicity profile and the delineation of variable andconserved regions in a variability profile.     

BIOSITE: a program for the interactive comparison of aligned homologous protein sequences

A program, BIOSITE, providing for the interactive visual comparisonof aligned homologous amino-acid sequences is presented, includingan example of its application. The program allows for two typesof comparison sequence to be generated: an ‘identity’sequence and a ‘difference’ sequence. These maybe used on subsets of sequences and in further comparisons toidentify candidate sites involved in a distinct functional property.The program should prove a useful tool for biologists engagedin understanding sequence—function relationships.     

'Size leap' algorithm: an efficient extraction of the longest common motifs from a molecular sequence set. Application to the DNA sequence reconstruction

We propose a new method, called ‘size leap’ algorithm,of search for motifs of maximum size and common to two fragmentsat least. It allows the creation of a reduced database of motifsfrom a set of sequences whose size obeys the series of Fibonaccinumbers. The convenience lies in the efficiency of the motifextraction. It can be applied in the establishment of overlapregions for DNA sequence reconstruction and multiple alignmentof biological sequences. The method of complete DNA sequencereconstruction by extraction of the longest motifs (‘anchormotifs’) is presented as an application of the size leapalgorithm. The details of a reconstruction from three sequencedfragments are given as an example. Received on February 12, 1991; accepted on February 15, 1991     

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     

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     

Density distribution and size sorting in fish schools: an individual-based model

In fish schools the density varies per location and often individualsare sorted according to familiarity and/or body size. High densityis considered advantageous for protection against predatorsand this sorting is believed to be advantageous not only toavoid predators but also for finding food. In this paper, welist a number of mechanisms and we study, with the help of anindividual-based model of schooling agents, which spatial patternsmay result from them. In our model, schooling is regulated bythe following rules: avoiding those that are close by, aligningto those at intermediate distances, and moving towards othersfurther off. Regarding kinship/familiarity, we study patternsthat come about when agents actively choose to be close to relatedagents (i.e., ‘active sorting’). Regarding bodysize, we study what happens when agents merely differ in sizebut behave according to the usual schooling rules (‘sizedifference model’), when agents choose to be close tothose of similar size, and when small agents avoid larger ones(‘risk avoidance’). Several spatial configurationsresult: during ‘active sorting’ familiar agentsgroup together anywhere in the shoal, but agents of differentsize group concentrically, whereby the small agents occupy thecenter and the large ones the periphery (‘size differencemodel’ and ‘active sorting’). If small agentsavoid the risk of being close to large ones, however, smallagents end up at the periphery and large ones occupy the center(‘risk avoidance’). Spatial configurations are alsoinfluenced by the composition of the group, namely the percentageof agents of each type. Furthermore, schools are usually oblongand their density is always greatest near the front. We explainthe way in which these patterns emerge and indicate how resultsof our model may guide the study of spatial patterns in realanimals.     

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.     

The Hexagonal Branching Pattern of Rhizomes of Alpinia speciosa L. (Zingiberaceae)

Alpinia speciosa L. (Zingiberaceae) is a striking example ofa plant in which an organized architectural structure fulfilsa basic functional requirement - the economical explorationand exploitation of the substrate. This rhizomatous plant spreadslaterally in a predictable manner by vegetative growth to forma clone of separated ramets. A morphological study establishes‘rules of growth’ governing the success and failureof lateral branches (sympodial units), their lengths, and theirrelative angles. The basic branching pattern of this rhizome system approximatesto that of a hexagonal grid - the most economical structuralshape that uniformly ‘samples’ a plane surface.It is shown that the significant deviation of branching anglefound in Alpinia from that required to develop an exact hexagonalnetwork will virtually eliminate aerial shoot ‘clashes’in which the placing of one aerial shoot coincides with thatof another aerial shoot, whilst at the same time enhancing thebenefits of the hexagonal system. The broader implications ofthe organised architecture of plants are emphasised. rhizome, branching pattern, architecture, productivity     

Effect of Source of Nitrogen on the Growth of Fiskeby Soya Bean: the Carbon Economy of Whole Plants

Fiskeby V soya bean was grown from seed germination to seedmaturation with two contrasting patterns of nitrogen metabolism:either wholly dependent on dinitrogen fixation, or with an abundantsupply of nitrate nitrogen, but lacking root nodules. The carbonand nitrogen economies of the plants were assessed at frequentintervals by measurements of photosynthesis, shoot and rootrespiration, and organic and inorganic nitrogen contents. Plantsfixing atmospheric nitrogen assimilated only 25–30 percent as much nitrogen as equivalent plants given nitrate nitrogen:c. 40 per cent of the nitrogen of ‘nitrate’ plantswas assimilated after dinitrogen fixation had ceased in ‘nodulated’plants. The rates of photosynthesis and respiration of the shootsof soya bean were not markedly affected by source of nitrogen;in contrast, the roots of ‘nodulated’ plants respiredtwice as rapidly during intense dinitrogen fixation as thoseof ‘nitrate’ plants. The magnitude of this respiratoryburden was calculated to increase the daily whole-plant respiratory loss of assimilate by 10–15 per cent over thatof plants receiving abundant nitrate. It is concluded that ‘nodulated’plants grew more slowly than ‘nitrate’ plants inthese experiments for at least two reasons: firstly, the symbioticassociation fixed insufficient nitrogen for optimum growth and,secondly, the assimila tion of the nitrogen which was fixedin the root nodules was more energy-demanding in terms of assimilatethan that of plants which assimilated nitrogen by reducing nitratein their leaves.     

Phyllotactic Patterns: A Biophysical Mechanism for their Origin

The patterns seen in plant shoots and flowers, ‘phyllotaxis’,originate in an annular region. They are typically propagatedinward from this ring-like area. We show here that an initialundulating periodic pattern (a ‘whorl’ of hump-likeorgans) can arise in a flat unstructured annulus. The patternarises not from pre-localized pushes from below, but ratheras a spontaneous physical response of the expanding surfaceto lateral constraint. Physical properties of a uniform formativelayer (tunica) and a uniform substratum (corpus) provide thewavelength of the undulation and hence the number of organs.Establishment of the parameters for this buckling, as well asthe follow-through of organ development, is biological. We propose,however, that at the moment of periodic pattern initiation theplant tissue simply manifests the spontaneous but complex propertiesof a two-layered inanimate sheet. Phyllotaxis; tunica; corpus; patterning; shoot apex; morphogenesis; biophysics; buckling     

Pattern of Respiration of a Perennial Ryegrass Crop in the Field

‘Dark’ respiratory losses of CO₂ were measured ona one year old sward of S24 perennial ryegrass (Lolium perenneL.) at intervals during a 74 day reproductive growth period,between April and June, and a 21 day vegetative growth period,in July and August. Part of the sward was shaded for one weekbefore measure ments commenced. Measurements of ‘dark’respiration continued for 46 hand it was possible to distinguishtwo components which are designated ‘maintenance’and ‘synthetic’ ‘Maintenance’ respiration was taken to be the meanrate of CO₂ efflux after 40–46 h darkness. When calculatedon a plant d. wt basis at 15°C it ranged between 6 to 32mgCO₂ g^-1 day^-1 during reproductive growth and 10–14 mgCO₂ g^-1 day^-1 during vegetative growth. During reproductivegrowth, sward protein content ranged between 7–23 percent and when maintenance respiration was recalculated on thebasis of protein content it changed relatively little throughoutthe growth period (90–140 mg CO₂ g pro tein^-1 day^-1);the value for vegetative growth ranged between 70–100mgCO₂ g protein-day^-1. Total ‘synthetic’ CO₂ flux was determined duringreproductive growth and a rate of ‘synthetic’ CO₂flux was determined during both reproductive and vegetativegrowth. Between 15 and 35 per cent of the CO₂ fixed in the previousphotoperiod was lost in ‘synthetic’ respirationof above-ground material in reproductive swards. Previous shadingincreased the proportion of ‘synthetic’ CO₂ lossfrom above ground. The rate of ‘synthetic’ CO₂ outputduring the first hours of darkness increased with amount ofCO₂ fixed in the previous photoperiod, although it was not proportionalto it. There is some evidence that assimilate is ‘carried-over’from one photoperiod to the next.     

Morphogenesis of 2,4-D Induced Abnormalities of the lnflorescence of Bread Wheat (Triticum aestivum, L.).

Treatment of Triticum plants with 2,4-D profoundly affects inflorescencemorphogenesis and results in the production of various abnormalities,amongst which are branched heads, whorls of spikelets. superimposedpairs of spikelets (‘banana’ twin spikelets) andpaired spikelets borne at the same level (‘yoked’spikets). Often more than one kind of abnormality is observedin a single head. Except for ‘banana’ twin spikelets,none of the induced abnormalities are duplicated by abnormalitieswhich occur spontaneously in untreated plants. Disturbance dueto treatment is only temporary and later the terminal regionof the apex recommences growth along a normal pattern of morphogenesis.     

The Potassium Relations of Lemna minor L.: I. POTASSIUM UPTAKE AND PLANT GROWTH

A simple expression has been derived to predict the rate ofnet K uptake into exponentially growing plants of Lemna minor.Net uptake predictions are in good quantitative agreement withmeasurements of ‘steady-state’ K influx, indicatingthat, in the ‘steady state’, K movements in theplant are essentially undirectional and that efflux is small.This close matching of inward K movement to the demands of theexpanding tissue is temporarily disturbed if plants are transferredto media of different K status. Uptake rates in the ‘step-up’are initially enhanced and then fall gradually towards a new‘steady-state’ rate. In contrast, the ‘step-down’causes an initial depression of uptake and then rates increasegradually towards the new ‘steady-state’ rate. Itis argued that these changes in uptake rates are associatedwith alterations in the cytoplasmic K content.     

Discovering simple DNA sequences by the algorithmic significance method

A new method, ‘algorithmic significance’, is proposedas a tool for discovery of patterns in DNA sequences. The mainidea is that patterns can be discovered by finding ways to encodethe observed data concisely. In this sense, the method can beviewed as a formal version of the Occam's Razor principle. Inthis paper the method is applied to discover significantly simpleDNA sequences. We define DNA sequences to be simple if theycontain repeated occurrences of certain ‘words’and thus can be encoded in a small number of bits. Such definitionincludes minisatellites and microsatellites. A standard dynamicprogramming algorithm for data compression is applied to computethe minimal encoding lengths of sequences in linear time. Anelectronic mail server for identification of simple sequencesbased on the proposed method has been installed at the Internetaddress pythia@anl.gov.     

Factors Affecting the Abscission of Reproductive Organs in Yellow Lupins (Lupinus luteus L.): III. ENDOGENOUS GROWTH SUBSTANCES IN VIRUS-INFECTED AND HEALTHY PLANTS AND THEIR EFFECT ON ABSCISSION

Extracts of small and mature-size lupin pods yielded four substancesaffecting the growth of wheat-coleoptile sections: one acidpromotor (A), two acid inhibitors(B and X), and one neutralinhibitor(Y). Inhibitor B was extremely active, however, coleoptile sectionsshowed no signs of toxic effects; they resumed growth at a rapidrate after rinsing them and adding ß-indolylaceticand (IAA) to the medium. 1 µg of IAA was required to counteractthe effect of ‘B’ extracted from 230 mg. Of tissue.On an equal fresh weight basis the inhibiting action of ‘B’in lupin pods was 500–1,500 times more potent than thatof ‘inhibitor ß’ in etiolated pea seedlings. Small pods of plants infected with pea-mosaic virus yielded3 times the amount of ‘A’ of healthy plants (equivalentto 1 µg. IAA 0.3 µg. IAA per 25 g. of tissue respectively),and approximately the amount of ‘B’. Mature podsof virus-infected plants again yielded more‘A’,but also 2? times more ‘B’ than pods of healthyplants. Healthy pods yielded more ‘A’ than virus-infectedpods, and there was no difference in ‘X’. A lupin abscission test was developed and the effects of proximaland distal application of -naphthyl acetic acid (NAA) are presented,and discussed with respect to results of other abscission tests. ‘A’ accelerated abscission when applied proximally,and delayed or prevented it when applied distally. ‘B’strongly accelerated abscission when applied in either way.A possible mechanism explaining the abscission-inducing effectof developing pods on later flowers is discussed in terms ofthe substances ‘A’ and ‘B’. The partlyprevented abscission observed on virus-infected plants was foundto agree well with the proposed mechanism.