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     

Characterization of RNA-dependent RNA Polymerases in Healthy and Tobacco Mosaic Virus-infected Tomato Plants

Healthy tomato plants were shown to contain high levels of RNA-dependentRNA polymerase activity, mainly in a ‘soluble’ form,but also partly in a ‘ bound’ form. The ‘bound’enzyme was solublized by EDTA treatment. Both forms of enzymewere partially purified and characterized. The ion and pH optimaof the two forms were identical at all stages of purification.Both enzymes exhibited uridylyl transferase activity, whichmade up 35 per cent of total incorporation. Infection with tobacco mosaic virus (TMV) increased activityof ‘soluble’ enzyme by twofold, and of solubilized‘bound’ enzyme by less than twofold. Uridylyl transferaseactivity was also increased by infection. General propertiesof the enzymes were unaltered by infection with one exception:in the presence of TMV RNA as added template, the ‘soluble’enzyme from infected plants incorporated ³H-UTP into productswith the electrophoretic properties and RNase sensitivitiesexpected for replicative form and replicative intermediate ofTMV. ‘Soluble’ enzyme from healthy plants, and solublized‘ bound’ enzyme from either healthy or infectedplants did not synthesize these products. The ‘soluble’ and solubilized ‘bound’enzymes behaved differently on ion-exchange chromatography.Under the conditions used, ‘soluble’ enzyme didnot bind to the column, whereas solublized ‘bound’enzyme did. No differences in chromatographic behaviour werefound between enzymes from healthy or infected plants. Withboth ‘soluble’ and solublized ‘bound’enzymes, the uridylyl transferase activity co-chromatographedwith the polymerase activity. Tomato, Lycopersicon esculentum, RNA-dependent RNA polymerase, tobacco mosaic virus, tobacco mosaic virus replicase     

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     

Base-pair probability profiles of RNA secondary structures

Dynamic programming algorithms are able to predict optimal andsuboptimal secondary structures of RNA. These suboptimal oralternative secondary structures are important for the biologicalfunction of RNA. The distribution of secondary structures presentin solution is governed by the thermodynamic equilibrium betweenthe different structures. An algorithm is presented which approximatesthe total partition function by a Boltzmann–weighted summationof optimal and suboptimal secondary structures at several temperatures.A clear representation of the equilibrium distribution of secondarystructures is derived from a two-dimensional bonding matrixwith base–pairing probability as the third dimension.The temperature dependence of the equilibrium distribution givesthe denaturation behavior of the nucleic acid, which may becompared to experimental optical denaturation curves after correctionfor the hypochromicities of the different base-pairs. Similarly,temperature-induced mobility changes detected in temperature-gradientgel electrophoresis of nucleic acids may be interpreted on thebasis of the temperature dependence of the equilibrium distribution.Results are illustrated for natural circular and synthetic linearpotato spindle tuber viroid RNA respectively, and are comparedto experimental data.     

The Developmental Anatomy of the Root System in Yam Bean, Pachyrhizus erosus Urban

Investigations revealed that the anatomy of the primary radicularroot of yam bean (Pachyrhizus erosus L.) was typically dicotyledonousexcept that the xylem was not completely developed centripetally.Most of the roots had tetrarch xylem, although a few triarchand pentarch roots were also observed. In both tuberous andnon-tuberous roots, secondary thickening occurred by the formationof the meristematic vascular cambium which formed secondarytissues in a normal fashion. Subsequently, tuberization wasinitiated in the secondary xylem by the development of anomalous‘secondary’ cambia from parenchyma cells surroundingvessel elements. Anomalous ‘secondary’ cambia alsodeveloped from parenchyma cells not associated with vessels.Subsequently, anomalous ‘tertiary’ cambia differentiatedfrom tissues produced by the anomalous ‘secondary’cambia. Activities of these anomalous cambia resulted in theproduction of parenchyma storage cells and were chiefly responsiblefor the growth of the mature tuber. Pachyrhizus erosus L., yam bean, tuberous root, anatomy, anomalous ‘secondary’ cambia, anomalous ‘tertiary’ cambia, centripetal xylem development     

Primary and Secondary Induction Requirements for Flowering of Contrasting European Varieties of Lolium perenne

The flowering requirements of six European varieties of Loliumperenne L. were studied in controlled environments. In experimentson primary induction, flowering was recorded after transferto long days (LD) in a greenhouse at 12–24°C. In experimentson secondary induction, primary induction was first accomplishedat 6°C/10 h daylength for 12 weeks. When evaluated by the50% heading criterion, the requirement for duration of primaryinduction at 6°C/8 h daylength was <3 weeks in Mediterranean,5–6 weeks in Central European and 7–8 weeks in Scandinavianvarieties. While ‘Veyo’ (Italy) flowered profuselyregardless of temperature or daylength during primary induction,critical temperatures for primary induction in SD and LD were15 and 11°C in ‘Baca’ (Czech Republic) and 11and 7°C in ‘Falster’ (Denmark). The criticalphotoperiod for secondary induction at 15°C ranged from12 h in ‘Veyo’ and 14 h in ‘Baca’ to16.5 h in ‘Falster’ and 17.5 in ‘Kleppe’(Norway). The critical number of LD cycles varied correspondingly.While the Central and North European varieties required fewerLD cycles for 50% heading at 18 than at 12°C, ‘Veyo’showed the opposite response. It is concluded that the requirementsfor both primary and secondary induction of Lolium perenne increasewith increasing latitude of origin of the germplasm. In oneexperiment, 39–87% of the inflorescences came from tillersthat were not visible on transfer from primary to secondaryinduction, thus it is also concluded that there is no juvenilestage in tillers of Lolium perenne. Copyright 2000 Annals ofBotany Company Daylength, flowering, juvenility, perennial ryegrass (Lolium perenne L.), primary induction, secondary induction, temperature, varieties, vernalization     

Phylogenetic comparative analysis of RNA structure on Macintosh computers

A Macintosh Hypertalk program (Hypercard ‘stack’)for use in phylogenetic comparative analysis of RNA structureis described. The program identifies covariations and compensatorychanges in RNA sequence alignments, for use in the constructionof secondary structure models or the identification of tertiaryinteractions. The results of an analysis are presented eitheras a list of positions in the alignment which covary, or asa 2-dimensional matrix in which potential helices in the secondarystructure appear as diagonal patterns. Received on January 7, 1991; accepted on March 19, 1991     

A toolkit for creating three-dimensional RNA pencil models

The advantages of nucleotide-resolution models over atomic-resolutionand cylinder models of large RNA structure are discussed, anda toolkit of RNA substructures for use in building ‘pencil’models is described. Prefabricated elements from the toolkitcan be used to quickly assemble complex RNA structure modelsfor the visualization of known RNA structures, or for exploringpotential tertiary structure configurations based on secondarystructure and other information.     

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     

Pyrimidine Nucleotide Biosynthesis in Vinca rosea Cells: Changes in the Activity of the de novo and Salvage Pathways during Growth in a Suspension Culture

Marked changes in the activity of the ‘de novo’and ‘salvage’ pathways of pyrimidine biosynthesisduring growth of Vinca rosea cells in a batch suspension culturewere observed. The activity of these pathways was investigated by determiningthe contribution of ¹⁴C of [2-¹⁴Cluracil, 12-¹⁴Cluridine. and[6-¹⁴Clorotate to the cell constituents and by measuring theactivity of the several enzymes of these pathways. During the lag phase of the culture, ‘uracil-’ and‘uridine-salvage’ pathways made the predominantcontribution to nucleotide biosynthesis, but, following theinitiation of cell division, the ‘de novo’ pathwayfor nucleotide biosynthesis operated appreciably. These results suggest that nucleotide synthesis during cellgrowth in a suspension culture can be divided into two stages:a ‘turnover stage’, during the lag phase of cellgrowth, and a ‘true biosynthetic stage’, which isinitiated in the cell division phase.     

Uptake and Metabolism of Sugars by Suspension cultured Catharanthus roseus Cells

p. 186, right column line 11 ‘27.2 KBq’ change to‘37.2 MBq’ p. 187, left column line 8 ‘27.2 KBq’ change to‘37.2 MBq’ line 10 ‘13.6 KBq’ change to ‘18.6 MBq’ line 11 ‘13.6 KBq’ change to ‘18.6 MBq’ line 21 ‘89%’ change to ‘80%’ right column line 24 ‘CLC-NH₄’ change to ‘CLC-NH₂’ P. 189, Table 1 appeared incorrectly: it should appear as indicated.     

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.     

Bioinformatics in the human interactome project

‘In the early days of the Human Interactome Project, ameeting was organized...’. Perhaps, a few years from now,newspapers will describe in those terms how straightforwardit was to plan the large-scale mapping of protein interactionsin human and other model organisms. Scientists attending thesecond Cold Spring Harbor Laboratory/Wellcome Trust symposiumon ‘Interactome Networks’¹ know well that thingsare not that easy. Important scientific, technical and sociologicalissues remain before the ‘Human Interactome Project’can be considered on its way. But things     

An electrophysiological investigation into the labellar lobe spreading response in the blowfly Protophormia terraenovae

Stimulation of single ‘largest’ or ‘marginal’labellar chemosensilla can evoke ipsi- and contralateral labellarlobe spreading responses in Protophormia. Measurements of reflexlatencies indicate that the response is triggered by messagescoming from the ‘largest’ ipsilateral chemosensilla.Input from the ‘marginal’ chemosensilla would playa role in maintaining the already triggered response.     

Olga--oligonucleotide primer design program for the Atari ST

A program to facilitate the design of oligonucleotide primnershas been devised. Olga is written in draft ANSI standard ‘C’and makes use of the implementation of Digital Research GEM(Graphics Environment Manager) on the Atari ST Olga is specificallysuited to the polymnerase chain reaction (PCR) allowing si analysisof two primer sequences. The advantage of Olga is that it providesin one program analyses for direct repeats, secondary structuresand primer dimerization as well as several useful ‘finishing’tools for workers engaged in PCR optimization and oligonucleotidesyntheses.     

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.     

Mycorrhizal Response of Two Tomato Genotypes Relates to their Ability to Acquire and Utilize Phosphorus

The purpose of this study was to determine how a plant's responseto colonization by mycorrhizal fungi relates to its abilityto acquire and utilize phosphorus for growth and reproduction.Two tomato genotypes previously found to be either responsive(‘LA1709’) or unresponsive (‘large cherry’)to mycorrhizal colonization during early vegetative growth wereexamined in detail. Plants were grown at four levels of addedphosphate or with mycorrhizal inoculum. Vegetative and reproductivegrowth, phosphorus uptake and root length density were measuredduring the course of plant development. Mycorrhizal symbiosissignificantly increased above-ground dry mass, root length,phosphorus content and yield under low phosphorus conditionsin ‘LA1709’, while it had less effect on these characteristicsin ‘large cherry’. When uninfected, however, ‘LA1709’grew and reproduced poorly unless high amounts of phosphoruswere added to the soil, while ‘large cherry’ grewwell under very low phosphorus conditions. This was because‘large cherry’ had significantly higher root lengthdensities than ‘LA1709’, enabling plants from thisgenotype to explore more soil volume and acquire greater amountsof phosphorus when grown without mycorrhizal fungi in low phosphorussoil. ‘Large cherry’ also had higher phosphorususe efficiency and allocated a greater proportion of phosphorusto reproduction when uninfected than ‘LA1709’. Itappears traits that affect a plant's ability to acquire andutilize phosphorus efficiently for growth and reproduction canalso affect its response to mycorrhizal colonization in tomato.Copyright1998 Annals of Botany Company. Tomato,Lycopersicon esculentum,mycorrhiza,Glomus etunicatum,phosphorus, reproduction, lifespan.     

Studies in the Regeneration of Horseradish: I. A Re-examination of the Morphology and Anatomy of Regeneration

1. Horseradish roots reach a stage of ‘ripeness to regenerate’at the age of 1–2 months, when secondary thickening hasbegun, a phellogen has formed, and the primary cortex has beenshed; provided that they are then detached from the parent plant. 2. New primordia arise (as is already known) only in associationwith the scars of lateral roots; but they are produced, notas previously believed from a callus, but individually as organizedmeristems whose cells are derived only from the phellogen ofthe main root. 3. The primordia appear to be undetermined (‘indifferent’)in nature; their subsequent differentiation into buds or rootsis described.     

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.