The 'Original Article' inAnnals of Botany

I have become aware that uncertainty exists in some quartersover what is or is not acceptable for submission as an originalresearch paper to this and similar journals. It appears thatthe essential characteristics of such articles are not alwaysfully appreciated, suggesting pressure to lower the basic standardsthat prescribe the peer-reviewed research paper. This editorialmakes it clear that theAnnals of Botanystrongly resists suchpressures. It views the successful peer-reviewed paper as theprincipal hallmark of success for individual scientists andthe ‘gold standard’ that defines tangible progressin science. I will not try to delineate all the features expectedof a satisfactory research paper but, instead, point to theparamount necessity of their being original works. Readers mustbe able to take it on trust that the contents of published papershave not been stolen from others or published in substantivemeasure elsewhere by the author. Protecting that trust is oneof the Journal's foremost concerns and it is no coincidencethat the opening sentence of our ‘Instructions to Authors’begins with the phrase ‘Contributions must be original'.Some other journals also adopt similar wording and authors shouldtake note of this most basic requirement. It underpins the credibilityand good standing of the standard peer-reviewed research paper.There is some risk of ambiguity concerning what is meant by‘original’ when an author writes on a similar subjectin both a refereed journal and in a non-refereed format suchas a chapter in a book. While this practice is entirely legitimate,the reader has the right to a scholarly reworking of ideas,substance and content in both cases. The reader is also entitledto expect appropriate cross-referencing between the two formsof communication and for the research paper to be recognizedas the primary source. Such cross-referencing is but a partof the larger requirement of being open about sources of knowledgeand about the influences that bear on the research being described.Scientific publishing of peer-reviewed science is serious workand theAnnals of Botanyendeavours to maintain the highest possiblestanding for its ‘Original Articles’. It takes promptpublic action whenever basic precepts essential to maintainingthis high standing are discovered to have been ignored by anyof its contributors.Copyright 1999 Annals of Botany Company     

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     

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     

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.     

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.     

A multiple sequence alignment algorithm for homologous proteins using secondary structure information and optionally keying alignments to functionally important sites

The programs described herein function as part of a suite ofprograms designed for pairwise alignment, multiple alignment,generation of randomized sequences, production of alignmentscores and a sorting routine for analysis of the alignmentsproduced. The sequence alignment programs penalize gaps (absencesof residues) within regions of protein secondary structure andhave the added option of ‘fingerprinting’ structurallyor functionally important protein residues. The multiple alignmentprogram is based upon the sequence alignment method of Needlemanand Wunsch and the multiple alignment extension of Barton andSternberg. Our application includes the feature of optionallyweighting active site, monomer-monomer, ligand contact or otherimportant template residues to bias the alignment toward matchingthese residues. A sum-score for the alignments is introduced,which is independent of gap penalties. This score more adequatelyreflects the character of the alignments for a given scoringmatrix than the gap-penalty-dependent total score describedpreviously in the literature. In addition, individual aminoacid similarity scores at each residue position in the alignmentsare printed with the alignment output to enable immediate quantitativeassessment of homology at key sections of the aligned chains.     

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     

Software for the development and evaluation of probabilistic identification matrices

A number of programs are described for the development and evaluationof probabilistic identification matrices for use with computer-assistedidentification. The program BEST reads an initial matrix ofper cent probabilities for all the binary characters examinedduring a cluster analysis and determines the most useful setof tests for distinguishing taxa in the matrix. Program RESORTcreates from the initial matrix an identification matrix inwhich the order of the tests may be different or the numberof tests reduced. A printed version of a matrix can be producedby MATPRJNT, which creates tables giving the per cent probabilityof a positive test result and the test results presented as‘–’, ‘v’ and ‘+’ dependingon a user-specified threshold. Program IDSC evaluates an identificationmatrix by calculating the best identification score for eachtaxon in the matrix using the expected result for each test.The programs were written in FORTRAN 77 and can be run on anymicrocomputer using the PC/MS-DOS operating system. Received on April 27, 1990; accepted on November 5, 1990     

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.     

Instant notes in plant biology, 2nd edn. * Lack A, Evans D. 2005. * Oxford: Taylor and Francis. {pound}18.99 (paperback). 351 pp.

The ‘InstantNotes’ series from Bios will probably be familiar to manyreaders. The series' success is evident in the second editionsthat are appearing, e.g. the current volume—albeit nowunder the Taylor and Francis label. Content This book does what it says on the label; it provides noteson (probably) all of the topics within the compass of present-day‘plant biology’. Primarily, it deals with anatomy,growth and development, physiology, reproduction, and economicuses and ecology of flowering plants (angiosperms). However,it does cover other phyla of the Kingdom Plantae (principallyin two ‘taxonomy/evolution’ sections), and algae(along     

Ayala, F.J., Fitch, W.M. and Clegg, M.T. Variation and evolution in plants and microorganisms: toward a new synthesis 50 years after Stebbins

In January 2000, an impressive cohort of evolutionary biologistsconvened in Irvine, California, to celebrate the 50th anniversaryof the publication of G. Ledyard Stebbins’ Variation andevolution in plants. The brief introductory appreciation ofStebbins by Peter Raven describes Variation as ‘the mostimportant book on plant evolution of the 20th century’(p. 5). This strongly worded claim is not entirely without justification.Among the ‘New Synthesists’, Stebbins achieved forbotanists what Theodosius Dobzhansky (later to be a colleagueof Stebbins at UC Davis) had previously achieved for geneticists,Ernst Mayr for zoologists and G. G. Simpson for palaeontologists.Admittedly, the     

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.     

Narrow-leafed Lupins with Restricted Branching

Crop phenology is one of the most important characters influencingproductivity in a given environment. Narrow-leafed lupin (Lupinusangustifolius L.) is a major grain legume crop in southern Australiawith general phenological adaptation to this Mediterranean-typeenvironment. However, it is an indeterminate crop with severalassociated limitations to productivity, such as overlappingvegetative and reproductive growth, late grain filling and sometimesexcessive vegetative growth. Here we studied two novel typesof narrow-leafed lupin with restricted branching, which mightbe useful for overcoming these problems. These restricted branchinglupins arose spontaneously within a breeding population, inthe case of ‘Tallerack’, and within a farmer's cropin the case of ‘ Hurst’ and we compared them withthe ‘Merrit’, which is widely grown and has thenormal indeterminate branching habit. The morphology and developmentof the main shoot of these genotypes were similar. However,‘Hurst’ had much larger leaves. There were alsostriking differences in the lateral branches of the restrictedbranching types; they had fewer leaves than ‘Merrit’and flowered earlier. These differences were most marked in‘ Hurst’, where the upper main stem branches werereduced to a single floret in the axil of main stem leaves,and these flowers often exhibited abnormal morphology. Copyright2000 Annals of Botany Company Lupinus angustifolius L., narrow-leafed lupin, adaptation, development, morphology, branching, leaves, mutant, plastochron, phyllochron, floral initiation, flowering.     

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 Effect of Bud Position on Branch Growth and Bud Abscission in Quercus petraea (Matt.) Liebl.

The time at which a bud began to expand was related to its positionnot only on an individual shoot but also within the crown. Thedistribution of buds and branches on the shoot was uneven; theshoot tip, where they were densely clustered, was termed the'whorl; and the remainder of the shoot, where they were widelyspaced, the ‘interwhorl’ stem. In spring, the terminalbud started expanding before the ’whorl’ buds whichpreceded the ‘interwhorl’ stem buds; completionof the flush of growth, determined by the end of leaf expansion,occurred in the reverse order, ‘interwhorl’     

Black, M. and Pritchard, H.W. (eds). Desiccation and survival in plants. Drying without dying

This excellent volume provides a very readable and comprehensivecoverage of desiccation tolerance in plants. The opening chapter,from which the subtitle ‘Drying without dying’ isdrawn, gives a splendid overview of what desiccation toleranceis and how plants accommodate this potentially lethal stress.It includes a history of research into plant desiccation andthe development of ideas, its occurrence within the plant kingdomand its ecological significance. The subsequent chapters buildmasterfully upon this introduction, in     

Theodoropoulos, D.I. Invasion biology. Critique of a pseudoscience.

The back cover of this book states that ‘contrary to theclaims of the nativists, research shows that man-dispersed speciesincrease biological diversity, benefit ecosystems, and act asan important force for healing the planet’. This is anuncompromising statement, and David Theodoropoulos divides hisdevelopment of the arguments supporting this statement intothree parts. Part I (Chapters 1–6) is ‘Nature, Dispersaland Reaction’. Part II (Chapters 7 and 8) is ‘Why?Psychology, Politics and Pseudoscience’. Part III (Chapters9–11) is ‘Humanity and Diversity’. There isalso an ‘Introduction’ including a summary of findingsand ‘An outline for a new theory of anthropogenic dispersal’,     

Integrated Analysis of Growth and Light Interception in Winter Lettuce II. Differences between Cultivars

‘Integrated growth analysis’ (emphasizing aspectsof crop and plant structure) and ‘light conversion analysis’(stressing the efficiency of interception and photosyntheticconversion of light) have been used to investigate the wintergrowth of different cultivars of butterhead and crisphead typesof glasshouse lettuce. Measurements from ‘Ambassador’ (large-framed butterhead),‘Renate’ (medium-sized butterhead) and ‘Cristallo’(crisphead) were made, statistical progressions were fittedto the primary data and hence estimates of all the analyticalcomponents were derived. Curves for crop growth rate, like those for most other components,followed a generally similar pattern for all three cultivars.In integrated growth analysis, the biomass curve for Ambassadorlay above the curves for the other cultivars. The weight advantagewas initially 60 per cent and it persisted with only a smallreduction (to 40 per cent) until the final harvest. Relativegrowth rate varied little between cultivars because differencesobserved in leaf area ratio were complementary to those seenin net assimilation rate. In light conversion analysis, differences in light interceptingefficiency between cultivars were not statistically significant,though Ambassador attained full interception 4 days earlierthan Renate and 6 days earlier than Cristallo. Differences inlight utilizing efficiency were small and non-significant exceptduring the post-rosette stage when the value for Renate waslower than that of either Ambassador or Cristallo. Deviationsaround the fitted curves were correlated with fluctuations inthe light regime. An assessment is made of the utility and limitations of thetwo procedures. It is concluded that both approaches can assistin analyzing the rate of dry matter production in crops or plantstands. Integrated growth analysis is advantageous when theneed arises to treat individual and population-based attributessimultaneously, while light conversion analysis provides a meansof explicitly incorporating the primary environmental variableinfluencing growth. Lactuca sativa L., lettuce cultivars, growth analysis, crop growth rate, relative growth rate, light interception, light utilization     

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 Suction Potential of Plant Cells and Some Related Topics

This paper is a theoretical discussion of the concept of suctionpotential or suction pressure as applied to plant cells, especiallywith reference to the possible occurrence of ‘active’water-secreting mechanisms. Following an attempt to define whatis meant by suction potential there is a discussion of the distinctionbetween ‘active’ and ‘passive’ agenciesin relation to water movement and a tabulation of such agencies. Some of the less commonly considered mechanisms are discussedin some detail, and an attempt is made to evaluate how effectivethey might be in producing increments of turgor pressure. Theconclusion is reached that if active mechanisms are operativein cell-water relations, then suction potential cannot adequatelybe denned in the ordinary way—in fact the ‘water-absorbingeffort’ of a cell cannot be completely specified in termsof pressure alone. There are appendixes on the possible role of frictional or contactelectrification in cell physiology; on the increase of permeabilityof the plasma membrane to ions and water caused by electricalforces; and on the energy requirement of active water-secretingmechanisms.