Pollination Biology in a TropicalAcaciaHybrid (A. mangiumWilld. xA. auriculiformisA. Cunn. ex Benth.)

Floral biology and pollination mechanism of theAcaciahybrid(A. mangiumWilld. xA. auriculiformisA. Cunn. ex Benth.) growingin Thailand are investigated using light and electron microscopy.The hybrid is andromonoecious. A floral spike consists of about150 loosely arranged flowers. Flowers are cream coloured, fragrantand have no floral nectaries. The pistil has a solid style witha smooth, wet stigma and amphitropous ovules with immature integuments.The anther consists of eight loculi, each bearing only one 16-grainpolyad. The flowers are weakly protogynous. Anthesis is completeat 0500–0600 h but peak female receptivity begins at 0200–0300h and is completed that day. The stigmatic exudate is of thelipophilic type and is secreted from the stigmatic cells bya holocrine mechanism. Pollen is the main floral reward forthe insect pollinators. There are several floral characteristicswhich facilitate pollen transfer from anthers and depositionon stigmas.Apis melliferaandCeratinasp. are the most effectivepollinators because they are the most common visitors and carrya heavy load of hybrid polyads. However, their behaviour inforaging for pollen in the same tree and weak protogynous dichogamymay promote self-pollination in the hybrid. The hybrid has lowpollination success due to low pollinator number. An increasein exposure time of flowers to pollinators or pollinator numbermay increase pollination success but may not affect the rateof pollen deposition on stigmas due to the relatively smallsize of the stigma in relation to the polyad.Copyright 1998Annals of Botany Company Acaciahybrid,Acacia mangium, Acacia auriculiformis, pollination, pistil receptivity, anthesis, pollinators.     

A new algorithm for cluster analysis of genomic methylation: the Helicobacter pylori case

Motivation: The genomic methylation analysis is useful to typebacteria that have a high number of expressed type II methyltransferases.Methyltransferases are usually committed to Restriction andModification (R-M) systems, in which the restriction endonucleaseimposes high pressure on the expression of the cognate methyltransferasethat hinder R-M system loss. Conventional cluster methods donot reflect this tendency. An algorithm was developed for dendrogramconstruction reflecting the propensity for conservation of R-MType II systems. Results: The new algorithm was applied to 52 Helicobacter pyloristrains from different geographical regions and compared withconventional clustering methods. The algorithm works by firstgrouping strains that share a common minimum set of R-M systemsand gradually adds strains according to the number of the R-Msystems acquired. Dendrograms revealed a cluster of Africanstrains, which suggest that R-M systems are present in H.pylorigenome since its human host migrates from Africa. Availability: The software files are available at http://www.ff.ul.pt/paginas/jvitor/Bioinformatics/MCRM_algorithm.zip Contact: filipavale{at}fe.ucp.pt Supplementary information: Supplementary data are availableat Bioinformatics online. Associate Editor: Martin Bishop     

ConFunc--functional annotation in the twilight zone

Motivation: The success of genome sequencing has resulted inmany protein sequences without functional annotation. We presentConFunc, an automated Gene Ontology (GO)-based protein functionprediction approach, which uses conserved residues to generatesequence profiles to infer function. ConFunc split sets of sequencesidentified by PSI-BLAST into sub-alignments according to theirGO annotations. Conserved residues are identified for each GOterm sub-alignment for which a position specific scoring matrixis generated. This combination of steps produces a set of feature(GO annotation) derived profiles from which protein functionis predicted. Results: We assess the ability of ConFunc, BLAST and PSI-BLASTto predict protein function in the twilight zone of sequencesimilarity. ConFunc significantly outperforms BLAST & PSI-BLASTobtaining levels of recall and precision that are not obtainedby either method and maximum precision 24% greater than BLAST.Further for a large test set of sequences with homologues oflow sequence identity, at high levels of presicision, ConFuncobtains recall six times greater than BLAST. These results demonstratethe potential for ConFunc to form part of an automated genomicsannotation pipeline. Availability: http://www.sbg.bio.ic.ac.uk/confunc Contact: m.sternberg{at}imperial.ac.uk Supplementary information: Supplementary data are availableat Bioinformatics online. Associate Editor: Dmitrij Frishman     

Single-Seeded Fruits and Seedling Establishment in Dalbergia miscolobium Benth. (Papilionaceae)1

Dalbergia miscolobium (Papilionaceae) is a tree of the Brazilian cerrado that produces ovaries with two ovules. Only one ovule usually matures, but when two mature, they are smaller than seeds of single-seeded pods. Germination percentage was lower in small seeds than in medium or large seeds. In general, small seeds gave rise to smaller seedlings (dry mass) than did medium and large seeds. The root/shoot ratio, however, was very similar for the first six months, indicating that this ratio is consistent across seedling sizes. There was no correlation between seed size and relative growth rate. Single-seeded fruit production in D. miscolobium resulted in greater seed reserves and increased fruit dispersal distance; single-seeded fruits were lighter than double-seeded ones. Together, these two features should increase the probability of successful seedling establishment of seeds from single-seeded versus double-seeded fruits.     

3D-Garden: a system for modelling protein-protein complexes based on conformational refinement of ensembles generated with the marching cubes algorithm

Motivation: Reliable structural modelling of protein–proteincomplexes has widespread application, from drug design to advancingour knowledge of protein interactions and function. This workaddresses three important issues in protein–protein docking:implementing backbone flexibility, incorporating prior indicationsfrom experiment and bioinformatics, and providing public accessvia a server. 3D-Garden (Global And Restrained Docking ExplorationNexus), our benchmarked and server-ready flexible docking system,allows sophisticated programming of surface patches by the uservia a facet representation of the interactors’ molecularsurfaces (generated with the marching cubes algorithm). Flexibilityis implemented as a weighted exhaustive conformer search foreach clashing pair of molecular branches in a set of 5000 modelsfiltered from around 340 000 initially. Results: In a non-global assessment, carried out strictly accordingto the protocols for number of models considered and model qualityof the Critical Assessment of Protein Interactions (CAPRI) experiment,over the widely-used Benchmark 2.0 of 84 complexes, 3D-Gardenidentifies a set of ten models containing an acceptable or bettermodel in 29/45 test cases, including one with large conformationalchange. In 19/45 cases an acceptable or better model is rankedfirst or second out of 340 000 candidates. Availability: http://www.sbg.bio.ic.ac.uk/3dgarden (server) Contact: v.lesk{at}ic.ac.uk Supplementary information: Supplementary data are availableat Bioinformatics online. Associate Editor: Burkhard Rost     

Combining multiple positive training sets to generate confidence scores for protein-protein interactions

Motivation: High-throughput experimental and computational methodsare generating a wealth of protein–protein interactiondata for a variety of organisms. However, data produced by currentstate-of-the-art methods include many false positives, whichcan hinder the analyses needed to derive biological insights.One way to address this problem is to assign confidence scoresthat reflect the reliability and biological significance ofeach interaction. Most previously described scoring methodsuse a set of likely true positives to train a model to scoreall interactions in a dataset. A single positive training set,however, may be biased and not representative of true interactionspace. Results: We demonstrate a method to score protein interactionsby utilizing multiple independent sets of training positivesto reduce the potential bias inherent in using a single trainingset. We used a set of benchmark yeast protein interactions toshow that our approach outperforms other scoring methods. Ourapproach can also score interactions across data types, whichmakes it more widely applicable than many previously proposedmethods. We applied the method to protein interaction data fromboth Drosophila melanogaster and Homo sapiens. Independent evaluationsshow that the resulting confidence scores accurately reflectthe biological significance of the interactions. Contact: rfinley{at}wayne.edu Supplementary information: Supplementary data are availableat Bioinformatics Online. Associate Editor: Burkhard Rost     

中国黄檀属植物(豆科)二新记录种

报道了2种黄檀属植物,即绒叶黄檀(Dalbergia velutina Benth.)和卵叶黄檀(D.ovata Graham ex Benth.)在中国云南的分布新记录。     

Unequal group variances in microarray data analyses

Motivation: In searching for differentially expressed (DE) genesin microarray data, we often observe a fraction of the genesto have unequal variability between groups. This is not an issuein large samples, where a valid test exists that uses individualvariances separately. The problem arises in the small-samplesetting, where the approximately valid Welch test lacks sensitivity,while the more sensitive moderated t-test assumes equal variance. Methods: We introduce a moderated Welch test (MWT) that allowsunequal variance between groups. It is based on (i) weightingof pooled and unpooled standard errors and (ii) improved estimationof the gene-level variance that exploits the information fromacross the genes. Results: When a non-trivial proportion of genes has unequalvariability, false discovery rate (FDR) estimates based on thestandard t and moderated t-tests are often too optimistic, whilethe standard Welch test has low sensitivity. The MWT is shownto (i) perform better than the standard t, the standard Welchand the moderated t-tests when the variances are unequal betweengroups and (ii) perform similarly to the moderated t, and betterthan the standard t and Welch tests when the group variancesare equal. These results mean that MWT is more reliable thanother existing tests over wider range of data conditions. Availability: R package to perform MWT is available at http://www.meb.ki.se/~yudpaw Contact: yudi.pawitan{at}ki.se Supplementary information: Supplementary data are availableat Bioinformatics online. Associate Editor: Martin Bishop     

Pollen Tube Growth and Fertilization Efficiency in Salpiglossis sinuata: Implications for the Involvement of Chemotropic Factors

The possible involvement of chemotropic factors influencingpollen tube growth in the style and ovary of Salpiglossis wasstudied. Pollen deposited at the base of excised styles germinatedreadily, with pollen tubes penetrating the transmitting tissueand growing towards the stigma, implying that no chemotropicrequirement exists for pollen tube growth in the style. However,the position and high efficiency of seed set following limited-pollinationof intact pistils would support the involvement of localizedchemotropism operating within the ovary. Chemotropism, limited pollination, fertilization efficiency, Salpiglossis sinuata     

Model-based deconvolution of genome-wide DNA binding

Motivation: Chromatin immunoprecipitation followed by hybridizationto a genomic tiling microarray (ChIP-chip) is a routinely usedprotocol for localizing the genomic targets of DNA-binding proteins.The resolution to which binding sites in this assay can be identifiedis commonly considered to be limited by two factors: (1) theresolution at which the genomic targets are tiled in the microarrayand (2) the large and variable lengths of the immunoprecipitatedDNA fragments. Results: We have developed a generative model of binding sitesin ChIP-chip data and an approach, MeDiChI, for efficientlyand robustly learning that model from diverse data sets. Wehave evaluated MeDiChI's performance using simulated data, aswell as on several diverse ChIP-chip data sets collected onwidely different tiling array platforms for two different organisms(Saccharomyces cerevisiae and Halobacterium salinarium NRC-1).We find that MeDiChI accurately predicts binding locations toa resolution greater than that of the probe spacing, even foroverlapping peaks, and can increase the effective resolutionof tiling array data by a factor of 5x or better. Moreover,the method's performance on simulated data provides insightsinto effectively optimizing the experimental design for increasedbinding site localization accuracy and efficacy. Availability: MeDiChI is available as an open-source R package,including all data, from http://baliga.systemsbiology.net/medichi. Contact: dreiss{at}systemsbiology.org Supplementary information: Supplementary data are availableat Bioinformatics online. Associate Editor: Martin Bishop     

PETALIFERA HABEI, A NEW SPECIES FROM JAPAN ADDENDUM

Since Petalifera habei was described in the Proceedings, 34,1, 12–18, April 1960, I have received from Dr. K. Babaa short account of the same species in Publ. Seto. mar. biol.Lab. 7, 3, 337–338. December, 1959, under the title "Thegenus Petalifera and a new species, P. ramosa, from Japan".I was unaware that Dr. Baba intended to describe it. As hispaper antedates mine, his name, Petalifera ramosa, must replaceP. Habei.     

Mining SARS-CoV protease cleavage data using non-orthogonal decision trees: a novel method for decisive template selection

Motivation: Although the outbreak of the severe acute respiratorysyndrome (SARS) is currently over, it is expected that it willreturn to attack human beings. A critical challenge to scientistsfrom various disciplines worldwide is to study the specificityof cleavage activity of SARS-related coronavirus (SARS-CoV)and use the knowledge obtained from the study for effectiveinhibitor design to fight the disease. The most commonly usedinductive programming methods for knowledge discovery from dataassume that the elements of input patterns are orthogonal toeach other. Suppose a sub-sequence is denoted as P₂P₁P_1'P_2',the conventional inductive programming method may result ina rule like ‘if P₁ = Q, then the sub-sequence is cleaved,otherwise non-cleaved’. If the site P₁ is not orthogonalto the others (for instance, P₂, P_1' and P_2'), the predictionpower of these kind of rules may be limited. Therefore thisstudy is aimed at developing a novel method for constructingnon-orthogonal decision trees for mining protease data. Result: Eighteen sequences of coronavirus polyprotein were downloadedfrom NCBI (http://www.ncbi.nlm.nih.gov). Among these sequences,252 cleavage sites were experimentally determined. These sequenceswere scanned using a sliding window with size k to generateabout 50 000 k-mer sub-sequences (for short, k-mers). The valueof k varies from 4 to 12 with a gap of two. The bio-basis functionproposed by Thomson et al. is used to transform the k-mers toa high-dimensional numerical space on which an inductive programmingmethod is applied for the purpose of deriving a decision treefor decision-making. The process of this transform is referredto as a bio-mapping. The constructed decision trees select about10 out of 50 000 k-mers. This small set of selected k-mers isregarded as a set of decisive templates. By doing so, non-orthogonaldecision trees are constructed using the selected templatesand the prediction accuracy is significantly improved. Availability: The program for bio-mapping can be obtained byrequest to the author. Contact: z.r.yang{at}exeter.ac.uk     

Light Gradients and the Transverse Distribution of Chlorophyll Fluorescence in Mangrove andCamelliaLeaves

The light gradient and transverse distribution of chlorophyllfluorescence in mangrove andCamellialeaves, which have differentmorphological characteristics, were examined using a micro-fluorescenceimaging system reported previously (Takahashiet al., Plant,Cell and Environment17: 105–110, 1994). Epidermal cellsscattered light strongly, resulting in an increase in the fluencerate in epidermal cells. For theCamellialeaf, a light gradientwas formed by absorption of light by photosynthetic pigmentsassociated with the induction of chlorophyll fluorescence. Forthe mangrove leaf, a light gradient was formed by backward scatteredlight within a thick layer of non-assimilatory cells. Lightwith a low absorption coefficient (515 nm) penetrated deeperthan that with a higher absorption coefficient (477 nm and 488nm) in theCamellialeaf, while light of both wavelengths showedsimilar profiles in the mangrove leaf. In the mangrove leaves,scattered light declined significantly in the non-assimilatorycell layer which is in front of the assimilatory cells. Light,the intensity of which was reduced to approx. 10% of the maximum,was well scattered and induced a considerable amount of chlorophyllfluorescence in the assimilatory cells, which appear to be wellorganized to capture weak light.Copyright 1998 Annals of BotanyCompany fluorescence, intact leaf, light gradient, mangrove (Rhizophora mucronataLamk.),Camellia japonicaL.     

ELECTROPHORETIC AND MORPHOMETRIC CHARACTERS IN POPULATION DIFERENTIATION OF THE PEARL OYSTER, PINCTADA RADIATA (LEACH), FROM AROUND BAHRAIN

Variation at the leucine aminopeptidase (Lap), glucose phosphateisomerase (Gpi) and tetrazolium oxidase (To) loci was investigatedin samples of three populations, Al-Mayana (MAY), Shigita (SH)and Mina Salman (MS), of Pinctada radiata from pearl oysterbeds around Bahrain. The To locus was monomor-phic. SignificantLap and Gpi heterozygote deficiencies were evident and it issuggested that these were generated by selection. The MS population,to the East of Bahrain, differed significantly in Gpi allelefrequencies from both Northern populations (MAY, SH) and Nei'sgenetic identity indicates a close relationship between theNorthern populations. Measurements of shell morphometrics were used both as ratiosof one dimension to another, and as regressions of one dimensionon another to examine relatedness between populations. Boththese mor-phometric approaches gave different results from eachother and also differed from the electrophoretic data. It isconcluded that estimates of relatedness in pearl oysters basedon electrophoretic data will be more reliable than those basedon shell shape. (Received 20 November 1990; accepted 12 April 1991)     

Violastyrene and isoviolastyrene,cinnamylphenols from Dalbergia miscolobium

The heartwood of Dalbergia miscolobium contains, in addition to the neoflavonoids (S)-4-methoxydal-bergione, (S)-4′-hydroxy-4-methoxydalbergione and dalbergin, the isoflavone di-O-methyldaidzein, the benzophenone cearoin and two cinnamylphenols, violastyrene [E-1-(3-hydroxy-2,4-dimethoxybenzyl)-2-phenylethylene] and isoviolastyrene [E-1-(4-hydroxy-2,3-dimethyoxybenzyl)-2-phenylethylene]. The structural determination of the cinnamylphenols relied on spectra, degradations and synthesis.