CORRIGENDUM

EAMES, F. E., 1968. New name for a Pakistan Eocene Turbonilla.Proc. malac. Soc. Lond. 38, 167. Line 4 : For J. Conch., Lond. p. 95, read Ann. Mag. Nat. Hist.(6) (6), 95.     

ERRATUM

The publishers apologize for the following errors, which appearedin Plant Geosensors by L. J. Audus (pp. 1051–1073): Page 1058, line 9: the expression should read P = (L²/D)/(l/q) Page 1068, paragraph (c) line 11: should read ‘reticulum, which was fairly uniformly peripheralin vertical roots, aggregated on the’     

ERRATA

p. 5, l. 22 for Dr. Frank read Dean p. 48, footnote 10 for Oxyxypræa read Oxyeypræa p. 51, footnote 18 for Dantzenberg read Dautzenberg p. 77, l. 29 for toxodont read taxodont p. 194, l. 10 for Rhytidia read Rhytida p. 227, l. 24 for chronological read conchological      

ERRATA

p. 136, 1. 25, for bombayana (Melvill) read bombayana (Sowerby). p. 138, 1. 24, for Trophora read Triphora. p. 255, 1. 6, for 1853 read 1856.      

Slider--maximum use of probability information for alignment of short sequence reads and SNP detection

Motivation: A plethora of alignment tools have been createdthat are designed to best fit different types of alignment conditions.While some of these are made for aligning Illumina SequenceAnalyzer reads, none of these are fully utilizing its probability(prb) output. In this article, we will introduce a new alignmentapproach (Slider) that reduces the alignment problem space byutilizing each read base's probabilities given in the prb files. Results: Compared with other aligners, Slider has higher alignmentaccuracy and efficiency. In addition, given that Slider matchesbases with probabilities other than the most probable, it significantlyreduces the percentage of base mismatches. The result is thatits SNP predictions are more accurate than other SNP predictionapproaches used today that start from the most probable sequence,including those using base quality. Contact: nmalhis{at}bcgsc.ca Supplementary information and availability: http://www.bcgsc.ca/platform/bioinfo/software/slider Associate Editor: Dmitrij Frishman     

ERRATA

p. 210. alternatus ... This entry is out of alphabetical orderand should follow after alsiosus. p. 225. caracteristicus. For x read xi. p. 236. cutis-auguina. Read cutis-anguina. p. 247. fabula. After Chem. add ) p. 271. maculosus Sow. Delete 3*. p. 279. muriculatus Sow. Delete 1. p. 302. reissi. For Sauto read Santo. p. 311. stercutius. Delete full stop after as.     

ERRATA

WARBURG, M. R., 1965. On the water economy of some Australianland snails. Proc. malac. Soc. Lond. 36, 297–305. Page 298: second line from bottom, should read ‘within± 1 µg for Themapupa’. Page 300: Fig. 2 legend, should read ‘Evaporative waterloss from Sinumelon remissum (a), Pleuroxia sp. (b) and Themapupaadelaidae (c)’. Page 300: section 4 heading, should read ‘Continuous curvesfor water loss’. Page 301: second line, for ‘Fig. 9’ read ‘Fig.3’. Page 301: Table 1, last line, for ‘0.120024’ read‘0.12024’. Present address: Israel Institute for Biological Research, Ness-Ziona,Israel.     

Gut evacuation rates and ingestion rates of Eudiaptomus graciloides measured by means of the gut fluorescence method

Journal of Plankton Research, 8, 973–983, 1986 FIg. 2. Time-dependent changes in the gut content (percentageof initial ng pigment) of E. gro.ciloides at different temperaturesunder simultaneous feeding. Fig. 4. The relationship between instantaneous evacuation rateand temperature of E. graciloides. The regresston equation forfeeding animals: y = 0.0044 e(0.141 ) (r² = 0.90). For comparisonthe results of non-feeding animals are indicated with open circles.     

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.     

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     

Effects of Interactions Between Low and High Temperature Treatments on Flowering of Spring Rape (Brassica napusvar.annua)

Exposure to high temperature (30 °C) before or after exposureto low temperature (0, 4 or 8 weeks at 4 °C) consistentlyincreased the number of leaf nodes at flowering and delayedflowering in a range of genotypes of spring rape(Brassica napusvar.annuaL.).Four days of prior exposure to high temperature had more effectthan 2 d, and the effect of subsequent exposure to high temperaturewas maximized when exposure commenced 1 week after the end ofthe low-temperature treatment. In genotypes that showed a vernalizationresponse (i.e. in which the number of leaf nodes at floweringwas reduced or flowering was advanced by low temperature), thisresponse was reduced or eliminated by either prior high-temperaturetreatment (antivernalization) or subsequent high-temperaturetreatment (devernalization). A biochemical model to accountfor these effects is proposed.Copyright 1998 Annals of BotanyCompany Brassica napusvar.annua, spring rape, antivernalization, devernalization, vernalization     

Effect of photoinhibition on algal photosynthesis: a dynamic model

Recent evidence from algal physiology and molecular biologyconfirms that photoinhibition is directly related to D1 proteindamage and recovery, and D1 protein damage leads to a decreasein electron transfer or an increase in turnover time of theelectron transfer chain. In this study, the turnover time ofthe electron transfer chain is defined as a function of therelative concentration of D1 protein in reaction centre II andthe photoinhibition processes due to D1 protein degradationare incorporated into a model of photosynthesis, initiated byDubinsky et al. (Plant Cell Physiol., 27, 1335–1349, 1986)and developed by Sakshaug et al. (Limnol. Oceanogr., 34, 198–205,1989). D1 protein damage is assumed to be both light and D1protein concentration dependent, and to be proportional to thecross-section of PSII (     

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     

ERRATA

p. 1, 1. 23, for Specimens read Specimens. p. 58, last line, for 15th March, read 13th March. p. 60, 1. 2, for Toredo read Teredo. p. 141, 1. 35, for Plates I and II read Plates 13 and 14. p. 142, 1. 3, for Plate 4 read Plato 16. p. 142, 1. 4, for Plate 4, 5, read Plate 16, 5.      

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     

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)     

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.     

Action Spectra for Inhibition by Light of Accumulation of Bacteriochlorophyll and Carotenoid during Aerobic Growth of Photosynthetic Bacteria

Action spectra for the inhibition by light of the accumulationof photosynthetic pigments during the aerobic growth of a photosyntheticbacterium, Rhodobacter sphaeroides, and an aerobic photosyntheticbacterium, Erythrobacter sp. strain OCh 114, were determinedover the range of wavelengths from 380 to 870 nm. The actionspectra for the inhibition of accumulation of bacteriochlorophyllin both R. sphaeroides and Erythrobacter sp. strain OCh 114indicated that the maximum inhibition occurred at approximately400 nm and a low level of inhibition occurred at 575 and 770nm. In R. sphaeroides, the action spectrum for the inhibitionof accumulation of carotenoid paralleled that for the inhibitionof accumulation of bacteriochlorophyll over the same range ofwavelengths. These results indicate that in both species, grownunder aerobic conditions, the same photoreceptor is involvedin the inhibition. One possible candidate for the relevant photoreceptormay be the precursor(s) to bacteriochlorophyll. It is possiblethat the photoreceptor is decomposed by light absorbed by itselfor by an unidentified photoreceptor that absorbs blue light(a photo-sensitizer). It is suggested that the accumulationof carotenoid is dependent on the stability of the bacteriochlorophyll. (Received September 16, 1988; Accepted March 2, 1989)     

Studies on the Physiology of Nodule Formation: With two Figures in the Text: A Reappraisal of the Effect of Preplanting

Nutman (Arm. Bot. 21, 321, 1957) found that preplanting agarslopes with Trifolium pratense L. or Medicago sativa L. advancedthe time when second lots of plants of these species grown onthe same slopes initiated nodules, and depressed the total numberof nodules formed. He attributed these effects to root secretionswhich at low concentration hasten initial nodulation but athigher concentrations inhibit nodule formation. Further workhas now shown that initial nodulation is stimulated becausethe preplant removes traces of nitrate from the medium. Theamount of nitrate in the tap water used to prepare the medium(6?5 p.p.m. N) also increases the number of nodules formed onthe control plants, and this effect explains to a considerableextent the depression of nodule numbers by preplanting. Initial nodulation was delayed by small amounts of nitrate andnitrite but not by other forms of combined nitrogen (ammonium,asparagine, and urea). All forms of combined nitrogen testedincreased the number of nodules formed over a period of 8 weekswhen supplied at an initial concentration of 20 p.p.m. N.     

Corrections

Vol. 30, parts 1 and 2 page 45, line 7 for "Canyon" read "Cayman". page 46 line 27for "2G; 7.xi.l937" read "36; 2.vi.l938". page 50 line 5 for "31" read "27". delete "dredged at 3 &metres". page 50 line 32 for "26; 7.xi.l937" read "30; 2.vi.l938". page 53 line 6 for "19.x.l937" read "8.v.l938". page 10, line 35, for "niiudula" read nitidula. page 21, figure 29, for "L. 8248" read "L. 82482". page 61, line 12, for "holotype (B.M. 43100)" read "syntypes(B.M. 43106, L. 82350)". page 64, line 23, for "Coriopsis" read "Cordiopsis". p. 64, lines 34 and 3G, for "lyell" read "lyellii". page 76, line 37, "Rzymowska 1914" should follow "Taylor (1900)"in line 36. page 77, line 43, for "Xerotrhicha" read "Xerotricha". page 87, line 1, for "twelve" read "ten". page 90, lines 44 and 45, for "marginal (M)" read "lateral",and for "two lateral teeth (L₁ L₂)" read "two marginal teeth".In figure 2, for "esehalent" read "exhalent". pp. 123, 125, 127, 129, headings, for "Pseudoneptunia" read"Pseudoneptunea" p. 124, line 34, for "highgatenis" read "highgatensis". p. 125, The locality of the Sedgwick Museum specimens C. 12891of Siphonalia ferroviae should be given as Titchfield, Hants.,and not as Portsmouth Dock.