Estimating the capacity for improvement in risk prediction with a marker

Consider a set of baseline predictors X to predict a binaryoutcome D and let Y be a novel marker or predictor. This paperis concerned with evaluating the performance of the augmentedrisk model P(D = 1|Y,X) compared with the baseline model P(D= 1|X). The diagnostic likelihood ratio, DLR_X(y), quantifiesthe change in risk obtained with knowledge of Y = y for a subjectwith baseline risk factors X. The notion is commonly used inclinical medicine to quantify the increment in risk predictiondue to Y. It is contrasted here with the notion of covariate-adjustedeffect of Y in the augmented risk model. We also propose methodsfor making inference about DLR_X(y). Case–control studydesigns are accommodated. The methods provide a mechanism toinvestigate if the predictive information in Y varies with baselinecovariates. In addition, we show that when combined with a baselinerisk model and information about the population distributionof Y given X, covariate-specific predictiveness curves can beestimated. These curves are useful to an individual in decidingif ascertainment of Y is likely to be informative or not forhim. We illustrate with data from 2 studies: one is a studyof the performance of hearing screening tests for infants, andthe other concerns the value of serum creatinine in diagnosingrenal artery stenosis.     

Reproductive Isolation in a Native Population of Petunia sensu Jussieu (Solanaceae)

Reproductive isolation was studied in four syntopic speciesof Petunia sensu Jussieu (Solanaceae) at a site in Rio Grandedo Sul State, Brazil. Reciprocal artificial crossing experimentsconfirmed that a genetic barrier exists between Petunia(P. axillarisand P. integrifolia) andCalibrachoa (C. parviflora and C. heterophylla),and also between C. parviflora andC. heterophylla . Petuniaaxillaris(white, nocturnally scented flower) is geneticallycompatible with the syntopic and allotopic P. integrifolia(coloured,unscented flower). Reproductive isolation appears to be maintainedby the two species having different pollinators: nocturnallyactive hawkmoths (Manduca contracta andM. diffissa subsp. petuniae)pollinate P. axillaris while a diurnally active bee (Hexanthedasp.) pollinates P. integrifolia. Flowers of P. integrifoliaexhibit diurnal opening and closing movements synchronous withthe activity period of the bee. Other than a probable nectarrobber (a carpenter bee, Xylocopa augusti), no insect visitedflowers of P. axillaris in the day. Amounts of floral nectarin P. axillaris and P. integrifolia were within the range ofhawkmoth- and bee-pollinated flowers, respectively. Reproductiveisolating mechanisms in the genus Petunia sensu Jussieu arediscussed. Copyright 2001 Annals of Botany Company Calibrachoa, hawkmoth, Petunia, Petunia axillaris, Petunia integrifolia, pollinator, reproductive isolation, Solanaceae     

Electrophoretic Variation in Esterases, Peroxidases and Acid Phosphatases in Some Native Greek Taxa of the Genera Hordeum and Taeniatherum

Horizontal starch gel electrophoresis has been applied to thestudy of esterase, peroxidase and acid phosphatase patternsin seven taxa, namely Hordeum diploids (2n=14) (H. marinum,H. marinum I and H. hystrix), tetraploids (2n=28) (H. bulbosumand H. murinum subsp. leporinum) and Taeniatherum (2n=14) (T.caput-medusae and T. caput-medusae I) in order to elucidatetheir phylogenetic relationships. On the basis of our experimentalresults the seven taxa may be placed in the following threegroups; (1) diploid Hordeum (H. marinum, H. marinum I, H. hystrix);(2) tetraploid Hordeum (H. bulbosum, H. murinum subsp. leporinum);(3) Taeniatherum (T. caput-medusae, T. caput-medusae I). Esterase, peroxidase and acid phosphatase patterns of the twoHordeum diploid taxa (H. marinum and H. marinum I) are verysimilar suggesting their close phylogenetic relationship; thesame is true for both the taxa of the genus Taeniatherum (T.caput-medusae and T. caput-medusae I). The taxa of the Taeniatherumgroup compared with the diploid Hordeum (H. marinum, H. marinumI, H. hystrix) and the tetraploid Hordeum (H. bulbosum, H. murinumsubsp. leporinum) show a lower degree of phylogenetic relationshipand seem to be equally distant from them. The tetraploid Hordeumgroup shows a higher phylogenetic relationship with diploidHordeum group than with the Taeniatherum group. These results confirm that the genus Taeniatherum, previouslyconsidered as part of the genus Hordeum, should be regardedas a separate genus. Gramineae (Poaceae), Hordeum L., Taeniatherum Nevski., esterase, peroxidase and acid phosphatase patterns, phylogenetic relationships     

Water Import Rate in Tomato Fruit: A Resistance Model

A model of the water import rate in tomato fruit is proposed.It compares the fruit to a hollow sphere (P) with external radiusR and internal radius R_G, corresponding to pericarp, and containingan internal spherical part (G). The pathway limiting water inputrate at any point I at a distance r from the fruit centre wasassumed to be proportional: (a) in P, to the length of the arcwhich has a radius r and which goes from I to the pedicel extension;(b) in G, to r. The water input rate at I was modelled basedon a law similar to Darcy's law which takes into account thedifference between the water potential at entry of fruit andthe water potential at point I. This latter potential was thesum of fruit osmotic potential and pressure potential due toresistance of tissue to deformation. This potential was proportionalto R-r or R_G -r. The model was expressed at fruit level by alaw such that water mass imported per unit time per unit surfacearea of fruit (f_rw) was a linear function of R. The model wascompared to linear regressions of this rate in terms of R whichhad been found during fruit swelling from published results,and which were obtained at different values of nutrient solutionsalinity. The results suggested that water input in tomato fruitis conditioned by passive forces depending on fruit size.Copyright1994, 1999 Academic Press Fruit, growth, model, resistance, salinity, size, tomato, transfer, water     

Background context and decision making in hoarding gray jays

If decision makers assign stable fitness-related values to options, preference for the most valuable of simultaneously encounteredoptions should be independent of background context (i.e.,prior options). The tendency to choose optionx versus y shouldbe unaffected by whether the decision maker has already beengiven a choice betweenx' and y' or between x' and y'. Here, food-hoarding gray jays (Perisoreus canadensis) were given aninitial choice between x' (one raisin, 0.5 m into a tube) and y' (three raisins, 0.5 m) or between x' and y' (both identicalto x'). All subjects were then given a choice between x' (oneraisin, 0.3 m) and y' (three raisins, 0.7 m). In violationof the principle of irrelevant alternatives, the "market share"ofx depended on prior options. Subjects initially exposed tocontext {x', y'} showed a stronger preference for x than did subjects initially exposed to {x', y'}, which implies thatthe jays did not assign a fixed value to each option. Subjectsthat initially could obtain a large reward (y') for about thesame "price" (perceived danger) as a small reward (x') apparentlydevalued the large reward (y) in the subsequent choice. Thiseffect may be the joint byproduct of cognitive constraints andan adaptive tendency to use information provided by the context.     

Systematic revision of Jorunna Bergh, 1876 (Nudibranchia: Discodorididae) with a morphological phylogenetic analysis

The genus Jorunna is characterized by a dorsum covered withcaryophyllidia, a prostate with two sections, a penis usuallyunarmed but occasionally armed with hooks, a copulatory spine,the presence of an accessory gland and a labial cuticle smoothor armed with jaw elements. The examination of 216 non-typespecimens, 30 types, and a review of the literature show thatthere are 16 valid species of the genus Jorunna: J. tomentosa(Cuvier, 1804); J. funebris (Kelaart, 1859); J. pantherinaAngas,1864; J. rubescens (Bergh, 1876); J. labialis (Eliot, 1908);J. parva (Baba, 1938); J. spazzola (Marcus, 1955); J. hartleyi(Burn, 1958); J. alisonaeMarcus, 1976; J. lemchei (Marcus, 1976);J. evansi (Eliot, 1906); J. pardusBehrens & Henderson, 1981;J.ramicolaMiller, 1996 and J. onubensis Cervera, García-Gómez& García, 1986. In addition, two new species fromthe Eastern Pacific are described: J. osae n. sp. and J. tempisquensisn. sp. We propose two new combinations: Jorunna parva and J.evansi. New records for the genus Jorunna are provided fromItaly, Algeria, Seychelles, Madagascar, Thailand, Marshall Islands,New Caledonia, Île de la Réunion, Sudan, PapuaNew Guinea, Indonesia, Panama, Costa Rica, Bahamas, and SouthernMexico. We present the first preliminary phylogenetic analysisof this cryptobranch dorid genus, based on morphological anatomicaldata, and discuss the biogeography and evolution of severalcharacters in this group. The phylogeny supports the hypothesisthat the genus Jorunna is a monophyletic group and shows thatKentrodoris is nested within it. (Received 31 December 2004; accepted 10 January 2008)     

Shell characters and taxonomy of Latirus and related fasciolariid groups

The neogastropod family Fasciolariidae contains a complex ofgenera related to Latirus Montfort, 1810, many of which havetraits unusual for the family. In a taxonomic revision of someof these genera, based on shell characters, we restrict Latirusto a mainly Indo-West Pacific group of Pliocene to Recent species,which closely resemble the middle Miocene to Recent pantropicalgenus Hemipolygona Rovereto, 1899. Hemipolygona stenomphalus(Habe & Kosuge, 1966) is synonymized with H. recurvirostris(Schubert & Wagner, 1829). Lathyropsis Oostingh, 1939, basedon a small Pliocene species from Indonesia, is here tentativelysubsumed under Polygona Schumacher, 1817. The latter genus,ranging from the late Oligocene to Recent, occurs mainly inthe New World and eastern Atlantic, and contains at least twospecies groups centered on P. infundibulum Schumacher, 1817(type of genus) and P. angulatus (Röding, 1798). Taxa assignedby many authors to Latirulus Cossmann, 1889, are here reassignedto the new genus Turrilatirus (type species: Voluta turritaGmelin, 1791), from the Pliocene to Recent of the Indo-WestPacific. Latirulus is restricted to Eocene species. We assignvarious early Miocene to Recent species from the western Atlanticand eastern Pacific to the new genus Pustulatirus (type species:Latirus mediamericanus, Hertlein & Strong, 1951a). Taxaformerly assigned to Latirus but here removed from Fasciolariidaeinclude Latirus ewekoroensis Adegoke, 1977; the Eocene RusculaCasey, 1904; Lathyrus granifer and L. compactilis, both of Martin,1931; Latirus kirbyi Clark, 1938; Latirus tortilis var. nanafaliusHarris, 1899; and Latirus quercotillaensis Olsson, 1931. (Received 6 September 2005; accepted 29 May 2006)     

Flower Morphology and Pollination Mechanism in Three Sympatric Goodyerinae Orchids from Southeastern Brazil

The pollination biology of Aspidogyne argentea, Aspidogyne longicornuandErythrodes arietina was studied in south-eastern Brazil.The three species are self-compatible but are pollinator-dependent.These three orchid species offer nectar as a reward to pollinatorsand flower visitors. The twoAspidogyne spp. have a dorsally-adhesiveviscidium, a feature which precludes pollinators other thanbees. Erythrodes arietina flowers are protandrous and show aventrally-adhesive viscidium. Aspidogyne argentea is visitedby halictid bees (here ranked as probable pollinators) and Hesperiidaebutterflies. Aspidogyne longicornu is pollinated by femalesof Euglossa(Euglossini) and visited by the hummingbird Phaethornisruber and by the euglossine bees Eulaema seabrai(females) andEulaema cingulata(males). The pollinarium adheres to the ventralsurface of the bee labrum, a very difficult place for bees toclean. The dorsally adhesive viscidium in Aspidogyne parallelsthat of the Spiranthinae genera of the so-called ‘Pelexiaalliance’. This condition seems to be particularly adaptativeunder conditions of low-frequency pollinator visits. Erythrodesarietina is pollinated by bees of the genera Paratetrapediaand Osiris which carry the pollinarium on the dorsal surfaceof their proboscis. Occasionally, these bees remove pollinariafrom their mouthparts using their forelegs. In general, in thespecies studied, a combination of both pollinator behaviourand morphological peculiarities promotes cross-pollination.Copyright 2001 Annals of Botany Company Orchids, Goodyerinae, Aspidogyne, Erythrodes, pollination, bees, hummingbirds, butterflies, morphology, viscidium, protandry     

Wide-Range Distribution of Insertion Sequences Identified in B. halodurans among Bacilli and a New Transposon Disseminated in Alkaliphilic and Thermophilic Bacilli

All of the insertion sequences (ISs) except for IS663 and agroup II intron identified in the alkaliphilic Bacillus haloduransC-125 genome were also detected in nine other strains of thesame species by PCR and Southern blot analysis. The transposaseof IS653 identified in the genomes of the 10 strains of B. haloduranswas found to have become the most diversified of all ISs identifiedin the genomes of 10 strains. A new IS element designated IS661belonging to the IS1380 family with inverted repeats (IRs) 17bp in length was present within IS658 identified in the genomeof B. halodurans A59. In addition, a new transposon designatedTn3271bh was identified within the IS642 element in the A59genome, which is similar to a transposon identified in thermophilicGeobacillus stearothermophilus T-6. The new transposon, Tn3271bh,generated an 8-bp duplication of the target site sequence andcarries a 21-bp IR. On the other hand, all kinds of ISs exceptfor IS643 and IS658 were distributed in the genome of obligatelyalkaliphilic Bacillus alcalophilus. Three ISs (IS652, IS653,and IS660) and a group II intron (Bh.Int) were widely dispersedin other Bacillus species without a correlation with the phylogeneticplacement based on 16S rDNA sequences.     

Leaf Properties Related to the Photosynthetic Response to Drought in Upland and Lowland Rice Varieties

Four upland and two lowland varieties were grown on floodedand dry soil in pots in a glasshouse. Photosynthetic rate (P),transpiration rate (T), and water content (W) of the secondexpanded leaf from the top of the main stem were measured undercontrolled aeration and illumination in a leaf chamber in thelaboratory, together with leaf area (La), dry matter content(DM), nitrogen content (N), stomatal frequency (Sf), and totalvessel cross-sectional area at the base of the leaf blade (Va).P/La was positively related to T/La and Sf/La among six varietieswhen they were grown on flooded soil. IR 8, a semidwarf indicalowland variety, showed the highest P/La with the highest Sf/Laand T/La. When grown on dry soil P/La was positively correlatedwith W/DM, the latter being negatively related to T/Va. Twoupland varieties, African Moroberekan and Brazilian IAC 1246,showed the highest P/La on dry soil, keeping a higher W/DM witha lower T/La and a lower T/Va. Daytime leaf diffusive conductance(l/r_L) and leaf water potential (_L) measured on the same orthe same stage leaf in the glasshouse were positively correlatedwith the W/DM measured in the laboratory among varieties grownon dry soil. Simultaneous observation of P, T and W in the laboratoryindicated nonstomatal reduction in P/La due to leaf water deficitin sensitive varieties, although these varieties also showeda markedly lower daytime l/r_L in the glasshouse as comparedwith resistant varieties. Oryza sativa L., rice, drought resistance, photosynthesis, transpiration, water deficit, stomatal frequency, vessel size     

Can phaeopigments be used as markers for Daphnia grazing in Lake Constance?

The formation of chlorophyll a degradation products was measuredwith natural phytoplankton from Lake Constance and Daphnia magnaand native Daphnia as grazers in grazing experiments duringspring bloom conditions using high-pressure liquid chromatography(HPLC). Chlorophyll a start concentrations were between 1.2and 16.3 µg l^–1; phaeopigment weights constituted5% of chlorophyll a weight. Only phaeophorbide a was a markerfor Daphnia grazing; concentrations of other phaeopigments (phaeophytina, chlorophyllide a and two unidentified phaeopigments) didnot increase during Daphnia grazing. Conversion efficiencies(chlorophyll a to phaeophorbide a) were between 0 and 43% ona weight basis, and between 0 and 65% on a molar basis. Conversionefficiencies were highest at high grazer density (40 Daphnial^–1) and after a 24 h exposure time. Grazing by microzooplanktonprobably led to the formation of the two unidentified phaeopigments.In Lake Constance, Daphnia density was significantly positivelycorrelated with the phaeophorbide a/chlorophyll a ratio whenit was <5000 Daphnia m^–3. However, when higher Daphniadensities were included in calculations, then Daphnia densitywas positively, but insignificantly, correlated with the phaeophorbidea/chlorophyll a ratio. This suggests that when the level offood per Daphnia is low, then grazing is more efficient withless production of phaeophorbide a and a higher production ofcolourless products.     

ANATOMICAL STUDIES REVEAL NEW PHYLOGENETIC INTERPRETATIONS IN LISSACHATINA (PULMONATA: ACHATINIDAE)

This is essentially a preliminary report on the revision ofsubgenus Lissachatina of the African land snail family Achatinidae.It extends the conchological revisionary work of J.C. Bequaert(1950) along the complementary line of comparative anatomicalstudies of the reproductive tracts. This is directed towardthe goal of a better understanding of phylo-geny in this family.Species emphasized are Achatina albopicta E.A. Smith,1878; A.allisa Reeve, 1849; A. fulica Bowdich, 1822; A. loveridgei Clench& Archer, 1930; A. zanzibarica Bourguignat, 1879, and thenew species A. eleanorae. Relegated tosynonymy are A. albicansPfeiffer, 1851; A. delorioli Bonnet, 1864; and A. iredalei Preston,1910. Tangible anatomical characters separate subgenera Lissachatinaand Achatina. A. capelloi Furtado, 1886; A. craveni E.A. Smith,1881; and A. connollyi Preston, 1912 are transferred from Lissachatinato Achatina s.s. Other transfers are in progress. (Received 26 September 1994; accepted 25 November 1994)     

Cloning, Nucleotide Sequences and Differential Expression of the nifH and nifH-Like (frxC) Genes from the Filamentous Nitrogen-Fixing Cyanobacterium Plectonema boryanum

The frxC gene, found in liverwort chloroplast DNA, encodes aprotein of unknown function. The deduced amino acid sequenceof the protein shows significant homology to that of ni-trogenaseFe-protein encoded by the nifH gene. We have cloned the frxCand nifH genes from the nitrogen-fixing cyanobacterium Plectonemaboryanum, using frxC- and nifH-specific probes, and have determinedtheir nucleotide sequences. The amino acid sequence deducedfrom the frxC gene of P. boryanum exhibits 83% homology to thatof the protein encoded by the/rxCgene from liverwort, whereasit exhibits only 34% homology to that encoded by the nifH genefrom the same organism, namely, P. boryanum. Northern blot analysisshowed that the frxC gene was transcribed more actively undernitrogenase-repressed conditions than under nitrogenase-inducedconditions, suggesting that the FrxC protein has a functiondistinct from nitrogen fixation. These results, together withthe phylogenetic relationship between the nifH and frxC genes,indicate that the frxC and nifH genes are derived from a commonancestral gene but have evolved independently to encode proteinswith different functions. (Received April 27, 1991; Accepted August 12, 1991)     

家蚕基质金属蛋白酶基因Bm-MMP的克隆、序列分析及表达研究

基质金属蛋白酶（matrix metalloproteinases, MMPs）家族是一类蛋白水解酶, 能够降解基底膜和细胞外基质中大部分蛋白质。为了研究MMPs对家蚕Bombyx mori基本生理功能的影响, 本文利用RACE和RT-PCR方法, 首次从家蚕蛹中克隆了一个MMP基因的全长cDNA, 命名为Bm-MMP。序列分析表明, Bm-MMP的mRNA存在两个选择性剪切变体, 分别命名为Bm-MMP-V1和Bm-MMP-V2。其中Bm-MMP-V1 cDNA全长为2 257 bp, 包含一个1 686 bp的开放阅读框, 编码561个氨基酸, 预测蛋白质分子量约为62.3 kD; Bm-MMP-V2 cDNA全长为2 188 bp。同源性分析表明, Bm-MMP-V1和Bm-MMP-V2的氨基酸序列与蜡螟Galleria mellonella的Gm1-MMP的氨基酸序列同源性最高, 均为88.8%;与黑腹果蝇Drosophila melanogaster的Dm1-MMP的氨基酸序列同源性, 分别为61.2%和64.3%。将Bm-MMP-V1的编码区连接到表达载体pET28a(+)上, 并在大肠杆菌BL21中进行原核表达, SDS-PAGE和Western blot分析结果表明, 带有6×His标签的融合蛋白被成功表达。半定量RT-PCR分析表明, Bm-MMP-V1和Bm-MMP-V2在4龄眠蚕、熟蚕、吐丝后36及48 h、预蛹中的表达量比5龄中食期与化蛹后的表达量高, 推测该基因与家蚕幼虫蜕皮变态有关;LPS诱导5龄3 d的幼虫, 其Bm-MMP-V1和Bm-MMP-V2在血液中的表达量升高, 推测Bm-MMP可能与免疫相关。本研究为进一步研究Bm-MMP在家蚕体内的作用机制奠定了基础。     

Predation by a photosynthetic dinoflagellate Gyrodinium instriatum on loricated ciliates

Feeding of a naked photosynthetic dinoflagellate, Gyrodiniuminstriatum, on loricated ciliates was investigated. Gyrodiniuminstriatum preyed on Favella azorica and Eutintinnus tubulosusby engulfment through the posterior end of the sulcus. In thecase of E.tubulosus, G.instriatum preyed on this small ciliatekeeping the original gymnodinioid cell shape. On the other hand,G.instriatum preyed on Favella taraikaensis by absorbing thecell contents of this large ciliate, which resulted in a balloonlike inflation of its body size. It seemed that G.instriatumcan change its feeding style according to the size of prey.Thus, the present study shows, by using direct observationson the feeding of G.instriatum on loricated ciliates, a reversalof energy flow processes in the food chain in which photosyntheticorganisms eat primary consumers. The growth of G.instriatumafter feeding on F.taraikaensis and E.tubulosus is also describedbriefly.