Addenda Clavariacea. III

1. The following noveltiea are described, with notes on otherspecies of their genera : Aphelaria subgen. Tremellodendropsis for the A. tuberosa alliancewith subtremellaceous basidia: A. amboinensis (Lév.)comb. nov. Chaetotyphula gelatinosa sp. nov. and C. tetraspora sp. nov.from Tropical America, whence C. hyalina (Jungh.) Corner isalso recorded. Clavariadelphus junceus (Fr.) Corner is recorded from Brazil. Mucronella flava sp. nov. from Iowa. Phaeoapheloria austra1iensis gen. et sp. nov. is intermediatebetween Aphelaria and stereoid fungi. Pistillaria trispora sp. nov. from Iowa: P. tucumanensis (Speg.)comb. nov. for Typhula tucumanensis Speg. Phistillina calyx Heim is excluded as marasmioid. 2. The Physalacria-subseriea is reviewed, and the followingare described aa new: Hormomitaria albidula sp. nov. from Brazil Pseudotyhula gen. nov. from West Africa: P. ochracea sp. nov.as the typespecies : P. tenuipes (Lloyd) comb. nov. (= Mucronellatenuipes Lloyd).     

Cloning and Characterization of New Repetitive Sequences in Field Bean (Vicia faba L.)

Annals of Botany83: 535–541, 1999 It is regretted that Figure 1 of this paper was incorrect; itshould have appeared as follows: Fig. 1. Genomic organization of new repetitive sequences. Southernblots of field bean genomic DNA digested using various restrictionenzymes (H, Hind III; Hc, Hinc II; T,Taq I; A, Alu I; R, RsaI; M, Mbo I; F, Fok I) were probed with the individual repeats.The bands from which the sequences were isolated are markedby arrows. The bands from which full length sequence of T133and TIII17 repeats were isolated are marked by asterisks.     

Relationship between Plant Weight and Growing Period for Vegetable Crops in the United Kingdom

A generalized equation is derived that relates total dry matterproduction to time from emergence for crops grown in the fieldwith adequate water and nutrients. It is: w+K₁lnw+W₀=K₂t where w is the plant dry weight in t ha^–1, t is time indays after emergence, K₂ and K₁ are constants and W₀ equals–(w₀+K₁lnw₀) where w₀ is the value of w at the start ofthe growing period. The increases in the dry matter of 18 different types of vegetablecrop were measured at intervals during growth in the field.In every case the data fitted the equation very satisfactorilywith K₁ set equal to 1 t ha^–1. The fitted values of K₂were similar for many crops; those of W₀ varied considerablybut were always similar to the values calculated from the individualseed weight and the plant population. Good fits were also obtainedwhen time in days was replaced with cumulative evaporation froman open water surface. It is concluded that the growth-time curves of many differentvegetable crops can be described by the same simple equationand that the variation between curves can be largely attributedto differences in seed weight and plant population.     

Photosynthesis and Light Activation of Ribulose 1, 5-bisphosphate Carboxylase in the Presence of Starch

Owing to a typographical error three equations were omittedfrom page 1294. The correct paragraphs are set out below. The component K₁ corrected for the difference in temperaturebetween the enzyme assay and the leaf and was calculated accordingto the Arrhemus equation. where v10 and v18 are the reaction velocities of carboxylationat 10?C and 18?C, respectively and A is the activation energy(A = 90 kJ mol^–1, as determined for purified wheat RuBPCOby M?chler, Keys and Cornelius, 1980) The components K2 corrected for the difference in CO₂ partialpressure between enzyme assay and leaf and for competitive inhibitionof carboxylation by O₂ and was calculated according to the modifiedMichaelis Menten equation where v_c, is the carboxylation velocity under leaf conditions,V_c. is the maximum carboxylation velocity as determined in theenzyme assay, K_c, and K_o are the Michaelis constants for carboxylationand oxygenation, respectively (K_o = 159 Pa CO₂. K_o = 35.3 kPaO₂, as interpolated for 18?C from spinach data as determinedby Jordan and Ogren, 1984), O is oxygen partial pressure inair and C₁ is intercellular CO₂ partial pressure in leaves (C₁= 29.1 ? 0.8 Pa (? s c , n = 15)) The component K3 corrected for the decrease in CO₂ fixationin leaves due to photorespiration and was calculated accordingto equation 3 Equation 3 is denved from the equation for the substrate specificityof RuBPCO, S= v_c/v_oC (Laing, Ogren, and Hageman, 1974), andfrom the equation for the stoichiometry of photorespiratoryCO₂ release, F=v_c–1/2 v_o, where v_c, and v_c are reactionvelocities of carboxylation and oxygenation, O and C are partialpressures of 02 and intercellular CO₂, F is net photosynthesisand S is the substrate specificity of RuBPCO (S= 3061 Pa/Pa,as interpolated for 18?C from spinach data as determined byJordan and Ogren, 1984)     

Protein-O-glycosylation in yeast: protein-specific mannosyltransferases

S.cerevisiae contains at least six genes (PMT1–6) fordolicholphosphate-D-mannose: protein-O-D-mannosyltransferases.The in vivo mannosylation of seven O-mannosylated yeast proteinshas been analyzed in a number of pmt mutants. The results clearlyindicate that the various protein O-mannosyltransferases havedifferent specificities for protein substrates. Five of theproteins tested (chitinase, a-agglutinin, Kre9p, Bar1p, Pir2p/hsp150)are mainly underglycosylated in pmt1 and pmt2 mutants, wherebyqualitative differences exist among the various proteins. Twoof the O-mannosylated proteins (Ggp1p and Kex2p) are not atall affected in pmt1 and pmt2 mutants but are clearly underglycosylatedwhen PMT4 is mutated. Although the PMT4 gene product is shownto be responsible for O-mannosylating a Ser-rich region of Ggp1pin vivo, a penta-seryl-peptide is not an in vitro substratefor this transferase. A PMT3 mutation does affect O-manno-sylationof chitinase only in the genetic background of a pmt1pmt2 doublemutation, indicating that PMT1 and PMT2 can compensate for adeleted PMT3 gene. dolichol-phosphate PMT gene family protein glycosylation S. cerevisiae     

家蝇细胞凋亡起始酶Caspase-1基因的克隆及在不同虫态的表达

为了研究Caspases家族在昆虫发育变态中的作用,通过RT-PCR扩增并结合RACE技术,克隆得到家蝇Musca domestica Caspase-1基因1条,命名为Mdom-Caspase-1（GenBank中cDNA序列号为EU854472, 氨基酸序列号为ACF71490）。该基因全长1 295 bp,阅读框序列870 bp,共编码289个氨基酸,理论分子量32.83 kDa,等电点8.67。 Mdom-Caspase-1蛋白有5个保守的半胱氨酸位点QACQG, 具有Caspase的典型特征; 整个分子呈现亲水性, 有8个区域共89个氨基酸为亲酯性, 蛋白质二级结构主要由11个α螺旋区、7个β-折叠区、17个β-转角区组成。昆虫间Caspase-1分子具有明显的保守性, Mdom-Caspase-1与黑腹果蝇Drosophila melanogaster、埃及伊蚊Aedes aegypti和致倦库蚊Culex quinquefasciatus的Caspase-1氨基酸序列相似性为65%~77%。RT-PCR半定量分析结果表明, Mdom-Caspase-1基因在家蝇各个虫态中均有表达, 但在卵期、3龄幼虫、预蛹、蛹和羽化5 d的雌虫中的表达量明显高于其他虫态。这些结果提示Caspase-1可能与昆虫发育变态关系密切, 为进一步研究昆虫Caspase-1功能、设计Caspase-1抑制剂提供了分子基础。     

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     

中华蜜蜂化学感受蛋白基因Acer-CSP1克隆与表达特征分析

化学感受蛋白(chemosensory proteins, CSPs)是昆虫化学感受系统中重要的组成部分之一。本研究克隆了中华蜜蜂Apis cerana cerana化学感受蛋白基因Acer-CSP1, 其核苷酸全长351 bp （GenBank登录号为FJ157352）, 编码116个氨基酸残基, 预测蛋白分子量为13.85 kD, 等电点为4.89, 且含有4个保守的半胱氨酸残基, 均符合昆虫CSPs的一般特征, 且与意蜂CSP1基因具有99.1%的相似性, 与其他昆虫也有45.3%~68.0%的相似性。利用2^-ΔΔCt法及绝对定量法的real-time PCR技术对Acer-CSP1在中蜂不同器官表达特征进行了研究, 得出的一致结论为Acer-CSP1显著水平地高丰度表达于中华蜜蜂触角, 其次大量表达于头部。由于触角为中华蜜蜂最主要的嗅觉器官, 而头部则具有发达的感觉神经系统和味觉系统, 这也提示Acer-CSP1极有可能参与中华蜜蜂的嗅觉以及其他化学感受功能。     

Identification of maize silicon influx transporters

Maize (Zea mays L.) shows a high accumulation of silicon (Si),but transporters involved in the uptake and distribution havenot been identified. In the present study, we isolated two genes(ZmLsi1 and ZmLsi6), which are homologous to rice influx Sitransporter OsLsi1. Heterologous expression in Xenopus laevisoocytes showed that both ZmLsi1 and ZmLsi6 are permeable tosilicic acid. ZmLsi1 was mainly expressed in the roots. By contrast,ZmLsi6 was expressed more in the leaf sheaths and blades. Differentfrom OsLsi1, the expression level of both ZmLsi1 and ZmLsi6was unaffected by Si supply. Immunostaining showed that ZmLsi1was localized on the plasma membrane of the distal side of rootepidermal and hypodermal cells in the seminal and crown roots,and also in cortex cells in lateral roots. In the shoots, ZmLsi6was found in the xylem parenchyma cells that are adjacent tothe vessels in both leaf sheaths and leaf blades. ZmLsi6 inthe leaf sheaths and blades also exhibited polar localizationon the side facing towards the vessel. Taken together, it canbe concluded that ZmLsi1 is an influx transporter of Si, whichis responsible for the transport of Si from the external solutionto the root cells and that ZmLsi6 mainly functions as a Si transporterfor xylem unloading.     

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.     

COMPARATIVE KARYOLOGICAL ANALYSIS OF FIVE SPECIES OF VIVIPARUS (GASTROPODA: PROSOBRANCHIA)

Karyological analysis was performed on Viviparus ater (Cristofori& Jan, 1832), V. acerosus Bourguignat, 1862, V. mamillatus (Kuster),V. viviparus (Linnaeus, 1758) and V. contectus (Millet, 1813),collected from different freshwater bodies of Switzerland, Hungary,Albania, Italy and Lithuania. The karyotypes of V. acerosusand V. mamillatus are described for the first time. The diploidnumber of chromosomes in V. contectus equals 14, whereas indiploid sets of other studied species, 18 chromosomes are present.The karyotype formula is in V. contectus (5m + 2sm, NF = 28,in V. ater, 7m + 1sm-m + 1 sm, in V. acerosus and V. viviparus,8m + 1sm, NF = 36, in V. mamillatus, 6m + 1m-sm + 1sm-m + 1sm,NF = 36. In females of V. ater, V. mamillatus and V. acerosus,the heteromorphism of chromosome pair no. 8 was observed, witha sex-determining mechanism — ZW female /ZZ male. Although,Z and W chromosomes are metacentric, significant differences(P > 0.05, or P > 0.001) in their size were determined.The interspecific significant differences (P > 0.05) in karyotypesof V. ater, V. mamillatus, V. acerosus and V. viviparus weredetected by using one-way ANOVA and Bonferronis Multiple Comparisontests. Only chromosomes of the pair no. 5 were of similar shapein all of these species. The smallest interspecific differencewas between V. viviparus and V. acerosus. The intraspecifickaryological differences in relative chromosome length and centromericindex of V. contectus from lakes Garda (Italy), Olauka andAsveja (Lithuania) were observed in the chromosome pair no.5. (Received 29 March 1999; accepted 19 October 1999)     

Some Aspects of the Nesting Behavior and Reproductive Biology of Sea Turtles

Basic reproductive data from 21 green turtle (Chelonia mydas),8 leatherback (Dermochelys coriacea), 7 hawksbill (Eretmochelysimbricata), 7 olive ridley (Lepidochelys olivacea),6 loggerhead(Caretta caretta), 1 Kemp's ridley (Lepidochelys kempi), and1 flatback (Chelonia depressa) populations are provided. Someintraspecific and interspecific relationships between size ofnester and clutch, egg size and hatchling size are analyzed.Measurements of reproductive rates (=numbers of hatchlings perfemale per year) in 11 populations varied from 35 to 200 inan olive ridley and loggerhead colony, respectively. Nestingbehavior of each species is described in terms of type of nestingemergence and time spent on the nesting beach (=chelonery).The relatively large number of yolkless eggs laid by many leatherbacksand by some hawksbills invites further study. Some aspects ofsea turtle nesting behavior and reproduction are compared tothose of other chelonians.     

Isolation of a Tobacco cDNA Encoding Sar1 GTPase and Analysis of Its Dominant Mutations in Vesicular Traffic Using a Yeast Complementation System

The cDNA clone of NtSARl, a gene encoding the small GTPase Sar1pwhich is essential for vesicle formation from the endoplasmicreticulum (ER) membrane in yeast, has been isolated from Nicotianatabacum BY-2 cells. NtSAR1 as well as AtSAR1 cDNA isolated fromArabidopsis thaliana [d'Enfert et al. (1992) EMBO J. 11: 4205]could complement the lethality of the disruption of SARI inyeast cells in a temperature-sensitive fashion. They also suppressedyeast sec12 and sec16 temperature-sensitive mutations as yeastSARI does. Using this complementation system, we analyzed thephenotypes of several mutations in plant SAR1 cDNAs in yeastcells. The expression of NtSAR1 H74L and AtSAR1 N129I showeddominant negative effect in growth over the wild-type SARI,which was accompanied by the arrest of ER-to-Golgi transport.Such dominant mutations will be useful to analyze the role ofmembrane trafficking in plant cells, if their expression canbe regulated conditionally. (Received October 29, 1997; Accepted March 17, 1998)     

Structure of N-glycans on the S3- and S6-stylar self-incompatibility ribonucleases of Nicotiana alata

Self-incompatibility is a mechanism developed by many plantsto prevent inbreeding. The products of the selfincompatibility(S)-locus in the styles of solanaceous plants are a series ofglycoproteins with ribonuclease activity. In this study, wereport on the N-glycans from the stylar selfincompatibilityS₃- and S₆-ribonucleases of Nicotiana alata, which were enzymicallyreleased and fractionated by high-pH anion-exchange HPLC. Atotal of 14 N-glycans were identified and characterized by acombination of electrospray-ionization mass-spectrometry, ¹H-NMRspectroscopy, chemical degradation, and methylation analyses.This pattern of N-glycosylation is much more complex than thatpreviously found on the N.alata S₁- and S₂-RNases each of whichcontained only four N-glycans. N-glycan Nicotiana alata ribonuclease selfincompatibility     

Flow Cytometric Determination of Relative Nuclear DNA Contents in Bicellulate and Tricellulate Pollen

Nuclear DNA content in mature pollen was measured with a flowcytometer Pollen of Lilium longiflorum, Dendranthema grandiflora(syn Chrysanthemum monfolium) and Zea mays was chopped and stainedwith the DNA fluorochrome DAPI DNA levels, expressed as arbitraryC values, were compared with those of nuclei isolated from leafor root material of the same plants In mature tricellulate pollen the generative cell is dividedafter second pollen mitosis into two sperm cells Tricellulatepollen from maize and chrysanthemum gave rise to one large 1Cpeak and, only in the case of chrysanthemum, a much smallerone at the 2C level These results suggest that the haploid nucleiof the vegetative as well as both sperm cells in tricellulatepollen are arrested in the G₁ stage of nuclear division Thesmall 2C peak in the case of chrysanthemum probably arose froma fraction of pollen with the sporophytic chromosome number(2n pollen) In contrast to this, mature bicellulate lily pollengave rise to two identical peaks at the 1C and the 2C levelFrom this result it was concluded that in bicellulate pollen,the 1C peak is caused by the signal of the haploid vegetativenucleus arrested in the G₁ stage of nuclear division, whereasthe 2C peak originates from the haploid generative nucleus whichhas already undergone DNA synthesis and is arrested in G₂ Lilium longiflorumThunb, lily, Dendranthema grandiflora Tzelev (syn Chrysanthemum morifolium Ramat ), chrysanthemum, Zea maysL, maize, male gametophytic cells, vegetative cells, generative cells, sperm cells, unreduced pollen, sporophytic cells, relative nuclear DNA contents, replication stage