Construction of Oryza sativa genome contigs by fingerprint strategy

We described the construction of BAC contigs of the genome of a indica variety of Oryza sativa.Guang Lu Ai 4. An entire representative(Sixfold coverage of rice chromosomes)and genetically stable BAC library of rice genome constructed in this lab has been systematically analysed by restriction enzyme fragmentation and polyacrylamide gel electrophoresis.And all the images thus obtained were subject to image-processing,which consisted of preliminary location of bands,cooperative tracking of lanes by correlation of adjacent bads.a precise densitometric pass,alignment at the marker bands with the standard,optional interactive editing,and normalization of the accepted bands.The contigs were generated based on the Computer Software specially designed for genome mapping.The number of contigs with 600 kb in length on average was 464.of contigs with 1000kb in length on average was 107; of contigs with 1500 kb in length on average was Construction of Oryza Sativa genome contigs.23.Therefor,all the contigs we have obtained ampunted up to 420 megabases in length.Considering the size of rice genome(430 megabased),the contigs generated in this lab have covered nearly 98% of the rice genome.We are now in the process of mapping the contigs to chromosomes.     

A TYROSINASE-LIKE ENZYME IN CEPAEA NEMORALIS AND ITS POSSIBLE RELATION WITH SHELL BANDING POLYMORPHISM

Shell banding polymorphism in Cepaea nemoralis may be relatedto tyrosinase activity in this gastropod, as the hyalozonatephenotype shows bands with no pigmentation. We aimed to establishif there is tyrosinase activity in Cepaea, and this activitywas analyzed for different organs on electrophoresis gel slabsand oxygen electrode. We have found two isocnzymatic forms,one of them polymorphic, with high activity in the foot andmantle, organs both involved with the pigmentation of body andshell. We propose that several isoenzymatic forms are functional inthe melanosome. These may be activated during the cell lysis,as hyalozonate samples display tyrosinase activity. (Received 22 June 1988; accepted 5 September 1988)     

A new interactive protein sequence alignment program and comparison of its results with widely used algorithms

A computer program that allows interactive sequence comparisonis described. It graphically displays a search matrix usingresidue physicochemical characteristics and multilength segmentalcomparisons. The user selects through a mousing device and screenpointer the sequence spans to be matched. The results of thismethod are compared with those of ALIGN and BESTFIT. Received on August 23, 1988; accepted on December 6, 1988     

A fast and sensitive multiple sequence alignment algorithm

A two-step multiple alignment strategy is presented that allowsrapid alignment of a set of homologous sequences and comparisonof pre-aligned groups of sequences. Examples are given demonstratingthe improvement in the quality of alignments when comparingentire groups instead of single sequences. The modular designof computer programs based on this algorithm allows for storageof aligned sequences and successive alignment of any numberof sequences. Received on August 23, 1988; accepted on December 6, 1988     

Chaos: principles and implications in biology

In this paper we review some of the basic principles of thetheory of dynamical systems. We introduce the reader to thedefinition of chaos and strange attractors and we discuss theirimplications in biology. Received on June 9, 1988; accepted on October 24, 1988     

Matrix algebra routines for the Acorn Archimedes microcomputer: example applications

A set of matrix algebra routines have been written, as BASICVprocedures, for the Acorn Archimedes microcomputer. It is shownthat these procedures are executed so quickly that programs,which require matrix algebra computations, can be written ininterpreted BASIC. Two example applications, reciprocal averagingand principal components analysis, are demonstrated. Received on January 19, 1988; accepted on February 9, 1988     

FEEDING OBSERVATIONS ON ACTEON TORNATILIS (LINNAEUS) (OPISTHOBRANCHIA: ACTEONIDAE)

The prey of the opisthobranch Acteon tornatilis (Linnaeus) andthe method of attack by the predator are described. The resultsof a series of choice experiments suggest that the preferredprey is the polychaete Owenia fusiformis Delle Chiaje, althoughLanice conchilega (Pallas) is also favoured. (Received 5 February 1988; accepted 29 April 1988)     

Multiple DNA and protein sequence alignment on a workstation and a supercomputer

This paper describes a multiple alignment method using a workstationand supercomputer. The method is based on the alignment of aset of aligned sequences with the new sequence, and uses a recursiveprocedure of such alignment. The alignment is executed in areasonable computation time on diverse levels from a workstationto a supercomputer, from the viewpoint of alignment resultsand computational speed by parallel processing. The applicationof the algorithm is illustrated by several examples of multiplealignment of 12 amino acid and DNA sequences of HIV (human immunodeficiencyvirus) env genes. Colour graphic programs on a workstation andparallel processing on a supercomputer are discussed. Received on April 26, 1988; accepted on July 7, 1988     

GELENT: a sequence gel entry program for keyboard and sonic digitizer input

A program is described for sequence data entry which allowsflexible program control by responding to both the keyboardand a sonic digitizer concurrently. Simplification of the initializationstage of each gel reading has been achieved, in comparison withother programs. Received on July 7, 1988; accepted on January 10, 1989     

A set of Macintosh computer programs for the design and analysis of synthetic genes

Computer programs that can be used for the design of syntheticgenes and that are run on an Apple Macintosh computer are described.These programs determine nucleic acid sequences encoding aminoacid sequences. They select DNA sequences based on codon usageas specified by the user, and determine the placement of basechanges that can be used to create restriction enzyme siteswithout altering the amino acid sequence. A new algorithm forfinding restriction sites by translating the restriction endonucleasetarget sequence in all three reading frames and then searchingthe given peptide or protein amino acid sequence with theseshort restriction enzyme peptide sequences is described. Examplesare given for the creation of synthetic DNA sequences for thebovine prethrombin-2 and ribonuclease A genes Received on October 18, 1988; accepted on December 9, 1988     

Fast and sensitive multiple sequence alignments on a microcomputer

A strategy is described for the rapid alignment of many longnucleic acid or protein sequences on a microcomputer. The programdescribed can handle up to 100 sequences of 1200 residues each.The approach is based on progressively aligning sequences accordingto the branching order in an initial phylogenetic tree. Theresults obtained using the package appear to be as sensitiveas those from any other available method. Received on October 7, 1988; accepted on December 6, 1988     

A REVIEW OF POECILOGONY IN GASTROPODS

All alleged cases of poecilogony in marine gastropods, involvingplanktotrophic and non planktotrophic larval development withina single species, are reviewed. It is concluded that there ispresently no known case of poecilogony in prosobranchs and shelledopisthobranchs, although indisputable poecilogony exists inAscoglossa and possibly nudibranchs. The multispiral or paucispiralform of the protoconch, which is a reflecxtion of planktotrophicor non-planktotrophic larval development respectively, can therefore,with a very high degree of confidence, be considered a species-specificcharacter that can be used in routine taxonomical work on bothRecent and fossil material. (Received 29 January 1988; accepted 11 April 1988)     

POEMS: program for outliers elimination in multidimensional space

A Program for Outliers Elimination in Multidimensional Space(POEMS), which allows the user to eliminate outliers from trainingspaces as a prior step to any statistical study, is presented.Even though the program can be applied to any scientific field,the characteristics of POEMS makes it particularly suitablefor ‘series design’ on Quantitative Structure -Activity Relationships studies. Received on March 1, 1988; accepted on May 3, 1988     

Correlation between meiotic behavior and breakpoints with respect to G-bands in two X-4 mouse translocations: T(X;4)7R1 and T(X;4)8R1

The meiotic synaptic behavior of male mice heterozygous for one of two X-4 translocations was examined to test a recently advanced hypothesis (Ashley, 1988) suggesting that it is possible to predict the synaptic behavior (nonhomologous vs. homologous) and recombinational parameters (suppression vs. nonsuppression of crossing-over) of a chromosome aberration from mitotic G-band breakpoint data. The hypothesis was based on prior observations of synaptic behavior in a series of X-autosome translocations in mice. The breakpoints of the translocation T(X;4)7R1 are both in G-light bands. As predicted by the hypothesis, synapsis was restricted to homology. In contrast, one breakpoint of the translocation T(X;4)8R1 lies in a "stippled" band of the standard diagrams of Nesbitt and Francke (1981). As predicted (Ashley, 1988), "stippled" bands are shown here to synapse nonhomologously, i.e., they behave as "G-dark." The linkage data, as they relate to the synaptic data and the predictions of the hypothesis, are also discussed.     

Methods for calculating the probabilities of finding patterns in sequences

This paper describes the use of probability-generating functionsfor calculating the probabilities of finding motifs in nucleicacid and protein sequences. Equations and algorithms are givenfor calculating the probabilities associated with nine differentways of defining motifs. Comparisons are made with searchesof random sequences. A higher level structure-the pattern-isdefined as a list of motifs. A pattern also specifies the permittedranges of spacing allowed between its constituent motifs. Equationsfor calculating the expected numbers of matches to patternsare given. Received on March 1, 1988; accepted on September 30, 1988     

THE CILIATED RIM OF THE VELUM OF LARVAE OF PECTEN MAXIMUS (BIVALVIA: PECTINIDAE)

During the early development of Pecten maximus, the prototrochof the trochophore becomes the rim of the velum of the veliger.The prototroch consists of a tract of randomly-distributed cilia,but in the veliger an ordered pattern of ciliation with somecompound cilia develops. The thin epithelium connecting thevelum to the body of the larva bears no cilia, nor does theupper surface of the velum (except for an apical tuft); themuch thicker epithelium of the velum rim, however, is profuselyciliated. The cilia are arranged in five bands or rings eachextending round the rim of the velum. The ring closest to theupper (i.e. ventral) surface of the velum is the inner preoralring of single cilia. Below this are two rings of much longercilia grouped to form blade-shaped cirri, which each consistof 2 or 3 rows of 10-15 cilia. The cilia substructures indicatethat the direction of active beat of the cirrus is along theaxis of the rows. This beating generates the main swimming current.The energy demands of beating are reflected in the numerouslarge mitochondria in the cells bearing the cirri. Nerve processesin the velum may control beating. Below the cirri are an adoraltract of shorter cilia and then a ring of postoral cilia. Thevelum anatomy is that of a typical bivalve veliger, but somefeatures distinguish Pecten maximus from other bivalves. Theonfiguration of the bands of cilia and the orientation of theirbeating suggest that the veliger captures food particles bythe ‘opposed band’ method. This configuration islikely to be homologous with those of other spiralian larvae. ^*Present address: School of Biological Scrences, PortsmouthPolytechnic, King Henry I Street, Portsmouth, PO1 2DY, U.K. (Received 30 September 1988; accepted 1 December 1988)     

A microcomputer program to evaluate the saturation of complex solutions with respect to biominerals

The program described is written in BASIC and enables calculationof ionic activity products and degrees of saturation for solutionswith respect to minerals of biological interest. The programtakes into account ion-pair formation by association of anionsand cations. The number of constituent species, whether or notinvolved in mineral formation or in ion-pair formation, appearsto be unlimited. The computation fulfils the conditions of conservationof matter and electrical neutrality. Successful computationis achieved even for systems with highly unfavourable ratiosbetween cations and anions with high affinities. The programis easily re-orientated towards any mineral/solution system. Received on March 1, 1988; accepted on April 19, 1988     

HAS THE POPULATION DECLINE DUE TO TBT POLLUTION AFFECTED SHELL-SHAPE VARIATION IN THE DOG-WHELK, NUCELLA LAPILLUS (L.)?

The number of dog-whelks on sheltered rocky shores of southernBritain has greatly declined during the last twenty years, followingthe use of TBT antifouling paints on the hulls of yachts andother small craft. In July 1988, dogwhelks were apparently absentfrom some sites around Dale Roads (Milford Haven: South Wales)where, formerly, they had been common. But, where animals couldbe found, there had been no detectable changes in mean shellshape since 1966/1971. That is, the survivors appear to representa random selection of the shell shapes shown by the former largepopulations. In a smaller inlet. Water-mouth Cove (N. Devon),the true sheltered shore form was apparently extinct: all thesurvivors, living on shores of intermediate exposure in theentrance to the cove, have less elongated shells. It will beinteresting to monitor the recolonisation process. (Received 5 October 1988; accepted 18 October 1988)     

A Macintosh Hypercard stack for calculation of thermodynamically-corrected buffer recipes

This paper describes a stack for the Apple Macintoshl^TM, Hypercard^TMenvironment that facilitates the calculation of a set of thermodynamically-correctedpH buffers. Presented in the familiar Macintosh mouse-basedenvironment, the program allows comprehensive buffer designand gives the user full control of buffer species, temperature,ionic strength, pH and choice of counter-ion to maintain theionic strength at a fixed value. Addition of new buffers tothe stack is straightforward and the recipes that are generated,including the weights of the various components, can be displayedon the screen or saved to a disk file for subsequent printing. Received on May 18, 1988; accepted on July 15, 1988     

HAEMOCYTES OF THE FRESHWATER SNAIL VIVIPARUS ATER (GASTROPODA, PROSOBRANCHIA)

Morphological and functional characteristics of the haemocytesof Viviparus ater were studied. Only one cell type occurs inthe haemolymph: the spreading haemocyte. These cells have thesame functions as blood cells belonging to the spreading typefound in other gastropods. It is also suggested that the spreadinghaemocytes represent the ancestral cell responsible for defencemechanisms. (Received 18 May 1988; accepted 19 August 1988)