Biomedical subjects

L Cardle

Publications and source records attributed to L Cardle.

7 recordsLinked to original sources

PubMed2000

UK CropNet: a collection of databases and bioinformatics resources for crop plant genomics.

The UK Crop Plant Bioinformatics Network (UK CropNet) was established in 1996 in order to harness the extensive work in genome mapping in crop plants in the UK. Since this date we have published five databases from our central UK CropNet WWW site (http://synteny.nott.ac.uk/) with a further three to follow shortly. Our resource facilitates the identification and manipulation of agronomically important genes by laying a foundation for comparative analysis among crop plants and model species. In addition, we have developed a number of software tools that facilitate the visualisation and analysis of our data. Many of our tools are made freely available for use with both crop plant data and with data from other species.

Crops, Agricultural↗

PubMed2000

Computational and experimental characterization of physically clustered simple sequence repeats in plants.

The type and frequency of simple sequence repeats (SSRs) in plant genomes was investigated using the expanding quantity of DNA sequence data deposited in public databases. In Arabidopsis, 306 genomic DNA sequences longer than 10 kb and 36,199 EST sequences were searched for all possible mono- to pentanucleotide repeats. The average frequency of SSRs was one every 6.04 kb in genomic DNA, decreasing to one every 14 kb in ESTs. SSR frequency and type differed between coding, intronic, and intergenic DNA. Similar frequencies were found in other plant species. On the basis of these findings, an approach is proposed and demonstrated for the targeted isolation of single or multiple, physically clustered SSRs linked to any gene that has been mapped using low-copy DNA-based markers. The approach involves sample sequencing a small number of subclones of selected randomly sheared large insert DNA clones (e.g., BACs). It is shown to be both feasible and practicable, given the probability of fortuitously sequencing through an SSR. The approach is demonstrated in barley where sample sequencing 34 subclones of a single BAC selected by hybridization to the Big1 gene revealed three SSRs. These allowed Big1 to be located at the top of barley linkage group 6HS.

Arabidopsis↗

PubMed2000

A simple sequence repeat-based linkage map of barley.

A total of 568 new simple sequence repeat (SSR)-based markers for barley have been developed from a combination of database sequences and small insert genomic libraries enriched for a range of short simple sequence repeats. Analysis of the SSRs on 16 barley cultivars revealed variable levels of informativeness but no obvious correlation was found with SSR repeat length, motif type, or map position. Of the 568 SSRs developed, 242 were genetically mapped, 216 with 37 previously published SSRs in a single doubled-haploid population derived from the F(1) of an interspecific cross between the cultivar Lina and Hordeum spontaneum Canada Park and 26 SSRs in two other mapping populations. A total of 27 SSRs amplified multiple loci. Centromeric clustering of markers was observed in the main mapping population; however, the clustering severity was reduced in intraspecific crosses, supporting the notion that the observed marker distribution was largely a genetical effect. The mapped SSRs provide a framework for rapidly assigning chromosomal designations and polarity in future mapping programs in barley and a convenient alternative to RFLP for aligning information derived from different populations. A list of the 242 primer pairs that amplify mapped SSRs from total barley genomic DNA is presented.

Chromosome Mapping↗

PubMed1999

Intimate association of microsatellite repeats with retrotransposons and other dispersed repetitive elements in barley.

Simple sequence repeat (SSR)-based genetic markers are being actively developed for the majority of crop plant species. In barley, characterization of 290 dinucleotide repeat-containing clones from SSR-enriched libraries has revealed that a high percentage are associated with cereal retrotransposon-like and other dispersed repetitive elements. Associations found were with BARE-1, WIS2-1A, PREM1 and the dispersed repetitive element R173. Additional similarities between different SSR clones, which have no matches in DNA sequence databases, indicate that this phenomenon is probably widespread in the barley genome. Sequence homologies to the non-coding regions of several cereal genes were also explained by homology to mobile genetic elements. The SSRs found can therefore be classified into two types: (1) those with unique sequences on either flank, and (2) those which are intimately associated with retro-transposons and other dispersed repetitive elements. As the cereal genome is thought to consist largely of this type of DNA, some random association would be expected. However, the conserved positions of the SSRs, relative to repetitive elements, indicate that they have arisen non-randomly. Furthermore, this class of SSRs can be classified into three subtypes: (1) those which are positioned 3' of a transposable element with unique sequence on the other flank, (2) those positioned 5' of a transposable element, and (3) those which have arisen from an internal sequence and so have transposable element sequence on both flanks. The first appear to be analogous to the class of SSRs in mammalian systems which are associated with Alu elements and SINEs (short interspersed elements) and which have been postulated to arise following integration of an extended and polyadenylated retro-transcript into the host genome, followed by mutation of the poly(A) tract and expansion into an SSR. For the second, we postulate that a proto-SSR (A-rich sequence) has acted as a 'landing pad' for transposable element insertion (rather than being the result of insertion), while the third includes those which have evolved as a component of an active transposable element which has spread throughout the genome during bursts of transposition activity. The implications of these associations for genome and SSR evolution in barley are discussed.

Base Sequence↗

PubMed1997

Foci of amino acid residue conservation in the 3D structures of the Kunitz BPTI proteinase inhibitors: how do variants from snake venom differ?

The Kunitz BPTI proteinase inhibitor family is divisible into subgroups based on source and bioactivity. Variants from snake venoms are of special interest because some show only weak inhibitory activity against the common proteinases while others are neurotoxic. We analysed the sequences for each subgrouping in the context of the common chain fold to predict the 3D location of interactive sites. The method used was an enhanced from of the previously devised 'regiovariation analysis.' This revealed the foci in 3D of amino acid side chain conservation in each subgroup. Locally high levels of side-chain conservation extending substantially in three dimensions can be associated more with the preservation of function than conformation, hence the foci probably reveal the most functionally relevant sites. For the inhibitor variants that do not originate from snake venom, regiovariation analysis gave an exact prediction of the antiproteinase site revealed by X-ray crystallography of inhibitor-enzyme complexes. However, this site is not the principal focus of evolutionary conservation in the inhibitors from snake venom, and other areas of the molecular surface are more prominent. The neurotoxic variants from snake venom (the dendrotoxins) have the principal focus of conservation near their C-terminal region, so this may be the origin of their special properties.

Amino Acid Sequence↗

PubMed1994

Identification of important functional environs in protein tertiary structures from the analysis of residue variation in 3-D: application to cytochromes c and carboxypeptidases A and B.

A simple methodology is described to apply to aligned protein sequence sets for which at least one representative 3-D C alpha structure is known. The evolutionary variation observed at each residue position in the sequence alignment is qualified by taking into account the residue variation that has occurred at other positions located within 7 A (according to the probable chain fold). This expresses the evolutionary behaviour of any residue position in the more appropriate context of its immediate surroundings and distinguishes between invariant residues on the basis of the variation of their environment. The highest mechanistic significance is attached to conserved residues in conserved surroundings, but the quantitative nature of the analysis means that all residue vicinities can be ranked and merged according to the degree of conservation that they exhibit and the residue positions that comprise them. Therefore, with the aid of the chain fold, contour maps can be constructed that show graded foci of evolutionary conservation in the underlying superstructure of the protein type, and the irregular shapes and extents of large conserved areas. To test the methodology, it was applied to cytochromes c and the carboxypeptidases A and B.

Biological Evolution↗

PubMed1993

Solution conformational analysis of the alpha-zein proteins of maize.

Small angle x-ray scattering and viscometric analyses of the alpha-zeins of maize in solution indicated that the molecules were asymmetric. Structure predictions of consensus sequences for the two classes of alpha-zeins, Z19 and Z22, were in good agreement with the alpha-helical contents determined by circular dichroism. Dimensions determined by small angle x-ray scattering and viscometry indicated a predominantly alpha-helical conformation. The data are discussed in relation to models for the solution conformation and to earlier models for alpha-zeins structure.

Amino Acid Sequence↗