Biomedical subjects

Ian N Roberts

Publications and source records attributed to Ian N Roberts.

10 recordsLinked to original sources

PubMed2006

Tracing the origin and co-phylogeny of the caliciviruses.

Caliciviruses infect a wide range of mammalian hosts and include the genus Norovirus, the major cause of food-borne viral gastroenteritis in humans. Using publicly available sequence data and phylogenetic analysis tools, the origins and virus-host co-phylogeny of these viruses were investigated. Here, evidence is presented in support of host switching by caliciviruses, but showing that zoonotic transfer does not appear to have occurred in the history of these viruses. The age or demography of the caliciviruses cannot yet be estimated with any firm degree of support, but further studies of this family, as new dated sequences become available, could provide key information of importance to human health and in understanding the emergence of food-borne disease.

Animals↗

PubMed2005

High throughput sequence analysis reveals hitherto unreported recombination in the genus Norovirus.

Viruses of the Norovirus genus (Caliciviridae family) are a major cause of human gastroenteritis. In some viruses, recombination is an important evolutionary process and therefore we should try to discover the quantity and characteristics of such events in Noroviruses. In order to identify recombination events, multiple sequence alignments were assembled from publicly available strains, and were tested using RAT, a recently developed software tool. Strains identified by RAT as putative recombinants were tested further, using a phylogenetic approach, the LARD software, and a Monte Carlo method, to gain additional support for their status. The identification of two previously described recombinants, WUG1 and Snow Mountain, was made. Furthermore, three instances of hitherto unreported recombination implicating Norovirus strains MD 145-12, Gifu'96 and Saitama U4 were found, with good statistical support for the latter two of these cases. Lordsdale-like viruses were highlighted as major contributors to recombination events during Norovirus evolution. Finally, the relevance of recombinants to the worldwide transmission of Norovirus is discussed.

Caliciviridae Infections↗

PubMed2005

Inferences of evolutionary relationships from a population survey of LTR-retrotransposons and telomeric-associated sequences in the Saccharomyces sensu stricto complex.

The Saccharomyces sensu stricto complex consists of six closely related species and one natural hybrid. Intra- and inter- species variability in repetitive elements can help elucidate the population structure and evolution of these close relatives. The chromosome positions of several telomeric associated sequences (TASs) and LTR-retrotransposons have been determined, using PFGE, in 112 isolates. Most of the repetitive elements studied are found in multiple copies in each strain, although in some subpopulations these elements are present in low copy number or are absent. Hybridization patterns and copy numbers of the repetitive elements correlate with geographic distribution. These patterns may yield interesting clues as to the origins and evolution of some TASs and retrotransposons, e.g. we can infer that Y' originated on the left end of chromosome XIV. There is strong evidence for horizontal transfer of Ty2 between S. cerevisiae and S. mikatae. Ty1 and Ty5 are either lost easily or frequently horizontally transferred. We have also found some gross chromosomal rearrangements in isolates within species and a few new natural hybrids between species, indicating that these processes occur in the wild and are not limited to conditions of human influence. DNA sequences have been deposited with the EMBL/GenBank database under Accession Nos AJ632279-AJ632293.

Base Sequence↗

PubMed2005

Molecular evidence for the existence of natural hybrids in the genus Zygosaccharomyces.

26S rDNA D1/D2 sequencing was used to characterise a number of food-associated Zygosaccharomyces rouxii strains held at the National Collection of Yeast Cultures. In the course of this study, four strains (NCYC 1682, NCYC 3042, NCYC 3060 and NCYC 3061) were identified which appeared, based on their D1/D2 sequences, to belong to a novel Zygosaccharomyces species. However, subsequent sequence analysis showed that NCYC 1682, NCYC 3060 and NCYC 3061 possess two highly divergent copies of the nuclear-encoded ADE2, HIS3 and SOD2 genes, indicating these three strains are in fact hybrids. NCYC 3042, however, does appear to represent a novel species which may be hypothesized to have crossed with Z. rouxii and given rise to hybrid strains. Additional approaches to define precise taxonomic status and mechanisms of hybrid genome formation amongst yeast species are discussed.

Carboxy-Lyases↗

PubMed2004

Recombination Analysis Tool (RAT): a program for the high-throughput detection of recombination.

MOTIVATION: Recombination can be a prevailing drive in shaping genome evolution. RAT (Recombination Analysis Tool) is a Java-based tool for investigating recombination events in any number of aligned sequences (protein or DNA) of any length (short viral sequences to full genomes). It is an uncomplicated and intuitive application and allows the user to view only the regions of sequence alignments they are interested in. RESULTS: RAT was applied to viral sequences. Its utility was demonstrated through the detection of a known recombinant of HIV and a detailed analysis of Noroviruses, the most common cause of viral gastroenteritis in humans. AVAILABILITY: RAT, along with a user's guide, is freely available from http://jic-bioinfo.bbsrc.ac.uk/bioinformatics-research/staff/graham_etherington/RAT.htm.

DNA, Viral↗

PubMed2003

Engineering evolution to study speciation in yeasts.

The Saccharomyces 'sensu stricto' yeasts are a group of species that will mate with one another, but interspecific pairings produce sterile hybrids. A retrospective analysis of their genomes revealed that translocations between the chromosomes of these species do not correlate with the group's sequence-based phylogeny (that is, translocations do not drive the process of speciation). However, that analysis was unable to infer what contribution such rearrangements make to reproductive isolation between these organisms. Here, we report experiments that take an interventionist, rather than a retrospective approach to studying speciation, by reconfiguring the Saccharomyces cerevisiae genome so that it is collinear with that of Saccharomyces mikatae. We demonstrate that this imposed genomic collinearity allows the generation of interspecific hybrids that produce a large proportion of spores that are viable, but extensively aneuploid. We obtained similar results in crosses between wild-type S. cerevisiae and the naturally collinear species Saccharomyces paradoxus, but not with non-collinear crosses. This controlled comparison of the effect of chromosomal translocation on species barriers suggests a mechanism for the generation of redundancy in the S. cerevisiae genome.

Aneuploidy↗

PubMed2003

Genetic differentiation of the Aspergillus section Flavi complex using AFLP fingerprints.

Twenty-four isolates of Aspergillus sojae, A. parasiticus, A. oryzae and A. flavus, including a number that have the capacity to produce aflatoxin, have been compared using amplified fragment length polymorphisms (AFLPs). Based on analysis of 12 different primer combinations, 500 potentially polymorphic fragments have been identified. Analysis of the AFLP data consistently and clearly separates the A. sojae/A. parasiticus isolates from the A. oryzae/A. flavus isolates. Furthermore. there are markers that can be used to distinguish the A. sojae isolates from those of A. parasiticus, which form the basis for species-specific markers. However, whilst there were many polymorphisms between isolates within the A. oryzae/A. flavus subgroup, no markers could be identified that distinguish between the two species. Sequencing of the ribosomal DNA ITS (internal transcribed spacers) from selected isolates also separated the A. sojae/A. parasiticus subgroup from the A. oryzae/A. flavus subgroup, but was unable to distinguish between the A. sojae and A. parasiticus isolates. Some ITS variation was found between isolates within the A. oryzae/A. flavus subgroup, but did not correlate with the species classification, indicating that it is difficult to use molecular data to separate the two species. In addition, sequencing of ribosomal ITS regions and AFLP analysis suggested that some species annotations in public culture collections may be inaccurate.

Aflatoxins↗

PubMed2003

Current approaches to whole genome phylogenetic analysis.

It has long been known that evolutionary trees (phylogenies) can be estimated by comparing the DNA or protein sequences of homologous genes across different organisms. More recently, attempts have been made to estimate phylogenies by comparing entire genomes. These attempts have focused largely on comparisons of gene content and gene order. Many different methods have been proposed for making these comparisons. These include primarily maximum parsimony and distance methods, although more recently maximum likelihood and Bayesian methods are being developed. This paper discusses each of these approaches in turn, including their merits and limitations, and any software which is available to make use of them.

Evolution, Molecular↗

PubMed2002

Determining a unique defining DNA sequence for yeast species using hashing techniques.

MOTIVATION: Yeasts are often still identified with physiological growth tests, which are both time consuming and unsuitable for detection of a mixture of organisms. Hence, there is a need for molecular methods to identify yeast species. RESULTS: A hashing technique has been developed to search for unique DNA sequences in 702 26S rRNA genes. A unique DNA sequence has been found for almost every yeast species described to date. The locations of the unique defining sequences are in accordance with the variability map of large subunit ribosomal RNA and provide detail of the evolution of the D1/D2 region. This approach will be applicable to the rapid identification of unique sequences in other DNA sequence sets. AVAILABILITY: Freely available upon request from the authors. SUPPLEMENTARY INFORMATION: Results are available at http://www.sys.uea.ac.uk/~jjw/project/paper

Algorithms↗

PubMed2002

Zygosaccharomyces kombuchaensis: the physiology of a new species related to the spoilage yeasts Zygosaccharomyces lentus and Zygosaccharomyces bailii.

Zygosaccharomyces kombuchaensis was recently discovered in the 'tea fungus' used to make fermented tea. Z. kombuchaensis was shown by ribosomal DNA sequencing to be a novel species, and a close relative of Zygosaccharomyces lentus, from which it could not be distinguished by conventional physiological tests. Z. lentus was originally established as a new taxon by growth at 4 degrees C, sensitivity for heat and oxidative stress, and lack of growth in aerobic shaken culture at temperatures above 25 degrees C. Subsequent analysis of Z. kombuchaensis reveals that this species shares these unusual characteristics, confirming its close genealogical relationship to Z. lentus. Detailed physiological data from a number of Z. kombuchaensis and Z. lentus strains clearly demonstrate that these two species can in fact be distinguished from one another based on their differing resistance/sensitivity to the food preservatives benzoic acid and sorbic acid. The spoilage yeasts Zygosaccharomyces bailii and Z. lentus are resistant to both acetic acid and sorbic acid, whereas Z. kombuchaensis is resistant to acetic acid but sensitive to sorbic acid. This would indicate that Z. kombuchaensis strains lack the mechanism for resistance to sorbic acid, but possess the means of resistance to acetic acid. This observation would therefore suggest that these two resistance mechanisms are different, and that in all probability acetic and sorbic acids inhibit yeast growth by different modes of action. Z. kombuchaensis strains were also sensitive to benzoic acid, again suggesting inhibition dissimilar from that to acetic acid.

DNA, Ribosomal↗