School of BioSciences - Research Publications

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    Generation and analysis of Siah2 mutant mice
    Frew, IJ ; Hammond, VE ; Dickins, RA ; Quinn, JMW ; Walkley, CR ; Sims, NA ; Schnall, R ; Della, NG ; Holloway, AJ ; Digby, MR ; Janes, PW ; Tarlinton, DM ; Purton, LE ; Gillespie, MT ; Bowtell, DDL (AMER SOC MICROBIOLOGY, 2003-12)
    Siah proteins function as E3 ubiquitin ligase enzymes to target the degradation of diverse protein substrates. To characterize the physiological roles of Siah2, we have generated and analyzed Siah2 mutant mice. In contrast to Siah1a knockout mice, which are growth retarded and exhibit defects in spermatogenesis, Siah2 mutant mice are fertile and largely phenotypically normal. While previous studies implicate Siah2 in the regulation of TRAF2, Vav1, OBF-1, and DCC, we find that a variety of responses mediated by these proteins are unaffected by loss of Siah2. However, we have identified an expansion of myeloid progenitor cells in the bone marrow of Siah2 mutant mice. Consistent with this, we show that Siah2 mutant bone marrow produces more osteoclasts in vitro than wild-type bone marrow. The observation that combined Siah2 and Siah1a mutation causes embryonic and neonatal lethality demonstrates that the highly homologous Siah proteins have partially overlapping functions in vivo.
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    A conserved supergene locus controls colour pattern diversity in Heliconius butterflies
    Joron, M ; Papa, R ; Beltran, M ; Chamberlain, N ; Mavarez, J ; Baxter, S ; Abanto, M ; Bermingham, E ; Humphray, SJ ; Rogers, J ; Beasley, H ; Barlow, K ; ffrench-Constant, RH ; Mallet, J ; McMillan, WO ; Jiggins, CD ; Noor, MAF (PUBLIC LIBRARY SCIENCE, 2006-10)
    We studied whether similar developmental genetic mechanisms are involved in both convergent and divergent evolution. Mimetic insects are known for their diversity of patterns as well as their remarkable evolutionary convergence, and they have played an important role in controversies over the respective roles of selection and constraints in adaptive evolution. Here we contrast three butterfly species, all classic examples of Müllerian mimicry. We used a genetic linkage map to show that a locus, Yb, which controls the presence of a yellow band in geographic races of Heliconius melpomene, maps precisely to the same location as the locus Cr, which has very similar phenotypic effects in its co-mimic H. erato. Furthermore, the same genomic location acts as a "supergene", determining multiple sympatric morphs in a third species, H. numata. H. numata is a species with a very different phenotypic appearance, whose many forms mimic different unrelated ithomiine butterflies in the genus Melinaea. Other unlinked colour pattern loci map to a homologous linkage group in the co-mimics H. melpomene and H. erato, but they are not involved in mimetic polymorphism in H. numata. Hence, a single region from the multilocus colour pattern architecture of H. melpomene and H. erato appears to have gained control of the entire wing-pattern variability in H. numata, presumably as a result of selection for mimetic "supergene" polymorphism without intermediates. Although we cannot at this stage confirm the homology of the loci segregating in the three species, our results imply that a conserved yet relatively unconstrained mechanism underlying pattern switching can affect mimicry in radically different ways. We also show that adaptive evolution, both convergent and diversifying, can occur by the repeated involvement of the same genomic regions.
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    The extent and importance of intragenic recombination.
    de Silva, E ; Kelley, LA ; Stumpf, MPH (Springer Science and Business Media LLC, 2004-11)
    We have studied the recombination rate behaviour of a set of 140 genes which were investigated for their potential importance in inflammatory disease. Each gene was extensively sequenced in 24 individuals of African descent and 23 individuals of European descent, and the recombination process was studied separately in the two population samples. The results obtained from the two populations were highly correlated, suggesting that demographic bias does not affect our population genetic estimation procedure. We found evidence that levels of recombination correlate with levels of nucleotide diversity. High marker density allowed us to study recombination rate variation on a very fine spatial scale. We found that about 40 per cent of genes showed evidence of uniform recombination, while approximately 12 per cent of genes carried distinct signatures of recombination hotspots. On studying the locations of these hotspots, we found that they are not always confined to introns but can also stretch across exons. An investigation of the protein products of these genes suggested that recombination hotspots can sometimes separate exons belonging to different protein domains; however, this occurs much less frequently than might be expected based on evolutionary studies into the origins of recombination. This suggests that evolutionary analysis of the recombination process is greatly aided by considering nucleotide sequences and protein products jointly.
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    Evolution of pathogenicity and sexual reproduction in eight Candida genomes
    Butler, G ; Rasmussen, MD ; Lin, MF ; Santos, MAS ; Sakthikumar, S ; Munro, CA ; Rheinbay, E ; Grabherr, M ; Forche, A ; Reedy, JL ; Agrafioti, I ; Arnaud, MB ; Bates, S ; Brown, AJP ; Brunke, S ; Costanzo, MC ; Fitzpatrick, DA ; de Groot, PWJ ; Harris, D ; Hoyer, LL ; Hube, B ; Klis, FM ; Kodira, C ; Lennard, N ; Logue, ME ; Martin, R ; Neiman, AM ; Nikolaou, E ; Quail, MA ; Quinn, J ; Santos, MC ; Schmitzberger, FF ; Sherlock, G ; Shah, P ; Silverstein, KAT ; Skrzypek, MS ; Soll, D ; Staggs, R ; Stansfield, I ; Stumpf, MPH ; Sudbery, PE ; Srikantha, T ; Zeng, Q ; Berman, J ; Berriman, M ; Heitman, J ; Gow, NAR ; Lorenz, MC ; Birren, BW ; Kellis, M ; Cuomo, CA (NATURE PUBLISHING GROUP, 2009-06-04)
    Candida species are the most common cause of opportunistic fungal infection worldwide. Here we report the genome sequences of six Candida species and compare these and related pathogens and non-pathogens. There are significant expansions of cell wall, secreted and transporter gene families in pathogenic species, suggesting adaptations associated with virulence. Large genomic tracts are homozygous in three diploid species, possibly resulting from recent recombination events. Surprisingly, key components of the mating and meiosis pathways are missing from several species. These include major differences at the mating-type loci (MTL); Lodderomyces elongisporus lacks MTL, and components of the a1/2 cell identity determinant were lost in other species, raising questions about how mating and cell types are controlled. Analysis of the CUG leucine-to-serine genetic-code change reveals that 99% of ancestral CUG codons were erased and new ones arose elsewhere. Lastly, we revise the Candida albicans gene catalogue, identifying many new genes.
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    Helpers and egg investment in the cooperatively breeding acorn woodpecker: testing the concealed helper effects hypothesis
    Koenig, WD ; Walters, EL ; Haydock, J (SPRINGER, 2009-09)
    In cooperatively breeding acorn woodpeckers (Melanerpes formicivorus), helper males have a large positive effect on fledging success in good acorn crop years but only a small positive effect in poor acorn crop years, while helper females exhibit the opposite pattern. Based on these findings, we tested the "concealed helper effects" hypothesis, which proposes that laying females reduce investment in eggs (with respect to their size, number, or quality) in a way that confounds helper effects and results in an absence of a relationship between helpers and breeding success. Results generally failed to support the hypothesis. Mean egg size was positively related to temperatures during the 10 days prior to egg-laying and negatively related to the food supply as indexed by the prior fall's acorn crop, but there were no significant differences vis-à-vis helpers except for interactions with the acorn crop that only partly corresponded to those predicted. With respect to clutch size, females laid larger clutches when assisted by female helpers, opposite the pattern predicted. Although our results suggest that egg size is adjusted to particular ecological circumstances, we conclude that neither egg nor clutch size is adjusted in a way that confounds the apparent effects of helpers, as proposed by the concealed helper effects hypothesis.
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    Methylenetetrahydrofolate reductase polymorphism and susceptibility to breast cancer
    Campbell, IG ; Baxter, SW ; Eccles, DM ; Choong, DYH (BIOMED CENTRAL LTD, 2002)
    BACKGROUND: A growing body of evidence suggests that variations in the levels of folate may contribute to the development of cancer. A functional polymorphic variant (C-->T substitution at nucleotide 677) in the 5,10-methylenetetrahydrofolate reductase (MTHFR) gene results in the conversion of an alanine to a valine and may modify the risk of breast and other cancers. METHOD: We have investigated the possible influence of this MTHFR variant on breast cancer risk in a case-control study of 233 healthy women and 335 women who had breast cancer that occurred under the age of 40 years, bilateral breast cancer or a family history of breast cancer. RESULTS: A significant excess of the valine genotypes was observed among the cases (odds ratio 1.43, 95% confidence interval 1.02-2.00). The effect was more pronounced among the cases with a breast cancer diagnosis under the age of 40 years, with an odds ratio of 1.66 (95% confidence interval 1.12-2.41). A nonsignificant excess of the valine genotypes was observed among the cases with a family history of breast cancer or bilateral breast cancer. CONCLUSIONS: The low activity C677T (valine) genotype of MTHFR may increase the risk of early onset breast cancer.
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    What makes a mitochondrion?
    Heazlewood, JL ; Millar, AH ; Day, DA ; Whelan, J (BMC, 2003)
    Experimental analyses of the proteins found in the mitochondria of yeast, humans and Arabidopsis have confirmed some expectations but given some surprises and some insights into the evolutionary origins of mitochondrial proteins.
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    AMPDB: the Arabidopsis Mitochondrial Protein Database
    Heazlewood, JL ; Millar, AH (OXFORD UNIV PRESS, 2005-01-01)
    The Arabidopsis Mitochondrial Protein Database is an Internet-accessible relational database containing information on the predicted and experimentally confirmed protein complement of mitochondria from the model plant Arabidopsis thaliana (http://www.ampdb.bcs.uwa.edu.au/). The database was formed using the total non-redundant nuclear and organelle encoded sets of protein sequences and allows relational searching of published proteomic analyses of Arabidopsis mitochondrial samples, a set of predictions from six independent subcellular-targeting prediction programs, and orthology predictions based on pairwise comparison of the Arabidopsis protein set with known yeast and human mitochondrial proteins and with the proteome of Rickettsia. A variety of precomputed physical-biochemical parameters are also searchable as well as a more detailed breakdown of mass spectral data produced from our proteomic analysis of Arabidopsis mitochondria. It contains hyperlinks to other Arabidopsis genomic resources (MIPS, TIGR and TAIR), which provide rapid access to changing gene models as well as hyperlinks to T-DNA insertion resources, Massively Parallel Signature Sequencing (MPSS) and Genome Tiling Array data and a variety of other Arabidopsis online resources. It also incorporates basic analysis tools built into the query structure such as a BLAST facility and tools for protein sequence alignments for convenient analysis of queried results.
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    Mergers and acquisitions: Malaria and the great chloroplast heist
    McFadden, GI (Springer Nature, 2000-12-01)