School of BioSciences - Research Publications

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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, 2006-10-01)
    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 (Springer Science and Business Media LLC, 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, 2009-09-01)
    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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    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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    Birth and Death of Genes and Functions in the beta-Esterase Cluster of Drosophila
    Robin, C ; Bardsley, LMJ ; Coppin, C ; Oakeshott, JG (SPRINGER, 2009-07-01)
    Here we analyze the molecular evolution of the beta-esterase gene cluster in the Drosophila genus using the recently released genome sequences of 12 Drosophila species. Molecular evolution in this small cluster is noteworthy because it contains contrasting examples of the types and stages of loss of gene function. Specifically, missing orthologs, pseudogenes, and null alleles are all inferred. Phylogenetic analyses also suggest a minimum of 9 gene gain-loss events; however, the exact number and age of these events is confounded by interparalog recombination. A previous enigma, in which allozyme loci were mapped to beta-esterase genes that lacked catalytically essential amino acids, was resolved through the identification of neighbouring genes that contain the canonical catalytic residues and thus presumably encode the mapped allozymes. The originally identified genes are evolving with selective constraint, suggesting that they have a "noncatalytic" function. Curiously, 3 of the 4 paralogous beta-esterase genes in the D. ananassae genome sequence have single inactivating (frame-shift or nonsense) mutations. To determine whether these putatively inactivating mutations were fixed, we sequenced other D. ananassae alleles of these four loci. We did not find any of the 3 inactivating mutations of the sequenced strain in 12 other strains; however, other inactivating mutations were observed in the same 3 genes. This is reminiscent of the high frequency of null alleles observed in one of the beta-esterase genes (Est7/EstP) of D. melanogaster.
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    A p21-activated kinase is required for conidial germination in Penicillium marneffei
    Boyce, KJ ; Andrianopoulos, A ; Cormack, BP (PUBLIC LIBRARY SCIENCE, 2007-11-01)
    Asexual spores (conidia) are the infectious propagules of many pathogenic fungi, and the capacity to sense the host environment and trigger conidial germination is a key pathogenicity determinant. Germination of conidia requires the de novo establishment of a polarised growth axis and consequent germ tube extension. The molecular mechanisms that control polarisation during germination are poorly understood. In the dimorphic human pathogenic fungus Penicillium marneffei, conidia germinate to produce one of two cell types that have very different fates in response to an environmental cue. At 25 degrees C, conidia germinate to produce the saprophytic cell type, septate, multinucleate hyphae that have the capacity to undergo asexual development. At 37 degrees C, conidia germinate to produce the pathogenic cell type, arthroconidiating hyphae that liberate uninucleate yeast cells. This study shows that the p21-activated kinase pakA is an essential component of the polarity establishment machinery during conidial germination and polarised growth of yeast cells at 37 degrees C but is not required for germination or polarised growth at 25 degrees C. Analysis shows that the heterotrimeric G protein alpha subunit GasC and the CDC42 orthologue CflA lie upstream of PakA for germination at both temperatures, while the Ras orthologue RasA only functions at 25 degrees C. These findings suggest that although some proteins that regulate the establishment of polarised growth in budding yeast are conserved in filamentous fungi, the circuitry and downstream effectors are differentially regulated to give rise to distinct cell types.
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    A Mouse Model of Harlequin Ichthyosis Delineates a Key Role for Abca12 in Lipid Homeostasis
    Smyth, I ; Hacking, DF ; Hilton, AA ; Mukhamedova, N ; Meikle, PJ ; Ellis, S ; Slattery, K ; Collinge, JE ; de Graaf, CA ; Bahlo, M ; Sviridov, D ; Kile, BT ; Hilton, DJ ; Beier, DR (PUBLIC LIBRARY SCIENCE, 2008-09-01)
    Harlequin Ichthyosis (HI) is a severe and often lethal hyperkeratotic skin disease caused by mutations in the ABCA12 transport protein. In keratinocytes, ABCA12 is thought to regulate the transfer of lipids into small intracellular trafficking vesicles known as lamellar bodies. However, the nature and scope of this regulation remains unclear. As part of an original recessive mouse ENU mutagenesis screen, we have identified and characterised an animal model of HI and showed that it displays many of the hallmarks of the disease including hyperkeratosis, loss of barrier function, and defects in lipid homeostasis. We have used this model to follow disease progression in utero and present evidence that loss of Abca12 function leads to premature differentiation of basal keratinocytes. A comprehensive analysis of lipid levels in mutant epidermis demonstrated profound defects in lipid homeostasis, illustrating for the first time the extent to which Abca12 plays a pivotal role in maintaining lipid balance in the skin. To further investigate the scope of Abca12's activity, we have utilised cells from the mutant mouse to ascribe direct transport functions to the protein and, in doing so, we demonstrate activities independent of its role in lamellar body function. These cells have severely impaired lipid efflux leading to intracellular accumulation of neutral lipids. Furthermore, we identify Abca12 as a mediator of Abca1-regulated cellular cholesterol efflux, a finding that may have significant implications for other diseases of lipid metabolism and homeostasis, including atherosclerosis.
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    Gain and loss of elongation factor genes in green algae
    Cocquyt, E ; Verbruggen, H ; Leliaert, F ; Zechman, FW ; Sabbe, K ; De Clerck, O (BIOMED CENTRAL LTD, 2009-02-12)
    BACKGROUND: Two key genes of the translational apparatus, elongation factor-1 alpha (EF-1alpha) and elongation factor-like (EFL) have an almost mutually exclusive distribution in eukaryotes. In the green plant lineage, the Chlorophyta encode EFL except Acetabularia where EF-1alpha is found, and the Streptophyta possess EF-1alpha except Mesostigma, which has EFL. These results raise questions about evolutionary patterns of gain and loss of EF-1alpha and EFL. A previous study launched the hypothesis that EF-1alpha was the primitive state and that EFL was gained once in the ancestor of the green plants, followed by differential loss of EF-1alpha or EFL in the principal clades of the Viridiplantae. In order to gain more insight in the distribution of EF-1alpha and EFL in green plants and test this hypothesis we screened the presence of the genes in a large sample of green algae and analyzed their gain-loss dynamics in a maximum likelihood framework using continuous-time Markov models. RESULTS: Within the Chlorophyta, EF-1alpha is shown to be present in three ulvophycean orders (i.e., Dasycladales, Bryopsidales, Siphonocladales) and the genus Ignatius. Models describing gene gain-loss dynamics revealed that the presence of EF-1alpha, EFL or both genes along the backbone of the green plant phylogeny is highly uncertain due to sensitivity to branch lengths and lack of prior knowledge about ancestral states or rates of gene gain and loss. Model refinements based on insights gained from the EF-1alpha phylogeny reduce uncertainty but still imply several equally likely possibilities: a primitive EF-1alpha state with multiple independent EFL gains or coexistence of both genes in the ancestor of the Viridiplantae or Chlorophyta followed by differential loss of one or the other gene in the various lineages. CONCLUSION: EF-1alpha is much more common among green algae than previously thought. The mutually exclusive distribution of EF-1alpha and EFL is confirmed in a large sample of green plants. Hypotheses about the gain-loss dynamics of elongation factor genes are hard to test analytically due to a relatively flat likelihood surface, even if prior knowledge is incorporated. Phylogenetic analysis of EFL genes indicates misinterpretations in the recent literature due to uncertainty regarding the root position.