Biological Sciences, Department of

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Characterization of the Astacin Family of Metalloproteases in C. elegans

Peer reviewed: 
Yes, item is peer reviewed.
Date created: 
2010
Abstract: 

Background: Astacins are a large family of zinc metalloproteases found in bacteria and animals. They have diverseroles ranging from digestion of food to processing of extracellular matrix components. The C. elegans genomecontains an unusually large number of astacins, of which the majority have not been functionally characterized yet.Results: We analyzed the expression pattern of previously uncharacterized members of the astacin family to tryand obtain clues to potential functions. Prominent sites of expression for many members of this family are thehypodermis, the alimentary system and several specialized cells including sensory sheath and sockets cells, whichare located at openings in the body wall. We isolated mutants affecting representative members of the varioussubfamilies. Mutants in nas-5, nas-21 and nas-39 (the BMP-1/Tolloid homologue) are viable and have no apparentphenotypic defects. Mutants in nas-6 and nas-6; nas-7 double mutants are slow growing and have defects in thegrinder of the pharynx, a cuticular structure important for food processing.Conclusions: Expression data and phenotypic characterization of selected family members suggest a diversity offunctions for members of the astacin family in nematodes. In part this might be due to extracellular structuresunique to nematodes.

Document type: 
Article

Computing Evolutionary Distinctiveness Indices in Large Scale Analysis

Peer reviewed: 
Yes, item is peer reviewed.
Date created: 
2012
Abstract: 

We present optimal linear time algorithms for computing the Shapley values and ‘heightened evolutionarydistinctiveness’ (HED) scores for the set of taxa in a phylogenetic tree. We demonstrate the efficiency of these newalgorithms by applying them to a set of 10,000 reasonable 5139-species mammal trees. This is the first time theseindices have been computed on such a large taxon and we contrast our finding with an ad-hoc index formammals, fair proportion (FP), used by the Zoological Society of London’s EDGE programme. Our empirical resultsfollow expectations. In particular, the Shapley values are very strongly correlated with the FP scores, but provide ahigher weight to the few monotremes that comprise the sister to all other mammals. We also find that the HEDscore, which measures a species’ unique contribution to future subsets as function of the probability that closerelatives will go extinct, is very sensitive to the estimated probabilities. When they are low, HED scores are less thanFP scores, and approach the simple measure of a species’ age. Deviations (like the Solendon genus of the WestIndies) occur when sister species are both at high risk of extinction and their clade roots deep in the tree.Conversely, when endangered species have higher probabilities of being lost, HED scores can be greater than FPscores and species like the African elephant Loxondonta africana, the two solendons and the thumbless batFuripterus horrens can move up the rankings. We suggest that conservation attention be applied to such speciesthat carry genetic responsibility for imperiled close relatives. We also briefly discuss extensions of Shapley valuesand HED scores that are possible with the algorithms presented here.

Document type: 
Article

Evolution and Connectivity in the World-Wide Migration System of the Mallard: Inferences from Mitochondrial DNA

Peer reviewed: 
Yes, item is peer reviewed.
Date created: 
2011
Abstract: 

Background: Main waterfowl migration systems are well understood through ringing activities. However, inmallards (Anas platyrhynchos) ringing studies suggest deviations from general migratory trends and traditions inwaterfowl. Furthermore, surprisingly little is known about the population genetic structure of mallards, andstudying it may yield insight into the spread of diseases such as Avian Influenza, and in management andconservation of wetlands. The study of evolution of genetic diversity and subsequent partitioning thereof duringthe last glaciation adds to ongoing discussions on the general evolution of waterfowl populations and flywayevolution. Hypothesised mallard flyways are tested explicitly by analysing mitochondrial mallard DNA from thewhole northern hemisphere.Results: Phylogenetic analyses confirm two mitochondrial mallard clades. Genetic differentiation within Eurasia andNorth-America is low, on a continental scale, but large differences occur between these two land masses (FST =0.51). Half the genetic variance lies within sampling locations, and a negligible portion between currentlyrecognised waterfowl flyways, within Eurasia and North-America. Analysis of molecular variance (AMOVA) atcontinent scale, incorporating sampling localities as smallest units, also shows the absence of population structureon the flyway level. Finally, demographic modelling by coalescence simulation proposes a split between Eurasiaand North-America 43,000 to 74,000 years ago and strong population growth (~100fold) since then and littlemigration (not statistically different from zero).Conclusions: Based on this first complete assessment of the mallard’s world-wide population genetic structure weconfirm that no more than two mtDNA clades exist. Clade A is characteristic for Eurasia, and clade B for North-America although some representatives of clade A are also found in North-America. We explain this pattern byevaluating competing hypotheses and conclude that a complex mix of historical, recent and anthropogenic factorsshaped the current mallard populations. We refute population classification based on flyways proposed byornithologists and managers, because they seem to have little biological meaning. Our results have implications forwetland management and conservation, with special regard to the release of farmed mallards for hunting, as wellas for the possible transmission of Avian Influenza by mallards due to migration.

Document type: 
Article

Widespread Horizontal Genomic Exchange does not Erode Species Barriers among Sympatric Ducks

Peer reviewed: 
Yes, item is peer reviewed.
Date created: 
2012
Abstract: 

Background: The study of speciation and maintenance of species barriers is at the core of evolutionary biology.During speciation the genome of one population becomes separated from other populations of the same species,which may lead to genomic incompatibility with time. This separation is complete when no fertile offspring isproduced from inter-population matings, which is the basis of the biological species concept. Birds, in particularducks, are recognised as a challenging and illustrative group of higher vertebrates for speciation studies. There aremany sympatric and ecologically similar duck species, among which fertile hybrids occur relatively frequently innature, yet these species remain distinct.Results: We show that the degree of shared single nucleotide polymorphisms (SNPs) between five species ofdabbling ducks (genus Anas) is an order of magnitude higher than that previously reported between any pair ofeukaryotic species with comparable evolutionary distances. We demonstrate that hybridisation has led to sustainedexchange of genetic material between duck species on an evolutionary time scale without disintegrating speciesboundaries. Even though behavioural, genetic and ecological factors uphold species boundaries in ducks, wedetect opposing forces allowing for viable interspecific hybrids, with long-term evolutionary implications. Based onthe superspecies concept we here introduce the novel term “supra-population” to explain the persistence of SNPsidentical by descent within the studied ducks despite their history as distinct species dating back millions of years.Conclusions: By reviewing evidence from speciation theory, palaeogeography and palaeontology we propose afundamentally new model of speciation to accommodate our genetic findings in dabbling ducks. This model, weargue, may also shed light on longstanding unresolved general speciation and hybridisation patterns in higherorganisms, e.g. in other bird groups with unusually high hybridisation rates. Observed parallels to horizontal genetransfer in bacteria facilitate the understanding of why ducks have been such an evolutionarily successful group ofanimals. There is large evolutionary potential in the ability to exchange genes among species and the resultingdramatic increase of effective population size to counter selective constraints.

Document type: 
Article

Evolution of Embryonic Developmental Period in the Marine Bird Families Alcidae and Spheniscidae: Roles for Nutrition and Predation?

Peer reviewed: 
Yes, item is peer reviewed.
Date created: 
2010
Abstract: 

Background: Nutrition and predation have been considered two primary agents of selection important in theevolution of avian life history traits. The relative importance of these natural selective forces in the evolution of avianembryonic developmental period (EDP) remain poorly resolved, perhaps in part because research has tended to focuson a single, high taxonomic-level group of birds: Order Passeriformes. The marine bird families Alcidae (auks) andSpheniscidae (penguins) exhibit marked variation in EDP, as well as behavioural and ecological traits ultimately linkedto EDP. Therefore, auks and penguins provide a unique opportunity to assess the natural selective basis of variation in akey life-history trait at a low taxonomic-level. We used phylogenetic comparative methods to investigate the relativeimportance of behavioural and ecological factors related to nutrition and predation in the evolution of avian EDP.Results: Three behavioural and ecological variables related to nutrition and predation risk (i.e., clutch size, activitypattern, and nesting habits) were significant predictors of residual variation in auk and penguin EDP based on modelspredicting EDP from egg mass. Species with larger clutch sizes, diurnal activity patterns, and open nests hadsignificantly shorter EDPs. Further, EDP was found to be longer among birds which forage in distant offshore waters,relative to those that foraged in near shore waters, in line with our predictions, but not significantly so.Conclusion: Current debate has emphasized predation as the primary agent of selection driving avian life historydiversification. Our results suggest that both nutrition and predation have been important selective forces in theevolution of auk and penguin EDP, and highlight the importance of considering these questions at lower taxonomicscales. We suggest that further comparative studies on lower taxonomic-level groups will continue to constructivelyinform the debate on evolutionary determinants of avian EDP, as well as other life history parameters.

Document type: 
Article

Structural and Micro-Anatomical Changes in Vertebrae Associated with Idiopathic-Type Spinal Curvature in the Curveback Guppy Model

Peer reviewed: 
Yes, item is peer reviewed.
Date created: 
2010
Abstract: 

Background: The curveback lineage of guppy is characterized by heritable idiopathic-type spinal curvature thatdevelops during growth. Prior work has revealed several important developmental similarities to the human idiopathicscoliosis (IS) syndrome. In this study we investigate structural and histological aspects of the vertebrae that areassociated with spinal curvature in the curveback guppy and test for sexual dimorphism that might explain a femalebias for severe curve magnitudes in the population.Methods: Vertebrae were studied from whole-mount skeletal specimens of curved and non-curved adult males andfemales. A series of ratios were used to characterize structural aspects of each vertebra. A three-way analysis of variancetested for effects of sex, curvature, vertebral position along the spine, and all 2-way interactions (i.e., sex and curvature,sex and vertebra position, and vertebra position and curvature). Histological analyses were used to characterize microarchitecturalchanges in affected vertebrae and the intervertebral region.Results: In curveback, vertebrae that are associated with curvature demonstrate asymmetric shape distortion,migration of the intervertebral ligament, and vertebral thickening on the concave side of curvature. There is sexualdimorphism among curved individuals such that for several vertebrae, females have more slender vertebrae than domales. Also, in the region of the spine where lordosis typically occurs, curved and non-curved females have a reducedwidth at the middle of their vertebrae, relative to males.Conclusions: Based on similarities to human spinal curvatures and to animals with induced curves, the concaveconvexbiases described in the guppy suggest that there is a mechanical component to curve pathogenesis incurveback. Because idiopathic-type curvature in curveback is primarily a sagittal deformity, it is structurally more similarto Scheuermann kyphosis than IS. Anatomical differences between teleosts and humans make direct biomechanicalcomparisons difficult. However, study of basic biological systems involved in idiopathic-type spinal curvature incurveback may provide insight into the relationship between a predisposing aetiology, growth, and biomechanics.Further work is needed to clarify whether observed sex differences in vertebral characteristics are related to the femalebias for severe curves that is observed in the population.

Document type: 
Article

A Major QTL Controls Susceptibility to Spinal Curvature in the Curveback Guppy

Peer reviewed: 
Yes, item is peer reviewed.
Date created: 
2011
Abstract: 

Background: Understanding the genetic basis of heritable spinal curvature would benefit medicine andaquaculture. Heritable spinal curvature among otherwise healthy children (i.e. Idiopathic Scoliosis and Scheuermannkyphosis) accounts for more than 80% of all spinal curvatures and imposes a substantial healthcare cost throughbracing, hospitalizations, surgery, and chronic back pain. In aquaculture, the prevalence of heritable spinal curvaturecan reach as high as 80% of a stock, and thus imposes a substantial cost through production losses. The geneticbasis of heritable spinal curvature is unknown and so the objective of this work is to identify quantitative trait loci(QTL) affecting heritable spinal curvature in the curveback guppy. Prior work with curveback has demonstratedphenotypic parallels to human idiopathic-type scoliosis, suggesting shared biological pathways for the deformity.Results: A major effect QTL that acts in a recessive manner and accounts for curve susceptibility was detected inan initial mapping cross on LG 14. In a second cross, we confirmed this susceptibility locus and fine mapped it toa 5 cM region that explains 82.6% of the total phenotypic variance.Conclusions: We identify a major QTL that controls susceptibility to curvature. This locus contains over 100 genes,including MTNR1B, a candidate gene for human idiopathic scoliosis. The identification of genes associated withheritable spinal curvature in the curveback guppy has the potential to elucidate the biological basis of spinalcurvature among humans and economically important teleosts.

Document type: 
Article

Functional Genomics of Human Bronchial Epithelial Cells Directly Interacting with Conidia of Aspergillus Fumigatus

Peer reviewed: 
Yes, item is peer reviewed.
Date created: 
2010
Abstract: 

Background: Aspergillus fumigatus (A. fumigatus) is a ubiquitous fungus which reproduces asexually by releasingabundant airborne conidia (spores), which are easily respirable. In allergic and immunocompromised individuals A.fumigatus can cause a wide spectrum of diseases, including allergic bronchopulmonary aspergillosis, aspergilloma andinvasive aspergillosis. Previous studies have demonstrated that A. fumigatus conidia are internalized by macrophagesand lung epithelial cells; however the exact transcriptional responses of airway epithelial cells to conidia are currentlyunknown. Thus, the aim of this study was to determine the transcriptomic response of the human bronchial epithelialcell line (16HBE14o-) following interaction with A. fumigatus conidia. We used fluorescence-activated cell sorting (FACS)to separate 16HBE14o- cells having bound and/or internalized A. fumigatus conidia expressing green fluorescentprotein from cells without spores. Total RNA was then isolated and the transcriptome of 16HBE14o- cells was evaluatedusing Agilent Whole Human Genome microarrays.Results: Immunofluorescent staining and nystatin protection assays demonstrated that 16HBE14o- cells internalized30-50% of bound conidia within six hrs of co-incubation. After FAC-sorting of the same cell culture to separate cellsassociated with conidia from those without conidia, genome-wide analysis revealed a set of 889 genes showingdifferential expression in cells with conidia. Specifically, these 16HBE14o- cells had increased levels of transcripts fromgenes associated with repair and inflammatory processes (e.g., matrix metalloproteinases, chemokines, andglutathione S-transferase). In addition, the differentially expressed genes were significantly enriched for Gene Ontologyterms including: chromatin assembly, G-protein-coupled receptor binding, chemokine activity, and glutathionemetabolic process (up-regulated); cell cycle phase, mitosis, and intracellular organelle (down-regulated).Conclusions: We demonstrate a methodology using FACs for analyzing the transcriptome of infected and uninfectedcells from the same cell population that will provide a framework for future characterization of the specific interactionsbetween pathogens such as A. fumigatus with human cells derived from individuals with or without underlying diseasesusceptibility.

Document type: 
Article

A Glycine Zipper Motif Mediates the Formation of Toxic Beta-Amyloid Oligomers in Vitro and in Vivo

Peer reviewed: 
Yes, item is peer reviewed.
Date created: 
2011
Abstract: 

Background: The b-amyloid peptide (Ab) contains a Gly-XXX-Gly-XXX-Gly motif in its C-terminal region that hasbeen proposed to form a “glycine zipper” that drives the formation of toxic Ab oligomers. We have tested thishypothesis by examining the toxicity of Ab variants containing substitutions in this motif using a neuronal cell line,primary neurons, and a transgenic C. elegans model.Results: We found that a Gly37Leu substitution dramatically reduced Ab toxicity in all models tested, as measuredby cell dysfunction, cell death, synaptic alteration, or tau phosphorylation. We also demonstrated in multiplemodels that Ab Gly37Leu is actually anti-toxic, thereby supporting the hypothesis that interference with glycinezipper formation blocks assembly of toxic Ab oligomers. To test this model rigorously, we engineered second sitesubstitutions in Ab predicted by the glycine zipper model to compensate for the Gly37Leu substitution andexpressed these in C. elegans. We show that these second site substitutions restore in vivo Abtoxicity, furthersupporting the glycine zipper model.Conclusions: Our structure/function studies support the view that the glycine zipper motif present in the Cterminalportion of Ab plays an important role in the formation of toxic Ab oligomers. Compounds designed tointerfere specifically with formation of the glycine zipper could have therapeutic potential.

Document type: 
Article