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Multiscale modelling of auxin transport in the plant-root elongation zone (2012)
Journal Article
Band, L. R., & King, J. R. (2012). Multiscale modelling of auxin transport in the plant-root elongation zone. Journal of Mathematical Biology, 65(4), https://doi.org/10.1007/s00285-011-0472-y

In the root elongation zone of a plant, the hormone auxin moves in a polar manner due to active transport facilitated by spatially distributed influx and efflux carriers present on the cell membranes. To understand how the cell-scale active transport... Read More about Multiscale modelling of auxin transport in the plant-root elongation zone.

Carbohydrate binding and gene expression by in vitro and in vivo propagated Campylobacter jejuni after Immunomagnetic Separation (2012)
Journal Article
King, R. M., Day, C. J., Hartley-Tassell, L. E., Connerton, I. F., Tiralongo, J., Mcguckin, M. A., & Korolik, V. (2012). Carbohydrate binding and gene expression by in vitro and in vivo propagated Campylobacter jejuni after Immunomagnetic Separation. Journal of Basic Microbiology, 53(3), 240-250. https://doi.org/10.1002/jobm.201100466

Campylobacter jejuni is an important human food-borne intestinal pathogen, however relatively little is known about its mechanisms of pathogenesis or pathogen-host interactions. To monitor changes in gene expression and glycan binding of C. jejuni wi... Read More about Carbohydrate binding and gene expression by in vitro and in vivo propagated Campylobacter jejuni after Immunomagnetic Separation.

Adenosine methylation in Arabidopsis mRNA is associated with the 3? end and reduced levels cause developmental defects (2012)
Journal Article
Bodi, Z., Zhong, S., Mehra, S., Song, J., Graham, N., Li, H., …Fray, R. G. (2012). Adenosine methylation in Arabidopsis mRNA is associated with the 3′ end and reduced levels cause developmental defects. Frontiers in Plant Science, 3(48), Article 48. https://doi.org/10.3389/fpls.2012.00048

We previously showed that the N6-methyladenosine (m6A) mRNA methylase is essential during Arabidopsis thaliana embryonic development. We also demonstrated that this modification is present at varying levels in all mature tissues. However, the require... Read More about Adenosine methylation in Arabidopsis mRNA is associated with the 3? end and reduced levels cause developmental defects.

Statistical inference of in vivo properties of human DNA methyltransferases from double-stranded methylation patterns (2012)
Journal Article
Fu, A. Q., Genereux, D. P., Stöger, R., Burden, A. F., Laird, C. D., & Stephens, M. (2012). Statistical inference of in vivo properties of human DNA methyltransferases from double-stranded methylation patterns. PLoS ONE, 7(3), Article e32225. https://doi.org/10.1371/journal.pone.0032225

DNA methyltransferases establish methylation patterns in cells and transmit these patterns over cell generations, thereby influencing each cell's epigenetic states. Three primary DNA methyltransferases have been identified in mammals: DNMT1, DNMT3A a... Read More about Statistical inference of in vivo properties of human DNA methyltransferases from double-stranded methylation patterns.

Testing the FMR1 promoter for mosaicism in DNA methylation among CpG sites, strands, and cells in FMR1-expressing males with fragile X syndrome (2011)
Journal Article
Stöger, R., Genereux, D. P., Hagerman, R. J., Hagerman, P. J., Tassone, F., & Laird, C. D. (2011). Testing the FMR1 promoter for mosaicism in DNA methylation among CpG sites, strands, and cells in FMR1-expressing males with fragile X syndrome. PLoS ONE, 6(8), Article e23648. https://doi.org/10.1371/journal.pone.0023648

Variability among individuals in the severity of fragile X syndrome (FXS) is influenced by epigenetic methylation mosaicism, which may also be common in other complex disorders. The epigenetic signal of dense promoter DNA methylation is usually assoc... Read More about Testing the FMR1 promoter for mosaicism in DNA methylation among CpG sites, strands, and cells in FMR1-expressing males with fragile X syndrome.

Maize grain and soil surveys reveal suboptimal dietary selenium intake is widespread in Malawi (2011)
Journal Article
Chilimba, A. D. C., Young, S. D., Black, C. R., Rogerson, K. B., Ander, E. L., Watts, M. J., …Broadley, M. R. (2011). Maize grain and soil surveys reveal suboptimal dietary selenium intake is widespread in Malawi. Scientific Reports, 1(72), https://doi.org/10.1038/srep00072

Selenium is an essential element in human diets but the risk of suboptimal intake increases where food choices are narrow. Here we show that suboptimal dietary intake (i.e. 20–30 mg Se person21 d21) is widespread in Malawi, based on a spatial integra... Read More about Maize grain and soil surveys reveal suboptimal dietary selenium intake is widespread in Malawi.

Setting the stage – Building and working in an ancient DNA laboratory (2011)
Journal Article
Knapp, M., Clarke, A. C., Horsburgh, K. A., & Matisoo-Smith, E. A. (2012). Setting the stage – Building and working in an ancient DNA laboratory. Annals of Anatomy, 194(1), 3-6. https://doi.org/10.1016/j.aanat.2011.03.008

With the introduction of next generation high throughput sequencing in 2005 and the resulting revolution in genetics, ancient DNA research has rapidly developed from an interesting but marginal field within evolutionary biology into one that can cont... Read More about Setting the stage – Building and working in an ancient DNA laboratory.

Cost-effective fluorescent amplified fragment length polymorphism (AFLP) analyses using a three primer system (2010)
Journal Article
Stolting, K. N., Clarke, A. C., Meudt, H. M., Blankenhorn, W. U., & Wilson, A. B. (2011). Cost-effective fluorescent amplified fragment length polymorphism (AFLP) analyses using a three primer system. Molecular Ecology Resources, 11(3), 494-502. https://doi.org/10.1111/j.1755-0998.2010.02957.x

The amplified fragment length polymorphism (AFLP) technique is a widely used multi-purpose DNA fingerprinting tool. The ability to size-separate fluorescently labelled AFLP fragments on a capillary electrophoresis instrument has provided a means for... Read More about Cost-effective fluorescent amplified fragment length polymorphism (AFLP) analyses using a three primer system.

Parasitoid developmental mortality in the field: patterns, causes and consequences for sex ratio and virginity (2010)
Journal Article
Kapranas, A., Hardy, I. C., Morse, J. G., & Luck, R. F. (in press). Parasitoid developmental mortality in the field: patterns, causes and consequences for sex ratio and virginity. Journal of Animal Ecology, 80, https://doi.org/10.1111/j.1365-2656.2010.01767.x

1. Sex ratio theory predicts that developmental mortality can affect sex ratio optima under Local Mate Competition and also lead to ‘virgin’ broods containing only females with no sibling-mating opportunities on maturity. 2. Estimates of development... Read More about Parasitoid developmental mortality in the field: patterns, causes and consequences for sex ratio and virginity.

Paper mulberry (Broussonetia papyrifera) as a commensal model for human mobility in Oceania: anthropological, botanical and genetic considerations (2010)
Journal Article
Seelenfreund, D., Clarke, A., Oyanedel, N., Piña, R., Lobos, S., Matisoo-Smith, E., & Seelenfreund, A. (2010). Paper mulberry (Broussonetia papyrifera) as a commensal model for human mobility in Oceania: anthropological, botanical and genetic considerations. New Zealand Journal of Botany, 48(3-4), 231-247. https://doi.org/10.1080/0028825X.2010.520323

Paper mulberry (Broussonetia papyrifera (L.) Vent.) was one of the most widely distributed crop species in prehistoric Oceania, occurring from continental East Asia to the Polynesian islands. Its broad distribution is largely due to human-mediated di... Read More about Paper mulberry (Broussonetia papyrifera) as a commensal model for human mobility in Oceania: anthropological, botanical and genetic considerations.

Genetic diversity analysis and single-nucleotide polymorphism marker development in cultivated bulb onion based on expressed sequence tag-simple sequence repeat markers (2008)
Journal Article
McCallum, J., Thomson, S., Pither-Joyce, M., Kenel, F., Clarke, A., & Havey, M. J. (2008). Genetic diversity analysis and single-nucleotide polymorphism marker development in cultivated bulb onion based on expressed sequence tag-simple sequence repeat markers. Journal of the American Society for Horticultural Science, 133(6), 810-818. https://doi.org/10.21273/jashs.133.6.810

Bulb onion (Allium cepa L.) is a globally significant crop, but the structure of genetic variation within and among populations is poorly understood. We broadly surveyed genetic variation in a cultivated onion germplasm using simple sequence repeat (... Read More about Genetic diversity analysis and single-nucleotide polymorphism marker development in cultivated bulb onion based on expressed sequence tag-simple sequence repeat markers.

Optimizing Automated AFLP Scoring Parameters to Improve Phylogenetic Resolution (2008)
Journal Article
Holland, B. R., Clarke, A. C., & Meudt, H. M. (2008). Optimizing Automated AFLP Scoring Parameters to Improve Phylogenetic Resolution. Systematic Biology, 57(3), 347-366. https://doi.org/10.1080/10635150802044037

The amplified fragment length polymorphism (AFLP) technique is an increasingly popular component of the phylogenetic toolbox, particularly for plant species. Technological advances in capillary electrophoresis now allow very precise estimates of DNA... Read More about Optimizing Automated AFLP Scoring Parameters to Improve Phylogenetic Resolution.

Distinct migratory and non-migratory ecotypes of an endemic New Zealand eleotrid (Gobiomorphus cotidianus) – implications for incipient speciation in island freshwater fish species (2008)
Journal Article
Michel, C., Hicks, B. J., Stölting, K. N., Clarke, A. C., Stevens, M. I., Tana, R., …van den Heuvel, M. R. (2008). Distinct migratory and non-migratory ecotypes of an endemic New Zealand eleotrid (Gobiomorphus cotidianus) – implications for incipient speciation in island freshwater fish species. BMC Evolutionary Biology, 8(1), https://doi.org/10.1186/1471-2148-8-49

Background. Many postglacial lakes contain fish species with distinct ecomorphs. Similar evolutionary scenarios might be acting on evolutionarily young fish communities in lakes of remote islands. One process that drives diversification in island fre... Read More about Distinct migratory and non-migratory ecotypes of an endemic New Zealand eleotrid (Gobiomorphus cotidianus) – implications for incipient speciation in island freshwater fish species.

Monitoring the Effects of Pulp and Paper Effluent Is Restricted in Genetically Distinct Populations of Common Bully (Gobiomorphuscotidianus) (2007)
Journal Article
van den Heuvel, M. R., Michel, C., Stevens, M. I., Clarke, A. C., Stölting, K. N., Hicks, B. J., & Tremblay, L. A. (2007). Monitoring the Effects of Pulp and Paper Effluent Is Restricted in Genetically Distinct Populations of Common Bully (Gobiomorphuscotidianus). Environmental Science and Technology, 41(7), 2602-2608. https://doi.org/10.1021/es061922q

The common bully (Gobiomorphuscotidianus), a small-bodied New Zealand native fish species, was used to monitor population impacts of multiple effluents in the Tarawera River, New Zealand. In an initial survey, the absence of reproductive development... Read More about Monitoring the Effects of Pulp and Paper Effluent Is Restricted in Genetically Distinct Populations of Common Bully (Gobiomorphuscotidianus).

Almost Forgotten or Latest Practice? AFLP applications, analyses and advances (2007)
Journal Article
Meudt, H. M., & Clarke, A. C. (2007). Almost Forgotten or Latest Practice? AFLP applications, analyses and advances. Trends in Plant Science, 12(3), 106-117. https://doi.org/10.1016/j.tplants.2007.02.001

Amplified fragment length polymorphism (AFLP) DNA fingerprinting is a firmly established molecular marker technique, with broad applications in population genetics, shallow phylogenetics, linkage mapping, parentage analyses, and single-locus PCR mark... Read More about Almost Forgotten or Latest Practice? AFLP applications, analyses and advances.

Volatile emission by contest losers revealed by real-time chemical analysis (2006)
Journal Article
Goubault, M., Batchelor, T. P., Linforth, R. S., Taylor, A. J., & Hardy, I. C. (2006). Volatile emission by contest losers revealed by real-time chemical analysis. Proceedings of the Royal Society B: Biological Sciences, 273(1603), 2853-2859. doi:10.1098/rspb.2006.3655

Animal interactions often involve chemical exchange but simultaneous evaluation of chemistry and behaviour has been problematical. Here we report findings from a novel method, atmospheric pressure chemical ionization-mass spectrometry (APCI-MS) coupl... Read More about Volatile emission by contest losers revealed by real-time chemical analysis.

Genetic mapping of a major gene affecting onion bulb fructan content (2006)
Journal Article
McCallum, J., Clarke, A., Pither-Joyce, M., Shaw, M., Butler, R., Brash, D., …Havey, M. J. (2006). Genetic mapping of a major gene affecting onion bulb fructan content. TAG Theoretical and Applied Genetics, 112(5), 958-967. https://doi.org/10.1007/s00122-005-0199-5

The non-structural dry matter content of onion bulbs consists principally of fructose, glucose, sucrose and fructans. The objective of this study was to understand the genetic basis for the wide variation observed in the relative amounts of these car... Read More about Genetic mapping of a major gene affecting onion bulb fructan content.

Reconstructing the Origins and Dispersal of the Polynesian Bottle Gourd (Lagenaria siceraria) (2006)
Journal Article
Clarke, A. C., Burtenshaw, M. K., McLenachan, P. A., Erickson, D. L., & Penny, D. (2006). Reconstructing the Origins and Dispersal of the Polynesian Bottle Gourd (Lagenaria siceraria). Molecular Biology and Evolution, 23(5), 893-900. https://doi.org/10.1093/molbev/msj092

The origin of the Polynesian bottle gourd (Lagenaria siceraria), an important crop species in prehistoric Polynesia, has remained elusive. Most recently, a South American origin has been favored as the bottle gourd could have been introduced from thi... Read More about Reconstructing the Origins and Dispersal of the Polynesian Bottle Gourd (Lagenaria siceraria).