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Exploitation of interspecific diversity for monocot crop improvement (2013)
Journal Article
King, J., Armstead, I., Harper, J., Ramsey, L., Snape, J., Waugh, R., …King, I. (2013). Exploitation of interspecific diversity for monocot crop improvement. Heredity, 110(5), 475-483. https://doi.org/10.1038/hdy.2012.116

In many cultivated crop species there is limited genetic variation available for the development of new higher yielding varieties adapted to climate change and sustainable farming practises. The distant relatives of crop species provide a vast and la... Read More about Exploitation of interspecific diversity for monocot crop improvement.

Construction of a doxycycline inducible adipogenic lentiviral expression system (2013)
Journal Article
Liu, Q., Hill, P., Karamitri, A., Ryan, K., Chen, H., & Lomax, M. A. (2013). Construction of a doxycycline inducible adipogenic lentiviral expression system. Plasmid, 69(1), https://doi.org/10.1016/j.plasmid.2012.10.001

To provide a tool for research on regulating adipocyte differentiation, tetracycline inducible (Tet on) lentiviral expression vectors under the control of an adipose-specific promoter were constructed. The lowest basal expression in the absence of do... Read More about Construction of a doxycycline inducible adipogenic lentiviral expression system.

DNA and Pacific Commensal Models: Applications, Construction, Limitations, and Future Prospects (2013)
Journal Article
Storey, A. A., Clarke, A. C., Ladefoged, T., Robins, J., & Matisoo-Smith, E. (2013). DNA and Pacific Commensal Models: Applications, Construction, Limitations, and Future Prospects. Journal of Island and Coastal Archaeology, 8(1), 37-65. https://doi.org/10.1080/15564894.2012.761299

Components of the Pacific transported landscape have been used as proxies to trace the prehistoric movement of humans across the Pacific for almost two decades. Analyses of archaeological remains and DNA sequences of plants, animals, and microorganis... Read More about DNA and Pacific Commensal Models: Applications, Construction, Limitations, and Future Prospects.

Analysis of ripening-related gene expression in papaya using an Arabidopsis-based microarray (2012)
Journal Article
Fabi, J. P., Seymour, G. B., Graham, N. S., Broadley, M. R., May, S., Lajolo, F. M., …Oliveira do Nascimento, J. R. (in press). Analysis of ripening-related gene expression in papaya using an Arabidopsis-based microarray. BMC Plant Biology, 12, Article 242. https://doi.org/10.1186/1471-2229-12-242

Background Papaya (Carica papaya L.) is a commercially important crop that produces climacteric fruits with a soft and sweet pulp that contain a wide range of health promoting phytochemicals. Despite its importance, little is known about transcrip... Read More about Analysis of ripening-related gene expression in papaya using an Arabidopsis-based microarray.

Ethnobiology: The missing link in ecology and evolution (2012)
Journal Article
Saslis-Lagoudakis, C. H., & Clarke, A. C. (2013). Ethnobiology: The missing link in ecology and evolution. Trends in Ecology and Evolution, 28(2), 67-68. https://doi.org/10.1016/j.tree.2012.10.017

Evolutionary biologists and ecologists increasingly appreciate the value of local knowledge of human communities for research into the past, present, and future of biodiversity. However, there are often significant problems accessing and interpreting... Read More about Ethnobiology: The missing link in ecology and evolution.

Adaptation for protein synthesis efficiency in a naturally occurring self-regulating operon (2012)
Journal Article
Herman, D., Thomas, C. M., & Steke, D. J. (2012). Adaptation for protein synthesis efficiency in a naturally occurring self-regulating operon. PLoS ONE, 7(11), Article e49678. https://doi.org/10.1371/journal.pone.0049678

The korAB operon in RK2 plasmids is a beautiful natural example of a negatively and cooperatively self-regulating operon. It has been particularly well characterized both experimentally and with mathematical models. We have carried out a detailed inv... Read More about Adaptation for protein synthesis efficiency in a naturally occurring self-regulating operon.

Modulation of pluripotency in the porcine embryo and iPS Cells (2012)
Journal Article
Rodríguez, A., Allegrucci, C., & Alberio, R. (2012). Modulation of pluripotency in the porcine embryo and iPS Cells. PLoS ONE, 7(11), Article 12. https://doi.org/10.1371/journal.pone.0049079

The establishment of the pluripotent ICM during early mammalian development is characterized by the differential expression of the transcription factors NANOG and GATA4/6, indicative of the epiblast and hypoblast, respectively. Differences in the mec... Read More about Modulation of pluripotency in the porcine embryo and iPS Cells.

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.