Aberdeen has a wide range of genomics projects, covering the range of biological and medical research at the University. The following provide a small sample of the types of projects that the Centre is involved in:
- Whole genome resequencing for variant detection in a wide range of organisms, including microbial (bacterial and fungi) plant and animal pathogens and clinical isolates, plants, nematodes
- De novo sequencing of novel fungal pathogens
- Single cell de novo whole genome sequencing of archaea
- A genetic dissection of traits required for sustainable water use in rice using Genome Wide Association Studies (GWAS)
- Human exome sequencing of archived samples
- 16S profiling of metagenomes in complex microbial communities in a wide range of samples, including soil, glaciers, marine sediments, animal (models and non-models) and human stool.
- Functional gene profiling of metagenomes in complex microbial soil communities
- De novo transcriptomes, including sharks and parasites
- Differential gene expression using RNAseq and microarrays in bacteria, fungi, mammals
- Exome sequencing of family trios for linkage studies in cancer and developmental disorders
- WGS ancient DNA from herbarium samples and ancient fur, stool and bone samples.
- Epigenome/Methylation Analysis using targeted BIS-seq and BIS-RNA-seq in humans and Siberian hamster
- Human cancer panels for precision medicine, including a Stratified Medicine Scotland SMS-IC Exemplar project (link).
The centre currently supports the research of several post-graduate students. More details about these projects can be found here.
Single cell de novo whole genome sequencing of archaea
Fasimoye, R.Y., Spencer, R.E.B., Soto-Martin, E., Eijlers, P., Elmassoudi, H., Brivio, S., Mangana C., Sabele, V., Rechtorikova, R., Wenzel, M., Connolly, B., Pettitt, J., Müller, B. (2022) A novel, essential trans-splicing protein connects the nematode SL1 snRNP to the CBC-ARS2 complex, Nucleic Acids Research, Volume 50, Issue 13, 22 July 2022, Pages 7591–7607. Link.
Sheridan PO, Louis P, Tsompanidou E, Shaw S, Harmsen HJ, Duncan SH, Flint HJ, Walker AW. Distribution, organization and expression of genes concerned with anaerobic lactate utilization in human intestinal bacteria. Microb Genom. 2022 Jan;8(1):000739. doi: 10.1099/mgen.0.000739. PMID: 35077342; PMCID: PMC8914356. Link.
Shaw, S., Berry, S., Thomson, J., Murray, G.I., El-Omar, E., Hold, G.L. (2022) Gut mucosal microbiome signatures of colorectal cancer differ according to BMI status. Frontiers in Medicine, Volume 8:800566. Link.
Oyedemi OT, Shaw S, Martin JC, Ayeni FA, Scott KP. Changes in the gut microbiota of Nigerian infants within the first year of life. PLoS One. 2022 Mar 17;17(3):e0265123. doi: 10.1371/journal.pone.0265123. PMID: 35298505; PMCID: PMC8929609. Link.
Lorgen-Ritchie M, Murray AD, Staff R, Ferguson-Smith AC, Richards M, Horgan GW, Phillips LH, Hoad G, McNeil C, Ribeiro A, Haggarty P. Imprinting methylation predicts hippocampal volumes and hyperintensities and the change with age in later life. Sci Rep. 2021 Jan 13;11(1):943. doi: 10.1038/s41598-020-78062-2. PMID: 33441584; PMCID: PMC7806645. Link.
Faber, M., Yoon, S., Shaw, S., de Paiva Alves, E., Wang, B., Zhitao, Q., Okamura, B., Hartikainen, H., Secombes, C.J., Holland, J.W. (2021) Comparative transcriptomics and host-specific parasite gene expression profiles inform on drivers of proliferative kidney disease. Scientific Reports. Link.
Melendrez M.C., Shaw, S., Brown, C.T., Goodner, B.W., Kvall, C. (2021) Editorial: Curriculum appplications in Microbiology: Bioinformatics in the Classroom. Frontiers in Microbiology, 12, 705233. Link.
Derous D, Sahu J, Douglas A, Lusseau D, Wenzel M. Comparative genomics of cetartiodactyla: energy metabolism underpins the transition to an aquatic lifestyle. Conserv Physiol. 2021 Jan 16;9(1):coaa136. doi: 10.1093/conphys/coaa136. PMID: 33505701; PMCID: PMC7816800. Link.
Smith, N.M., Maloney, N.G., Shaw, S., Horgan, G.W., Fyfe, C., Martin, J.C., Suter, A., Scott, K.P., Johnstone, A.M. (2020) Daily Fermented Whey Consumption Alters the Fecal Short-Chain Fatty Acid Profile in Healthy Adults. Frontiers in Nutrition. Link.
Wenzel, M., Johnston, C., Müller, B., Pettitt, J. & Connolly, B. (2020) Resolution of polycistronic RNA by SL2 trans-splicing is a widely-conserved nematode trait. RNA. Link.
Afouda, B., Nakamura, Y., Shaw, S., Charney, R. M., Paraiso, K. D., Blitz, I. L., Cho, K. W. Y. & Hoppler, S. (2020) Foxh1/Nodal defines context-specific direct maternal Wnt/β-catenin target gene regulation in early development. iScience. Link.
Edwards CH, Christie CR, Masotti A, Celluzzi A, Caporali A, Campbell EM. Dendrimer-coated carbon nanotubes deliver dsRNA and increase the efficacy of gene knockdown in the red flour beetle Tribolium castaneum. Sci Rep. 2020 Jul 24;10(1):12422. doi: 10.1038/s41598-020-69068-x. PMID: 32709999; PMCID: PMC7381663. Link.
Krol, E., Noguera, P., Shaw, S., Costelloe, E., Gajardo, K., Valdenegro, V., Bickerdike, R., Douglas, A. & Martin, S. (2020) Integration of transcriptome, gross morphology and histopathology in the gill of sea farmed Atlantic salmon (Salmo salar): Lessons from multi-site sampling. Frontiers in Genetics. Link.
Hijazi, K., Morrison, R.W., Mukhopadhya, I., Martin, B., Gemmell, M., Shaw, S. & Santoro, F. (2020) Oral bacterial diversity is inversely correlated with mucosal inflammation. Oral Diseases. Link.
Gusachenko, O.N., Woodford, L., Balbirnie-Cumming, K., Campbell, E.M., Christie, C.R., Bowman, A.S., & Evans, D.J. (2020) Green Bees: Reverse Genetic Analysis of Deformed Wing Virus Transmission, Replication, and Tropism. Viruses. 12(5), 532. Link.
McFarland, M.R., Keller, C.D., Childers, B.M., Adeniyi, S.A., Corrigall, H., Raguin, A., Carmen Romano, M. & Stansfield, I. (2020) The molecular aetiology of tRNA synthetase depletion: induction of a GCN4 amino acid starvation response despite homeostatic maintenance of charged tRNA levels. Nucleic Acids Research. 48 (6), 3071–3088. Link.
Beaurepaire, A., Piot, N., Doublet, V., Antunez, K., Campbell, E., Chantawannakul, P., Chejanovsky, N., Gajda, A., Heerman, M., Panziera, D., Smagghe, G., Yañez, O., de Miranda, J.R. & Dalmon, A. (2020) Diversity and Global Distribution of Viruses of the Western Honey Bee, Apis mellifera. Insects. 11(4), 239. Link.
Alessi, A.M., Gray, V., Farquharson, F.M., Flores‐López, A., Shaw, S., Stead, D., Wegmann, U., Shearman, C., Gasson, M., Collie‐Duguid, E.S.R, Flint, H.J. & Louis P. (2020) β‐glucan is a major growth substrate for human gut bacteria related to Coprococcus eutactus. Environmental Microbiology. Link.
Laverde Gomez JA, Mukhopadhya I, Duncan SH, Louis P, Shaw S, Collie-Duguid E, Crost E, Juge N, Flint HJ. Formate cross-feeding and cooperative metabolic interactions revealed by transcriptomics in co-cultures of acetogenic and amylolytic human colonic bacteria. Environ Microbiol. 2019 Jan;21(1):259-271. doi: 10.1111/1462-2920.14454. Epub 2018 Nov 22. PMID: 30362296; PMCID: PMC6378601. Link.
Redmond AK, Zou J, Secombes CJ, Macqueen DJ, Dooley H. Discovery of All Three Types in Cartilaginous Fishes Enables Phylogenetic Resolution of the Origins and Evolution of Interferons. Front Immunol. 2019 Jul 12;10:1558. doi: 10.3389/fimmu.2019.01558. PMID: 31354716; PMCID: PMC6640115. Link.
Siemienowicz, K., Filis, P., Shaw, S., Douglas, A., Thomas, J., Mulroy, S., Howie, F., Fowler, P., Duncan, W.C. & Rae, M. (2019) Fetal androgen exposure is a determinant of adult male metabolic health. Scientific Reports. 9: 20195 (2019). Link.
Figeac, N., Mohamed, A.D., Sun, C., Schönfelder, M., Marallanas, D., Garcia-Munoz, A., Missiaglia, E., Collie-Duguid, E., De Mello, V., Pobbati, A.V., Pruller, J., Jaka, O., Harridge, S.D.R., Hong, W., Shipley, J., Vargesson, N., Zammit, P.S. & Wackerhage, H. (2019) VGLL3 operates via TEAD1, TEAD3 and TEAD4 to influence myogenesis in skeletal muscle. Journal of Cell Science. 132(13). Link.
Hiraga SI, Monerawela C, Katou Y, Shaw S, Clark KR, Shirahige K, Donaldson AD. Budding yeast Rif1 binds to replication origins and protects DNA at blocked replication forks. EMBO Rep. 2019 Jul;20(7):e48152. doi: 10.15252/embr.201948152. Epub 2019 Jun 26. Erratum for: EMBO Rep. 2018 Sep;19(9): PMID: 31267726; PMCID: PMC6607008. Link.
Perez Calderon LJ, Gontikaki E, Potts LD, Shaw S, Gallego A, Anderson JA, Witte U. Pressure and temperature effects on deep-sea hydrocarbon-degrading microbial communities in subarctic sediments. Microbiologyopen. 2019 Jun;8(6):e00768. doi: 10.1002/mbo3.768. Epub 2018 Nov 16. PMID: 30444300; PMCID: PMC6562134. Link.
Wasi, M., Khandelwal, N.K., Moorhouse, A.J., Nair, R., Vishwakarma, P., Bravo Ruiz, G., Ross, Z.K., Lorenz, A., Rudramurthy, S.M., Chakrabarti, A., Lynn, A.M., Mondal, A.K., Gow, N.A.R. & Prasad, R. (2019) ABC Transporter Genes Show Upregulated Expression in Drug-Resistant Clinical Isolates of Candida auris: A Genome-Wide Characterization of ATP-Binding Cassette (ABC) Transporter Genes. Frontiers in Microbiology. 10:1445. Link.
Lahari, Z., Ribeiro, A., Talukdar, P., Martin, B., Heidari, Z., Gheysen, G., Price, A.H. & Shrestha, R. (2019) QTL-seq reveals a major root-knot nematode resistance locus on chromosome 11 in rice (Oryza sativa L.). Euphytica. 215:117. Link.
Hsu, T., Gemmell, M.R., Franzosa, E.A., Berry, S., Mukhopadhya, I., Hansen, R., Michaud, M., Nielsen, H., Miller, W.G., Nielsen, H., Bajaj-Elliott, M., Huttenhower, C., Garrett, W.S. & Hold, G.L. (2019) Comparative genomics and genome biology of Campylobacter showae. Emerging Microbes and Infections. 8(1):827-840. Link.
Derous, D., Sahu, J., Douglas, A., Lusseau, D. & Wenzel, M. (2019) Adaptations of energy metabolism in cetaceans have consequences for their response to foraging disruption. bioRxiv. Link.
Lopes, B.S., Strachan, N.J.C., Ramjee, M., Thomson, A., MacRae, M., Shaw, S. & Forbes, K. (2019) Nationwide stepwise emergence and evolution of multidrug-resistant Campylobacter jejuni sequence type 5136, United Kingdom. Emerging Infectious Disease. 25(7). Link
Wenzel, M.A., Johnston, C., Müller, B., Pettitt, J., & Connolly, B. (2019) Deep evolutionary origin of nematode SL2 trans-splicing revealed by genome-wide analysis of the Trichinella spiralis transcriptome. bioRxiv. Link.
Pascoe, B., et al. (2019) Domestication of Campylobacter jejuni NCTC 11168. Microbial Genomics. 10.1099/mgen.0.000279. Link
Redmond AK, Ohta Y, Criscitiello MF, Macqueen DJ, Flajnik MF, Dooley H. Haptoglobin Is a Divergent MASP Family Member That Neofunctionalized To Recycle Hemoglobin via CD163 in Mammals. J Immunol. 2018 Oct 15;201(8):2483-2491. doi: 10.4049/jimmunol.1800508. Epub 2018 Sep 7. PMID: 30194112; PMCID: PMC6179929. Link.
Afouda BA, Lynch AT, de Paiva Alves E, Hoppler S. Genome-wide transcriptomics analysis identifies sox7 and sox18 as specifically regulated by gata4 in cardiomyogenesis. Dev Biol. 2018 Feb 1;434(1):108-120. doi: 10.1016/j.ydbio.2017.11.017. Epub 2017 Dec 8. PMID: 29229250; PMCID: PMC5814753. Link.
Redmond AK, Macqueen DJ, Dooley H. Phylotranscriptomics suggests the jawed vertebrate ancestor could generate diverse helper and regulatory T cell subsets. BMC Evol Biol. 2018 Nov 15;18(1):169. doi: 10.1186/s12862-018-1290-2. PMID: 30442091; PMCID: PMC6238376. Link.
Brunner, K., John, C.M., Phillips, N.J., Alber, D.G., Gemmell, M.R., Hansen, R., Nielsen H.L., Hold, G.L., Bajaj-Elliott, M., & Jarvis, G.A. (2018) Novel Campylobacter concisus lipooligosaccharide is a determinant of inflammatory potential and virulence. Journal of Lipid Research. 59: 1893-1905. Link.
Norton, G.J., Travis, A.J., Douglas, A., Fairley, S., De Paiva Alves, E., Ruang-areerate, P., Naredo, M.E.B., McNally, K.L., Hossain, M., Islam, R.M. & Price, A.H. (2018) Genome wide association mapping of grain and straw biomass traits in the rice Bengal and Assam Aus Panel (BAAP) grown under alternate wetting and drying and permanently flooded irrigation. Frontiers in Plant Science. 9:1223. Link.
Derous D, Mitchell SE, Green CL, Wang Y, Han JDJ, Chen L, Promislow DEL, Lusseau D, Douglas A, Speakman JR. The Effects of Graded Levels of Calorie Restriction: X. Transcriptomic Responses of Epididymal Adipose Tissue. J Gerontol A Biol Sci Med Sci. 2018 Mar 2;73(3):279-288. doi: 10.1093/gerona/glx101. PMID: 28575190; PMCID: PMC5861923. Link.
Dalby, M.J., Aviello, G., Ross, S., Walker, A.W., Barrett, P. & Morgan, P.J. (2018) Diet induced obesity is independent of metabolic endotoxemia and TLR4 signalling, but markedly increases hypothalamic expression of the acute phase protein, SerpinA3N. Scientific Reports. 8: 15648. Link.
Perez Calderon, L.J., Gontikaki, E., Potts, L.D., Shaw, S., Gallego, A., Anderson, J.A. & Witte, U. (2018) Effects of pressure and temperature on deep sea hydrocarbon-degrading microbial communities in subartic sedmiments. Microbiology Open. 16(e768). Link
Mukhopadhya, I., Gomez, J., Duncan, S., Louis, P., Shaw, S., Collie-Duguid, E., Crost, E., Juge, N. & Flint, H. (2018) Formate cross-feeding and cooperative metabolic interactions revealed by transcriptomics in cocultures of acetogenic and amylolytic human gut bacteria. Environmental Microbiology. Link.
Wenzel, M.A., Douglas, A. & Piertney, S.B. (2018) Microbiome composition within a sympatric species complex of intertidal isopods (Jaera albifrons). PLoS ONE 13(8): e0202212. Link
Hiraga, S., Monerawela, C., Katou, Y., Shaw, S., Clark, K., Shirahige, K. & Donaldson, A. (2018) Budding yeast Rif1 bind to replication origins and protects DNA at blocked replication forks. EMBO reports. e46222. Link.
Edwards, C., Baird, J., Zinser, E., Woods, D., Shaw, S., Campbell, E.M. & Bowman, A. (2018) RNA-interference in the cat flea, Ctenocephalides felis: approaches for sustained gene knockdown and evidence of involvement of Dicer-2 and Argonaute2. International Journal for Parasitology. S0020-7519(18)30207-8. Link.
Gemmell, M.R., Berry, S., Mukhopadhya, I., Hansen, R., Nielsen, H.L., Bajaj-Elliott, M., Nielsen, H., & Hold, G.L. (2018) Comparative genomics of Campylobacter concisus: Analysis of clinical strains reveals genome diversity and pathogenic potential. Emerging Microbes & Infections. 7:116. Link.
Garg, M., Hendy, P., Ding, J.N., Shaw, S., Hold, G., & Hart, A. (2018) The effect of vitamin D on intestinal inflammation and faecal microbiota in patients with ulcerative colitis. Journal of Crohn's and Colitis. jjy052. Link.
Hansen, R., Gibson, S., de Paiva Alves, E., Goddard, M., MacLaren, A., Karcher, A.M., Berry, S., Collie-Duguid, E., El-Omar, E., Munro, M., & Hold G.L. (2018) Adaptive response of neonatal sepsis-derived Group B Streptococcus to bilirubin. Scientific Reports. 8:6470. Link.
Afouda, B.A., Lynch, A.T., de Paiva Alves, E., & Hoppler, S. (2018) Genome-wide transcriptomics analysis of genes regulated by GATA4, 5 and 6 during cardiomyogenesis in Xenopus laevis. Data in Brief. Link.
Robertson FM, Gundappa MK, Grammes F, Hvidsten TR, Redmond AK, Lien S, Martin SAM, Holland PWH, Sandve SR, Macqueen DJ. Lineage-specific rediploidization is a mechanism to explain time-lags between genome duplication and evolutionary diversification. Genome Biol. 2017 Jun 14;18(1):111. doi: 10.1186/s13059-017-1241-z. PMID: 28615063; PMCID: PMC5470254. Link.
Redmond AK, Pettinello R, Dooley H. Outgroup, alignment and modelling improvements indicate that two TNFSF13-like genes existed in the vertebrate ancestor. Immunogenetics. 2017 Mar;69(3):187-192. doi: 10.1007/s00251-016-0967-1. Epub 2017 Jan 9. PMID: 28070614; PMCID: PMC5316386. Link.
Afouda, B.A., Lynch, A.T., de Paiva Alves, E., & Hoppler, S. (2017) Genome-wide transcriptomics analysis identifies sox7 and sox18 as specifically regulated by gata4 in cardiomyogenesis. Developmental Biology. Link.
Pettinello R, Redmond AK, Secombes CJ, Macqueen DJ, Dooley H. Evolutionary history of the T cell receptor complex as revealed by small-spotted catshark (Scyliorhinus canicula). Dev Comp Immunol. 2017 Sep;74:125-135. doi: 10.1016/j.dci.2017.04.015. Epub 2017 Apr 19. PMID: 28433528. Link.
Swortwood, M.J., Bartock, S.H., Scheidweiler, K.B., Shaw, S., Filis, P., Douglas, A., O'Shaughnessy, P.J., Soffientini, U., Lucendo-Villarin, B., Iredale, J.P., Hay, D.C., Fowler, P.A., Huestis, M.A. (2017) Quantification of ethyl glucuronide, ethyl sulfate, nicotine, and its metabolites in human fetal liver and placenta. Forensic Toxicology. Link.
Sun, C., De Mello, V., Mohamed, A., Ortuste Quiroga, H.P., Garcia-Munoz, A., Al Bloshi, A., Tremblay, A.M., von Kriegsheim, A., Collie-Duguid, E., Vargesson, N., Matallanas, D., Wackerhage, H., & Zammit, P.S. (2017) Common and distinctive functions of the Hippo effectors Taz and Yap in skeletal muscle stem cell function. Stem Cells. epub ahead of print. Link.
Pradhan, A., Herrero-de-Dios, C., Belmonte, R., Budge, S., Garcia, A.L., Kolmogorova, A., Lee, K.K., Martin, B.D., Ribeiro, A., Bebes, A., Yuecel, R., Gow, N.A.R., Munro, C., MacCallum, D.M., Quinn, J., & Brown, A.J.P. (2017) Elevated catalase expression in a fungal pathogen is a double-edged sword of iron. PLoS Pathogens. 13(5):e1006405. Link.
Morrice, N., McIlroy, G.D., Tammireddy, S., Reekie, J., Shearer, K.D., Doherty, M.K., Delibegovic, M., Whitfield, P.D., & Mody, N. (2017) Elevated Fibroblast growth factor 21 (FGF21) in obese, insulin resistant states is normalised by the synthetic retinoid Fenretinide in mice. Scientific Reports. 7: 43782. Link.
Derous D, Mitchell SE, Wang L, Green CL, Wang Y, Chen L, Han JJ, Promislow DEL, Lusseau D, Douglas A, Speakman JR. The effects of graded levels of calorie restriction: XI. Evaluation of the main hypotheses underpinning the life extension effects of CR using the hepatic transcriptome. Aging (Albany NY). 2017 Jul 31;9(7):1770-1824. doi: 10.18632/aging.101269. PMID: 28768896; PMCID: PMC5559174. Link.
Dehler, C. E., Secombes, C. J., & Martin, S. A. (2016). Environmental and physiological factors shape the gut microbiota of Atlantic salmon parr (Salmo salar L.). Aquaculture. Link.
Carroll, A., Cheng, R., Collie-Duguid, E., Meharg, C., Scholz, M. E., Fiering, S. N., Fields, J. L., Palmer, A. A., Lionikas, A. (2017) Fine mapping of genes determining extrafusal fiber properties in murine soleus muscle. Physiological Genomics Jan 13:physiolgenomics.00092.2016. Link.
Ballou, Elizabeth R., et al. "Lactate signalling regulates fungal β-glucan masking and immune evasion." Nature Microbiology 2 (2016): 16238. Link.
Watt, E., Gemmell, M. R., Berry, S., Glaire, M., Farquharson, F., Louis, P., ... & Hold, G. L. (2016). Extending colonic mucosal microbiome analysis—assessment of colonic lavage as a proxy for endoscopic colonic biopsies. Microbiome, 4(1), 61. Link.
Ikeh, M. A., Kastora, S. L., Day, A. M., Herrero-de-Dios, C. M., Tarrant, E., Waldron, K. J., ... & MacCallum, D. M. (2016). Pho4 mediates phosphate acquisition in Candida albicans and is vital for stress resistance and metal homeostasis. Molecular Biology of the Cell, 27(17), 2784-2801. Link.
Hijazi, K., Mukhopadhya, I., Abbott, F., Milne, K., Al-Jabri, Z. J., Oggioni, M. R., & Gould, I. M. (2016). Susceptibility to chlorhexidine amongst multidrug-resistant clinical isolates of Staphylococcus epidermidis from bloodstream infections. International journal of antimicrobial agents. Link.
Shaw, S., Le Cocq, K., Paszkiewicz, K., Moore, K., Winsbury, R., de Torres Zabala, M., Studholme, D., Salmon, D., Thornton, C.R. and Grant, M.R., (2016). Transcriptional reprogramming underpins enhanced plant growth promotion by the biocontrol fungus Trichoderma hamatum GD12 during antagonistic interactions with Sclerotinia sclerotiorum in soil. Molecular plant pathology. Link.
Leach, M. D., Farrer, R. A., Tan, K., Miao, Z., Walker, L. A., Cuomo, C. A., ... & Cowen, L. E. (2016). Hsf1 and Hsp90 orchestrate temperature-dependent global transcriptional remodelling and chromatin architecture in Candida albicans. Nature communications, 7. Link.
Nakamura, Y., de Paiva Alves, E., Veenstra, G.J.C. & Hoppler, S. (2016) Tissue- and stage-specific Wnt target gene expression is controlled subsequent to β-catenin recruitment to cis-regulatory modules. Development; 143(11):1914-25. Link.
Lehtovirta-Morley, L. E., Ross, J., Hink, L., Weber, E. B., Gubry-Rangin, C., Thion, C., ... & Nicol, G. W. (2016). Isolation of ‘Candidatus Nitrosocosmicus franklandus’, a novel ureolytic soil archaeal ammonia oxidiser with tolerance to high ammonia concentration. FEMS microbiology ecology, 92(5), fiw057. Link.
Derous D, Mitchell SE, Green CL, Wang Y, Han JD, Chen L, Promislow DE, Lusseau D, Speakman JR, Douglas A. The effects of graded levels of calorie restriction: VII. Topological rearrangement of hypothalamic aging networks. Aging (Albany NY). 2016 May;8(5):917-32. doi: 10.18632/aging.100944. PMID: 27115072; PMCID: PMC4931844. Link.
Derous D, Mitchell SE, Green CL, Chen L, Han JD, Wang Y, Promislow DE, Lusseau D, Speakman JR, Douglas A. The effects of graded levels of calorie restriction: VI. Impact of short-term graded calorie restriction on transcriptomic responses of the hypothalamic hunger and circadian signaling pathways. Aging (Albany NY). 2016 Apr;8(4):642-63. doi: 10.18632/aging.100895. PMID: 26945906; PMCID: PMC4925820. Link
Ribeiro, A., A. Golicz, C.A. Hackett, I. Milne, G. Stephen, D. Marshall, A.J. Flavell, and M. Bayer. 2015. An investigation of causes of false positive single nucleotide polymorphisms using simulated reads from a small eukaryote genome. BMC Bioinformatics 16(1):1–16. Link
Li, R., Redmond, A. K., Wang, T., Bird, S., Dooley, H., & Secombes, C. J. (2015). Characterisation of the TNF superfamily members CD40L and BAFF in the small-spotted catshark (Scyliorhinus canicula). Fish & shellfish immunology, 47(1), 381-389. Link.
Strachan NJ, Rotariu O, Lopes B, MacRae M, Fairley S, Laing C, Gannon V, Allison LJ, Hanson MF, Dallman T, Ashton P, Franz E, van Hoek AH, French NP, George T, Biggs PJ, Forbes KJ. Whole Genome Sequencing demonstrates that Geographic Variation of Escherichia coli O157 Genotypes Dominates Host Association. Sci Rep. 2015 Oct 7;5:14145. doi: 10.1038/srep14145. PMID: 26442781; PMCID: PMC4595763. Link.
Lusseau, D., Mitchell, S.E., Barros, C., Derous, D., Green, C., Chen, L., et al. (2015) The effects of graded levels of calorie restriction: IV. Non-linear change in behavioural phenotype of mice in response to short-term calorie restriction. Sci Rep. 5:13198. Link
Shearer, K., Morrice, N., Henderson, C., Reekie, J., McIlroy, G., McCaffery, P., Delibegovic, M., Mody, N. (2015) Fenretinide prevents obesity in female mice via the interaction between retinoid and estrogen signalling. Obesity; 23:1655-62. Link
Mitchell, S.E., Tang, Z., Kerbois, C., Delville, C., Konstantopedos, P., Bruel. A, et al. (2015) The effects of graded levels of calorie restriction: I. impact of short term calorie and protein restriction on body composition in the C57BL/6 mouse. Oncotarget; 6:15902–15930. Link
Mitchell, S.E., Delville, C., Konstantopedos, P., Hurst, J., Derous, D., Green, C., et al. (2015) The effects of graded levels of calorie restriction: II. impact of short term calorie and protein restriction on circulating hormone levels, glucose homeostasis and oxidative stress in male C57BL/6 mice. Oncotarget. 6:23213–23237. Link
Mitchell, S.E., Delville, C., Konstantopedos, P., Derous, D., Green, C.L., Chen, L., et al. (2015) The effects of graded levels of calorie restriction: III. impact of short term calorie and protein restriction on mean daily body temperature and torpor use in the C57BL/6 mouse. Oncotarget. 6:18314–18337. Link
Zou, J., Redmond, A.K., Qi, Z., Dooley, H., Secombes, C.J. (2015) The CXC chemokine receptors of fish: insights into CXCR evolution in the vertebrates. Gen Comp Endocrinol; 215:117-31. Link
Weber, E.B., Lehtovirta, L.E., Prosser, J.I., Gubry-Rangin, C. (2015). Ammonia oxidation is not required for growth of Group 1.1c soil thaumarchaea. FEMS Microbiology Ecology; 91:3 Link
Flink, L. G., Allen, R., Barnett, R., Malmström, H., Peters, J., Eriksson, J., ... & Larson, G. (2014). Establishing the validity of domestication genes using DNA from ancient chickens. Proceedings of the National Academy of Sciences, 111(17), 6184-6189. Link.
Some of the research supported by CGEBM:
MRC Programme Grant (2016-2021): Impact of fungal adaptation upon host recognition and pathogenesis. PI, Professor Alistair Brown. CoIs, Professors Neil Gow, Lars Erwig, Mihai Netea. Award £1,981,419
Wellcome Trust WTSA PhD Studentship (2015-2018): The transition from fungal commensalism to systemic infection. PI, Professor Alistair Brown. CoIs, Professor Gordon Brown, Dr Donna MacCallum. Award £108,653
BBSRC project grant (2012-2018): A genetic dissection of traits required for sustainable water use in rice using Genome Wide Association Studies (GWAS). PI, Professor Adam Price with multiple Co-Is in Aberdeen, Lancaster, Bangladesh and the International Rice Research Institute. Award £1.2M (Aberdeen component £930K).
FACCE-ERA-NET+ project grant (2014-2017): GreenRice: Seven partners in 4 countries coordinated by CIRAD, Montpellier. Aberdeen. Lead: Professor Adam Price: Award €1,447K (Aberdeen component €878K).
MRC Research Grant (2014-2017): The human fetal liver: development and response to maternal drug use. PI, Professor Paul Fowler. CoIs Paul O'Shaughnessy, Dr Panagiotis Filis, Dr Alex Douglas & Dr Susan Fairley.
NHS Endowment Grant (2014-2016): Chlorhexidine baths and emergence of multidrug resistant staphylococci in intensive care units. PIs Drs Karolin Hijazi & Ian Gould.
BBSRC Grant (2013-2016): Mechanisms directing stress-specific outputs from a regulatory hub in C. albicans. PI, Professor Alistair Brown (Collaboration with Jan Quinn, Newcastle). Award £429,137
European Commission (FP7) (2012-2016): Microbicide Optimization Through Innovative Formulation. PI, Dr Karolin Hijazi. CoI, Dr Georgina Hold. Award £450,840
Wellcome Trust ISSF Grant (2015): Impact of the gut microbiota and diet upon Candida colonisation and infection. PI, Professor Alistair Brown. CoIs, Dr Alan Walker, Dr Megan Lenardon. Award £19,748
Tenovus Scotland (2013-2015): Oral Microbiota in Patients with Recurrent Aphthous Stomatitis. PI, Dr Karolin Hijazi. CoI, T Foley & Dr Georgina Hold. Award £10,000
NERC fellowship (NERC-1026-CR; NE/J019151/1) (2012-2015): Evolutionary adaptation in archaea. PI, Dr Cecile Gubry-Rangin. Award £362,498
ERC Advanced Grant (2010-2015): Spatial and temporal regulation of the fungus-host interaction during life-threatening fungal infections. PI, Professor Alistair Brown.
BBSRC SABR Grant (2008-2014): Combinatorial responses of fungal pathogens to their human hosts: an Integrative Systems Biology approach (CRISP). PI, Professor Alistair Brown. CoIs, Professor Celso Grebogi, Professor George Coghill, Dr Alessandro de Moura, Professor Marco Thiel, Dr Carmen Romano, Professor Neil Gow.
BBSRC EastBio PhD studentship: Exploring and exploiting the biosynthesis of myriocin, a potent fungal metabolite. PIs, Dr Alexandra Brand & Professor Dominic Campopiano. Award £71,077
Biosciences KTN BBSRC CASE: Drug target identification in the cat flea by transcriptomics and gene knockdown. PI, Dr Alan S. Bowman (Uni Aberdeen). CoIs, Dr Debra Woods (Zoetis Animal Health, Kalamzoo,USA). Student, Catriona McIntosh. Award £127,000
Friends of Anchor: Obesity and colorectal cancer – do microbes hold the key. PI, Dr Georgina Hold. Award £10,000
GI Research funds: Assessment of microbial diversity in colorectal cancer progression. PI, Dr Georgina Hold. Award £5,000
GI Research funds: Is faecal aspirate a good proxy for intestinal biopsy in IBD patients: 16S V3/V4. PI, Dr Georgina Hold. Award £5,000
ISSF Seedcorn: Role of the enteric virome and its interaction with the bacterial and fungal microbiome in the aetiopathogenesis of Crohn’s disease. PI, Dr Indrani Mukhopadhya. CoI, Dr Georgina Hold. Award £22,087
MRC PhD studentship & NHS Grampian neonatal endowments funding: Assessment of the antimicrobial properties of bilirubin in relation to Group B streptococcus infection. PI, Dr Georgina Hold. CoIs. Mike Munro, Richard Hansen. Award £140,000
NHS Grampian endowments: CAMPY-GAP Camplyobacter–genome annotation project. PI, Dr Georgina Hold. CoI, Dr Indrani Mukhopadhya. Award £12,000
RESAS Programme Theme 3.2.1 Importance of Healthy Diets. PI, Dr Janice Drew. CoIs, Stephanie Andraos. Award £886,398
RESAS Programme Theme 3.2.2. Dietary components of healthy diets and their effects. PI, Dr Alan Walker. Award £1,465,271
St Marks Foundation: Vitamin D and the intestinal microbiome in IBD. PI, Dr Georgina Hold. Award £14,710
Wellcome Trust Investigator Award: Making and breaking of fungal cell walls. PI, Professor Neil Gow.
- Community Engagement
Community engagement is important to increase the knowledge and interest of the public and create future enthusiatic scientists.
Please contact us if you are interested in working with us for a community engagement event.
Cell Block Science
An initiative established at the University of St. Andrews, and funded by the Wellcome Trust to be taken nationwide, sees researchers heading into prisons to educate inmates about the science being undertaken at university's close to them. With help from PERU, The CGEBM team visited HMP Grampian with a day of activities surrounding DNA, with fun facts about how DNA research impacts every day life, and a short activity extracting DNA from strawberries.
May Festival School's Programme
Aimed at local primary schools, the CGEBM team presented Genes Unzipped! as a part of both the 2017 and 2019 May Festival School's Programme. This interactive workshop aimed to teach children about DNA, with activities demonstrating what things contain DNA, how DNA is translated to proteins, and a hands-on activity extracting DNA from strawberries. This event took place as a part of the wider May Festival School's Programme.
Doors Open Day
The CGEBM team have held a stall in the Institute of Medical Sciences in both 2016 and 2018 as part of the Annual Aberdeen doors open day. This event sees hundreds of buildings open their doors for the public for free. The CGEBM team had fun activities on offer for all of the family including science puzzles, DNA putt-putt, "make-your-own" DNA bracelets, and real life samples to peer at under the microscope. The team also talked about some of the work being undertaken in the Centre and offered tours of the laboratory.
For more information about Doors Open Day, including a list of all buildings that are took part, visit the website - http://www.doorsopendays.org.uk/.
The CGEBM team held a stall on Friday 30th September as part of Explorathon 2016. This event is a Scottish wide event to celebrate European Researcher's night. The CGEBM team was available to answer any questions that members of the public have about the research being undertaken, and to teach interesting facts and basic concepts of genomics through fun family activities. Activities included DNA mini golf, DNA origami and "Pin the eye on the Mendelian" kids games.
For more information about Explorathon, including a list of locations that took part, visit the website - http://www.explorathon.co.uk/. For more information about European Researchers Night, visit the website - http://ec.europa.eu/research/researchersnight/index_en.htm.