Impact

2024 

Then CK, Paillas S, Moomin A, Misheva MD, Moir RA, Hay SM, Bremner D, Roberts (nee Nellany) KS, Smith EE, Heidari Z, Sescu D, Wang X, Suarez-Bonnet A, Hay N, Murdoch SL, Saito R, Collie-Duguid ESR, Richardson S, Priestnall SL, Wilson JM, Gurumurthy M, Royle JS, Samuel LM, Ramsay G, Vallis KA, Foster KR, McCullagh JSO, Kiltie AE. Dietrary fibre supplementation enhances radiotherapy tumour control and alleviates intestinal radiation toxicity. Microbiome 2024, 12, 1, 22, p89  Link

Ghazal A., Clarke D., Abdel-Rahman M.A., Ribeiro A., Collie-Duguid E., Pattinson C., Burgoyne K., Muhammad T., Alfadhel S., Heidari Z., Samir R., Gerges M.M., Nkene I., Colamarino R.A., Hijazi K., Houssen W.E., Venomous gland transcriptome and venom proteomic analysis of the scorpion Androctonus amoreuxi reveal new peptides with anti-SARS-CoV-2 activity, Peptides, Volume 173, March 2024. Link

Hyötyläinen T., McGlinchey A., Salihovic S., Schubert A., Alex Douglas A., Hay D.C., O'Shaughnessy P.J., Iredale J.P., Shaw S., Fowler P.A., Orešič M., In utero exposures to perfluoroalkyl substances and the human fetal liver metabolome in Scotland: a cross-sectional study. Articles, Volume 8, Issue 1, E5-E17, January 2024. Link

2023

Ward, A.B., Harris, P.A., Argo, C.McG., Watson, C., Neacsu, M., Russell, W.R., Ribeiro, A., Collie-Duguid, E., Heidari, Z., Morrison, P.K. Homemade Nucleic Acid Preservation Buffer Proves Effective in Preserving the Equine Faecal Microbiota over Time at Ambient Temperatures. Animals 2023, 13, 3107. Link

Ward, A., Harris, P. A., Argo, C. M., Watson, C., Neacsu, M., Russell, W., Ribeiro, A., Collie-Duguid, E., Heidari, Z. & Morrison, P. K. Effect of sampling and storage conditions upon equine fecal microbial community. Journal of Equine Veterinary Science. 2023, Special Issue ed. Vol. 124. 104308. Link

Simonettia, S., Collie-Duguid, E., Fernandez Martin, C., Louis, P., Pu, J., Smith, E. & Dionisi, D. Effect of feed concentration and residence time on anaerobic fermentation in CSTR and SBR to produce short-chain organic acids. Journal of Environmental Engineering. 2023, 11, 5, October 2023, 110461. Link

Collins, F.L., Roelofs A.J., Symons R.A., Kania, K., Campbell, E., Collie-Duguid E.S.R, Riemen A.H.K. Clark, S.M., De Bari C. Taxonomy of fibroblasts and progenitors in the synovial joint at single-cell resolution. Annals Rheum. Dis. 2023, 82, 3, 428-437. Link

2022

Mukhopadhya, I., Martin, J. C., Shaw, S., McKinley, A. J., Gratz, S. W. & Scott, K. P. Comparison of microbial signatures between paired faecal and rectal biopsy samples from healthy volunteers using next-generation sequencing and culturomics. 2022, Microbiome. 10, 1, 17 p., 171. Link

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. Gut mucosal microbiome signatures of colorectal cancer differ according to BMI status. Frontiers in Medicine, 2022, 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. 

Nikolov, V., Malavia, D. & Kubota, T. SWI/SNF and the histone chaperone Rtt106 drive expression of the Pleiotropic Drug Resistance network genes. 2022, Nature Communications. 13, 16 p., 1968. Link

2021

Solano-Collado, V., Colamarino, R. A., Calderwood, D. A., Baldassarre, M., & Spanò, S. (2021). A Small-Scale shRNA Screen in Primary Mouse Macrophages Identifies a Role for the Rab GTPase Rab1b in Controlling Salmonella Typhi Growth. Frontiers in cellular and infection microbiology, 11, [660689]. Link. 

Lorgen-Ritchie, M., Clarkson, M., Chalmers, L., Taylor, J. F., Migaud, H., & Martin, S. A. M. (2021). A Temporally Dynamic Gut Microbiome in Atlantic Salmon During Freshwater Recirculating Aquaculture System (RAS) Production and Post-seawater Transfer. Frontiers in Marine Science, 8, [869]. 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.

2020

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.

2019

Duvenage, L., Walker, L. A., Bojarczuk, A., Johnston, S. A., MacCallum, D. M., Munro, C. A., & Gourlay, C. W. (2019). Inhibition of Classical and Alternative Modes of Respiration in Candida albicans Leads to Cell Wall Remodeling and Increased Macrophage Recognition. mBio, 10(1), [e02535-18]. 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. 

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

Zafeiri, A., Filis, P., Shaw, S., Iredale, J. P., Swortwood, M. J., Mitchell, R. T., Hay, D. C., O'Shaughnessy, P. J. & Fowler, P. A. Maternal Smoking during Pregnancy and Changes in Prostaglandin Enzymes in the Human Fetus. 2019, Reproductive Sciences. 26, Supplement 1, p. 244A-244A 1 p., F-103. Link

2018

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.

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.

2017 

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.

2016

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

2015

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

2014

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 Equipment – World class labs. Capital equipment award (2023).  Spatial biology platform.  MRC Award £458129, Total Investment £610839
PI, Dr Jenna Gregory, CoIs, Dr Elaina Collie-Duguid, Professor Paul Fowler, Gillian Milne.

Tenovus Scotland (2023-2024). Bioinformatics analysis of single cell SEQUENCing of Human PBMC in acutE cardiac disease: SEQUENCE study. PI, Dr Mohammad Khan, CoIs, Professor Dana Dawson, Dr Elaina Collie-Duguid. Award £18966

Medical Research Scotland (2022 – 2026). Determining the biological basis for, and de-stigmatising, problematic alcohol use and anxiety. PI, Professor Alasdair MacKenzie, CoIs, Dr Elaina Collie-Duguid, Dr John Mooney.

Global Challenges research Fund (GCRF) Covid-19 response (2020 – 2021). Development of novel modified scorpion venom peptides as anti-SARS-CoV-2 virus. PI, Dr Wael Houssen, Cis, Dr ESR Collie-Duguid, Dr Sergio Dall’ Angelo, Dr Mohamed Abdel-Rahman. Award £48,550

Leverhulme Trust doctoral training programme (2018 – 2023). Centre for doctoral training in sustainable production of chemicals and materials led by School of Natural and Computing Science. Professor Davide Dionisi, Anaerobic digestion work theme (Engineering, Biological Sciences, Medical Sciences), Dr Elaina Collie-Duguid: Academic co-supervisor. Award, £1,050,000

University of Aberdeen Development Trust (2018). Single Cell Genomics Chromium System. PI, E Collie-Duguid. Award £34520

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.

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

Update:  The centre supports the research of post-graduate students. More details about some of our student projects can be found here.

Single cell de novo whole genome sequencing of archaea

The CGEBM recruited its first cohort of graduate students early in 2013. These genomics enabled studentships include informatics and biology focused projects in ecology, evolution, agriculture, microbiology, nutrition, human disease and biomaterials within world leading research teams in the University. The CGEBM support the personal and scientific development of their students through provision of an extended training programme in genomics, bioinfromatics and critical scientific skills.

CGEBM supported studentships include;

Publications 

• Ward, A.B., Harris, P.A., Argo, C.McG., Watson, C., Neacsu, M., Russell, W.R., Ribeiro, A., Collie-Duguid, E., Heidari, Z., Morrison, P.K. Homemade Nucleic Acid Preservation Buffer Proves Effective in Preserving the Equine Faecal Microbiota over Time at Ambient Temperatures. Animals 2023, 13, 3107. Link
• Ward, A., Harris, P. A., Argo, C. M., Watson, C., Neacsu, M., Russell, W., Ribeiro, A., Collie-Duguid, E., Heidari, Z. & Morrison, P. K. Effect of sampling and storage conditions upon equine fecal microbial community. Journal of Equine Veterinary Science. 2023, Special Issue ed. Vol. 124. 104308. Link
• Simonettia, S., Collie-Duguid, E., Fernandez Martin, C., Louis, P., Pu, J., Smith, E. & Dionisi, D. Effect of feed concentration and residence time on anaerobic fermentation in CSTR and SBR to produce short-chain organic acids. Journal of Environmental Engineering. 2023, 11, 5, October 2023, 110461. 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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. 
• 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, S.E., Green, C.L., Chen, L., Han, J.J., Wang, Y., et al. (2016) 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. 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 
• 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
• 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
• 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
• 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
• 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

PhD Opportunities

PhD students are also being recruited in the Pathways to a Healthy Life Theme and the Environment and Food Security Theme.

Please apply for studentships via the Graduate School.

You can find more PhD Opportunities here.

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.

2024

BBSRC EastBio Thematic Meeting – April 2024 "Using bioinformatics to address the 'Rules of Life'"

CGEBM bioinformatician Louie van de Lagemaat was invited to give the keynote lecture at this event held at the University of Aberdeen and led by the University’s BBSRC EastBio (East of Scotland Biosciences consortium) cohort as part of the EastBio Doctoral Training partnership. The event was attended by students from the University of Aberdeen and other Scottish Universities. There was lots of enthusiasm to learn how bioinformatics is transforming research.  In particular, attendees learned about next-generation sequencing and how it can be applied to address a large diversity of aspects of fundamental cell biology, which might be termed the "Rules of Life". These range from the obvious genome and RNA sequencing to studies of genomic sequence variation, methylation, chromatin state, binding of protein to RNA or DNA, transcription rate, splicing, isoform abundance, mRNA turnover and translation efficiency, to name a few. Further applications include abundance measurement of gut and environmental microbial communities.

Further discussion centred around single-cell RNA sequencing and multiomics, applications of long-read sequencing, and newer methods involving instruments that spatially resolve mRNA and protein abundance to explore the transcriptome and proteome in distinct cell populations in complex tissues. Participants also learned about high-performance computing, how expert bioinformaticians can participate seamlessly in a broader biology project, how appropriate training can jump-start a self-directed bioinformatic analysis, and how web-based graphical user interfaces such as Galaxy offer a more intuitive interface to a wide array of bioinformatic tools. These discussions highlighted services that the Centre for Genome-Enabled Biology (CGEBM) offers to the University of Aberdeen and the broader community.

2023

Wellcome ISSF Public Engagement event – January 2023 “What’s in my Pond?”

Between January and March 2023, CGEBM carried out three, two-day interactive workshops for over 60, S3 level pupils, from St Machar and Northfield Academies. Workshops were held on site at the University in the Cruickshank Botanical Gardens, the Aberdeen Biodiversity Centre, with laboratory-based activities carried out in the Science Teaching Hub. 

Each program started with an introduction to genomes, sequencing, and computational biology. This was followed up with pond dipping and identification of fauna and flora using traditional identification keys.

Water samples were also collected to identify species using DNA sequencing to demonstrate to the pupils that species can be identified from environmental DNA using genomics. Over the course of the workshop, students used vacuum pumps to filter and capture environmental DNA, extracted this DNA from filter membranes, prepared DNA libraries from samples using an Oxford Nanopore Voltrax device and then sequenced the libraries in real time using a MinION sequencer. 

We discussed with students how DNA sequencing is used directly in health, such as through sequencing of the gut microbiome of patients with varying conditions and showed how the sequencing technologies are being used in “real-life” research within health, such as the variant monitoring of the Covid outbreak, and for development of diagnostic tests for disease. 

Bioinformaticans from the CGEBM went through analysis of the sequencing data with the students who had the opportunity to interrogate the data and find out “What’s In My Pond?”.

Pupils also had a walking tour of the University and a discussion with Career and Access professionals.

Funding for this event was through a competitive Wellcome ISSF Public Engagement grant. 

The workshops built stronger ties with the University and the two schools involved and more regular curriculum linked workshops are planned to aid STEM teaching and encourage more pupils to consider further or higher education in STEM subjects.

2019

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. 

2018

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/.

2016

Explorathon 2016

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.