Campus Directory: James Thomas

University of Lethbridge

James Thomas
Faculty
Biological Sciences Department
Office: D886 (University Hall)
Phone: (403) 329-2467
Fax: (403) 329-2082
Email:
Faculty (AgBio Coord)
Agricultural Biotechnology
Office: D886 (University Hall)
Phone: (403) 329-2467
Fax: (403) 329-2082
Lab
Room: D840 (University Hall)
Phone: (403) 329-2317

Expertise

Cell & molecular biology, Environmental microbiology, Food and water borne bacterial pathogens, Agricultural bioechnology, Plant breeding and biochemical characterization of functional foods such as fenugreek

Office Hours

Open: Please call or email for an appointment. 9:00 AM to 4:30 PM

About Me

I initially trained as a cell and molecular biologist at McMaster University in Hamilton, Ontario, receiving my PhD in 1980. Since then, I did post-doctoral work at the University of Toronto and later at the University of Calgary. I received a position at the University of Lethbridge in southern Alberta, Canada in 1988, and currently hold a position as a Professor in Cell and Molecular Biology. In total I have published about 100 peer reviewed papers and abstracts. Much of my work is collaborative in nature.
I have been working with Surya Acharya, Agriculture and Agri-Food Canada, Manjula Bandara, Alberta Agriculture and Food, and Darcy Driedger, Alberta Agriculture and Food, to develop new forages for the livestock and dairy industries and, new value added crops to help diversify our agricultural industry. These studies helped lead to development of ACE-1 PC rye, a new perennial cereal rye which is adapted for growth in semi-arid climates with reduced water and, has excellent feed characteristics as either silage, hay or pasture (released by Agriculture and Agri-Food Canada, Lethbridge Research Centre). We also have been developing new lines of fenugreek which produce good forage and mature seed within the ~100 frost-free days that we have available for growth in southern Alberta. The crop is an annual legume which can be used in crop rotations and, is adapted for growth on dry land or with limited irrigation. The plant produces diosgenin, a steroid hormone precursor which has potential to promote weight gain in livestock and increased milk production in dairy cattle. New varieties with enhanced production qualities are being developed as a potential source of steroid hormones for the pharmaceutical industry, as a dietary supplement for the nutraceutical industry and, as artificial maple flavoring for the food industry.

Part of my research focus also is in the area of microbiology, looking at cause and effect associations in the occurrence of waterborne pathogens, in particular in relation to agriculture, ecology and urban/industrial activities. In collaboration with Vic Gannon, Public Health Agency of Canada, and Eduardo Taboada, Public Health Agency of Canada, we have been looking at genomic characterization, bioinformatic analysis and metabolic fingerprinting of environmental isolates of E. coli O157:H7, Enterococcus, Campylobacter and Salmonella as a means of bacterial source tracking, and identification of environmental isolates of bacterial pathogens. Much of this work on water quality has been done within the Oldman River basin of southern Alberta using geographical information systems to assess spatial and temporal distribution of fecal coliform bacteria within the watershed. I also have been collaborating with Tim McAllister (Agriculture and Agri-Food Canada), Kim Stanford and Tim Reuter (Alberta Agriculture and Food) to look at development of clinical assays for enteric pathogens, as well as mitigation strategies for enteric pathogens in food and water. In general, this data is being related to land use, agricultural, urban and industrial applications.

Biography

Teaching

Introductory Biology - Biology 1010 - Cellular Basis of Life
Cell/Molecular Biology - Biology 3105 - Signal Transduction
Biology 4110 - Advances in Genetics, Molecular and Celluar Biology
Biochemistry 2000 - Introductory Biochemistry

Selected Publications

1. Sottie, E.T., Acharya, S.N., McAllister, T.A., Thomas, J., Wang, Y., and Iwaasa, A.D. (2014). "Alfalfa pasture bloat can be eliminated by intermixing with newly-developed sainfoin population.", Agronomy Journal, 106(4): 1470-1478. doi : 10.2134/agronj13.0378
2. Conrad, C.C., Stanford, K., McAllister, T.A., Thomas, J., Reuter, T. (2014) Further development of sample preparation and detection methods for O157 and the top 6 non-O157 STEC serogroups in cattle feces. J. Microbiol. Meth. 105: 22-30. http://www.sciencedirect.com/science/article/pii/S0167701214001833
3. Hallewell, J., Niu, Y.D., Munns, K., McAllister, T.A., Johnson, R.P., Ackermann, H.W., Thomas, J.E., Stanford, K., Niu, Y.D., Munns, K., McAllister, T.A., Johnson, R.P., Ackermann, H.W., Thomas, J.E., and Stanford, K. (2014) Populations of endemic bacteriophage differ between cattle shedding high and low numbers of Escherichia coli O157:H7 in feces. Appl Environ Microbiol. 80(13):3819-3825. Apr 18. [Epub ahead of print]
4. Hallewell, J., Barbieri, L.R., Thomas, J.E., Stanford, K., and McAllister, T.A. (2013) Fecal shedding in cattle inoculated with Escherichia coli O157:H7 and fed corn or wheat distillers' dried grain with solubles. J. Food Prot. 76(1):114 - 118. doi: 10.4315/0362-028X.
5. Laing, C., Taboada, E.N., Kruczkiewicz, P., Thomas, J.E., Gannon, V.P.J. (2013) A Dynamic Whole-genome Database for Comparative Analyses, Molecular Epidemiology and Phenotypic Summary of Bacterial Pathogens. BIOINFORMATICS 2013: 304-307. SciTePress, (2013)
6. Kruczkiewicz, P., Mutschall, S., Barker, D., Thomas, J., Van Domselaar, G., Gannon, V.P.J., Carrillo, C. D., and Taboada, E. N. (2013). MIST: a tool for rapid in silico generation of molecular data from bacterial genome sequences.
BIOINFORMATICS 2013: 316-323. SciTePress, (2013) https://bytebucket.org/peterk87/microbialinsilicotyper/wiki/mist_paper.pdf
7. Kovalchuk, A., Aladedunye, F., Rodriguez-Juarez, R., Li, D., Thomas, J., Kovalchuk, O., and Przybylski, R. Novel antioxidants are not toxic to normal tissues but effectively kill cancer cells. (2013) Cancer Biology & Therapy 14:907 - 915; PMID: 23917379.
8. Kovalchuk, I., Walz, P., Thomas, J., and Kovalchuk, O. (2013) Genomic Instability in Liver Cells Caused by an LPS-Induced Bystander-Like Effect. PLoS ONE 8(7): e67342. http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0067342
9. Hallewell, J., McAllister, T.A., Thomas, J., Booker, C.W., Hannon, S., Jim, G.K., Burciaga-Robles, L.O., May, M.L., Peterson, R.E., Flaig, C., Hussey E.M. and Stanford, K. (2012) Effects of wheat or corn distillers' dried grains with solubles on feedlot performance, fecal shedding and persistence of Escherichia coli O157:H7. J. Anim. Sci. 90(8): 2802-10. doi: 10.2527 / jas.2011-4856.
10. Taboada, E.N., Ross, S.L., Mutschall, S.K., MacKinnon, J.M., Robertsa, M.J., Buchanan, Kruczkiewicz, P., Jokinen, C.C., Thomas, J.E., Nash, J.H.E., Gannon, V.P.J., Marshall, B., Pollarid, F. and Clarke, C.G. (2012) Development and Validation of a Comparative Genomic Fingerprinting Method for High-Resolution Genotyping of Campylobacter jejuni. J. Clin. Microbiol. 50 (3): 788-797.
11. Laing, C., Zhang, Y., Gilmour, M.W., Allen, V., Johnson, R., Thomas, J.E., and Gannon, V.P.J. (2012) A comparison of Shiga-toxin 2 bacteriophage from classical Enterohemorrhagic Escherichia coli serotypes and the German E. coli O104:H4 outbreak strain. PLOS 1. 7(5): 1-12.
12. Jokinen, C.C., Edge, T.A., Koning, W., Laing, C.R., Lapen, D.R., Miller, J., Mutschall, S., Scott, A., Taboada, E.N., Thomas, J.E., Topp, E., Wilkes, G. and Gannon, V.P.J. (2012) Spatial and temporal drivers of zoonotic pathogen contamination of an agricultural watershed. J. Environ. Qual. 41:242-252.
13. Thomas, J.E., Bandara, M., Driedger, D. and Lee, E.L. (2011) Fenugreek in Western Canada. Americas J. Plant Sci. Biotech (Focus on Canada III) 5 (Special Issue 2):32-44.
14. Bandara, M., Lee, E.L. and Thomas, J.E. (2011) Gotu kola (Centella asiatica L.): an under-utilized herb. Americas J. Plant Sci. Biotech (Focus on Canada III) 5 (Special Issue 2):20-31.
15. Laing, C.R., Villegas, A., Taboada, E.N., Kropinski, A., Thomas, J.E. and Gannon, V.P.J. (2011) Identification of Salmonella enterica species- and subgroup-specific genomic regions using Panseq 2.0. Infect. Genet. Evol. 11 (8): 2151-2161. http://www.sciencedirect.com/science/article/pii/S1567134811003509
16. Laing, C.R., Zhang, Y., Thomas, J.E. and Gannon, V.P.J. (2011) Everything At Once: comparative analysis of the genomes of bacterial pathogens. Vet. Microbiol. 153:13-26. http://www.sciencedirect.com/science/article/pii/S0378113511003427
17. Jokinen, C.C, Edge, T.A., Suzanne Ho, S., Koning, W., Laing, C., Mauro, W., Medeiros, D., Miller, J., Robertson, W., Taboada, E., Thomas, J.E., Topp, E., Ziebell, K., Gannon, V.P.J. (2010) Molecular subtypes of Campylobacter spp., Salmonella enterica and Escherichia coli O157:H7 isolated from faecal and surface water samples in the Oldman River watershed, Alberta, Canada. Water Research 45:1247-1257. http://www.sciencedirect.com/science/article/pii/S0043135410006962#
18. Thomas, J.E., Bandara, M., Lee, E.L., Driedger, D. and Acharya, S.N. (2011) Biochemical monitoring in fenugreek to develop functional food and medicinal plant variants. New Biotechnology: International Society of Biotechnology and Biochemistry - Special Issue. New Biotech. 28 (2): 110-117.
19. Laing, C., Buchanan, C., Taboada, E.N., Zhang, Y., Kropinski, A., Thomas, J.E. and Gannon, V.P.J. (2010) Pan-genome sequence analysis using Panseq: an online tool for the rapid analysis of core and accessory genomic regions. BMC Bioinform. 11: 461-475. (http://www.biomedcentral.com/1471-2105/11/461)
20. Zhang, Y., Laing, C., Zhang, Z., Hallewell, J., You, C., Ziebell, K., Johnson, R.P., Kropinski, A.M., Thomas, J.E., Karmali, M. and Gannon, V.P.J. (2010) Lineage and Host-Source are Both Correlated with Levels of Shiga toxin 2 Production by Escherichia coli O157:H7 Strains. Appl. Environ. Microbiol. 76 (2): 474-482.
21. Jokinen, C.C., Schreier, H., Mauro, W., Taboada, E., Isaac-Renton, J.L., Topp, E., Edge, T., Thomas, J.E., Gannon, V.P. (2010) The occurrence and sources of Campylobacter spp., Salmonella enterica and Escherichia coli O157:H7 in the Salmon River, British Columbia, Canada. J. Water Health 8 (2): 374-386.
22. Basu, S.K., Acharya, S.N., Bandara, M.S., Friebel, D. and Thomas, J.E. (2009) Effects of genotype and environment on seed and forage yield in fenugreek (Trigonella foenum-graecum L.) grown in western Canada. AJCS 3(6): 305-314.
23. Laing, C.R., Buchanan, C., Taboada, E.N., Zhang, Y., Karmali, M.A., Thomas, J.E. and Gannon, V.P.J. (2009) In silico genomic analyses reveal three distinct lineages of Escherichia coli O157:H7, one of which is associated with hyper-virulence. BMC Genomics 10: 287 (doi:10.1186/1471-2164-10-287).


Monographs
1. Prasad, R., Acharya S., and Thomas, J. (2014) Identification Of High Seed Yielding And Stable Fenugreek Mutants. Lambert Academic Publishing. ISBN-10: 3659478857 | ISBN-13: 978-3659478857
2. Basu, S., Acharya, S.N. and Thomas, J.E. (2009) Production of High Quality Fenugreek (Trigonella foenum-graecum L.): Selecting for optimized yield and early seed maturation. pp. 176. VDM Verlag (Publisher). ISBN: 3639123786
3. Acharya, S.N. and Thomas, J.E. (Eds) (2007) Advances in Medicinal Plant Research. pp. 550. This book contains 22 invited chapters from leading scientists doing research on medicinal plants from around the world. All chapters were peer reviewed by two experts from the area of each submitted author's work. Research Signpost (Publisher). ISBN: 81-7736-255-0

In The Media

Magazine Articles
1. Thomas, J.E. (2012) Editorial: Uncovering the chemical benefits of medicinal plants and functional foods presents new challenges and untold opportunities. Medicinal Aromatic Plants 2012, 1:4 (http://dx.doi.org/10.4172/map)
2. Acharya, S.N., Thomas, J.E. and Basu, S.K. (2008) Fenugreek: A new crop to cope with agricultural restructuring and diminishing water supplies. (Crops, Soils, Agronomy) CSA News 53 (6): 5-6.
3. Acharya, S.N., Mir, Z., Moyer, J.R., Blade, S., Thomas, J. E., Basu, S.K., Bandara, M. and Friebel, D.R. (2008) New dryland forage crops for sustainable agriculture in southern Alberta. NESA Newsletter. 11(2): 2-4.

Research Interests

Research

Cell & Molecular Biology / Biochemistry

Environmental Microbiology: Microbial assessment of water quality (Member of the Canadian Water Network; National Centre of Excellence); Assessment of microbial diversity.

Molecular Genetics / Biochemistry: Host / Pathogen interactions.

Agricultural Biotechnology: collaborative research on development of new forage crops in support of the livestock industry; Use of wood ash as a soil amendment for forages and canola.



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