Duedu:Vacancies
Student Projects
The are some projects that are available to various groups of students in the area of microbial biotechnology. Interested students are to send an email to the project lead - Dr. Kwabena Duedu. We are looking for students with innovative thinking to work on these discovery projects. Hence students who express interest will be interviewed by the project team. Interviews will be conducted at the end of November or the first week in December 2016. Students intending to register for postgraduate programmes may indicate that in the email. If you require expedite interview, you may request.
Molecular characterisation of pathogens
Kwabena O. Duedu1*, Grace Kpeli1, Orish Verna2, Adjoa A. Boakye1
1 Department of Biomedical Sciences, University of Health and Allied Sciences, Ghana
2 School of Medicine, University of Health and Allied Sciences, Ghana
*Project Lead/Principal Investigator: Email: kduedu@uhas.edu.gh
Microbes are an important part of our environment. In humans and animals microbial communities that constitute the microbiome are involved in many processes that regulate life processes as well as lead to various disease states. Similarly, in the environment, microbes are involved processes such as food poisoning, decay of materials, among others. Our understanding of microbes and microbial processes strongly depend on our knowledge of what microbes are found where. In order to build this knowledge, we employ molecular tools to investigate the diversity, distribution and abundance of microbial communities under different settings. Some of the projects include:
1. Characterization diarrhoea pathogens from stool
Using polymerase chain reaction this project aims to identify the carriage of diarrhoeal pathogens from stool samples. Our biobank contains a few hundreds of stool samples from school children and adults in communities that we have studied. We also have a library of primers for identification of stool pathogens such as parasites (Giardia spp, Entamoeba spp and Cryptosporidium spp), bacteria (various diarhhoeagenic Escherichia coli (EHEC, EPEC, EAEC, O157:H7, etc), Listeria monocytogenes, Salmonella spp, and Shigella spp). In addition, we've also got molecular systems for investigating soil transmitted helminths (eg. Hookworms, Ascaris, Trichuris trichiura, and Shistosoma spp. In addition to routine nucleic acid extraction, purification and polymerase chain reaction (PCR) tools, these projects may also employ restriction fragment length polymorphism (RFLP) tools for characterization of some of these pathogens.
Microbial biofuel projects
Kwabena O. Duedu1*, Eugene K. A. Fletcher2, Adjoa A. Boakye1, Innocent Afeke3
1 Department of Biomedical Sciences, University of Health and Allied Sciences, Ghana
2 Novo Nordisk Foundation Center for Biosustainability, DTU Biosustain, Denmark
3 Department of Medical Laboratory Sciences, University of Health and Allied Sciences, Ghana
*Project Lead/Principal Investigator: Email: kduedu@uhas.edu.gh
There is increasing call for the development of sustainable energy sources such as biofuels to replace declining oil reserves. Not only are the world’s oil reserves declining but also fossil fuels are harmful to the environment due to their high CO2 emissions. The use of biofuels is not new. In 1900, Rudolf Diesel demonstrated an engine he constructed running on groundnut oil (Knothe 2001). Biofuels were also reported during the 1920s and 1930s as well as during World War II (NCB 2011). Henry Ford, founder of Ford Motor Company is also quoted to have said in 1925 that “The fuel of the future is going to come from fruit like that sumac out by the road, or from apples, weeds, sawdust - almost anything. There is fuel in every bit of vegetable matter that can be fermented. There’s enough alcohol in one year’s yield of an acre of potatoes to drive the machinery necessary to cultivate the fields for a hundred years”. Years later, major advances and applications of plant-derived fuels have been seen with bioethanol and biodiesel (Antoni et al. 2007; Dale 2008). Plant biomass is the most abundant and ideal feedstock for biofuel production. Biofuels may be produced from plant biomass by biochemical conversion using microorganisms (bacteria and fungi) in two major steps: 1. digestion and 2. fermentation. Biomass digestion, also referred to as biomass degradation or biomass conversion leads to the production of sugars (and other products). The products are then fermented to form the bioalcohols. There hasn’t been any single microorganism found to perform both digestion and fermentation. Bioconversion has hence been achieved by combinatorial approaches with either microbes or microbes and enzymes isolated from microbes. Another challenge is that, most microbes capable of doing one of these steps are not industrially friendly, hence, the use of genetic engineering to transfer cellulose degradation capabilities to industrially friendly microbes such as Escherichia coli, Citrobacter freundii, and Bacillus subtilis (Lynd et al. 2005; French 2009; de Souza and de Oliveira Magalhaes 2010; Samanta et al. 2013; French et al. 2015; Duedu and French 2016; Lakhundi et al. 2016). The Duedu Lab at the School of Basic & Biomedical Sciences, UHAS is undertaking research on transferring cellulose degradation capabilities to industrially friendly microbes as well as discovery new microbes and enzymes that can be used in biomass conversion processes. Two projects are available in this area for students.
1 & 2. Isolation and characterization of microbial communities involved in lignocellulose and starch hydrolysis
1. Lignocellulase degrading microbes
We will be investigating forest floors for lignocellulosic degradation activities. Samples will be collected from sites where visible activities are identified. Biophysical and biochemical properties of these sites will be characterized. We will isolate and identify microbial communities involved in lignocellulose degradation and characterize this activity in a laboratory setting. Techniques to use will include microbiological culture and identification, DNA extraction, PCR, protein extraction, enzyme activity, biochemical analysis and biophysical condition evaluation.
2. Starch hydrolyzing microbes
Cassava processing is very common in Ghana. At local processing industries (eg. for gari and cassava dough), the liquid is often discarded into the environment together with other waste. These wastes have a potential of redefining the microbial ecosystem of the environment into becoming more of microbes capable of utilizing starch and complex carbohydrates. We aim to isolate and characterize microbes that are able to utilize these carbohydrates and determine the biochemical pathways by which they do this. Techniques to use will include microbiological culture and identification, DNA extraction, PCR, sequence analysis, protein extraction, enzyme activity, biochemical analysis and biophysical condition evaluation.
3. Construction of metagenomic libraries and and screening for lignocellulose and starch hydrolyzing enzymes
The problem of non-culturability limits what one can fine through culture-based screening of microbial communities. Functional genomics is a powerful tool that enables construction and screening of genomic libraries for genes as well as understand various pathways. The procedure is simple and involves extracting genomic DNA from a sample, cutting fragments and cloning into cosmids or fosmids. These are then cloned into a suitable expression system such as E. coli and screened for the presence of the desired genes or pathways. Next generation sequencing further makes this techniques very powerful and enables extensive studies and mining of metagenomes. In this project we will be constructing metagenomic libraries from microbial communities to mine for genes of lignocellylose and starch hydrolyzing enzymes.
Antimicrobial discovery projects
Kwabena O. Duedu1*, Adjoa A. Boakye1, Innocent Afeke2, Peter Atadja1
1 Department of Biomedical Sciences, University of Health and Allied Sciences, Ghana
2 Department of Medical Laboratory Sciences, University of Health and Allied Sciences, Ghana
*Project Lead/Principal Investigator: Email: kduedu@uhas.edu.gh
Treatment of microbial infections requires potent antimicrobial agents. In recent years, antimicrobial drug resistance has rendered many antimicrobial agents, useless. This has led to the development ‘super bugs’ which are now a global threat. Whilst searching for ways to curb the evolution and spread of antimicrobial resistance, there is an urgent need to discover and develop new potent antimicrobial agents. Antimicrobial agents dates back to 1921 and 1928 when Sir Alexander Fleming, a Scottish Biologist made discoveries of the enzyme lysozyme and antibiotic substance penicillin (Aminov 2010). Over the years antimicrobial agents have been developed using different methods including chemical synthesis and computer aided drug design. There has recent reports of antimicrobial activity of various microbes and natural products (Motta et al. 2004; Saravanan D et al. 2012; Bizuye et al. 2013; Gebreyohannes et al. 2013; Lihan et al. 2014; Mashoria et al. 2014; Yekkour et al. 2015). We are developing a robust screening pipeline for the discovery of antimicrobials from natural products. These pipelines allow us to screen both microbes and natural products for antimicrobial activities against various pathogens.
1. Functional screening of microbial communities from the soil and forest floors for antimicrobials
This project will involve isolation of microbial communities and their screening for antimicrobial activities. Antimicrobial activities will be tested against major bacteria and fungal pathogens using standard culture techniques as well as against genetically engineered antibiotic resistant bacteria. Techniques to be used in this project will include metagenomic cloning and library construction, microbiological culture and identification, extract preparation and screening of biomolecules, high performance liquid chromatography, DNA extraction and PCR, sequence analysis and biotyping.
2. Evaluation of the effects of natural products on bacteria commonly implicated in wound infections
Traditional African medicine has a wide range of remedies for treating diseases. Among these is a poorly curated library of mono preparations as well as cocktails that are used in treating infections. In this project we will be evaluating the antimicrobial effects of some of these preparations and determine extract fractions that contain the observed activities. Techniques to be used in this project will include metagenomic cloning and library construction, microbiological culture and identification, extract preparation and screening of biomolecules, high performance liquid chromatography, DNA extraction and PCR, sequence analysis and biotyping.
Further information for applicants
Potential applicants are advised to be innovative and bold in their thinking and approaches. Our lab is equipped with good microbiological, biochemical and molecular biology facilities. Training will be provided for using any of the facilities.
References Aminov, R.I. (2010) A brief history of the antibiotic era: lessons learned and challenges for the future. Front Microbiol 1, 134. Antoni, D., Zverlov, V.V. and Schwarz, W.H. (2007) Biofuels from microbes. Appl Microbiol Biotechnol 77, 23-35. Bizuye, A., Moges, F. and Andualem, B. (2013) Isolation and screening of antibiotic producing actinomycetes from soils in Gondar town, North West Ethiopia. Asian Pacific Journal of Tropical Disease 3, 375-381.
Dale, B. (2008) Biofuels: thinking clearly about the issues. J Agric Food Chem 56, 3885-3891. de Souza, P.M. and de Oliveira Magalhaes, P. (2010) Application of microbial alpha-amylase in industry - A review. Braz J Microbiol 41, 850-861. Duedu, K.O. and French, C.E. (2016) Characterization of a Cellulomonas fimi exoglucanase/xylanase-endoglucanase gene fusion which improves microbial degradation of cellulosic biomass. Enzyme and Microbial Technology 93–94, 113-121.
French, C.E. (2009) Synthetic biology and biomass conversion: a match made in heaven? J R Soc Interface 6 Suppl 4, S547-558. French, C.E., Horsfall, L., Barnard, D.K., Duedu, K., Fletcher, E., Joshi, N., Kane, S.D., Lakhundi, S.S., Liu, C.-K., Oltmanns, J., Radford, D., Salinas, A., White, J. and Elfick, A. (2015) Beyond Genetic Engineering: Technical Capabilities in the Application Fields of Biocatalysis and Biosensors. In Synthetic Biology eds. Giese, B., Pade, C., Wigger, H. and von Gleich, A. pp.113-137: Springer International Publishing.
Gebreyohannes, G., Moges, F., Sahile, S. and Raja, N. (2013) Isolation and characterization of potential antibiotic producing actinomycetes from water and sediments of Lake Tana, Ethiopia. Asian Pac J Trop Biomed 3, 426-435.
Knothe, G. (2001) Historical perspectives on vegetable oil-based diesel fuels. Inform 12, 1103-1107.
Lakhundi, S.S., Duedu, K.O., Cain, N., Nagy, R., Krakowiak, J. and French, C.E. (2016) Citrobacter freundii as a test platform for recombinant cellulose degradation systems. Letters in Applied Microbiology DOI: 101111/lam12668 (Accepted article available online).
Lihan, S., Lin, C.S., Ahmad, I., Sinang, F.M., Hua, N.K. and Sallehin, A.A. (2014) Antimicrobial producing microbes isolated from soil samples collected from Nanga Merit Forest in Sarawak, Malaysian Borneo Eur J Exp Biol 4, 494-501.
Lynd, L.R., van Zyl, W.H., McBride, J.E. and Laser, M. (2005) Consolidated bioprocessing of cellulosic biomass: an update. Curr Opin Biotechnol 16, 577-583. Mashoria, A., Lovewanshi, H.S. and Rajawat, B.S. (2014) Isolation of antimicrobial producing bacteria from soil samples collected from Bhopal Region of Madhya Pradesh, India. Int J Curr Microbiol App Sc 3, 563-569.
Motta, A.S., Cladera-Olivera, F. and Brandelli, A. (2004) Screening for antimicrobial activity among bacteria isolated from the Amazon Basin. Brazilian Journal of Microbiology 35, 307-310. NCB (2011) Biofuels: ethical issues. London: Nuffield Council on Bioethics.
Samanta, A., Mitra, D., Roy, S.N., Sinha, C. and Pal, P. (2013) Characterization and Optimization of Amylase Producing Bacteria Isolated from Solid Waste. J Environ Protect 4, 647-652.
Saravanan D, Bharathi, S., Radhakrishnan, M. and Balagurunathan, R. (2012) Exploitation of bacteria from forest ecosystem for antimicrobial compounds. J Appl Pharm Sc 2, 120-123.
Yekkour, A., Meklat, A., Bijani, C., Toumatia, O., Errakhi, R., Lebrihi, A., Mathieu, F., Zitouni, A. and Sabaou, N. (2015) A novel hydroxamic acid-containing antibiotic produced by a Saharan soil-living Streptomyces strain. Lett Appl Microbiol 60, 589-596.
