At the end I have also included a summary the work that I have done as post-degree student at the University of Waterloo.
Undergraduate Research project: I explored the distribution and biochemistry of the killer phenomenon in industrial strains of Saccharomyces cerevisiae. Killer yeasts secrete polypeptide toxins that are fatal to other yeast strains, often of the same species as the one producing the killer toxin. The toxin is produced from genetic information carried by a linear double stranded RNA plasmid, designated as M. This plasmid is maintained by another double stranded RNA plasmid designated as L. To assess the potential impact of this phenomenon on the wine making industry, a survey of wine making yeasts wasperformed. Furthermore, the evolutionary origins of this toxin wereexplored by comparing codon usage in the killer M plasmid to that of several yeast genes. The results indicated that some potentialkiller yeast strains existed in the collection surveyed. However, attempts to prove this by analytical methods failed to yield any toxins.According to codon usage, the double stranded RNA plasmid is notrelated to yeast, and therefore represents the involvement of aforeign species in the evolution of yeast. For the undergraduate research project I worked onmy own without supervision for a semester, in addition to myother courses. At the end of the semester I submitted a paper,which was reviewed by three professors. Also I had to present mywork at a formal defense, which was attended by both studentsand faculty.
Molecular Genetics: This course explored the chemical nature of genetic material, transcription, and the control of gene expression. DNA cloning and the use of recombinant DNA molecules in modifying gene expression. In this course we were introduced to many techniques. These include the electrophoretic analysis of cellular proteins, we explored the amino acid substitution present in human sickle cell hemoglobin, and yeast ribosomal proteins. We also used radioactive isotopes and actinomycin D to compare the lifespans of twomRNA, one bacterial and one mammalian. Also in vitro transcriptionwas done using a crude nucleic preparation, which we made fromDrosophila and calf liver tissue. In this course we also comparedthe induction of tyrosine in Neurospora crassa by D-phenylalanine and a racemic mixture of ethonine with the induction of Beta--galactosidase in Eschericia coli with lactose. I also extractedand purified DNA and RNA, using SDS-chloroform and SDS-phenolrespectively. In another experiment I transformed an ampicillin-sensitivestrain of bacteria a resistant one, by the introduction of an R-plasmid. Using nucleic acids we were introduced to polyacylamideand agarose gel electrophoresis; something I later used in myresearch project. We also used restriction endonucleases to map lamda-phage DNA. The last experiment was DNA sequencing whichwas just demonstrated to us.
Applied Molecular Genetics: Genetic aspects of Biotechnology: Mutant selection, cell fusion, and gene expression in microbial hosts forthe production of industrially, agriculturally, and clinically significant gene products. Genetic engineering in eukaryotes andthe development of transgenic organisms. In the laboratory wetransformed yeast by introducing a plasmid in to the cell, splicednew DNA into a plasmid using restriction enzymes, and used it to transform E. coli. Then we again used restriction enzymes and agarose gel electrophoresis to analyze the plasmids. In thiscourse we also used agrobacterium to introduced novel DNA into a plant. We also used cell fusion on plant cells. The course also included using antibody affinity Chromatographyto purify Beta-galactosidase. We later tested the extractedprotein with antibodies and polyacrylamide gel electrophoresis.
Engineering Biotechnology: This course examined the application of engineering techniques to biotechnological processes. Areascovered included the use of chemical and biological reactions,kinetic models and system specific equations for mass transfer.We also compared the differences between batch and continuousflow reactors. Also covered was the measurement and control of the process, and the sterilization of bioreactors. As well as the estimation of equipment costs.
Concepts of Cell Culture: This course covered various techniques of cell culture. This included tissue, and cell culture of animals and plants. Topics covered included monoclonal antibodies, and tissueplasminogen activator. More importantly in the laboratory we preparedplant callus cultures and regenerated them back into whole plants.Cell culture was also used as a method of examining differentiationand cancers.
Analytical Biochemistry: This course covered the general topicof the purification of biomolecules. In the laboratory we did theBradford protein assay. We also precipitated the crude protein fractionof milk, and used it for anion exchange chromatography to extractalpha-lactalbumin. After that we purified the protein using gel filtration, then SDS-PAGE. Then we determined the pI ofthe protein. After which we hydrolyzed the protein and used thinlayer chromatography (both one and two dimensional) to determine its amino acid composition. We then studied the effect of alpha-lactalbumin on lactose synthase activity. In the secondpart of the course we isolated genomic DNA from chicken blood,and plasmid DNA from E. coli. Then we analyzed restrictionfragments of the DNA using Southern blotting and agarose gelelectrophoresis. We then used a non-radioactive probe to search for vitellogenin gene on the Nytran membrane from the Southern blot.That probe was vitellogenin DNA labeled with digoxigenin-dUDP.
Applied Biochemistry: This course covered the isolation, processingand application of carbohydrates, lipids, amino acids, proteins, enzymes, antibiotics, and vaccines in industry, medicine, and scientific research. Emphasis was placed on the innovative procedures for the exploitation of living cells.
Membrane Biochemistry: This course examined the cell membrane onthe molecular level, covering the structure and function of cellmembranes, cell surfaces, and the associated structures.
Metabolic Processes: This course was a detailed treatment of majormetabolic patterns in prokaryotic and eukaryotic systems. It covered glycolysis, the citric acid cycle, the catabolism offatty acids, and so on.
Microbial Technology: This course studied how the metabolism of microorganisms can be manipulated to produce goods and services.The means by which the yields of secondary metabolites, enzymes,and genetically selected products can be maximized were covered.Examples of specific processes were examined. As part of therequirements for this course I gave a seminar on the use ofcellulose wastes as substrate for certain fungi, which in theorycan be used as a feed stock for domestic animals.
Techniques in Microbiology: This course consisted mostly of laboratory work. We studied the kinetics of microbial cell growth,cell harvesting, cell disruption, separation, and the biochemicalanalysis of cell constituents. It was an open laboratory coursewhere in addition to the regular hours, we went in when we had the time to get the work done. The cell studied was Erwinia herbicula.
Industrial Microbiology: This course covered the fundamental andapplied aspects of industrial processes: yeast and bacterial anaerobic fermentations; vitamins and commercial enzyme productions;antibiotics; single cell protein; and utilization of industrialand agricultural wastes.
After I took this course the professor teaching it retired. His replacement in subsequent semesters tried some changes that included the addition of a lot of food microbiology material I was asked, by the new professor, to sit in on the lectures and and give him an opinion as to how well he was doing compared to previous years. I was happy to give him a positive review; although some of the weaker students were complaining about the heavy work load, the new version of the course was excellent.
Structure and Function in Biochemistry: This course was a survey thatcovered many aspects of biochemistry without too much detailbeing given on any particular one.
Microfungi: This was a survey course that covered the taxonomy, growth physiology, genetic systems and application of important yeasts and filimentous fungi. The course emphasized the classification, and nomenclature of yeasts.
Bacterial Physiology: This course covered the nature and structureof bacterial cell walls, and membranes. It covered the cytology,growth, as well as the influence of the physical and chemical environment on growth.
Introductory Biochemistry: This course gave a broad overview of biochemistry. It gave some coverage of enzyme structure, kinetics,and function, as well as an introduction to metabolism.
Introductory Genetics: This gave a general over view of Genetics.
General Microbiology II: In this course we studied the growth andadaptation of microorganisms, with an emphasis on basic physiologicalprocesses and factors affecting growth. The role of microorganismsin the natural cycles of elements was the subject of experimentationin the laboratory. The diversity of metabolic types was demonstrated byconsideration of phototrophic and autotrophic bacteria as well asmicrobes growing in extreme environments. Basic microbiological techniques were stressed; such as the microscopic examination,isolation, enumeration, and growth, of microbes was studied. Thelecture section tended to cover mostly the cell walls, membranes,and extracellular polysaccharides.
General microbiology I: This was an introductory course, it wassimple yet fun.
Introductory Biology: This was a survey course that coveredsome of everything from horticulture to microbiology. It wasa fun course.
Other Courses of Possible Interest:
Principles of disease: this course gave me a general overview of the medical aspects of human biology.
Soil Science: An agricultural course That I took as an elective, it covered in a general manner the quality of soil needed for crops, and how to care for the soil. Topics covered included the origin ofsoils , as well as their classification and interpretation in a modified environment. The course covered how soils were formed as a productof the natural environment, and the changes that would occur as they aremodified with use.
Beverage Management: This course covered the wine and spirits industry. It placed emphasis on the knowledge required forpurchasing, pricing, and quality control. It was a fourth year business course.
Beverage Technology: this course covered the production of beverages from soda pop to wines and spirits. It was a sciencecourse and covered a lot of material in detail.
Fundamental Chemistry I
Fundamental Chemistry II
Organic Chemistry I
Organic Chemistry II
Inorganic Chemistry I
Analytical Chemistry I
Analytical Chemistry II
Molecular Kinetics
Physical Chemistry I
Functions and Relations
Calculus I
Calculus II
An Introduction to Mechanics
Fundamental Laws of Physics
General Astronomy
Medieval Britain
Witchcraft, Folk Belief, and Popular Culture
The Emergence of Modern Russia
Critical Thinking
5000 Days
Post-degree work,
Fermentation Biotechnology:
This course covered the biology of industrial micro-organismsand the fermentation systems in which they are used. The raw materialsused, and the desired properties of them was covered. We studied the downstream processing of fermentation products. Areas that were emphasizedincluded the production of industrial chemicals, food additives, and enzymes.
Metabolism 1:
This course covered the metabolism of carbohydrates, lipids, and amino acids.
Metabolism 2:
The topics covered included the properties and metabolism of porphyrins, the synthesis and degradation of purines, and pyrimidines and biogenic amines. Also covered were the structural aspects of enzyme activity, as well as control and transportation mechanisms.
Patrick J. Cummings Post Office Box: 90619Tsim Sha TsuiHong Kong (SAR, China(p-cummin@calum.csclub.uwaterloo.ca)