Department of Microbial, Biochemical & Food Biotechnology ...

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Feb 12, 2013 (4 years and 4 months ago)

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Department of Microbial, Biochemical
& Food Biotechnology
University of the Free State

Thank you for considering to do your B.Sc. honours degree in this
Department of Biotechnology. In the society of today a B.Sc. degree is not
sufficient to guarantee good job prospects. Obtaining a B.Sc. Hons
qualification significantly enhances your skills and thus your employability,
preparing you for a variety of careers. A B.Sc. Hons degree also paves the
way to improving your qualifications even further by enrolling for an M.Sc.
degree, which involves full-time research in a specialist area of science.

The current department arose from the merger in 1988 of the departments of
Microbiology and Biochemistry (both founded in the early 1960s), and the
more recent merger with the department of Food Science in 2002. The
department now comprises two divisions, namely Microbiology &
Biochemistry, and Food Science (the latter division situated in the Agriculture
building). The department was awarded the status of a MIRCEN
(Microbiological Resources Centre) by UNESCO in 1996. Our MIRCEN
yeast culture collection is the largest of its kind in the southern hemisphere
and is a valuable research resource.

The division of Microbiology & Biochemistry comprises 15 academic staff
members. A particular strength of the department is the close association
between the disciplines of biochemistry and microbiology, resulting in a
dynamic interchange of ideas and expertise. Most of the academic staff in
the disciplines of microbiology and biochemistry have an NRF (National
Research Foundation) rating. This translates to our post-graduate students
being trained by nationally and internationally recognised and experienced
researchers. The focus areas of the research groups in the department
include Molecular Biology, Biotransformation, Fermentation Biotechnology,
Nanotechnology, Lipid Biotechnology & Yeast Taxonomy, Food
Microbiology, Veterinary Biotechnology, Extreme Biochemistry, High
Throughput Biology and Bioinformatics, Structural and Evolutionary Biology,
Human molecular genetics, Molecular virology.

Our B.Sc. honours programme is quite intensive, comprising several
theoretical modules, a literature review and a short research project. These
will expand not only your theoretical knowledge of the subject area, but you
will also learn to use a variety of laboratory techniques, gain experience in
the design and execution of laboratory experiments and the interpretation of
experimental results. During the course of your studies you will also acquire
the writing and communication skills that will be essential in your future
career. Our honours programme commences at the end of January and can
only be done on a full-time basis; we cannot accommodate part-time
students.
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Application for B.Sc. Honours
The applications of prospective students are screened by a departmental
selection committee before students apply for registration at UFS. Usually
you need an average mark of at least 65% in your major subject, but other
factors, such as the number of modules failed, are also taken into account.
Application forms are available from the departmental secretary or on our
website at www.ufs.ac.za/biotech.



HONOURS PROGRAMME STRUCTURE

BIOCHEMISTRY Study code 4511

Coordinator: Dr. A. van Tonder (Room 5, Biotechnology building)
Tel: 051-4012892 E-mail: vtondea@ufs.ac.za

The honours programme in Biochemistry consists of modules with a total credit value
of 128. In addition to BOC614, BOC622, BOC634, BOC674, BOC693 and BOC692
that are compulsory, students can select BOC654 or any other equivalent (credit
value) module
in Microbiology, Biotechnology, Genetics, Chemistry or any other
discipline, in consultation with the Coordinator and Departmental Chairperson.

Module code Credits
BOC614 - General analytical and chromatographic techniques
in Biochemistry 16
BOC634 - Protein structure and catalysis 16
BOC654* - Bioinformatics and Genomics 16
BOC674 - Advanced molecular biology 16
BOC622 - Oral examination of theory and practical 8
BOC693 - Research: Literature study 24
BOC692 - Research essay 32

* Or any other 16 credit module


B.Sc. Honours degree prerequisites

Biochemistry
At least 64 credits in Biochemistry at third year level. An average of 65% in
undergraduate Biochemistry modules. Admission is subject to a selection process.


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Biochemistry Syllabi

BOC614 (16 credits): General analytical and chromatographic techniques
in Biochemistry (1st quarter)
Research techniques in biochemistry: serological techniques, chromatographic,
spectroscopic and other analytical techniques for the analysis of biomolecules and
products.
BOC634 (16 credits): Protein structure and catalysis (3
rd
quarter)
Enzyme structure and the theory of catalysis: thermodynamic and kinetic principles,
mechanisms applied in catalysis. Enzyme reaction mechanisms, ligand binding and
design. Enzyme structure determination and prediction. Enzyme applications in
organic chemistry.

BOC654 (16 credits) : Bioinformatics and Genomics (2
nd
quarter)
Computational methods: databases and analysis of sequence data. The minimal
genome, genome sequencing, existing and emerging technologies, genome
annotation and metabolic pathway construction. Applications of genomics and
metagenomics

BOC674 (16 credits): Advanced molecular biology (2nd quarter)
Training in the reading and interpretation of publications in molecular biology and the
presentation of a seminar on a current molecular biology topic. The use of advanced
molecular biology techniques as well as training in computer software associated with
the analysis of DNA information. Students will also be expected to do self-study on
selected topics that are related to molecular biology.
BOC622 (8 credits): Oral examination of theory and practical (end of 4th
quarter)
The oral examination is normally scheduled for November. A panel consisting of
lecturers from the division of Microbiology & Biochemistry and including an external
examiner, is convened for this purpose. This -oral will test the general knowledge of
the student with respect to Biochemistry in general as well as aspects of the
Biochemistry Honours course. It is recommended that the student work through
course material covered previously. It is especially advisable that special attention be
paid to techniques and topics which relate to the research project.
BOC693 (24 credits): Research: Literature study (2nd and 3rd quarters).
Students carry out a literature survey, during the first semester, on a topic supplied to
them by a lecturer acting as mentor. A literature review covering the chosen topic is
written and also presented orally. The written portion of the module is evaluated by
the mentor as well as the external assessor and marks are allocated by both.
BOC692 (32 credits) Research essay (2nd – 4th quarter)
Students conduct research on a topic supplied to them during the first semester by a
lecturer acting as mentor. A written research report is prepared and also presented
orally. The written portion of the module is evaluated by the mentor as well as an
external assessor and marks are allocated by both.

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Biochemistry Honours Programme

FIRST SEMESTER

The honours programme commences towards the end of January; the date will
be communicated to successful applicants.

BOC614: General analytical and chromatographic techniques in
Biochemistry (first quarter)
BOC654: Bioinformatics and Genomics (second quarter)
BOC674: Advanced molecular biology (second quarter)
BOC693: Literature research (full year module; starts second quarter)

SECOND SEMESTER

BOC634: Protein structure and catalysis (third and fourth quarter)
BOC622: Oral exam on theory and practicals (end of year)
BOC692: Research essay (starts third quarter)


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Research Groups (Biochemistry)

For the purpose of the literature study and research for the research essay, each
student is allocated to a research group in the department. The preference of the
student will be taken into account in the placing. Students who subsequently elect to
continue with an M.Sc. study are free to switch to another research group, subject to
the availability of places in that group.

i) Extreme Biochemistry
Prof. E. van Heerden Proteomics and functional genomics of
organisms in extreme environments.

ii) High Throughput Biology and Bioinformatics
Prof. H-G. Patterton Epigenomics, mass spectrometry, proteomics
and bioinformatics.
Dr. Gabré Kemp Mass spectrometry, proteomics and small
molecule analysis.
Dr. Elize Patterton Cell aging and proteomics.

iii) Molecular Biology
Prof. J. Albertyn: Yeast and general molecular biology.

iv) Biotransformation
Prof. M.S. Smit The use of whole cells or enzymes to catalyse
specific reactions.

v) Structural and Evolutionary Biology
Dr. D.J. Opperman Determination of three-dimensional structure
of proteins by X-ray crystallography to analyze
structure-function relationships in natural
evolution and directed evolution studies.

vi) Human molecular genetics
Dr F.H. O’Neill Detection and characterisation of
polymorphisms that may affect cellular
detoxification

vii) Molecular virology
Dr. H.G. O’Neill Development of alternative rotavirus vaccines
using reverse genetics and the production of
virus-like particles in yeast


For more information on the research groups, go to www.ufs.ac.za/biotech
and click
on Divisions then on Microbiology and Biochemistry. On our home page, you may
also click on Academic Staff (at the bottom of the page) - Meet our Academic Staff for
a description of the field of interest of each academic.
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MICROBIOLOGY / BIOTECHNOLOGY

Coordinator: Prof. S.G. Kilian (Room 50, Biotechnology building)
Tel: 051-401 2780 E-mail: kiliansg@ufs.ac.za

The curriculum is compiled in consultation with the Departmental Chairperson. Studies
commence in January.

Microbial Biotechnology - Study code 4512
The honours programme in Biotechnology consists of modules with a total credit value
of 128. Apart from BTG622, BTG693, BTG692, BTG634 and BTG614/BOC614, which
are compulsory, the student must select additional honours modules from the
Microbiology, Biotechnology and Biochemistry syllabi. One 16 credit module from any
other discipline (e.g. Genetics, Chemistry or Food Science) may be chosen in
consultation with the Coordinator and Departmental Chairperson.
Modules Credits
BTG614 - Techniques in Biotechnology 16
BTG634 - Continuous and batch culture of micro-organisms 16
BTG622 - Oral exam on theory and practical work 8
BTG693 - Research: Literature study 24
BTG692 - Research essay 32
BOC634 - Enzymology 16
BOC654 - Advanced protein structure and function 16
BOC674 or MKB674 - Advanced molecular biology 16
MKB634 - Microbial diversity 16
MKB654 - Applied microbial physiology 16

Microbiology - Study code 4526
The honours programme in Microbiology consists of modules with a total credit value
of 128. Apart from MKB614, MKB622, MKB692 and MKB693, which are compulsory,
the student must select additional honours modules from the Microbiology and
Biotechnology Honours syllabi. One 16 credit honours module from any other
discipline (e.g. Biochemistry, Genetics, Chemistry or Food Science) may also be
chosen in consultation with the Coordinator and Departmental Chairperson.
Modules Credits
MKB614 - Techniques in Microbiology 16
MKB634 - Microbial diversity 16
MKB654 - Applied microbial physiology 16
MKB674 - Advanced molecular biology 16
MKB622 - Oral exam on theory and practical work 8
MKB693 - Research: Literature study 24
MKB692 - Research essay 32

B.Sc. Honours degree prerequisites

Microbiology
At least 64 credits in Microbiology at third year level. An average of 65% in
undergraduate Biology modules. These include VWS344 and BOC314. Admission is
subject to a selection process.

Microbial Biotechnology
At least 64 credits in Biochemistry or Microbiology at third year level or else in
consultation with the Departmental Chairperson. An average of 65% in undergraduate
Microbiology or Biochemistry modules. Admission is subject to a selection process.
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Microbiology / Biotechnology Syllabi

MKB / BTG614 (16 credits): Advanced techniques in Microbiology
Research techniques in Microbiology: handling and preservation of micro-organisms,
serological techniques, chromatographic, spectroscopic and other analytical
techniques for the analysis of organic compounds, Shake flask cultivation, GC &
HPLC analysis, cell breaking, bioreactor cultivation, advanced techniques in molecular
biology, centrifugation, pH measuring, microscopy, philosophy of science, project
proposal writing, chemical principles for biologists.
BTG634 (16 credits): Continuous and batch cultivation of micro-
organisms
Growth kinetics of batch cultures. Oxygen as substrate: volumetric oxygen transfer
coefficient; critical dissolved oxygen concentration. Chemostat theory: material
balances; Monod model; autoregulation; determination of kinetic and stoichiometric
parameters. Deviations from the Monod model: maintenance energy; double
substrate-limited growth; growth on mixtures of carbon substrates. Effect of growth
rate on cell composition and size. Product formation: kinetics; effect of environmental
factors. Complex chemostat systems and applications. Kinetics of fed-batch cultures.
Degree of reduction and carbon balances.
MKB634 (16 credits): Microbial diversity
Yeasts: Identification of yeasts as required for quality assurance in the brewing and
wine industry. Yeast taxonomy.
Fungi: Ecological concepts in mycology, endophytes, ecological succession, mating
types and vegetative compatibility. Taxonomy, collection, preservation and description
of fungi. Mycological techniques and the use of identification keys.
Bacteria: Bacterial nomenclature and classification. Numerical taxonomy. Serology
and chemotaxonomy. Nucleic acids in bacterial classification. Putative taxa of
prokaryotes. Polyphasic taxonomy. Chemical ecology.
Viruses: Practical aspects of the propagation of viruses and the use of PCR for the
identification of viruses.
MKB654 (16 credits): Applied microbial physiology
Food Microbiology: Physiology of food spoilage micro-organisms. The application of
micro-organisms in biological control. Food spoilage and its prevention. Mycotoxins.
The application of micro-organisms in food processing.
Microbial product formation: Principles and application of fermentative metabolism.
Metabolic regulation and its implication for microbial product formation. Industrial
processes based on microbial physiological activities.
MKB674 (16 credits): Advanced molecular biology
Training in the reading and interpretation of publications in molecular biology and the
presentation of a seminar on a current molecular biology topic. The use of advance
molecular biology techniques as well as training in computer usage that are
associated with the analysis of DNA information. Students are also expected to do
self-study on selected topics that are related to molecular biology.
MKB / BTG622 (8 credits): Oral examination in theory and practicals
The oral examination is taken in November. A panel consisting of lecturers of the
division of Microbiology & Biochemistry and which includes an external assessor is
constituted for this purpose. Students are expected to answer questions on
microbiology in general and evaluation is not limited to completed course contents.
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MKB / BTG693 (24 credits): Research literature study
Students conduct literature research on a topic supplied in the first semester by a
lecturer who serves as their mentor. A literature report is written on the topic, which is
also presented orally. The mentor as well as the external assessor for the module
evaluate the written report and both allocate marks.
MKB / BTG692 (32 credits): Research essay

Students complete a research project on a topic supplied in the first semester by a
lecturer who serves as their mentor. Students write a report on their results and also
present their work as an oral presentation. The mentor as well as the external
assessor evaluate the written report and both allocate marks.



Microbiology / Biotechnology Honours Programme

FIRST SEMESTER

The honours programme commences towards the end of January; the date will
be communicated to successful applicants.

BTG / MKB614: Advanced techniques (first quarter)
MKB654: Applied microbial physiology (second quarter)
MKB674: Advanced molecular biology (second quarter)
BTG634: Continuous and batch cultivation of micro-organisms (2nd quarter)
BTG / MKB693: Literature research (full year module; starts 2nd quarter)


SECOND SEMESTER

MKB 634: Microbial diversity (third and fourth quarter)
BTG / MKB622: Oral exam (end of year)
BTG / MKB692: Research essay (full-year module; starts third quarter)


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Research Groups (Microbiology & Biotechnology)

For the purpose of the literature study and research for the research essay, each
student is allocated to a research group in the Department. The preference of the
student will be taken into account in the placing. Students who subsequently elect to
continue with an M.Sc. study are free to switch to another research group, subject to
the availability of places in that group.

i) Molecular Biology
Prof. J. Albertyn: Yeast and general molecular
biology.

ii) Biotransformation
Prof. M.S. Smit The use of whole cells or enzymes
to catalyse specific reactions.

iii) Fermentation Biotechnology
Prof J.C. du Preez, Ms L. Steyn, Mr. D. Schabort
Microbial growth and product
formation. Production of
heterologous proteins by
genetically modified micro-
organisms. Bioethanol. Yeast
physiology. Continuous cultures.
Systems biology and metabolic flux
analysis.
Prof. S.G. Kilian Microbial physiology and
applications: Membrane transport,
hydrolytic enzymes, prebiotic oligo-
saccharides produced by microbes
and their effects.

iv) Nanotechnology, Lipid Biotechnology & Yeast Taxonomy
Prof. J.L.F. Kock Nanotechnology, lipid bio-
technology and yeast taxonomy.
Dr. C.H. Pohl Lipid metabolism of pathogenic
fungi.

v) Food Microbiology
Prof. B.C. Viljoen Characterization of food-related
yeasts, their

taxonomical status
and ecological advantages and
disadvantages.

Vi) Veterinary Biotechnology
Prof. R.R. Bragg Characterization of pathogens of
importance to animals and the
development of vaccines to
control these pathogens

For more information on the research groups, go to www.ufs.ac.za/biotech
and click
on Divisions then on Microbiology and Biochemistry. On our home page, you may
also click on Academic Staff (at the bottom of the page) - Meet our Academic Staff for
a description of the field of interest of each academic.
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SCHOLARSHIP / BURSARY APPLICATIONS

The closing date for NRF (National Research Foundation) honours bursaries is
normally towards the end of the year. Visit www.nrf.ac.za under the “student” link for
further information. Details will be provided by UFS to prospective students regarding
the application procedure and deadline for applications.

These scholarships are awarded on a competitive basis only to students of high
academic merit and who are South African citizens.
TYPE OF APPLICATION
VALUE OF AWARD
NRF Free-standing scholarship for Honours
Prerequisites: At least an aggregate of 60% in the final
year i.r.o. the relevant major subject and the degree must
have been completed in the minimum time period. An
exception is made for “black” students who may have
required an additional year.
R20 000 p.a.
NRF Innovation Scholarship for Honours
Only for Hons in Biotechnology, Cellular and Molecular
Biology, Nanotechnology
Prerequisites: At least an aggregate of 60% in the final
year i.r.o. the relevant major subject and the degree must
have been completed in the minimum time period. An
exception is made for “black” students who may have
required an additional year.
R35 000 p.a.
NRF Scarce Skills Scholarship for Honours
Only for Hons in Biotechnology or Agricultural Sciences.
Prerequisites: At least an aggregate of 60% in the final
year i.r.o. the relevant major subject and the degree must
have been completed in the minimum time period. An
exception is made for “black” students who may have
required an additional year.
R35 000 p.a.

The above information is subject to change on short notice.

The Faculty usually provides limited funds to be used for scholarships. It is the policy
of the Dept. of Microbial, Biochemical & Food Biotechnology that these scholarships are
preferentially awarded to honours students who do not qualify for NRF bursaries due to
race or citizenship. These faculty scholarships will be of a lower amount than the above
NRF scholarships.
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CONTACT DETAILS



Department of Microbial, Biochemical & Food Biotechnology
University of the Free State
P.O. Box 339
Bloemfontein 9301



Biochemistry
Coordinator: Dr. A. van Tonder (Room 5, Biotechnology building)
Tel: 051-4012892 E-mail: vtondea@ufs.ac.za


Microbiology / Biotechnology
Coordinator: Prof. S.G. Kilian (Room 50, Biotechnology building)
Tel: 051-4012780 E-mail: kiliansg@ufs.ac.za





Departmental Chairperson: Prof. J.C. du Preez
Tel: 051-401 2396
Fax: 051-401 9376
E-mail: dpreezjc@ufs.ac.za

Website: www.ufs.ac.za/biotech