3rd Year Biotechnology Microbiology Course

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12 Φεβ 2013 (πριν από 4 χρόνια και 9 μήνες)

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3rd Year Biotechnology Microbiology Course


Course coordinator:
Dr. Tom Barry

Phone Ext.
3189

e.mail:
thomas.barry@nuigalway.ie


1: THIRD BIOTECHNOLOGY MICROBIOLOGY LECTURE TIME TABLE




Monday

12
-
1 pm.


Tuesday

2
-
3 pm


Wednesday

12
-
1 pm


Thursd
ay

9
-
10 am


All lectures are held in the Tyndall Lecture Theatre, Dept. of Microbiology, NUIG.



2: THIRD SCIENCE MICROBIOLOGY PRACTICAL COURSE TIMETABLE:



Tuesday

3
-
6 pm


Thursday

10
-
1 pm


Upstairs and downstairs practical laboratories, Dept. of
Microbiology, NUIG.



Semester 1 Lectures


1: INTODUCTION: DR. T. BARRY
-
Sept. 8
th
(2pm)


This lecture is designed to provide students with an overview of the third year course
both theoretical and practical for Semester I and Semester II. Also covered
are the
requirements and standards that students must attain at the end of third year in order
to successfully enter fourth year microbiology. Relevant topics for discussion are
lecture timetable, practicals, continuous assessment, examination questioning
and
answering, examination marking breakdown, quality review of the course, etc.



2: FOOD MICROBIOLOGY

DR. C. O’BYRNE (10 LECTURES).

Sept. 9
th
to 24
th


Lecture 1:

Historical overview of food microbiology.
The role played by

Antony
van Leeuwenhoek and
Louis Pasteur in identifying the link between
microorganisms and processes of decay and putrefaction. The theory of
spontaneous generation.


Lecture 2:


Microbiology of beer production.
The process of beer production:
Malting, milling, mashing, wort boilin
g, fermentation, post
-
fermentation treatment. Biochemical changes that take place during the
fermentation.


Lecture 3:


Microbiology of wine production.
The producing process for red and
white wine: Crushing, partial fermentation (red), removal of grape
so
lids, fermentation, racking off, malolactic fermentation, fining and
clarification. Contribution of yeasts and bacteria to the flavour of the
wine. Microbiological quality problems in wine.


Lecture 4:

Microbiology of cheese production.
An overview of
the cheese
making process. Production of curds: the biochemistry of milk
coagulation, the role of the starter culture. The role of the secondary
flora in producing flavour and texture in cheese. Problems with
bacteriophage. Bacteriophage resistance mechani
sms in lactic acid
bacteria.


Lecture 5:

Factors that influence the growth of microorganisms in food.
The
inhibitory basis for high salt (low water activity), low pH, extremes of
temperature and REDOX potential.


Lecture 6:

Food poisoning 1.
Definitions of
food
-
borne infections, intoxications
and toxicoinfections.

Food
-
borne disease statistics from the US. Key
microorganisms implicated in food
-
borne disease. Relative importance
of bacteria, viruses and fungi.


Lecture 7&8:

Food poisoning 2: Food
-
borne intox
ications.
A closer look at
selected bacterial agents implicated in food borne intoxications:
Staphylococcus aureus, Closteridium botulinum
. Fungi involved in
food
-
borne intoxications.


Lecture 9:

Food poisoning 3: Food
-
borne infections.
Campylobacter
and

Salmonella.


Lecture 10:

Food poisoning 4: Food
-
borne toxicoinfections.
Bacillus cereus
and
Closteridium perfringens.



Recommended text:
Microbiology of Foods by Ayres, Mundt and Sandine,



Freeman & Co. (Most recent edition)



or

Modern Food Microbiology by J.M. Jay, Van Nostrand (Most recent edition)



3. INDUSTRIAL MICROBIOLOGY AND APPLIED STERILITY/ASEPSIS


Dr. GERARD FLEMING (10 LECTURES). Oct. 7
th
to Oct. 22
nd



Lecture 1: The Scope:
This course seeks t
o introduce students to those aspects of
applied microbiology which they are likely to encounter in microbially
-
based/medicare industries. Knowledge of the techniques of sterilisation and
inhibition are essential for good practice in any microbiology labo
ratory.


Outline of major groups of industrial fermentations.


Lecture 2: Research, development, and scale
-
up:




Typical objectives
-
qualitative and quantitative (titre, yield and
volumetric productivity) , and restraints.


Primary and secondary screenin
g
-
the use of shake flasks,lab.
fermenters and pilot plant. New approaches to screening.


Lectures 3 and 4: Organisms:


Choice and storage.

Process improvement by strain selection
-
avoiding induction,


repression and inhibition
-
use of auxotrophs


Lecture 5: Media:


Economic considerations
-
crude v defined
-
carbon sources
-

nitrogen sources
-
vitamins and growth factors
-
minerals
-
inducers
-

precursors
-
inhibitors.


Lecture 6 and 7: Process m
anipulation:


What is a bioprocessor (fermenter)
-
pH, temperature,
foam/antifoams and agitation/aeration.



Industrial batch cultures
-
inoculation development and
fermentation build up
-
when to harvest
-
fed batch cultures


Continuous cultures with and w
ithout recycling.


Lecture 8: Sterility and Asepsis
-
Definitions and reasons:


Why bother?


Tackling the problem
-
organisms,treatment and environment.


Lecture 9: Basic heat treatments:


Basic kinetics
-
k and nabla
-
effect of spores and mixed population
s


Steam and its characteristics
-
the danger of steam/air mixes,


Autoclaves, basic and advanced
-
autoclave monitoring.



Lecture 10:

Large (industrial) scale heat sterilisation:


Moist heat sterilisation and industrial fermentations
-
the options.


Desig
ning batch sterilisation for large volumes of themolabile
liquids (Richards’rapid method).


HTST (high temperature/short time) treatments, theory and practice
-
continuous sterilisers and pasteurisers.


Sterility, asepsis, and fermenter design and operat
ion.


Sterilisation by radiation / Disinfectants and antiseptics


Uses of UV and non
-
ionising radiation.

Filtration

Depth and absolute filters
-
filter testing. Types and uses.


Ethylene oxide (gas) sterilis
ation.



Recommended Text:
Principles of Fermentation Technology by P.F. Stanbury, A
Whitaker and S.J. Hall (2nd ed.) Pergamon Press, 1995.




4. AQUATIC MICROBIOLOGY

Dr. TOM BARRY (5 LECTURES). OCT

27
th


to NOV 3
rd


Lecture 1:

Microbial Ecology of Aqu
eous Environments
. Uses, sources and
barriers to the use of water. Categories of pollutants. Water bacteria. Water as a
vector of disease. Typical water
-
borne diseases caused by bacteria and viruses.


Lecture 2:

Biological Indicators of Pollution
. M
embrane Filtration / MPN
methodologies for detection of indicator organisms. Emerging rapid technologies for
enumeration and confirmation including Idex, MUG agar and Biolog systems. Water
standards.


Lecture 3 /4: Eutrophication
. Causes and effects.
Ogliotrophic v’s eutrophic lakes.
Production and respiration. Seasonal / temperature effects. Roles played by N and P
in eutrophication.


Lecture 5:

Physical Methods for Detection of Pollution
. TOC and COD
estimation. Principle of BOD test. Determinat
ion of BOD using gold
-
standard
Wrinkler method and D.O. meter. Troubleshooting. BOD water standards.



SEMESTER II LECTURES


5:

VIROLOGY

Dr. G. WALL (8 LECTURES).

Jan. 11
th
to Jan. 21
st
.


Lecture 1

How we classify viruses. Virologists use viral chara
cteristics such as genetic material
to put them into different classes / divisions. Students are introduced to the Baltimore
scheme of classification.


Lecture 2

The oncogenic viruses. How the
identification o
f viral oncogenes has helped to
define
the mole
cular basis of cancer
. Students are introduced to the functions of proto
-
oncogenes. We examine some specific viruses involved in the development of cancers
and a description of changes in the cell in tumour development.



Lecture 3

An examination of the as
sociation between infection with Epstein Barr virus and the
development of Burkitt’s lymphoma and nasopharangeal carcinoma. The relationship
between viruses and cervical cancer.



Lectures 4 & 5

The processes that ‘switch on’ oncogenes turning a proto
-
onco
gene into a cellular
-
oncogene. We examine the actions of chronic transforming retroviruses, chromosomal
transformation (using chronic myeloid leukaemia as a model) and activation by point
mutation.


Lecture 6

We use bladder cancer to illustrate point mutat
ions in oncogene activation. How lung
cancer can arise. The consequences of amplification and deletion of proto
-
oncogenes.
We also explore tumour
-
suppressor gene activity.


Lectures 7 & 8

Oncogene re
-
arrangements. The
f
unctions
of oncogene and proto
-
oncoge
ne p
rotein

p
roducts
and how they each contribute to the multi
-
step process of the development of
a cancer.


6:

BASIC AND APPLIED IMMUNOLOGY
-
PROF. A. MORAN (12
LECTURES).

Feb. 8
th
to Feb. 25
th
.


Lecture 1: Non
-
specific immunity (1):
Genetic resistance, s
train resistance,
physiological state of the host, mechanical and chemical barriers and the
protective role of host flora. Phagocytosis: macrophages and polymorphs.



Lecture 2: Non
-
specific immunity (2):
The process of phagocytosis. Inflammation:
acute an
d chronic.


Lecture 3: Non
-
specific immunity (3)
: Antimicrobial factors. Complement: role,
classical pathway and alternative pathway. Interferons.


Lectures 4 & 5: Acquired immunity
: Introduction. Actively acquired vs. passively
acquired. Development of th
e immune response. Properties of antigens: structure,
immunogenicity, adjuvants, haptens. Properties of antibodies: general structure
and antibody classes. Kinetics of the immune response.


Lecture 6: B cell activity in humoral immunity:
B cells. B cell di
fferentiation.
Polyclonal and monoclonal antibodies. Basis of antibody diversity.


Lecture 7: Cell
-
mediated immunity
: T cells: properties, antigen recognition and
role. Effector and regulator T cells. Lymphokines.


Lecture 8: Hypersensitivity
: Antibody
-
med
iated allergy, antibody
-
dependent
cytotoxicity/cytolyticity, immune complex disorders, delayed hypersensitivity.


Lectures 9 & 10: In vitro antibody tests (1)
: Conditions influencing reactions,
diagnosis of disease, other applications. Agglutination test:
slide agglutination,
tube agglutination, and haemagglutination.


Lecture 11: In vitro antibody tests (2)
: Precipitin tests: ring test, single diffusion
and double diffusion methods. Immunoelectrophoresis.
(3):
In vitro antibody
tests.


Lecture 12: Radioimm
unoassay
, enzyme
-
linked immunosorbent assay, complement
fixation tests, immunomicroscopic techniques.




Practicals (Semester 1 only)


a) Food Microbiology (5 Practicals)

b) Genetic Engineering (5 Practicals)

c) Industrial Microbiology (2.5 Practicals)


Total Practicals (12.5)





Examination




1 x 3 h examination in Spring (70%)



Written practical examination at the end of Semester I or early
Semester II (30%).