Bi7430 Molecular Biotechnology
1. Introductory lecture
Organisation of the course
Outline
 I n t ro d u c t i o n o f c o u rs e
 C o n t e n t o f c o u rs e a n d p ra c t i c a l c l a s s e s
 L e c t u r i n g a n d e v a l u a t i o n
 Re c o m m e n d e d l i te ra t u re
 B i o t e c h n o l o g y a t M U
 E xc u r s i o n i n L o s c h m i d t L a b o ra t o r i e s
Introduction of the course
EXTENSIVE MULTIDISCIPLINARITY
PREREQUISITES:
 basic knowledge of microbiology, molecular biology, biochemistry,
immunology and genetics
COURSE FOCUSE:
 the specific aspects of modern biotechnology
 examples of up to date applications and discoveries
(industry, agriculture, pharmacy, biomedicine
and environmental protection)
 the role of modern biotechnology in
sustainable living
Sustainability
 concept of sustainability
with the aim to promote a necessary “… development that meets the
needs of the present without compromising the ability of future
generations to meet their own needs”
World Commission on Environment and Development, 1987
 reduce waste production and environmental impact
 reduce consumption of resources (e.g., materials, energy, air, water)
 increase the recycling and use of renewable materials (e.g., biomass)
Sustainability
Biotechnology
 KEY TECHNOLOGY of 21st century
ENVIRONMENTAL ASPECTS
 natural processes (bioprocesses)
 sustainable and resource efficient
ECONOMICAL ASPECTS
 1/3 of worldwide production derived from bioprocesses in 2030
 biotechnology market 300 billion EUR*
Route to the Knowledge-Based Bioeconomy, 2007
Example of sustainable technology
BIOCATALYSIS (+30°C)
1000 t penicillin G
45 t ammonia
10,000 m3 water
1 t ENZYME
(1 $/kg 6-APA)
CHEMICAL PROCESS (-40°C)
1000 t penicillin G
160 t ammonia
300 t dimethylchlorosilane
800 t N,N-dimethylaniline
600 t phosphopentachloride
4,200 m3 dichloromethane
4,200 m3 n-butanol
 hy d r o l y s i s o f p e n i c i l l i n G
LECTURES
Organization info
Content of the course
2. Basics of Molecular Biotechnology
3. Methods of Gene Manipulations
4. Protein Engineering
5. Microfludics, Lab on a Chip
6. Biofuels
7. Molecular Biotechnology in Industry
8. Environmental Molecular Biotechnology
9. Molecular Biotechnology in Agriculture
10. Molecular Biotechnology in Medicine I.
11. Molecular Biotechnology in Medicine I I.
METHODOLOGICAL
LECTURES
TECHNOLOGICAL
LECTURES
Lecturers
Doc. RNDr. Zbyněk Prokop, Ph.D. (UČO 23696)
 protein engineering, microfluidics
 biotechnological applications
 Loschmidt Laboratories, lea der of research team
 co-founder of Enantis – 1st biotech spin-off at MU
Mgr. Sarka Bidmanova, Ph.D. (UČO 77580)
 bioanalytical devices for military and environment
 immobilization and characterization of enzymes
 Enantis and Loschmidt Laboratories, research
specialist
Mgr. Táňa Koudeláková, Ph.D. (UČO 39790)
 molekulární biologie a proteinové inženýrství
 řízená evoluce, enzymové biotechnologie
 Loschmidt Laboratories, research specialist
Instructions
 bring printed copy of the slides as handouts for notes
Instructions
 bring printed copy of the slides as handouts for notes
 find all materials including printed version of the slides at
http://is.muni.cz/
 be on time, come at least 5 min before lecture starts
 please,contact me if any problem with the lecture or material
 be active and participate in discussions
Lecturing system
 powerpoint slides as well as recommended literature in English
 lecturing, discussions and examination in Czech
 2 hrs per week
 lecture part I. (45 min)
BREAK (5 -10 min)
lecture part II. (45 min)
Activities and Evaluation
 reading the original literature
 review or book chapter for each lecture
 „Lecture 02 (READING).pdf“
 four progress written tests during the lecturing period
 at the beginning of lecture 4., 6., 8., and at the end of semester
 each 10-12 questions from lectures and reading
 questions a,b,c,d type, can be cumulative with multiple answers
 duration 10 min
 final written test during examination period
 50 questions from entire course / 1 hour
Recommended literature
 M. Wink (Ed.) 2011: An Introduction to Molecular Biotechnology :
Fundamentals, Methods and Applications, 2nd Edition, Willey-Blackwell
 B. R. Glick, J. J. Pasternak, C. L. Patten 2011: Molecular
Biotechnology: Principles and Applications of Recombinant DNA ,
4th Edition, ASM Press
 J. M. Walker, R. Rapley 2009: Molecular biology and biotechnology,
5th Edition, RSC Publishing
 A. Sonnino (Ed.) 2011: IntroductIon to molecular biology and genetic
engineering, Food and Agriculture organization of the united Nations,
Rome (pdf on IS materials)
PRACTICAL LESSONS
Organization info
Content of the course
1. Design of recombinant systems (LL, MU)
2. Preparation and testing of microfluidic chip (LL, MU)
3. Fermentation of recombinant microorganisms (LL, MU)
4. Preparation of enzymatic biosensor (Enantis)
5. Biodegradation of environmental pollutant
by recombinant bacterium (LL, MU)
6. Biocatalytic preparation of pharmaceutical precursor (Enantis)
7. Preparation and transformation of liposoms (VRI)
8. Analysis of liposoms by DLS, TEM etc. (VRI)
Instructors
Loschmidt laboratories, MU
Táňa Koudeláková, Ph.D. (UČO 39790)
Lukáš Chrást, M.Sc. (UČO 269981)
Tomáš Buryška, M.Sc. (UČO 323660)
Enantis, Ltd.
Šárka Bidmanová, Ph.D.
Veronika Štěpánková, Ph.D.
Veterinary Research Institute
PharmDr. Josef Mašek, Ph.D.
Ing. Štěpán Koudelka, Ph.D.
MVDr. Pavel Kulich, Ph.D.
RNDr. Jana Plocková
Lecturing system
 INTERACTIVE SYNOPSIS available on IS
 2 hrs per week (STARTS on Wednesday 12/10, A13 entrance 2.floor)
 CAPACITY: two groups of 10 students (10:00 – 12:00, 14:00 – 16:00)
 LANGUAGE: materials EN, spoken language CZ,
protocols and essays either EN or CZ
 ABSENCE (max. 1): official excuse in IS + substitute activity - written
essay EN or CZ, two A4 pages, 1.5 spaced, TNR 12 (template on IS)
 LECTURE ORGANISATION
 assignment (HOMEWORK)
 theoretical introduction given by lecturer
 experimental work in the laboratory
 protocol submitted in one week after each practical (template on IS)
Loschmidt Laboratories, MU
B I O C ATA LY S I S
B I O D E G R A D AT I O N
B I O S E N S I N G
Protein and metabolic engineering
Koudelakova et al. 2012. Biotech. J.
Biocatalysis
Prokop, Z., et al. 2004. WO 2006079295
D r u g s
F e r o m o n e s
B r a d y r h i s o b i u m
j a p o n i c u m
Prokop, Z., et al. 2010. Angew. Chem. 49: 6111–6115
Biodegradation
Prokop, Z., et al. 2005. WO 2006128390 Prokop, Z., et al. 2006. Biotech. J. 1: 1370-1380
S p h i n g o b i u m
j a p o n i c u m
Cl
Cl
Cl
Cl
Cl
Cl
Biodegradation
 1 , 2 , 3 - t r i c h l o r o p r o p a n e ( TC P )
 c h e m i c a l b u i l d i n g b l o c k , f u m i ga n t , s o l v e n t
 p e rs i s t e n t w a t e r a n d s o i l c o n t a m i n a n t
 t ox i c , c a rc i n o g e n i c
Biodegradation
R h o d o c o c c u s A g r o b a c t e r i u m
h a l o a l k a n e
d e h a l o g e n a s e
e p o x i d e
h y d r o l a s e
h a l o a l c o h o l
d e h a l o g e n a s e
E s c h e r i c h i a
r D N A
Biodegradation
Pavlova, et al. 2009. Nature Chem. Biol. 5: 727-733 Dvorak, et al. 2014. ChemBioChem. 15: 1891-1895
p r o t e i n
e n g i n e e r i n g
m o d e l l i n g
Immobilization of pathway
Dvorak, et al. 2014. ACS Environ. Sci. Tech. DOI 10.1021/es500396r
 L e n t i K a t s ® - p o l y v i n i l a l c o h o l p a r t i c l e s
 C L E A ® - c ro s s - l i n ke d e n z y m e a g re ga t e s
Immobilization of pathway
Dvorak, et al. 2014. ACS Environ. Sci. Tech. DOI 10.1021/es500396r
 p a c ke d b e d re a c t o r
 c o l u m n 1 ( 5 0 m l , D h a A )
 c o l u m n 2 ( 1 0 0 m l , H h e C + E c h A )
 2 . 5 m o n t h s a t 2 2 ° C
 9 7 % e f f i c i e n c y fo r TC P
 9 . 7 g o f TC P d e g ra d e d i n t o t a l
Biodegradation
Kurumbang, et al. 2014. ACS Synth. Biol. 3: 172–181
 o p t i m i ze d s y n t h e t i c p a t h w ay a s s e m b l e d i n E . c o l i
 p a i rs o f d u e t v e c t o rs ( p E T D u e t , p C D F, p A C YC )
t r a n s f o r m a t i o n
Biosensing
Bidmanova, et al. 2010. Anal. Bioanal. Chem. 398:1891–1898
Modern Biotechnology at MU
R e s e a r c h
D e v e l o p m e n t
A p l i c a t i o n s
E d u c a t i o n
Molekulární biotechnologie Bi7430
 Období: podzim (každoročně)
 Rozsah: přednáška 2 hodiny/týden, cvičení 2 hodiny/týden
 Přednášky: Doc. Prokop, Dr. Koudeláková, Dr. Bidmanová
 Cvičení: Dr. Bidmanová, Dr. Koudeláková, Dr. Štěpánková, Mgr. Buryška, Mgr. Chrást
 Osnova:
 proteinové a metabolické inženýrství
 genetické inženýrství rostlin a živočichů
 molekulární diagnostika a moderní vakcíny
 buněčná a genová terapie a regenerativní medicína
 molekulární biotechnologie v průmyslu a zemědělství
Proteinové inženýrství Bi7410
 Období: jaro
 Rozsah: přednáška 1 hodina/týden
 Vyučující: Mgr. Radka Chaloupková, Ph.D.
 Osnova:
 strukturně-funkční vztahy proteinů
 metody exprese a purifikace rekombinantních proteinů
 metody strukturní a funkční analýzy proteinů
 racionální design, semi-racionální design a řízená evoluce
 příklady využití proteinového inženýrství
Bioinformatika Bi5000+Bi9060+Bi9061
 Období: podzim
 Rozsah: přednáška 2 hodiny/týden, cvičení 2 hodiny/týden
 Vyučující: prof. Mgr. Jiří Damborský, Dr., doc. RNDr. Roman Pantůček, Ph.D.,
 Osnova:
 bioinformatické databáze a jejich prohledávání
 analýza nukleotidových a proteinových sekvencí
 hledání a identifikace genů
 analýza a předpověď struktury proteinů
Strukturní biologie Bi9410
 Období: podzim
 Rozsah: přednáška 2 hodiny/týden, cvičení 2 hodiny/týden
 Vyučující: Mgr. David Bednář
 Osnova:
 struktura, stabilita a dynamika biologických makromolekul
 makromolekulární interakce a komplexy
 stanovení a předpověď struktury, identifikace důležitých oblastí
 stanovení vlivu mutace na strukturu a funkci proteinu
 aplikace v biologickém výzkumu, návrhu léčiv a biokatalyzátorů