Midterm Flashcards
1
Q
Define industrial bioprocessing (biotechnology)
A
any commercial technique that uses living organisms or substances from those organisms to make or modify a product, to improve plants or animals, or to develop microorganisms for specific uses
2
Q
When did Van Leeuwhenhoak observe yeast cels in alcohol fermentation?
A
1680 AD
3
Q
What are the 3 stages of industrial bioprocessing?
A
- upstream processing
- fermentation
- downstream processing
3
Q
Define allogeneic
A
cells from antigenically-matched donor
4
Q
What are the 5 common properties of all industrial bioprocesses?
A
- produce a product in demand and has value
- active cells should function as intended consistency from batch to batch
- raw materials used to grow the cells should also be consistent and a high quality
- process steps should be consistent
- product should meet critical quality attributes (CQA) and be stable under shipping/storage conditions and maintains quality
- cost of goods (COGs) to make product should be low enough to make projected profit
5
Q
Define autologous
A
cells from patient to be treated
7
Q
When did Cagniard-Latour, Schwann, Kurtzing hypothesize living cells?
A
1837 AD
8
Q
The did Pasteur show living yeast cells ferment sugar to ethanol and CO2?
A
1857 AS
9
Q
When did Darwin publish the origin of species?
A
1859 AD
10
Q
When did Pasteur note the relationships between microbes and disease?
A
1877 AD
11
Q
When did Koch develop microbial technique and maintenance methods?
A
1881
12
Q
When was the 1st commercial production of lactic acid by anaerobic fermentation?
A
1881
13
Q
When did the UK produce acetone and butanol by anaerobic fermentation?
A
1881
14
Q
When did Flemming demonstrate that mode contamination of bacterial cultures causes bacterial death?
A
1929
15
Q
When did Florey & Chain isolate Penicillin, elucidated structure and demonstrated its bacterial properties on Gram positive bacteria?
A
1940
16
Q
When did Watson and Crick discover double helix structure of DNA?
A
1953
17
Q
When did Paul Berg & Colleagues isolate the first plasmid bacterial cloning vector and showed that it was self-replicating and separate from chromosomal DNA?
A
1971
18
Q
When did Boyer and Cohen start collaborating to develop a method to enable bacteria to take up plasmid DNA?
A
1972
19
Q
When did Boyer & Cohen isolate a new cloning vector pSC101 & create bacterial intra and inter species rDNA?
A
1972-1973
20
Q
When did John Morrow and colleagues clone & propagate ribosomal DNA genes from a eukaryote in E. coli?
A
1973
21
Q
When did Genetec start?
A
1976
22
Q
When did Sanger dideoxycytidine chain-termination DNA sequencing method develop becoming a standard method?
A
1977
23
Q
When did US supreme court rule that genetically engineered microorganisms can be patented?
A
1980
24
Q
When did Genetec develop recombinant hGH in E. coli?
A
1981
25
When did Eli Lilly get 1st ever FDA approval of a recombinant product insulin (humulin) in E. coli?
1982
26
When did PCR developed by Kary Mullis at Cetus Corp. and would go on to revolutionize rapid DNA sequencing?
1983
27
When did Kohler and Milstein produce monoclonal Ab in hybridomas in and win a Nobel prize?
1984
28
When did recombinant met-hGH somatropin produced in E. coli buy Genetec approved in USA?
1985
29
When did orthclone OKT3 (muoromonab-DCD3) produced in hybridoma cell line was the first mAb approved by the FDA?
1985
30
When was the 1st recombinant drug made in CHO cells was tissue plasminogen activator and approved by the FDA?
1987
31
When was the first approved gene therapy clinical trial was carried out, resulting in partial rostral of immunity which was temporary?
1990
32
When was recombinant erythropoietin made in CHO cells by Amgen was approved by the FDA for anemia treatment by the FDA (brands Epogen and epocrit)?
1990
33
When was the first commercialized genetically modified crop tomato marked by cal gene?
1994
34
When was dolly the sheep the first mammal successfully cloned at the Roslin institute in Scotland?
1996
35
When were improvements in clonal stability/better vectors, media optimization and feeding strategies improved?
late 1990s - early 2000s
36
When was sequencing of the whole human genome completed?
2003
37
When was anti-thrombin the first recombinant protein produce din the transgenic animals/goats was approved by the EMEA?
2006
38
When was the first recombinant protein vaccine against Newcastle disease virus made in plant cell culture transgenic tobacco approved by the USDA?
2006
39
When was the Craig centre institute (California) created the first synthetic cell by inserting the genome of Mycoplasma mucoides into the empty cytoplasm of related bacterium?
2010
40
When was the whole genome sequence of CHO K1 was published?
2011
41
When was the first manufactured set cell product prochymial Osiris therapeutics approved by health Canada for GvHD?
2012
42
When were Spanish researchers successfully reprogrammed mouse stem cells into iPSD and were first to grow iPSC in pretri plates?
2013
43
When was Japanese health agency approve the first use of stem cells in human clinical trials?
2013
44
When was GINTUIT the first allogeneic cell-based product approved by the FDA?
2012-present
45
When was the first autologous and genetically modified t-cel treatment - personalized medicine?
2017
46
When was ALOFISEL the first allogeneic stem cell treatment approved in the EU?
2018
47
Define primary metabolites
metabolites produced during active growth (Trophophase) and required for growth and maintenance of cellular functions
48
Define secondary metabolites
metabolites which are not required for growth and maintenance of cellular functions and are an end product of the primary metabolism
49
What phase is secondary metabolites normally produced in?
stationary phase (idiophase)
50
Define cellular therapeutics
cells, single or multi-cellular on a matrix are the product
51
What are the phases of cell growth?
lag, exponential, stationary, death phase
52
Who developed ABE fermentation?
Chaim Weizman
53
What is a similarity and a difference of how ABE fermentation is carried out to how yeast ferments sugars for ethanol?
- similar mechanism
| - different that organisms are strictly anaerobic in ABE
54
What is the class of bacteria usually carrying out ABE fermentation?
clostridia
55
What are the 6 stages of the biopharmaceutical research and development process?
1. basic research
2. drug discovery
3. pre clinical
4. clinical trials (phase I, II, II)
5. FDA review
6. post-approval research & monitoring
56
What is the relationship between product value and volume?
high volume, low value product
| low volume, high value product
57
What are the 6 things that determine the economics of fermentation?
- cost of raw materials
- utilities
- labour and maintenance
- fixed charges
- working capital charges
58
When a product is in very high demand annually, what happens to the price?
decreases significantly
59
When the production cost is high, what is the fermentation titre?
low
60
When using high-quality materials, what happens to labour and depreciation costs?
both decrease (because need less purification)
61
What is the next step after the initial evaluation of market demand, cell titre vs. cost and value of certain bio products?
deciding on the cell expression system
62
What are the 10 important elements in choosing an industrial cell expression system?
1. type of product
2. route of product biosynthesis should be well characterized
3. are you going to develop (growth conditions, metabolic engineering) an optimized cell line in-house, license out development, or license an existing cell production platform?
4. cell line should be stable during the projected time course of a full-scale fermentation (upstream process) & also during dry-storage
5. ability to grow in a low cost defined medium with limited addition of vitamins and other growth factors is a plus but not always possible (eg. mammalian cells)
6. amenability to genetic manipulation is desirable, especially in the case of recombinant processes.
7. safety, non-pathology and toxicity
8. a cell line that has well-established regulatory acceptance in the industry is optimal (eg. E. coli, CHO)
9. readily harvested from fermentation, if product is intracellular - readily breakable to release product
10. acceptable cell-related impurities profile to make product purification easier (downstream processing)
63
What is the benefit to in-house development of an optimized cell line?
control over OP and R&D
64
What is the downside to in-house development of an optimized cell line?
takes longer
65
What is the benefit to licensing a cell production platform?
takes less time
66
What is the downside to licensing a cell production platform?
high licensing fees
67
Are mAb glycosylated?
yes
68
Are multivalent vaccine (flublok) glycolsylated?
yes
69
Is insulin glycolsylated?
no
70
Is a difficult to express protein glycosylated?
No/yes
71
Is immunotherapy glycosylated?
yes
72
Is regenerative medicine glycosylated?
yes
73
Is mAb a secreted product?
yes
74
Is multivalent vaccine (flublok) a secreted product?
yes
75
Is insulin a secreted product?
No
76
Is a difficult to express protein a secreted product?
yes
77
Is immunotherapy a secreted product?
N/A
78
Is regenerative medicine a secreted product?
N/A
79
What cell type is used to produce mAb?
mammalian
80
What cell type is used to produce multivalent vaccine (flublok)?
insect
81
What cell type is used to produce insulin?
bacterial
82
What cell type is used to produce difficult to express protein?
yeast
83
What cell type is used to produce immunotherapy?
T-cell
84
What cell type is used to produce regenerative therapy?
stem-cells
85
What is a recommended cell/expression system for mAb?
CHO/fed-batch
86
What is a recommended cell/expression system for multivalent vaccine (flublok)?
SF9/baculovirus vector/fed-batch
87
What is a recommended cell/expression system for insulin?
E. coli/fed-batch
88
What is a recommended cell/expression system for difficult to express proteins?
P. pastoris/fed-batch
89
What is a recommended cell/expression system for immunotherapy?
human CAR-T/cell factory or fed-batch
90
What is a recommended cell/expression system for regenerative medicine?
induced pluripotent see cells (iPSC)/cell factory or fed-batch
91
What is the cell system rational for mAb?
- well characterized
- excellent yields
- many regulatory approvals
92
What is the cell system rational for multivalent vaccine (flublok)?
- multiple proteins can be made
- low immunogenicity
- moderate # reg approvals
93
What is the cell system rational for insulin?
- well characterized
- excellent yields
- many regulatory approvals
- cheap raw materials
94
What is the cell system rational for difficult to express proteins?
- excellent yields
- human glycosylation, some strains
- generally regarded as safe
- cheap raw materials
95
What is the cell system rational for immunotherapy?
- CAR-T cells are product
- specific targeting
- autologous or allogeneic
96
What is the cell system rational for regenerative medicine?
- iPSC are product
- cytodifferentiation
- tissue replacement
- personalized medicine
- autologous or allogeneic
97
What are 9 examples of targets for improving cell lines?
- growth rate
- genetic stability
- non-toxicity to humans
- cell size
- ability to use cheaper substrates
- modification of submerged morphology
- elimination of production of compounds that interfere with downstream processing
- permeability alterations to improve product secretion
- tagging protein products
98
What are some ways that make growth rate a target for improving cell lines?
optimizing growth rate by cell type or clone screening or culture conditions
99
What are some ways that genetic stability can be targeted to improve cell lines?
plasmid expression vectors that are maintained efficiently during culture in bacterial cells, or integrate in a stable manner into transcription hot spots in genomic DNA of mammalian cells
100
Why is cell size a target for improving cell lines?
larger cells are more easily separated from culture fluid at the end of culture, mammalian cells are easier to separate from broths than bacterial cells
101
Why is the ability to use cheaper substrates a target for improving cell lines?
cells that use minimal medium are best for processing efficiency (process control, analysis)
102
Who is the modification of submerged morphology mostly a concern for in improving cell lines?
fungi
103
Define cell culture medium
a liquid or gel designed to support the growth of microorganism, cells or small plants
104
How does cell culture media regulate the cell cycle?
because comprised of an appropriate source or energy and compounds to do that
105
What are the 7 main factors that affect the final choice of individual raw materials for culture media?
- cost and availability
- ease of handling
- sterilization requirements/potential denaturation
- formulation, mixing, complexing and viscosity characteristics
- levels and range of impurities
- health and safety implications
- thermal damage
106
Why does cost and availability affect the final choice of individual raw materials for the culture medium?
ideally the materials should be inexpensive, consistent quality and year-round availability
107
Why does ease of handling affect the final choice of individual raw materials for the culture medium?
associated with transport and storage costs (eg. temperature control requirements)
108
Why are inorganic salts added to media?
helps retain the osmotic balance and help in regulating membrane potential by providing sodium, potassium, and calcium ions and ions for cell attachment and enzyme cofactorsW
109
What are 3 things that are added to a media for metabolism (ie. building cellular structures)?
carbohydrates, nucleic acids, and amino acids
110
Why are vitamins, trace elements and lipids added to media?
metabolism and enzyme function
111
Define BSA
bovine serum albumin
112
Why is BSA added to media?
ruch source of growth factors and appropriate for cell cloning and growth of fastidious cells
113
What percentage does normal growth media often contain of BSA?
2-10%
114
What are the 8 functions that supplementation of media with fetal serum serves?
- provides basic nutrients
- provides growth factors and hormones (growth promotion and special cell function)
- provides several binding proteins to carry other molecules into cel (eg. albumin, transferrin)
- supplies proteins like fibronectin to promote attachment of cells to substrate and spreading factors to help cells spread out before division
- provides protease inhibitors (protects from proteolysis)
- provides minerals
- increases viscosity of medium (protects cells from mechanical damage)
- acts as buffer
115
What are the 6 advantages of serum in media?
- contains growth factors and hormones stimulating cell growth and functions
- helps attachment of cells
- acts as spreading factor
- acts as buffer agent to maintain pH
- functions as binding protein
- minimizes mechanical damages through increasing viscosity
116
What are the 5 disadvantages of serum in media?
- lack uniformity in composition
- testing needs to be done to maintain quality of each batch before using
- may contain growth inhibiting factors
- increase risk of contamination
- presence of serum in media may interfere with purification and isolation of cell culture products
117
Define CHO
Chinese hamster ovary
118
Why are mammalian cell lines like CHO the prevailing animal-derived cell system?
due to their suitability to produce conveniently glycosylated proteins
119
Define fermentation
cultivation of living organism or cells under controlled conditions to optimize growth and productions of products
120
What is controlled to achieve maximum yield and efficiency for fermentation/cell culture processes?
environmental conditions
121
How is optimization of fermentation/cell culture processes carried out?
- taking into account different factors and the interaction of these factors
- statistical approaches like factorial design are used to define model space for process control and operational space for parameters to reduce risk of process variability
122
Define the Hayflick limit
the finite number of generations of growth and it is characteristic of the cell type, age, and species of origin
123
What are the 4-ish phases of growth for finite cell lines?
Phase 1 - cells are adapting to culture, relatively slow growth
Phase 2 - cells are growing at doubling rate (~18-24h)
Crisis point - cells recognize own limited ability for cell division, growth slows
Phase 3 - growth slows further and eventually stops
124
Define anchorage-dependence
need for solid substrate to grow
125
Define density inhibition
maximum cell density, exhaustion of nutrients, complete cover of available growth surface
126
Defined transformed cells
cells that are treated with a mutagenic agent such as UV rays, virus, oncogenes or can arise spontaneously
127
When transformed cells acquire a capacity for infinite growth, what are they called?
established or continuous
128
What are the differences between carcinogenesis in vivo to transformation of cell in vitro?
- transformed cells are not necessarily malignant
- malignant transformation likely requires several mutations
- non-maligamt transformation requires a single mutation
129
Define genomic ploidy
the number of copies of each chromosome in a cell
130
What is the diploid chromosome number in normal human mammalian cells?
46
131
What are the 4 other properties of normal mammalian cells?
- anchorage dependence
- a finite lifespan
- nonmalignant (non-cancerous)
- density inhibition
132
What are the 3 characteristics and genomic policy in transformed mammalian cells (like CHO-K1)?
- polyploid (more than 2 copies/chromosome) and can be aneuploid (fragmented chromosome)
- infinite growth potential
- loss of anchorage dependence
133
What could explain some of the differences in performance of the mammalian cell lines in bioreactors?
there is evidence from whole genome analysis of different (clonal) CHO cell lines that there is clone-to-clone variability and aneuploidy
134
What did Howard Cooke observe about human germline chromosomes?
the caps at the end of them were longer than those found in somatic cells
135
What happens to human germline chromosomes with each generation of growth?
shortened (100 bases for human telomeres)
136
Define telomerase
telomerase reverse transcriptase (TERT) + telomerase RNA (TERC)
137
Who discovered telomerase?
Carol Greider & Elizabeth Blackburn
138
What is the purpose of telomeres?
protects the chromosomes from degradation
139
What is the function of telomerase?
builds telomere DNA (why transformed cells can keep growing)
140
Does bacterial DNA have telomeres?
no, because their chromosome is a closed circular loop (DNA)
141
Why does mammalian DNA need telomere caps?
because it is linear and susceptible to degradation
142
In a hybridoma cell line, is the hayflick limit still observed?
yes
143
Borrellia and Streptomyces are bacteria with linear DNA, do they have telomeres? If not, what do they have instead?
- Borrelia - linear ends closed with hairpin loops
| - Streptomyces - proteins attached to ends of linear strands (act as primer for DNA synthesis)
144
Define suspended growth
cells are freely dispersed in the growth medium and interact as a single or flocculated units
145
Define supported growth
cells develop as a biofilm, normally on an inert support material and result in the formation of a complex interacting community of cells
146
Define organ culture
slice tissue and displace at gas-liquid interface, usually passes through tissue and retains structural integrity
147
Define explant culture
tissue is at solid-liquid interface, the whole tissue organs are transplanted from fetus and planted ex-vivo
148
Define dissociated cell culture
tissue is separated into individual cells then grown onto 3D subs strip use disaggregated tissue
149
Define organotypic culture
culture of an organ collected from an organism that allows to analyze complex tissue organs and preservation of the cultured organ and structure
150
What are the 2 types of single-use shake flasks?
- with or without baffles
| - no baffles for mammalian cells?
151
Define OUR
oxygen uptake rate
152
What are the uses/advantages of single-use (disposable) microbioreactor systems? (5 things)
- process development with process conditions approximating he manufacturing scale (results scalable to larger bench-scale + manufacturing bioreactors)
- rapid tool for evaluating rate fo conditions and cell line/strain performance
- process robustness studies (what limits of process are and setting working parameter ranges)
- high culture development, more precise
- no clean up post experimentation
153
What are the 2 disadvantages of single-use (disposable) microbioreactor system?
- more costly than shake flasks
| - lots of training to operate and program runs
154
What are the advantages to single-use bioreactors? (10 things)
- reduces cleaning and sterilization needs
- plant set up, space and operational cost are lower than classic fixed ones (~60% savings)
- smaller footprint, less utilities/piping, can be changed quickly
- reduces risk of cross-contamination = biological/process safety
- cheaper & easier complex validation and quality control b/c no testing after each run
- contain fewer parts than conventional bioreactor so initial/maintenance costs lower
- flexibility in product output because of small max size so easy to add more bioreactors to increase production
- technology transfer from ss bioreactors to SUBs easy because they perform similarly.
- disposable sensors and probes
- some suppliers can customize ports and sensor array
155
What are the disadvantages of single-use bioreactors (SUBs)?
- because small max size, best suited to high yield producing high value products
- limiting factor is achievable oxygen transfer into solution, not suitable for bacterial processes (better for mammalian because oxygen transfer is lower)
- cost of the disposable bag bioreactors is high & quality concerns require testing
- generate lots of plastic wastes (environmental concern)
156
What are the disadvantages of single-use bioreactors (SUBs)?
- because small max size, best suited to high yield producing high value products
- limiting factor is achievable oxygen transfer into solution, not suitable for bacterial processes (better for mammalian because oxygen transfer is lower)
- cost of the disposable bag bioreactors is high & quality concerns require testing
- generate lots of plastic wastes (environmental concern)
157
What is the advantage of roller bottles?
changing process guest by varying number of bottles
158
What is the disadvantages of roller bottles? (2 things)
- difficult to precisely control parameters
| - cant match yield and precise control of stirred tanks
159
What is a disadvantage to cell factories?
difficult to monitor
160
Define batch
closed system with a definite beginning and end
161
Define fed-batch
closed system with extra nutrients added (continuously, intermittently, single)
162
Define continuous
open system where fresh medium is added while culture simultaneously is removed and the system is in a steady state (concentrations nutrients and cell number do not say)
163
What are 2 advantages of batch?
- initial low cost to operate
| - simple to implement and run
164
What are disadvantages of batch? (6)
- least effective for producing biomass
- least Volumetric productivity
- less control of bi-products (affect product yield and quality)
- high non-productive downtime (eg. cleaning)
- increased frequency of sterilization wears out instruments & probes
- running costs high because each batch requires a culture seed train prior to the production bioreactor
165
Batch product examples
- amino acids
- enzymes
- organic acids
- antibiotics
166
What are the 4 advantages of fed-batch?
- high cell density
- highest volumetric production (g/L)
- more control of bi-products which affect product yield and quality
- regulatory acceptance highest, because much precedent in approved products
167
What are the disadvantages of fed-batch? (6 things)
-optimal medium for production ≠ optimal for growth (increases prep complexity)
-though controlled better than batch, bi-products still impact the process
-high non-productive downtime (eg. cleaning)
-increased frequency of sterilization
wears out instruments & probes
-running costs high because each batch requires a culture seed train prior to the production Bioreactor
-more complex to run & control than batch
168
Fed-batch product examples
- alcoholic beverages
- most amino acids
- enzymes
- organic acids
- antibiotics
- recombinant proteins
- vaccines
169
What are the 6 advantages of continuous/perfusion?
- one medium for production & growth (no feeds), simpler
- high cell density
- highest specific productivity (g/L/day)
- best control of bi-products which affect product yield and quality
- reduced down-time
- low running costs
170
What are disadvantages of continuous/perfusion? (6 things)
-high initial investment
-sterility must be maintained through 20-50 days or more ( a lost run more costly than Batch or Fed-batch)
-larger tanks to store a supply of medium for continuous feeding
-long runs increase risk of low-yielding mutants developing in the culture
More technically demanding than fed-batch
-low volumetric production (g/L), makes downstream processing more difficult
171
Continuous/perfusion product examples
- biofuels
- biomass
- recombinant proteins
- vaccines
172
What are some controlled/measured physical parameters during industrial cell culture/fermentation? (5 things)
- temperature (electrode)
- airflow (meter)
- agitation/speed of agitation (meter)
- pressure (transducer)
- liquid flow (transducer)
173
What are some controlled/measured chemical parameters during industrial cell culture/fermentation? (8 things)
- dissolved O2 (electrode)
- dissolves CO2 (electrode)
- nutrients eg. glucose (electrodes)
- pH (electrode)
- metal ions (electrode)
- foam level/detection (electrode)
- acid/alkali addition (meter)
- on-line or off-line nutrient inflow and exhaust gas (mass spectra)
174
What are some controlled/measured biological parameters during industrial cell culture/fermentation? (3 things)
- biosensors for biologically active products (electrodes)
- products (mass spec)
- biomass (spectrophotometers - on-line and off-line)
175
Define in-line measurements
sensor directly attached
176
Define on-line measurements
take samples and recirculate in spectrometer
177
Define at-line measurements
take samples out and take to instrument in proximity
178
Define off-line measurement
taken to an instrument at a different lab bench (not close)
179
What are the 4 alternate strategies for controlling dissolved oxygen?
- change in air flow
- intermittent oxygen sparging
- control of gas composition
- spin filter isolates cells from sparged gas
180
How is the change in air flow rate a strategy for controlling dissolved oxygen?
filters bring in air which changes the concentration of dissolved O2
181
Define PID
proportional-integral-derivative controller
