The document provides an overview of upstream and downstream processes. Upstream processes involve cell culture and media preparation, such as inoculum development, media development, and cell culture. Downstream processes involve steps after fermentation like cell disruption, purification, and final product isolation. Physical, chemical and enzymatic methods can be used for cell disruption in downstream processing. The document also discusses the definition, examples, and importance of upstream and downstream processes.

1. UPS TREAM AND
DO WNS TREAM
PRO CES S ES

2. PRES ENTATIO N O VERVIEW
Here’s what you need to know about Upstream and Downstream Processes :
• Definition of Upstream and Downstream Processes
• Examples/list of Upstream and Downstream Processes
• Upstream, Fermentation and Downstream Processes
• Upstream Processes: Cell culture and Media Preparation
• Particle Separator
• Cell Disruption: Physical, Chemical and Enzymatic Methods
• Essence of Upstream and Downstream Processes in Industries

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The game is called “UPSTREAM & DOWNSTREAM:
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of colored squares. Some squares are numbered
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There are two type of clues:
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of words whose letters run horizontally (from
left to right) across the grid. Each across
question is assigned by a number. This number
corresponds to the number for its answer in the
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7. INTRO DUCTIO N
Bioprocessing is an expanding field encompassing any
process that uses living cells or their components (e.g.,
bacteria, enzymes, or chloroplasts) to obtain desired
products, such as biofuels and therapeutics.
Traditionally, bioprocess development is split into
“upstream” and “downstream” functional groups.
• Application of natural or genetically manipulated
(recombinant) whole cells/ tissues/ organs, or parts
thereof, for the production of industrially or
medically important product

8. What is Upstream
Processing
The upstream part of a bioprocess refers to
the initial stage in which microbes/cells are
grown, e.g.:
• Bacteria
• Yeast
• Mammalian Cell

9. What is Downstream
Processing (US P)?
The downstream part of a bioprocess refers to
the part where the cell mass from the
upstream are processed to meet purity and
quality requirements.
3 main sections: cell disruption, a purification
section and a polishing section.

10. List of Upstream and Downstream Processes
UPSTREAM
PROCESSES
DOWNSTREAM
PROCESSES
 Inoculum Development
 Media Development
 Improvement of Inoculum
 Inoculation  Removal of Particulates
 Primary Isolation
 Purification
 Final Product Isolation /
Polishing

11. Upstream, Fermentation and
Downstream Processes
UPSTREAM FERMENTATION DOWNSTREAM
Liquid
medium
Fermenter
Separation of cellular
product, purification,
conc, etc.
cell
transformation
Bio-products
substrate
Product Biosynthesis

12. Upstream, Fermentation and
Downstream Processes

13. Upstream processing is usually
divided into the following stages
S ubstrate Preparation Cell Culture
Media Preparation

14. The substances with which the enzymes react to
are called substrates.
What is a
S ubstrate?

15. Juice from sugarcane,
molasses
Corn Meal
Types of substrates that are used for Ethanol
roduction
Starch containing
substrate
Waste products from
wood or processed wood
Sulfite waste-liquor

16. Molasses is diluted with
water in 1 :5 ratio
Fortification with
Ammonium
ul ate
Addition of
Yeast
Dilution of
molasses
Addition of
S ul uric acid
UBS TRATE
PREPARATIO N

17. What is a Culture
Media?
It is critical to cell growth,
metabolism, and protein expression.
It provides for optimum pH,
osmolality, and nutrients in an
environment that is essential for cell
growth and survival.

18. BAS AL MEDIA
are those that may be used
for growth of bacteria that
do not need enrichment of
the media
ENRICHED
MEDIA
are enriched usually by adding
blood, serum or egg
S ELECTIVE MEDIA
favour the growth of a particular
bacterium by inhibiting the
growth of undesired bacteria
CLAS S IFICATIO N O F CULTURE
MEDIA
INDICATO R MEDIA
an indicator is included in the
medium
TRANS PO RT MEDIA
are used when specimen cannot
be cultured soon after
collection.
S TO RAG E MEDIA
used for storing the bacteria for
a long period of time.

19. MEDIA PREPARATIO N
Media is predominantly made up of various
components:
● Carbohydrate
● Nitrogen
● Fats
● Trace amounts of salts
is usually carried out in tanks, petri dishes,
carboys, bottles or bags to which the media is
introduced.

20. • The dispensing room is the location where raw
materials for use in the production process are
weighed or measured.
• In some biomanufacturing facilities, the
dispensing process can be electronic. However,
in many companies a manual system is still used.
Upstream Processing Areas
Dispensing room

21. • The air cleanliness classification of the
dispensing room is Class 1 00,000 which is
achieved using HEPA filtration of the air supply
to the room.
• The HVAC system also maintains the room at a
positive pressure with respect to the
surrounding rooms and corridors.
Upstream Processing Areas
Dispensing room

22. Vessels used during the biomanufacturing
process and all associated piping/hoses must
be free of any foreign substances prior to use.
Clean in Place (CIP) and Steam in Place (SIP)
are validated cleaning and sterilization
procedures that ensure the bioreactor is safe
for use.
CIP/SIP SYSTEMS

23. ● CIP involves automatic cleaning or process equipment with minimal setup and
shutdown and little or no operator intervention.
● SIP occurs when the vessels are sterilized with clean steam to establish a sterile
boundary which is critical to prevent contamination.
CIP/S IP S YS TEMS

24. is the process by which cells are grown
under controlled conditions, generally
outside their natural environment.
CELL CULTURE

25. ACTERIAL G RO WTH CURVE
If the bacterial population is measured periodically and
log of number of viable bacteria is plotted in a graph
against time, it gives a characteristic growth curve
which is known as growth curve or growth cycle.
The growth curve has following phases:
● Lag phase
● Log phase or exponential phase
● Stationary phase
● Death phase or decline phase

26. ACTERIAL G RO WTH CURVE
is characterized by the
period during which there is
no increase in number of cell
bacteria divides continuously at
constant rate and the number of
bacteria increase exponentially
bacteria growth reaches a
state during which there is no
net increase in bacterial
population.
number of bacteria decrease
continuously and
exponentially.
LO G PHAS E
DECLINE
PHAS E
AG PHAS E
PHAS E

27. Figure 1: Distinct phases of the growth cycle of a production bioreactor cell culture

28. Must be available in
sufficiently large volumes
Must be free of
contamination
Culture used to inoculate a fermentation satisfies
the following criteria:
Must be in a healthy,
active state
Must be in a suitable
morphological form
Must retain its product-
forming capabilities.

29. ● Cell culture hood
● Incubator
● Water bath
● Centrifuge
● Refrigerator and freezer (–20°C)
● Cell counter (e.g., Automated Cell
Counter or hemacytometer)
● Inverted microscope
● Liquid nitrogen (N2) freezer or
cryostorage container
● Sterilizer (i.e., autoclave)
Cell Culture Basic Equipments

30. Cell Culture Basic
Equipments
Cell Culture Hood
Although a separate tissue culture room is preferred, a
designated cell culture area within a larger laboratory
can still be used fort sterile handling, incubation, and
storage of cell cultures, reagents, and media. The
simplest and most economical way to provide aseptic
conditions is to use a cell culture hood.

31. The basic layout of a cell culture hood for right-handed workers

32. Cell Culture Basic Equipments
Incubator
The purpose of the incubator is to provide the
appropriate environment for cell growth. The
incubator should be large enough for your laboratory
needs.

33. Cell Culture Basic Equipments

34. Cell Culture Basic Equipments

35. CELL CULTURE
INO CULUM S PINNER PREFER
MENTERS
FERMENTER
thawing of a
frozen vial of cells 1 00-500mL 1 -3 prefermenter
cultures

36. S ERIAL DILUTION
The goal of the serial dilution
process is to obtain plates with
CFUs in the range of 30–300,
and the process usually
involves several dilutions in
multiples of 1 0 to simplify
calculation.
Serial dilution involves diluting a fixed volume of cells mixed with dilution solution using the previous
dilution as an inoculum. The result is dilution of the original culture by an exponentially growing factor.

37. TWO METHO DS O F INO CULATIO N
POUR PLATE METHOD

38. TWO METHO DS O F INO CULATIO N
SPREAD PLATE METHOD

39. CO NTAMINATIO N
Preventive measures include
ensuring proper cleaning of all materials,
proper gowning (e.g., gloves, face masks,
hair nets, etc.), and using proper aseptic
techniques is critical to prevent
contamination of the culture.

40. ● is essential for preventing the contamination
with any undesired microorganisms.
S TERILIZATIO N
There are two reliable methods used to sterilize
microbial culture media:
 Autoclave: at 1 21 °C (200 kPa) for 1 5 minutes
 Dry Heat Oven: at 1 70°C for 30 minutes

41. RO LE O F pH IN
CELL CULTURE
pH can affect growth and is referred to as a
“critical process parameter.” pH will not
remain stable for a long period of time in an
actively growing culture.
pH probe transmitter

42. O THER CULTURE PARAMETERS
TEMPERATUR E
● Optimal Temperature: 37°C
● Monitored by temperature probe
DIS S O LVED O XYG EN
● Controlled by DO probe and
computer system

43. MAINTAINING AND
MO NITO RING
CULTURE
Cell growth and viability is monitored
during culture by counting cell
methods.
Cell Counting
Tallies the number of viable and
non-viable cells. Accurate and
consistent cell counts is essential in
a robust production process.

44. CELL CO UNTING METHO DS
1. Manual Cell Counting with Hemocytometer
A device used for determining the
number of cells per unit volume of a
suspension is called a counting
chamber. The most widely used type
of chamber is called a
hemocytometer.

45. CELL CO UNTING METHO DS
2. Automated Cell Counters
Automated cell counters were
designed to be a faster, easier,
automated alternative to manual
counting. They use the same
principles of operation as
hemocytometers. They perform
multiple counts of cells within a
known area and average out the
results.

46. CELL
DIS RUPTIO N
Physical Methods

47. PHYS ICAL METHO DS
O smotic shock
In this technology, cells are first
exposed to either high or low salt
concentration. Then the conditions are
quickly changed to opposite conditions
which leads to osmotic pressure and
cell lysis.
Disadvantages:
● Low efficiency
● Requires addition of high
amounts of salts
● High water usage is high
● High downstream
processing costs

48. PHYS ICAL METHO DS
S onication
The method uses pulsed, high frequency sound
waves to agitate and lyse cells, bacteria, spores and
finely diced tissue. The sound waves are delivered
using an apparatus with a vibrating probe that is
immersed in the liquid cell suspension.
Disadvantages:
● High heat generation
● Noise Pollution.
● Expensive process.
● Generate free radicals

49. PHYS ICAL METHO DS
Thermolysis
Used to disrupt the bonds within cell
walls, and also to denature proteins.
Thermolysis has shown potential in
becoming more common in large scale
production.
Disadvantages:
● Cannot be used for heat
labile substances
● Spore forming bacteria
are also resistant to this
method.
● Periplasmic proteins in G(-) bacteria
are released when the cells are heated
up to 50ºC.
● Cytoplasmic proteins can be released
from E.coli within 1 0min at 90 ºC.

50. PHYS ICAL METHO DS
High Pressure omogenizer
It is a process that works to reduce particle size or to
lyse cells. The higher the amount of energy applied
during the homogenization process, the smaller the
particle size or the more complete the cell lysis. It is
mostly used for yeast cells. It is a vital unit in the
dairy production industry, for milk homogenization.
Disadvantages:
● High heat generation

51. PHYS ICAL METHO DS
Impingement
In this procedure, a stream of
suspended cells at high velocity and
pressure are forced to hit either a
stationary surface or a second stream
of suspended cells.
Advantages:
● It can be effectively used for disrupting
cells even at a low concentration
● Micro fluidizer is successfully
used for breaking E. coli cells

52. PHYS ICAL METHO DS
G RINDING WITH G LAS S BEADS
Bead Mills have been adapted for cell disruption in both small
scale and large scale production. It is an efficient way of
disrupting different microbial cells as different designs have
been developed.
Advantages:
● Useful for small sized materials
● Can be carried out in both batch and
continuous processes.
● Commonly used for disruption of yeast cells
and for grinding animal tissues.
Disadvantages:
● Large amount of heat generation
● Poor scale-up
● High chance of contamination

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54. S
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Across:
1. It is the process of releasing molecules or other materials from inside a
cell.
2. Media _________ is necessary to ensure that only the desired
microorganism is present to carry out the fermentation, that products are
made of predicted quality, that the environment is protected from
undesirable contamination, and that deterioration of products is prevented.
C R U
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1. Enzymatic cell disruption relies upon the addition of common cell
membrane disrupting enzymes such as ____________.
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56. B
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S I O N
Down:
1. A media that may be used for growth of
bacteria that do not need enrichment.
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Across:
1. It is characterized by the period during
which there is no increase in number of cell.
2. The method uses pulsed, high frequency
sound waves to agitate and lyse cells,
bacteria, spores and finely diced tissue.

57. CELL
DIS RUPTIO N
Chemical Methods

58. CHEMICAL METHO DS
DETERG ENTS
● Detergents damaged the lipoproteins of the
microbial cell membrane and lead to release of
intracellular components.
● Commonly used anionic detergent is sodium dodecyl
sulfate (SDS) which reorganizes the cell membrane
by disturbing protein-protein interactions.
● Detergents that are ionic in nature, cationic or
anionic can denature membrane proteins and lyse
the cells
DISADVANTAGES
● Proteins will be denatured in lysis process.
● Detergents may also disturbed subsequent downstream processing process.
● Additional purification step may be required after cell lysis.

59. CHEMICAL METHO DS
O RG ANIC
S O LVENTS
Solvents which
can be used for
cell lysis include
alcohols, dimethyl
sulfoxide, methyl
ethyl ketone or
toluene
Extract cell wall’s
lipid components
Leads to release
of intracellular
components

60. CHEMICAL METHO DS
ALKALI TREATMENT
Used for hydrolysis of
microbial cell wall material
provided that the desired
enzyme will tolerate a pH
of 1 0.5 to 1 2.5 for 20 to
30 minutes.
Disadvantages: Chemical
costs for neutralization of
alkali are high.
Disadvantages: Product
may not be stable in alkali
conditions.

61. CO NS EQ UENCES O F US ING CHEMICAL
METHO D
● Chemical Methods are risky to use for the disruption of sensitive cells,
as the used of solvents and detergents can cause protein denaturation,
damaging the final product.
● A significant issue is the removal and recovery of the chemical
disrupter, making chemical methods highly applicable at a laboratory
scale.
● Chemical methods also have low efficacy, making them more
expensive and less useful as disruption methods.
● The high consumption of solvents and water makes chemical methods
environmentally unfriendly.

62. CELL
DIS RUPTIO N
Enzymatic Methods

63. Cell Disruption: Enzymatic Method
Enzymatic cell disruption relies upon
the addition of common cell
membrane disrupting enzymes such as
lysozyme or other muramidases which
act by digesting the peptidoglycan
layer of bacteria.
The benefits of enzymatic cell lysis
includes:
 Specificity
 High rate of product release
 Mild nature of cell disruption

64. Cell Disruption: Enzymatic Method
LYSOZYME
Lysozyme is the most frequently used enzyme and is commercially available
(produced from hen egg white). It hydrolyses β-1 , 4-glycosidic bonds of the
mucopeptide in bacterial cell walls.
The Gram- positive bacteria (with high content of cell wall mucopeptides) are more
susceptible for the action of lysozyme. For Gram-negative bacteria, lysozyme in
association with EDTA can break the cells. As the cell wall gets digested by
lysozyme, the osmotic effects break the periplasmic membrane to release the
intracellular contents.
GLUCANASE, MANNANASE AND PROTEASE
For the lysis of yeast cell walls, glucanase and mannanase in
combination with proteases are used

65. Enzymatic Cell Disruption Methods
LYSOZYME
Lysozyme source/type
Lysozyme concentration
Cell concentration
Solution composition
Incubation time
Variables :
Pretreatment

66. Enzymatic Cell Disruption Methods
DNAse
DNAse source/type
DNAse concentration
DNA concentration
Solution composition
Incubation time
Variables :

67. Enzymatic Cell Disruption Methods
GENERAL ENZYME
Enzyme source/type
Cell density
Cell type
Protein of interest
Process Condition
Variables :
Pretreatment

68. BIO S EPARATIO N
DO WNS TREAM PRO CES S
Particles, from cellular to molecular, may be
separated from a solution based on their
differences in key physical chemical properties
such as:
● Size
● Density
● Solubility
● Diffusivity

70. S O LID LIQ UID S EPARATIO N
most commonly used to separate
biomass in culture medium.
Removal of Insoluble Methods

71. PO INTS TO BE CO NS IDERED WHILE
S ELECTING THE FILTER MEDIUM
● Ability to build the solid
● Minimum resistance to flow the filtrate
● Resistance to chemical attack
● Minimum cost
● Long Life

72. TYPES O F FILTERS US ED
PLATE AND FRAME
FILTERS
These are cheap and versatile - the
surface area can be adjusted by varying
the number of plates. Not suitable for the
removal of large quantities of solids from
broths as the plates have to be
dismantled for solids recovery. They are
used as polishing devices to filter out low
residual solids.

73. FILTER PRES S
A filter press is built of a sequence of
perforated plates alternating with hollow
frames. The plates are covered with a
suitable filter medium (cloths) that create a
series of chambers through which the slurry
can be forced. Solids are retained in the
chambers and the filtrate discharges into the
hollows on the plate surface and drain out.

74. VACCUM FILTERS
● It is one of the mot commonly used type
of filter in fermentation.
● The drum is pre-coated prior to filtration.
● A small agent of coagulation is added to
the broth before pump into the filter.
● Vacuum filters are used for clarification
of fermentation broths (containing 1 0-
40% solids by volume with particle sizes
ranging between 0.5-1 0 µm) due to
simplicity of operation and low cost.

75. S O LID LIQ UID S EPARATIO N
● It is used to separate particles of 1 00-0.1 micrometer
from liquid by gravitational forces.
● Use of the centrifugal force for the separation of
mixtures.
● More dense components migrate away from the axis
of the centrifuge.
● Less dense components migrates towards the axis.
CENTRIFUG ATIO N

76. NO ZZLE CENTRIFUG E
For large scale fermentations, solid recovery
has to be continuous and these centrifuges
need to have a solids discharge mechanism.
Nozzle discharge types are suitable for
recovery of yeast and bacteria but tend to get
clogged by fungal mycelium or large particulate
matter.

77. S O LIDS EJ ECTING
CENTRIFUG E
Solids ejecting centrifuges have
continuous or intermittent
mechanisms to discharge solids
and may be used for the recovery
of mycelia or bacterial biomass.

79. S O LID LIQ UID S EPARATIO N
When a gas is introduced into the liquid broth, it
forms bubbles. The cells and other solid particles
get adsorbed on gas bubbles. These bubbles rise
to the foam layer which can be collected and
removed. The presence of certain substances,
referred to as collector substances, facilitates
stable foam formation e.g., long chain fatty acids,
amines.

80. ● Process where a solute comes out of
solution in the form of flocs or flakes.
● In flocculation, the cells (or cell debris)
form large aggregates to settle down
for easy removal. The process of
flocculation depends on the nature of
cells and the ionic constituents of the
medium. Addition of flocculating
agents (inorganic salt, organic
polyelectrolyte, mineral hydrocolloid) is
often necessary to achieve appropriate
flocculation.
FLO CCULATIO N

81. EVAPO RATIO N
Water in the broth filtrate can be removed by a simple
evaporation process. The evaporators, in general,
have a heating device for supply of steam, and unit
for the separation of concentrated product and
vapour, a condenser for condensing vapour,
accessories and control equipment. The capacity of
the equipment is variable that may range from small
laboratory scale to industrial scale.

82. ● The concentration of biological products can be
achieved by transferring the desired product (solute)
from one liquid phase to another liquid phase, a
phenomenon referred to as liquid-liquid extraction.
● It is a separation process that takes advantage of the
relative solubilities of solute in immiscible solvents.
LIQ UID LIQ UID EXTRACTIO N

83. ADS O RPTIO N
● Involves the partitioning of a solute
between a bulk solution phase and a
typically porous or high surface area
solid.
● Common adsorbent used are
activated carbon, silica gel, alumina.

84. PRECIPITATIO N
● Organic solutes have solubilities dependent on solution
temperature, pH, composition, ionic strength and dielectric
constant.
● Solid formed is called the precipitate and the liquid
remaining above the solid is called the supernate.
● Salts such a ammonium and sodium sulphate are used for
proteins to precipitate.
● Organic solvents-methanol used to precipitate dextrans.
● Chilled ethanol and acetone used for protein precipitation.
● Non ionic polymer such as polyethylene glycol used in
precipitation.

85. MEMBRANE FILTRATIO N
Membrane filtration involves the use of
membrane technology for the separation of
biomolecules and particles and the concentration
of process fluids. During separation a
semipermeable membrane acts as a selective
barrier retaining the molecules/particles bigger
than the pore size while allowing the smaller
molecules to permeate through the pores.

86. ● Is governed by a screening principle and
dependent on particle size.
● Ultrafiltration membranes have a pore size
between 1 nm and 1 00nm.
● Typically, the process is suitable for
retaining biomolecules, bacteria, viruses,
polymers, colloidal particles and sugar
molecules.

88. ● Done to separate those contaminants that resemble
the product very closely in physical and chemical
properties.
● Require sensitive and sophisticated equipment,
Expensive to carry out.
PURIFICATIO N

89. CHRO MATO G RAPHY
● Separation of mixtures
● Passing a mixture dissoved in a
“mobile phase” through a stationary
phase, which separates the analyte to
be measured from other molecules in
the mixture and allows it to be
isolated.
● The biological products of
fermentation (proteins,
pharmaceuticals, diagnostic
compounds and research materials)
are very effectively purified by
chromatography.

90. CHRO MATO G RAPHY
● Affinity chromatography separates the protein
of interest on the bass of a reversible
interaction between it and its antibody coupled
to a chromatography bead or labeled as the
antigen.
● Affinity chromatography is based on an
interaction of a protein with an immobilized
ligand.

91. ● Used charged stationary phase to
separate charged compounds
● Resin that carries charged
functional which interact with
oppositely charged groups of the
compound to be retained.
● The pH determines the effective
charge on both the target
molecule and the Ion-exchanger.
EXCHANG E
CHRO MATO G RAPHY

92. S IZE EXCLUS IO N
CHRO MATO G RAPHY
● Gel permeation or Gel filtration
● Involves separation on the basis of
molecular size (molecular sieving)
● Particularly useful for desalting
protein preparations

93. LIQ UID
CHRO MATO G RAPHY
● Mobile Phase is a liquid
● In the HPLC technique, the sample is
forced through a column that is packed
with irregularly or spherically shaped
particles or a porous monolithic layer
(stationary phase) by a liquid (mobile
phase) at high pressure.

94. Distillation is used to recover fuel
alcohol, acetone and other
solvents from fermentation media
and for the production of potable
spirits. With ethanol, the
continuous process produces a
product with maximum ethanol
concentration of 96.5% (v/v).
DIS TILLATIO N
DISTILLATIO
N COLUMN
CONDENS
ER
REBOILE
R
OUTLET

95. Dialysis and Electrodialysis
These membrane separation techniques
are used for the removal of low molecular
weight solutes and inorganic ions from a
solution.

96. FO RMULATIO N
● End with packaging of the product in a
form that is stable, easily transported
and convenient.
● Remove or deactivate trace
contaminants which might compromise
product safety

97. ● Product crystallization may be
achieved by evaporation, low
temperature treatment, or the
addition of a chemical reactive
with the solute. The product’s
solubility cannot be reduced by
adding solvents, salts, polymers,
e.g., non-ionic PEG and
polyelectrolytes or by altering
the pH.
CRYS TALLIZATIO N FREEZE DRYING /
● Freezing the material
● Reducing the surrounding
pressure and adding enough
heat to allow the frozen
water in the material to
sublime directly from the
solid phase to gas.

98. S PRAY DRYING
● Spray drying is used for drying large
volumes of liquids.
● In spray drying, small droplets of liquid
containing the product are passed
through a nozzle directing it over a
stream of hot gas. The water
evaporates and the solid particles are
left behind.

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