Monday, 27 April 2020

Biochemistry: the Molecules of Life

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Thursday, 2 April 2020



Aeration, Agitation & its Kinetics
The majority of fermentation processes is aerobic and, therefore, requires the provision of oxygen. a microbial culture must be supplied with oxygen during growth at a rate sufficient to satisfy the organisms’ demand. The oxygen demand of an industrial fermentation process is normally satisfied by aerating and agitating the fermentation broth. However, the productivity of many fermentations is limited by oxygen availability and, therefore, it is important to consider the factors which affect a fermenter’s efficiency in supplying microbial cells with oxygen.
OXYGEN SUPPLY
Oxygen is normally supplied to microbial cultures in the form of air. The method varies with the scale of the process:
1. Laboratory-scale microbial cultures may be aerated by means of the shake-flask technique where the culture is grown in a conical flask shaken on a platform contained in a controlled environment chamber. Animal cell cultures are frequently grown in “T-flasks” which provide a large surface area for oxygen diffusion—the “T” referring to the total surface area available for cell growth; thus, a T-25 flask has a 25 cm2 growth area.
2. Microbial pilot- and industrial-scale fermentations are normally carried out in stirred, aerated vessels, termed fermenters. Laboratory scale experiments using culture volumes upward of approximately 500 cm3 are also performed in stirred, aerated fermenters as this enables the cultural conditions to be better monitored and controlled, and facilitates the addition of supplements and the removal of samples. Some fermenters are so designed that adequate oxygen transfer is obtained without agitation for example bubble columns and air-lift fermenters. Large-scale animal cell cultures have been grown in a range of fermenter types, including stirred aerated vessels based on microbial systems.
The rate of oxygen transfer from air bubble to the liquid phase may be described by the equation:
(1)
where CL is the concentration of dissolved oxygen in the fermentation broth (mmoles dm–3)
 t is time (hours)
dCL/dt is the change in oxygen concentration over a time period, that is, the oxygen-transfer rate (mmoles O2 dm–3 h–1)
KL is the mass transfer coefficient (cm h–1)
a is the specific gas/liquid interface area per liquid volume (cm2 cm–3)
C* is the saturated dissolved oxygen concentration (mmoles dm–3).
KL may be considered as the sum of the reciprocals of the resistances to the transfer of oxygen from gas to liquid, and the difference between the saturated dissolved oxygen concentration and the actual concentration in the fermentation broth (C*–CL) may be considered as the “driving force” across the resistances. It is extremely difficult to measure both KL and “a,” the gas–liquid interface area, in a fermentation and, therefore, the two terms are generally combined in the term KLa, the volumetric mass-transfer coefficient, the units of which are reciprocal time (h–1). The volumetric mass-transfer coefficient is used as a measure of the aeration capacity of a fermenter. The larger the KLa, the higher the aeration capacity of the system.
DETERMINATION OF KLa VALUES
The determination of the KLa of a fermenter is essential in order to establish its aeration efficiency and to quantify the effects of operating variables on the provision of oxygen. Dissolved oxygen is usually monitored using a dissolved oxygen electrode which records dissolved oxygen activity or dissolved oxygen tension (DOT) while the equations describing oxygen transfer are based on dissolved oxygen concentration.The solubility of oxygen is affected by dissolved solutes so that pure water and a fermentation medium saturated with oxygen would have different dissolved oxygen concentrations yet have the same DOT, that is, an oxygen electrode would record 100% for both. The dissolved oxygen concentration, for all practical purposes, will be zero and the KLa may then be calculated from the equation: (where OTR is the oxygen transfer rate.)
                                                           
  (2)


OXYGEN-BALANCE TECHNIQUE
The KLa of a fermenter may be measured during fermentation by the oxygen balance technique which determines, directly, the amount of oxygen transferred into solution in a set time interval. The procedure involves measuring the following parameters:
1. The volume of the broth contained in the vessel, VL (dm3).
2. The volumetric air flow rates measured at the air inlet and outlet, Qi and Qo, respectively (dm3 min–1).
3. The total pressure measured at the fermenter air inlet and outlet, Pi and Po, respectively (atm. absolute).
4. The temperature of the gases at the inlet and outlet, Ti and To, respectively (K).
5. The mole fraction of oxygen measured at the inlet and outlet, yi and yo, respectively.
The oxygen transfer rate may then be determined from the following equation:

(3)
Where 7.32 × 105 is the conversion factor equaling (60 min h–1) [mole/22.4 dm3 (STP)] (273 K/l atm).
The KLa may be determined, provided that CL and C* are known, from Eq. 1
(4)
EFFECT OF AIRFLOW RATE ON KLa
Non Mechanically agitated reactors Bubble columns and air-lift reactors are not mechanically agitated and, therefore, rely on the passage of air to both mix and aerate.
1. Bubble columns
The flow pattern of bubbles through a bubble column reactor is dependent on the gas superficial velocity. At gas velocities of below 1–4 cm s–1 the bubbles will rise uniformly through the medium and the only mixing will be that created in the bubble wake. This type of flow is referred to as homogeneous. At higher gas velocities bubbles are produced unevenly at the base of the vessel and bubbles coalesce resulting in local differences in fluid density. The differences in fluid density create circulatory currents and flow under these conditions is described as heterogeneous 

The KLa in a bubble column is essentially dependent on the superficial gas velocity. for most non viscous situations the equation is:
(5)
Where Vsc is the superficial air velocity corrected for local pressure. However, viscosity has an overwhelming influence on KLa in a bubble column that can be expressed as:
(6)
Where π is the liquid dynamic viscosity (N s m–2).
2. Air-lift reactors
The difference between a bubble column and an air-lift reactor is that liquid circulation is achieved in the air-lift in addition to that caused by the bubble flow. The reactor consists of a vertical loop of two connected compartments, the riser and downcomer. Air is introduced into the base of the riser and escapes at the top. The degassed liquid is denser than the gassed liquid in the riser and flows down the downcomer. Thus, a circulatory pattern is established in the vessel—gassed liquid going up in the riser and degassed liquid coming down the downcomer. Circulation in an air-lift results in the bubbles being in contact with the liquid for a shorter time than in a corresponding bubble column. Thus, the KLa obtained in an air-lift will be less than that obtained in a bubble column at the same superficial air velocity, that is, less than 0.32 (V s c) 0.7 . The advantage of the air-lift lies in the circulation achieved, but this is at the cost of a lower KLa value.

Excerpts : Principles of fermentation technology, Stanbury & Whitaker

Wednesday, 1 April 2020


Scintillation Counting

Liquid Scintillation Counting (LS Counting) is a lab based strategy that utilizes a Liquid Scintillation Counter (LSC) to check the radioactive emanations from a liquid sample. It is regularly utilized in the organic sciences to quantify the take-up of radioactive isotopes into biological materials. Radioactive isotopes interact with matter in two different ways, ionization and excitation.
Excitation drives an energized molecule or compound (known as a fluor) to emanate photons of light. The procedure is known as scintillation. when the light is recognized by a photomultiplier, it frames the premise of scintillation counting. Basically, a photomultiplier changes over the energy of radiation into an electrical sign, and the  strength of the electrical signal that outcomes is legitimately corresponding to the energy of the first radioactive occasion. This implies two, or significantly more, isotopes can  be independently identified and estimated in a similar example, if they have  adequately different energy emitting spectra.
Types of scintillation counting
Solid scintillation counting
In solid scintillation counting the sample is placed adjacent to a solid fluor (e.g. sodium iodide). Solid scintillation counting is particularly useful for gamma emitting isotopes. This is because they can penetrate the fluor. The counters can be small handheld devices with the fluor attached to the photomultiplier tube or larger bench-top machines with a well-shaped fluor designed to automatically count many samples.





Liquid Scintillation Counting
In liquid scintillation counting, the sample is mixed with a scintillation fluid containing a solvent and one or more dissolved fluors. This method is particularly useful in quantifying weak b-emitters such as 3 H, 14C and 35S, which are frequently used in biological work. Scintillation fluids are called ‘cocktails’ because there are different formulations, made up of a solvent (such as Toulene) & fluors such as 2,5-diphenyloxazole (PPO), 1,4-bis(5- phenyloxazol-2-yl)benzene (nicknamed POPOP, or 2-(40 -t-butylphenyl)-5-(400-bi-phenyl)-1,3,4-oxydiazole (butyl-PBD).


                                                Liquid Scintillation Counting

There are a number of physical processes that may disrupt LSC. These include:
Process
Explanation
Examples
Reduce Problem By
Chemiluminescence
Generation of light due to chemical processes.
Bleaching agents, dioxane-based scintillators
Equilibrate sample for a period of time in the LSC
Photoluminescence
Emission of photons from excited molecular species.
Vials, caps, other materials in the LSC. Some samples such as proteinaceous materials when dissolved in alkaline solubilisers such as hyamine.
Acidify samples; avoid exposure to sunlight or fluorescent lighting. Dark adapt samples for several hours before counting.
Quenching
Reduction in the scintillation count rate.
Photon quenching, chemical impurity quenching, colour quenching (see diagram below).
Use Internal Standards to account for quenching. A standard with a known CPM/DPM (Counts per minute/Disintegrations per minute) is added and measured and the reduction due to quenching adjusted for in the measured samples.

Examples of the use of LS Counting
  1. Viral Proteins: Proteins produced by viruses when they infect a cell are produced in very small amounts and are difficult to detect and purify. If virus-infected cells are fed a radioactive amino acid, then each time that amino acid is linked to form the growing protein a radioactive ‘label’ is attached to the protein. This radioactive ‘label’ is then used to monitor the identification and purification of the viral protein. Amino acids containing 3H, 14C and 35S are often used to label proteins. 35S is particularly useful as sulphur is only found in two amino acids – methionine and cysteine.
  2. Environmental Monitoring: Checking for 3H spills in the laboratory. Tritium is such a weak emitter that its presence cannot be detected by a Geiger-Mueller counter. Wipe testing is usually used. This is where suspect surfaces are wiped with a piece of tissue. The tissue is placed in LS Cocktail in a LS vial and counted in the LS Counter.
 References:
1. Principles & Techniques of Biochemistry, 5th Edition. Keith Wilson & john Walker



Monday, 30 March 2020

COMPLEMENT SYSTEM

Complement System
The complement system refers to a series of >20 proteins, circulating in the blood and tissue fluids. Most of the proteins are normally inactive, but in response to the recognition of molecular components of microorganisms they become sequentially activated in an enzyme cascade – the activation of one protein cleaves and activates the next protein in the cascade enzymatically. Complement can be activated through three different pathways,  each of which can cause the activation of C3, cleaving it into a large fragment, C3b, that acts as an opsonin, and a small fragment C3a (anaphylatoxin) that promotes inflammation. Activated C3 can trigger the lytic pathway, which can damage the plasma membranes of cells and some bacteria. C5a, produced by this process, attracts macrophages and neutrophils and also activates mast cells. Complement was discovered as a heat-labile component of normal plasma that causes the opsonisation and killing of bacteria.
Classical Pathway
This pathway involves complement components C1C2 and C4. The pathway is triggered by antibody-antigen complexes binding to C1, which itself has three subcomponents C1qC1r and C1s. The pathway forms a C3 convertase, C4b2a, which splits C3 into two fragments; the large fragment, C3b, can covalently attach to the surface of microbial pathogens and opsonise them; the small fragment, C3a, activates mast cells, causing the release of vasoactive mediators such as histamine.
Alternative Pathway
This pathway involves various factors, B, D, H I, which interact with each other, and with C3b, to form a C3 convertase, C3bBb, that can activate more C3, hence the pathway is sometimes called ‘the amplification loop’. Activation of the loop is promoted in the presence of bacterial and fungal cell walls, but is inhibited by molecules on the surface of normal mammalian cells.
Mannose-binding Lectin Pathway
This pathway is activated by the binding of mannose-binding lectin (MBL) to mannose residues on the pathogen surface. This in turn activates the MBL-associated serine proteases, MASP-1 and MASP-2, which activate C4 and C2, to form the C3 convertase, C4b2a.


Role of Complement in Disease
The complement system plays a critical role in inflammation and defence against some bacterial infections. Complement may also be activated during reactions against incompatible blood transfusions, and during the damaging immune responses that accompany autoimmune disease. Deficiencies of individual complement components or inhibitors of the system can lead to a variety of diseases (Tabulated), which gives some indication of their role in protection against disease.
Table . Diseases associated with complement deficiencies
Complement Deficiency
Disease
C3 and Factor B
Severe bacterial infections
C3b-INA, C6 and C8
Severe Neisseria infections
Deficiencies of early C components C1, C4, C2.
Systemic lupus erythematosus (SLE)

REFERENCES:
Zaahira Gani, Cambridge, UK
https://www.immunology.org/public-information/bitesized-immunology/systems-and-processes/complement-system
https://www.youtube.com/watch?v=mfCeCvkQbuI&t=63s