Free Biotechnology Notes

Proteases in leather Industry

2013-01-27T03:44:00.001-08:00

Proteases in leather Industry

Proteases belong to a group of proteolytic enzymes. They are obtained by microbial fermentations and are meant to use in leather industry for Dehairing, bating and soaking purposes. Their major use is in detergent industry too where they are used for breaking proteinaceous matter caused by body secretions, food stuffs and blood stains. These enzymes are obtained from plants, animals and microbial sources. Animal and Microbial Proteases from Fungi and bacteria re used in the pretanning processes of leather manufacture.

Animal Proteases are mixture of Trypsin, Chymotrypsin and various Peptidases which may contain amylase or lipase as secondary enzymes.

Proteases differ in their pH range as follows:

Acid Proteases: pH 2.5 – 6.0 derived from A. satoi

Alkaline Proteases: belong to group of serine proteases. More heat sensitive and heat

deactivate at 60⁰ C

Neutral Proteases: Obtained from Aspergillus and Penicillium spp.

Enzymes in Dehairing

Dehairing involves the digestion of basal cells of hair bulb and cells of malphigian layer. This is followed by loosening of hair with an attack on outermost sheath and breakdown of inner root sheath and parts of hair that are not keratinized.

Various Enzymes used in dehairing process are:

CLARIZYME: has been developed especially for dehairing of skins and hides. It is an alkaline protease derived from A. Flavus. It grows rapidly on wheat bran and produce large amount of protease.

Enzymes from bacteria have gained much importance because of commercial interest , easy production, high yield and easy recovery of enzyme. Examples are, Bacillus and Streptomyces spp.

Keratinases: hydrolyse Keratins are obtained from S. fradiae.

Enzymes in Soaking:

Soaking is the first operation where in hides and skins are cleaned and softened with water. Soaking is necessary for solubilisation and elimination of salts and globulin proteins contained within fibrous structures of hides and skins. It is carried out at alkaline conditions at temperature of 10-20⁰C.

Advantages of soaking are production of leather with less wrinkled skin.

Alkaline Proteases of Bacterial & Fungal origin has been used for soaking which reduces the need of chemicals.

Enzymes in Bating:

Bating is a process in which hides are softened by treating them in warm infusion of animal dung and product used for such purposes is called as BATE. Main objective of bating is to remove proteinaceous materials like albumin, globulins, mucoids from hides and skin and allow splitting up of collagen fibres to facilitate penetration of tanning materials and other chemicals, thereby giving finished leather with desired properties like feel, softness and pliability etc. Principal materials which a bate contains are proteolytic enzyme, a carrier for enzyme, wood flour and deliming agent like Ammonium chloride.

Enzymes from Aspergillus spp. are used in bating.

A combination of both mold and pancreatic enzymes are ideal bates.

Enzymes in Degreasing:

Degreasing is an essential step for production of glove and clothing leather. This process involves removal of excess natural fats from greasy skin. This grease results in defects like uneven dyeing, finishing and staining. Degreasing helps to obtain soft and pliable;e leather for garment manufacture.

It is carried out using aqueous emulsification with detergents or by solvent extraction since solvents are hazardous. So Lipase is used as an alternative for various solvents.

Acid Lipase from Rhizopus has been very effective in degreasing of sheep skins.

Fungal Lipase from A. Niger is also a good degreasing agent.

Alkaline Bacterial Lipase at pH of 9-9.4 is good for degreasing pig skin.

Enzyme (Cellulase ) Production

2013-01-26T03:59:00.000-08:00

CELLULASE PRODUCTION

Cellulase term is referred to all enzymes which cleave beta, 1-4 glycosidic linkages in cellulose. Many bacteria and fungi are celluloytic but preparations marketed for industrial applications are derived from Aspegillus niger, Neurospora and Trichoderma viridae. Aspergillus enzyme exerts good activity on CMC (carboxy methyl cellulose) but fails to attack on solid cellulose because it lacks a important component i.e. C₁ Cellulase. Cellulase is multienzyme complex with 2 important components called C₁ and C_x. Both have important functions.

C₁can attack upon native cellulose of higher crystallinity while C_x cannot attack such kind of cellulose but can split in turn the cellulose fragments which have been derived by action of C_1.

Trichoderma produces an enzyme complex with high levels of C₁ cellulase which extensively degrades insoluble cellulose.

Cultivation & Purification

In large scale fermentation A. niger is mostly cultured by wheat bran tray method. This process yields high levels of enzyme. Extraction of cellulose from solid substrate cultures is performed by percolation of dried mold bran with 0.02 to 0.1 M lactic acid.

Neurospora and Trichoderma are grown by submerged culture. For continuous culture it is advantageous that T. Viride produces a suspension of short mycelia threads, rarely forming pellets. For submerged cultivations bran and wheat straw pre-treated with alkali can be used as a source of cellulose. Ammonium ions can be used a suitable nitrogen source. A correct pH profile is necessary to give optimum enzyme yields in batch culture concentration and purification of enzyme is carried out by precipitation, adsorption and gel filtration techniques.

Ammonium sulphate is used for precipitation followed by centrifugation at 10,000 g for 10 minutes. After separating the sediment supernatant is subjected to re centrifugation for 10,000 g for 10 minutes. Precipitates are suspended in 0.5 M acetate buffer with pH 5 and crystallisation procedures are followed.

Industrial Uses

Ø Cellulase is currently used to improve texture and palatability of poor quality vegetables.

Ø It also accelerates drying of vegetables.

Ø A potential use of cellulose is conversion of cellulosic material to glucose and other sugars which in turn can be used as microbial substrates in variety of fermentations e.g. Alcohol.

Computer Applications in Fermentation Technology

2012-05-04T22:41:00.001-07:00

Computer Applications in Fermentation Technology

The use of computers for for modelling fermentation processes started in 1960s. Initially the use of computers was restricted because of the cost factor but reductions in the cost and the availability of the cheaper small computers has widened interest in their possible applications. The availability of efficient small computers has led their use for pilot plants and laboratory systems because the financial costs for the online computer systems counts the insignificant part of the whole system. There are three distinct systems areas of computer function postulated by Nyiri in 1972:

a) Logging of Process Data: This is performed by the data acquisition which has both hardware and software components. there is an interface between the sensors and the computer. the software should include the computer program for sequential; scanning of the sensor signals and the procedure of data storage.

b) Data Analysis: Data reduction is performed by the data analysis systems which is acomputer program based on a series of mathematical equations. the analysed information may be put on a print out, fed into data bank or utilized for process control.

c) process control: is also performed by a computer program. signals from the computer are fed tio the pumps, valves or switches via the interface. in addition to this computer program may contain instructions to display devices or teletypes to indicate alrms.

Components of Computer Linked system:

When a computer is linked to a fermenter to operate as a control and recording system, a number of factors must be considered to ensure taht all the components interact and function satisfactorily for the control a d data logging.An example is DDC (Direct Digital Control) system to explain the computer controlled addition of a liquid from a resrvoir to a fermenter.

A simple outline of the main components is as follows:

Sensor S in fermenter produces a signal which may need to be simplified and conditioned in the correct analogue form. at this stage it is necessary to convert the signal to a digital form which can be subsequently transmitte dto the computer. An interface is placed in the circuit at this point. The interface serves as the junction point for the inputs from the fermenter sensors to the computers and output signals from the computer to the fermenter controls such as a pump T attached to an additive reservoir.

A sensor will generate a small voltage proportional to the parameter it is going to measure. for example a temperature probe might generate 1V at 10^oC and 5V at 50^oC. But this signal cannot be understood by the computer and must be converted from an analogue to digital converter ( ADC) into digital form.

The accuracy will depend upon the number of bits it sends to the computer. AN 8-bit converter will work in the range of 0-255 and it is tehrefore able to divide a signal voltage into 256 steps. This will give amaximum accuracy of 100/256, which is pproximately 0.4%. However a 10- bit converter can give 1024 steps with a n accuracy of 100/1024, which is pproximately 0.1%. therefore when a parameter is to be monitored very accurately a converter of the appropraite degree of accuracy will be required. the time taken for an ADC to convert voltage signals to a digital output will vary with accuracy, but improved accuracy will lead to slower conversion and hence slower control responses. The small computers is often used for one or more fermenters. it is coupled to a real time clock, which determines how frequently readings from teh sensor should be taken and possibly recorded. Ancillary equipments include a VDU, a data store , a teletype, a graphic display unit, a print out, alarms and barometer.

It is also possible to develop online programs so that online instruments can be checked regularly and recalibrated when necessary.

P.S.

Next post will be about the details of three distinct areas.
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Most Astounding Fact About The Universe

2012-03-05T18:44:00.000-08:00

http://thenextweb.com/shareables/2012/03/06/the-most-outstanding-fact/

INDUSTRIAL ALCOHOL PRODUCTION

2012-03-01T18:40:00.002-08:00

Industrial Alcohol
The production of industrial alcohol, ethanol become commercially feasible on a large scale after 1906 when the Industrial Alcohol Act was passed. This act allowed the sale of tax-exempt alcohol, if it has first denatured to prevent its use in various Alcohol beverages. Industrial Alcohol is commonly employed as a solvent and to a lesser extent as a raw material for chemical synthesis. Smaller amounts are also used as a motor fuel like gasoline.
Microorganism:
Choice of fermentation microorganism for the alcohol production depends upon the type of carbohydrate employed in the medium. For example if starch and sugar are raw materials in the medium then specially selected strains of Saccharomyces crevisiae are utilized. Production from Lactose of whey is accomplished with Candida pseudotropicalis. If it is sulfur waste liquor fermentation the Candida utilis is the best organism, because of its ability to ferment pentoses. So particular strains of these various organisms actually employed for the fermentation are selected for several properties. They must grow rapidly, have higher tolerance to the high concentartions of sugar but at the same time they must be able to produce much larger amounts of alcohol and be resistant to the produced alcohol.
Media
The media for the commercial production includes:
Blackstrap Molasses / Corn (Blackstrap molasses has greater use)
Grains
Sulfite waste liquor
Whey
Patatoes
Wood Wastes

For Molasses fermentation , molasses must be diluted with water to a sugar conc. between 10 -18%. Concentrations greater than 20% are not employed as they could be detrimental to yeast. The pH of the medium is set between 4 -5 by adding sulfuric acids or lactic acids, or by employing Lactic acid bacteria to bring initial lactic acid fermentation. Microbial contaminants are usually inhibited by the low pH, high sugar conc. and anaerobic conditions of the fermentation and by the high alcohol production by the yeast.
Starchy media such as corn, rye and barley must undergo initial starch hydrolysis. This can be accomplished by mashing with barley malt, by addition of dilute acids or by utilizing fungal amylolytic enzymes (Aspergillus and Rhizopus).In most of the cases, malt is used to accomplish hydrolysis of starch By mixing 30% barley and 70% corn with water and carry on the mashing procedures similar to the wine or nbeer making procedures.
Fermentation:
Fermentation is carried out in large reactors at a temperature between 21 - 27^oC, but heat evolution might raise the temperature to 30^oC, so cooling coils are used to bring the temperature down. Fermentation lasts for about 2-3 days, but actual time period depends upon the substrate utilized and temperature. The fermentation broth at completion of fermentation ranges from 6 -9 percent alcohol by volume and this alcohol reflects the yield 0f 90 -98% theoretical conversion of substrate sugar to alcohol.So yileds should not be confused with "proof" as proofing means alcohol concentartion designation and it will be twice the percentage in vol of ethanol as dissolved in water e.g. 70% ethanol is 140 proof.

FERMENTATION ECONOMICS

2012-03-01T03:02:00.002-08:00

Fermentation Economics:

The objective of any successful fermenttaion process is the ability to produce a fermentation product. Thus the product must be sold to recover all the costs along with desired profit. But manufacturing should be done in accordance with the market demand. So there could be 2 possibilities:

First possibilty is : That the market for so called product already exist because the same or similar product has previously been sold by others.

Second possibilty is : a newly manufactured or discovered product e.g. a new antibiotic will require a market to be established.

This might include the approval by FDA ( food and drug adminstration)

There are certain obstacles regarding the marketing of a certain product like the semand of the product is low or it has relatively very few uses.so its quite obvious that for a product lke this it could be challenging to get patent coverage because of lack of utility.

for the products which are already in the market , there could be a fierce competition. so to succed in the competition the product must be cheap enough that it can be sold at or slightly less than the already existing selling price. So, in the nutshell, the whole fermentation process and its product must be able to compete on an economically sound basis with the similar products in the market.

The economic position of a fermentation product is closely tied to the costs associated with its production and distribution. These costs can be categorised into several classes as follows:

Media components:

The competitive postion and expected profits from a fermentation product are closely tied to the costs of the various components of the production medium. usually inoculum medium is less expensive because it is required to provide rapid cell growth only and not for converting large amount of carbon substarte into a fermentation product. However any medium component may be subject to fluctuations in context to availabilty and costs. so it is always advantageous to have a alternative medium for use if any unusual situation happens.

Labor Costs:

labor costs involve technical ad non technical trained personnel at all levels of competence. This includes handling of cultures, inoculum, production, product recovery and purification, packaging, cleaning and adminstartion and so forth. Labor costs vary from fermentation to fermentation.

Contamination and sterlization:

Contamination always add costs to any fermentation process. most fermentations cannot survive serious conmtaminations so the medium must be discardedmodertae fermentations does not require the medium to be discarded but it might affect the yields. Certain fermentations are more prone to contamination than others. This involves cases in which foaming is a problem. some are more sensitive to phage infections like bacterial fermentations. So there has to be an alternate method for the contaminant growth. Such methods include low pH of the medium, partial heat treatment of the medium and inclusion of certain chemicals so a sto retad contaminant growth.

Yield and Product Recovery:

Product Yield and Recovery are the prime considertaions of fermentation economics and in that context yield and recovery must be considered together, since high yield id of little value if the product cannot be recovered properly for sale.

Product Purity:

At one end of the scale some products, like antibiotic preprations must be sterile and free from pyrogens. In contrast other antibiotic preprations are sold in crude form for mixture with animal feeds. Thus the purity level required for the marketing of a fermentation product has a major effect on the costs associated with the product.Specific fermentation products can also be marketed at more than one concentartion as level of purity. For example, lactic acid is sold at strengths ranging from approx 20 - 85% and its purity levels range from crude technical grade to high purity edible and U.s.P. grades. Each of these grades of lactic acid has a place on the market.

Waste Disposal:

Costs attributed to waste disposal vary from minimal to maximal factor in fermentation process. A critical consideration is the acceptance of waste by Municipal's STW (Sewage Treatment Works); as they might want pre treatment of wastes before the acceptance. In the altter case the fermentation company must have its own waste treatment plant. Disposal of wastes is no longer simple in contrsat to historical disposal in the rivers, streams or other water bodies. Certain fermentations require the waste to be sterlized before disposal.

Research Costs:

Fermentation process must include those expenses incurred in the research that actually discovered the process nad developed it. These costs can be considerable for those fermentations where they provide new products .there are less tangible research costs that must also be considered in the overall cost of fermentation. This type of reserach is pursued in teh hope that teh resulting basic information obtained on the growth and synthetic activities of microbes will be of later value in defining areas of exploration and approaches for discovering new fermentation processed and bettering old processes.

An appraisal of the economic potential is required for the fermentation process which evaluate all the above categories under present and future market protential. but evaluation must be made as early as possible during process development. Also process must be evaluated at later stages during actual production. It is also important to consider present and future costs and a selling price for the product that market can bear.. All these points must be evaluated and then decide whether the fermentation product can be sold at an acceptable level of profit or not? If the decisons are negative then the alternatives are to abandon the whole process and carry out further reesarch on the product recovery. After all a great deal of money is at stake in these decisons!!!

Reference: Casida, L.E. Industrial Microbiology

Media Sterlization

2012-02-12T07:04:00.000-08:00

Media Sterlization:

Media can be treated by variety of methods like radiations, filtration, ultrasonic treatment and heat. Practically the universal and most favourable method for sterilization is the steam.

Kinetics of Sterlization:

The destruction of microorganisms by steam or the moist heat can be described by the first order chemical reaction and can be represented by the following equation:

- dN / dt = kN Eq no. 1

N is no. Of viable organisms present

t is the time of sterilization treatment.

k is the reaction rate constant or the specific death rate

Upon integration of equation no.1 we get:

N_t / N₀ = e ^–kt Eq no. 2

N₀is no. of viable organisms presentat the start of sterilization

N_tis the no. Of viable organisms after treatment period t

Upon taking natural logarithms of the Eq. No. 2 we get:

ln (N_t/ N₀) = -kt Eq no.3

A plot of natural logarithm of N_t/ N₀against time will yield a straight line ; the slope of which is equalto – k (see the fig. ABOVE)

So we can make 2 anomalous predictions from the plot:

1. An infinite time is required to achieve sterile conditions. ( Nt = zero)

2. After a certain period of time there will less than one viable cell present.

But the above plots can be observed only when the sterilization of pure culture is done in one physiological form only and that too under the ideal sterilization conditions. Thus, the value of k is not only species dependent but also on the physiological form of the cell e.g. endospores of genus Bacillus will be more heat resistant than the vegetative cells.

Considering this factor Richards in 1968 has produced a series of graphs (see Graphs below) which illustrate the deviation from the theory which can be expressed in the practice.

GRAPH 1

GRAPH 2

Above 3 graphs illustrate the effect of time of heat treatment on the survival of a population of bacterial endospores.

Graph 1 shows the initial population increase resulting from heat activation of spores in early stages of sterilization; followed by the decline in viable spore number. Activation o spores is significantly more than their destruction during early stages of the process and therefore viable number of spores increases before the observation of exponential decline.

Graph2 illustrates the initial stationary period followed by the decline; owing to the fact that the death of the spores is compensated by the heat activation of spores.

Graph 3 shows the population decline at a sub maximum rate due to the death of the spores.

GRAPH 3

Now we know that with any first order reaction, the reaction rate increases with temperature increase due to increase in the reaction rate constant which is the case of destruction of microorganisms (i.e.specific death rate constant; k).

Thus, the relationship between the temperature and reaction rate constant can be expressed by Arrhenius Equation:

dlnk/dT = E/RT²Eq no 4:

E is the Activation energy

R is gas constant

T is absolute temperature

Upon integration of Eq. no 4 we get:

k= Ae^{- E/RT}Eq. no 5:

A is Arrhenius constant

On taking natural Logarithms Eq no. 5 becomes:

ln k = ln A - E/Rt Eq. No.6:

By combining Eq. no. 3 and 5 following expression can be derived for heat sterilization of a pure culture at a constant temperature:

ln (N_t/ N₀) = A.t.e ^–E/Rt Eq. no. 7

Deindoerfer and Humphery used the term ln (N_t/ N₀) as a design criterion for the sterilization which has been called as DEL Factor or NABLA factor.

Del factor is a measure of fractional reduction of viable organism count produced by a certain heat and time regime. Therefore:

∇ = ln (N_t/ N₀₎

But; ln (N_t/ N₀₎ = kt

& kt = A.t. e ^–E/Rt

Thus, ∇ = A.t. e ^–E/Rt Eq. no. 8

On rearranging equation no. 8 becomes :

ln t = E/RT + ln ( ∇ /A) eq. no 9

Thus, a plot of the natural logarithm of the time required to achieve a certain ∇ value against the reciprocal of the absolute temperature will yield a straight line, the slope of which is dependent on the activation energy.( see fig below)

So a regime of time and temperature can be determined if we want to achieve the desired Del factor. However , as we know fermentation medium is not an inert mixture of components so it is very likely that deleterious reactions occur , resulting in loss of nutrient quality. Two types of reactions occur during sterilization as follows:

(i) Interactions between nutrient components of the medium. A common occurrence during sterilization is the Maillard-type browning reaction which results in discoloration of the medium as well as loss of nutrient quality. These reactions are normally caused by the reaction of carbonyl groups, usually from reducing sugars, with the amino groups of amino acids and proteins. Problems of this type are normally resolved by sterilizing the sugar separately from the rest of the medium and recombining the two after cooling.

(ii) Degradation of heat labile components. Certain vitamins, amino acids and proteins may be degraded during a steam sterilization regime. In extreme cases, such as the preparation of media for animal-cell culture, filtration may be used.

P.S I do not owe any of the above text.

References:

Shuler, M.L. and Kargi, F. (2002) Bioprocess Engineering: Basic Concepts. 2 nd Edition. Prentice Hall,

Stanbury, P. , Whittaker, A. (2004) Principles of Fermentation Technology

Facts About DNA

2012-02-06T06:02:00.000-08:00

Facts About DNA

DNA stands for deoxyribonucleic acid.
DNA is part of our definition of a living organism.
DNA is found in all living things.
DNA was first isolated in 1869 by Friedrich Miescher.
James Watson and Francis Crick figured out the structure of DNA.
DNA is a double helix.
The structure of DNA can be likened to a twisted ladder.
The rungs of the ladder are made up of “bases”
Adenine (A) is a base.
Thymine (T) is a base.
Cytosine (C) is a base
Guanine (G) is a base.
A always pairs with T in DNA.
C also pairs with G in DNA.
The amount of A is equal to the amoun tof T, same for C and G.
A+C = T+G
Hydrogen bonds hold the bases together.
The sides of the DNA ladder is made of sugars and phosphate atoms.
Bases attached to a sugar; this complex is called a nucleoside.
Sugar + phosphate + base = nucleotide.
The DNA ladder usually twists to the right.
There are many conformations of DNA: A-DNA, B-DNA, and Z-DNA are the only ones found in nature.
Almost all the cells in our body have DNA with the exception of red blood cells.
DNA is the “blueprint” of life.
Chromosomal or nuclear DNA is DNA found in the nucleus of cells.
Humans have 46 chromosomes.
Autosomal DNA is part of chromosomal DNA but does not include the two sex chromsomes – X and Y.
One chromosome can have as little as 50 million base pairs or as much as 250 million base pairs.
Mitochondrial DNA (mtDNA) is found in the mitochondria.
mtDNA is only passed from the mother to the child because only eggs have mitochondria, not sperm.
There’s a copy of our entire DNA sequence in every cell of our body with one exception.
Our entire DNA sequence is called a genome.
There’s an estimated 3 billion DNA bases in our genome.
One million bases (called a megabase and abbreviated Mb) of DNA sequence data is roughly equivalent to 1 megabyte of computer data storage space.
Our entire DNA sequence would fill 200 1,000-page New York City telephone directories.
A complete 3 billion base genome would take 3 gigabytes of storage space.
If unwound and tied together, the strands of DNA in one cell would stretch almost six feet but would be only 50 trillionths of an inch wide.
In humans, the DNA molecule in a non-sex cell would have a total length of 1.7 metres.
If you unwrap all the DNA you have in all your cells, you could reach the moon 6000 times!
Our sex cells–eggs and sperm–have only half of our total DNA.
Over 99% of our DNA sequence is the same as other humans’.
DNA can self-replicate using cellular machinery made of proteins.
Genes are made of DNA.
Genes are pieces of DNA passed from parent to offspring that contain hereditary information.
The average gene is 10,000 to 15,000 bases long.
The segment of DNA designated a gene is made up of exons and introns.
Exons have the code for making proteins.
Introns are intervening sequences sometimes called “junk DNA.”
Junk DNA’s function or lack thereof is a source of debate.
Part of “junk DNA” help to regulate the genomic activity.
There are an estimated 20,000 to 25,000 genes in our genome.
In 2000, a rough draft of the human genome (complete DNA sequence) was completed.
In 2003, the final draft of the human genome was completed.
The human genome sequence generated by the private genomics company Celera was based on DNA samples collected from five donors who identified themselves only by race and sex.
If all the DNA in your body was put end to end, it would reach to the sun and back over 600 times (100 trillion times six feet divided by 92 million miles).
It would take a person typing 60 words per minute, eight hours a day, around 50 years to type the human genome.
If all three billion letters in the human genome were stacked one millimeter apart, they would reach a height 7,000 times the height of the Empire State Building.
DNA is translated via cellular mechanisms into proteins.
DNA in sets of 3 bases, called a codon, code for amino acids, the building blocks of protein.
Changes in the DNA sequence are called mutations.
Many thing can cause mutations, including UV irradiation from the sun, chemicals like drugs, etc.
Mutations can be changes in just one DNA base.
Mutations can involve more than one DNA base.
Mutations can involve entire segments of chromosomes.
Single nucleotide polymorpshisms (SNPs) are single base changes in DNA.
Short tandem repeats (STRs) are short sequences of DNA repeated consecutively.
Some parts of the DNA sequence do not make proteins.
Genes make up only about 2-3% of our genome.
DNA is affected by the environment; environmental factors can turn genes on and off.
There are many ways you can analyze your DNA using commercially available tests.
Paternity tests compare segments of DNA between the potential father and child.
There are other types of relationship testing that compares DNA between siblings, grandparents and grandchild, etc.
DNA tests can help you understand your risk of disease.
A DNA mutation or variation may be associated with a higher risk of a number of diseases, including breast cancer.
DNA tests can help you understand your family history aka genetic genealogy.
DNA tests can help you understand your ethnic make-up.
DNA can be extracted from many different types of samples: blood, cheek cells, urine.
DNA can be stored either as cells on a cotton swab, buccal brush, or frozen blood or in extracted form.
In forensics, DNA analysis usually looks at 13 specific DNA markers (segments of DNA).
The odds that two individuals will have the same 13-loci DNA profile is about one in one billion.
A DNA fingerprint is a set of DNA markers that is unique for each individual except identical twins.
Identical twins share 100% of their genes.
Siblings share 50% of their genes.
A parent and child share 50% of their genes.
You can extract DNA at home from fruit and even your own cheek cells.
DNA is used to determine the pedigree for livestock or pets.
DNA is used in wildlife forensics to identify endangered species and people who hunt them (poachers).
DNA is used in identify victims of accidents or crime.
DNA is used to exonerate innocent people who’ve been wrongly convicted.
Many countries, including the US and UK, maintain a DNA database of convicted criminals.
The CODIS databank (COmbined DNA Index System) is maintained by the BI and has DNA profiles of convicted criminals.
Polymerase chain reaction (PCR) is used to amplify a sample of DNA so that there are more copies to analyze.
We eat DNA every day.
DNA testing is used to authenticate food like caviar and fine wine.
DNA is used to determine the purity of crops.
Genetically modified crops have DNA from another organism inserted to give the crops properties like pest resistance.
Dolly the cloned sheep had the same nuclear DNA as its donor mom but its mitochondrial DNA came from from the egg mom. (Does that make any sense?)
People like to talk about DNA even if it bears no relation to science or reality.
A group of bloggers who write regularly about DNA and genetics have banded to gether to form The DNA Network.
Lists about DNA can get a little boring.

INTERESTING????

GET MORE INFO HERE EYEONDNA.COM

AMAZING PHENOMENON OF SAND CASCADES ON MARS

2012-02-04T06:25:00.000-08:00

Dark Sand Cascades on Mars

They might look like trees on Mars, but they're not. Groups of dark brown streaks have been photographed by the Mars Reconnaissance Orbiter on melting pinkish sand dunes covered with light frost. This image was taken in 2008 April near the North Pole of Mars. At that time, dark sand on the interior of Martian sand dunes became more and more visible as the spring Sun melted the lighter carbon dioxide ice. When occurring near the top of a dune, dark sand may cascade down the dune leaving dark surface streaks -- streaks that might appear at first to be trees standing in front of the lighter regions, but cast no shadows. Objects about 25 centimeters across are resolved on this image spanning about one kilometer. Close ups of some parts of this image show billowing plumes indicating that the sand slides were occurring even when the image was being taken.

Image Credit: HiRISE, MRO, LPL (U. Arizona), NASA

WINE PRODUCTION

2011-12-14T06:48:00.000-08:00

WINE PRODUCTION

Wine is the product of grapes which can be obtained after alcoholic fermentation by yeast. Technically it is the transformation of sugars of grapes by yeast under anaerobic conditions into carbon dioxide, ethanol and some by products. Wine can also be produced by the fermentation of the fruit juices, honey and berries.

a) Wine from Grapes: Basically two types of grapes: Red and white ones are used for production of 2 different types of wines; namely RED WINE AND WHITE WINE. Grapes with a sugar content of 15- 20% are appropriate for extraction after harvesting. Whole process involves stemming, cleaning, crushing followed by addition of sodium or potassium meta-bisulphite to check the growth of undesirable organisms. Crushed grapes so obtained are known as MUST.

b)Fermentation: Fermentation is carried out by adding 2-5% of wine yeast namely: Saccharomyces crevisiae in the MUST. The contents should be mixed twice a day by punching the cap of floating grapes so as to allow the profuse growth of yeast due to increase in aeration. This step helps in extraction of colour. Thereafter mixing should be stopped and anaerobic fermentation is carried out by maintaining temperature at 24-27⁰C for about 3-6days (in case of red wine) and around 10 – 20⁰C for about 4-12 days (in case of white wine).

c)Recovery: Once the fermentation is completed the fermented juice is drawn off and stored under the atmosphere of CO₂for further fermentation for about 7 – 12 days temperature of 21-29⁰C.

Thereafter wine is pasteurized before aging. During pasteurization the protein is precipitated and removed. After filtering the wine is transferred in the wooden tanks. It is believed that aging is important for imparting flavour, aroma, sanctity and colour to the wine. After aging wine is ready to clarify and then it is bottled.

PRIMARY AND SECONDARY METABOLITES

2011-12-06T22:32:00.001-08:00

PRIMARY & SECONDARY METABOLITES

The metabolism can be defined as the sum of all the biochemical reactions carried out by an organism. It involves two pathways: Primary metabolic pathways (PMPs) produce too few end products while secondary metabolic pathways (SMPs) produce too many products.

PMPs require the cell to use nutrients in its surroundings such as low molecular weight compounds for cellular activity. There are three potential pathways for primary metabolism: the Embden Meyerhof-Parnas Pathway (EMP), the Entner-Dourdorof pathway and the hexose monophosphate (HMP) pathway. The EMP pathway produces two molecules of pyruvate via triose phosphate intermediates. This pathway occurs most widely in animal, plant, fungal, yeast and bacterial cells. Many microorganisms however use this pathway solely for glucose utilization. During primary metabolism hexoses such as glucose are converted to single cell protein (SCP) by yeasts and fungi. Yeasts from the Sachcharomyces species produce alcohol as cells grow during the log phase using an anaerobic primary metabolic pathway. This account for most of the alcohol found in nature and is widely used in the fermentation industry to produce beer, wine and spirits.

For example in the citric acid fermentation process involving Aspergillus Niger, hexoses are converted via the EMP pathway, to pyruvate and acetyl Co-A which condenses with oxaloacetate to form citrate in the first step of the TCA cycle. Ethanol, lactic acid and acetic acid were the first commercial products of the fermentation industry. Several of these products have applications as alternative energy sources, for example alcohol has been used to produce a cheaper alternative to petrol in developing countries such as Brazil and in Europe between World Wars I and II.

Secondary metabolism synthesises new compounds. Secondary metabolites are not vital to the cells survival itself but are more so for that of the entire organism. Relatively few microbial types produce the majority of secondary metabolites. Secondary metabolites are produced when the cell is not operating under optimum conditions e.g. when primary nutrient source is depleted. Secondary metabolites are synthesized for a finite period by cells that are no longer undergoing balanced growth. A single microbial type can produce very different metabolites. Streptomyces griseus and Bacillus Subtillus each produce more than fifty different antibiotics. Most secondary metabolites are produced by families as closely related compounds. The chemical structure and their activities cover a wide range of possibilities, including antibiotics, ergot alkaloids, naphtalenes, nucleosides, peptides, phenazines, quinolines, terpenoids and some complex growth factors. The production of economically important metabolites such as antibiotics by microbial fermentation is one of the major activities of the bioprocess industry.

Secondary metabolites such as penicillin are produced during the stationary phase (idiophase) of cell growth. Most of the knowledge concerning secondary metabolism comes from the study of commercially important microorganisms.

There are some similarities between the pathways that produce primary and secondary metabolites, namely that the product of one reaction is the substrate for the next and the first reaction in each case is the rate-limiting step. Also the regulation of secondary metabolic pathways is interrelated in complex ways to primary metabolic regulation.

Primary Metabolites

Fermentation products of primary metabolism such as ethanol, acetic acid, and lactic acid were the first commercial products of the fermentation industry. These industrial revelations were soon followed by citric acid production along with other products of fungal origin. Due to the high product yield and the low reproducibility costs, major interest has been shown in the respective markets. Production of cell constituents i.e. lipids, vitamins, polysaccharides as well as intermediates in the synthesis of cell constituents such as amino acids and nucleotides are also of great economic importance in present-day industry. The effectiveness of yeasts along with other microorganisms as sources of the B-group vitamins has been recognized for more than 50 years and like products of catabolic primary metabolism e.g. ethanol, citric acid etc. are of great commercial importance.

Citric acid is an organic acid that is of major economic use in today’s industry. It is a very important commercial product and is widely used in the food and beverage industries as a food additive. In addition to the beverage and food industry, citric acid is used in effervescent powders as well as being used in boiler and metal cleaning. Factors effecting citric acid production vary considerable and depend predominantly on the strain of A. niger used. Other factors that affect citric acid production include the type of raw material fermented, the amount of methyl alcohol present, the substrate’s initial moisture content as well as the fermentation time and temperature. Much research has been conducted over the years in order to increase the yield of citric acid production.

Nucleotides are used in the preparation of poly and oligonucleotides as well as being of potential nutritional and medical interest. However the greatest interest in nucleotides lies in the fact that they have the ability to enhance the flavour of foods. Yeast extract is extensively used as a flavouring agent in the food industry and is widely available either in powder or paste form. After autolysis and partial hydrolysis of RNA, ribonucleotides such as 5’-monophpsphate (GMP) and inosine 5’-monophosphate (IMP) may be extracted from the biomass. Flavour enhancement is a property of these purine ribonucleosides as well as the ribonucleoside, xanthylic acid (XMP). These food enhancers are responsible for meaty flavours found in foods and are available on the market worldwide. These products are of major importance in the food industry and currently international trade surpasses US $1.1 billion per year (23).

Secondary Metabolites

Antibiotics were first defined as a chemical compound produced by a microorganism, which has the capacity to inhibit the growth of and even destroy bacteria and microorganisms in dilute solutions. Sir Alexander Fleming first discovered the antibiotic properties of the mould Penicillin notatum in 1929 at St. Mary’s hospital in London, when he noticed that Penicillin

notatum destroyed a staphylococcus bacterium in culture. Penicillin is bactericidal to a number of gram-positive bacteria and acts by inhibiting transpeptidation thus preventing new cells from forming walls. It belongs to the beta-lactam family of antibiotics. During World war two research was moved to the USA where large-scale growth of the mould began. Firstly penicillin moulds were grown in small shallow containers on nutrient broth. Methods of growth were improved by using deep fermentation tanks with continuous sterile air supply and corn steep liquor as a source of nutrients. In 1943 a cantaloupe mould, P. Chysogenum was found to produce twice the amount of penicillin than P. notatum. Since then researchers continued to find higher yielding penicillin moulds and have also improved yields further by exposing moulds to x-rays and UV light. The first type of penicillin produced was Penicillin G, which had to be administered to patients parenterally because it is broken down by stomach acid. Penicillin V was later formulated so that it could be taken orally; unfortunately it was less active than Penicillin G.

The enhancement of antibiotic industrial yield has been achieved through traditional strain improvement programs based on random mutation and screening. Recombinant DNA techniques have existed since the 1970’s and involve the introduction of DNA fragments into host cells using a vector (a plasmid or phage) that contains a selection marker. The DNA fragments are integrated into the host genome or autonomously replicated as a plasmid. Transformants are then screened for improved characteristics. The pharmaceutical company Eli Lilly was responsible for the first recombinant DNA improvement of an antibiotic producing microorganism. Transformation of C. acremonium 394-4 caused an increase in the amount of antibiotic cephalosporin C excreted by the organism. Cephalosporins are beta-lactam compounds that are structurally and pharmacoligically related to penicillins. Cephalosporins resist hydrolysis by enzymes referred to as penecillinases, which are secreted by a number of bacteria. They are now one of the most widely prescribed antibiotics and are very effective for the treatment of hospital-acquired infections.

Actinomycetes are aerobic spore forming bacteria that originate from soil. A large number of antibiotics are produced by actinomycetes and in particular Streptomyces. They resemble a fungal mycelium in form, but have thinner filaments. These filaments are formed when cells divide to form long chains of up to 50 cells. Actinomyces griseus was first isolated from soil in the Andes, this bacterium produced a substance that killed many bacteria unaffected by penicillin, including Tuburculosis bacillus. The antibiotic was named streptomycin. However tubercle bacilli soon became resistant to streptomycin and it has since been replaced by para-amino-salicylic acid (PAS). Stretomycetes are still very important bacterial producers of antibiotics and cytostatics. Due to the emerging resistance of bacteria to common antibiotics, new technologies such as combitatorial biosynthesis are being used for the production of novel metabolites using streptomycetes. This technology involves the use of a combination of genes from different biosynthetic pathways to produce modified metabolites.

Ordinarily Actinomycetes use the EMP pathway to metabolise glucose because this pathway is a more efficient one than the ED pathway. The secondary metabolites of the fungi including Drechslera, Trichoderma, Aspergillus and Curvularia have the ability to produce green dyes / anthraquinones.. These dyes are from natural sources and do not cause the pollution to the environment associated with chemical dyes.

So in nutshell Industrially important primary microorganisms are continually being improved to optimize product yield and substrate utilization in order to minimize the cost of production. Primary products of microbial metabolism have made a significant contribution to the food and beverage industries. Primary metabolites have been used to produce petroleum derived products as well as ethanol for liquid fuels (gasohol). Considering the current trends in oil prices, microorganisms that have the ability to produce such products will no doubt be exploited to their full potential. In the not too distant future biomass energy could become a major contributor to the Earth’s energy requirements as petroleum resources run out. The introduction of antibiotics revolutionised the treatment of infectious disease in humans. Antibiotics are used in large quantities in animal farming to prevent infection as well as to treat diseases. Smaller doses are added to animal feed to promote growth. Fruits and vegetables are also treated for bacterial infections using antibiotics such as streptomycin and oxytetracycline. Owing to this widespread use, antibiotics have been found in liquid waste at animal feedlots and have spread into many surface and groundwater supplies. Residues of antibiotics have also been detected in sewage treatment plants and raw water resources in many European countries. The prescence of antibiotics has upset the delicate balance of microorganisms in the environment by depletion of microorganisms susceptible to antibiotics and providing favourable environments for the proliferation of resistant strains. Three EU projects were undertaken in 2003 to assess the presence and effects of antibiotics in the aquatic environment and in soils: the ERAVMIS, PEPHARMAWATER and POSEIDON projects. These projects also propose solutions to this problem, such as the removal of antibiotics from wastewater by ozonation and sunlight. Bioresearch Italia began a project to isolate previously unexploited microorganisms from actinomycetes and uncommon filamentous fungi in 2002. This project may provide some insight into methods of combating the increasing number of antibiotic resistant strains of bacteria.

References:

http://www.msu.edu/course/mmg/301/lec

Krishna, C., 19xx, Solid state fermentation systems - an overview, Journal of

Applied Microbiology, Vol. 25 Issues 1-2, pp1-30

Learry, E; Keegan, J; primary versus secondary metabolites

PENICILLIN PRODUCTION

2011-12-06T19:40:00.001-08:00

PENICILLIN PRODUCTION:

Penicillin was the first naturally occurring antibiotic discovered. It is obtained in a number of forms from Penicillium moulds. Penicillin is not a single compound but a group of closely related compounds, all with the same basic ring-like structure (a β-lactam) derived from two amino acids (valine and cysteine) via a tripeptide intermediate. The third amino acid of this tripeptide is replaced by an acyl group (R) and the nature of this acyl group produces specific properties on different types of penicillin.

There are two different types of penicillin.

Biosynthetic penicillin is natural penicillin that is harvested from the mould itself through fermentation.

Semi-synthetic penicillin includes semi synthetic derivatives of penicillin - like Ampicillin, Penicillin V, Carbenicillin, Oxacillin, Methicillin, etc. These compounds consist of the basic Penicillin structure, but have been purposefully modified chemically by removing the acyl group to leave 6-aminopenicillanic acid and then adding acyl groups that produce new properties.

These modern semi-synthetic penicillins have various specific properties such as resistance to stomach acids so that they can be taken orally, a degree of resistance to penicillinase (or β-lactamase) (a penicillin-destroying enzyme produced by some bacteria) and an extended range of activity against some Gram-negative bacteria. Penicillin G is the most widely used form and the same one we get in a hypodermic form.

PENICILLIN G

Penicillin G is not stable in the presence of acid (acid-labile). Since our stomach has a lot of hydrochloric acid in it (pH2.0), if we were to ingest penicillin G, the compound would be destroyed in our stomach before it could be absorbed into the bloodstream, and would therefore not be any good to us as a treatment for infection somewhere in our body. It is for this reason that penicillin G must be taken by intramuscular injection - to get the compound in our bloodstream, which is not acidic at all. Many of the semi-synthetic penicillins can be taken orally.

Penicillium chrysogenum that produce antibiotics, enzymes or other secondary metabolites frequently require precursors like purine/pyrimidine bases or organic acids to produce said metabolites. Primary metabolism is the metabolism of energy production for the cell and for its own biosynthesis. Typically, in aerobic organisms (Penicillium chrysogenum) it involves the conversion of sugars such as glucose to pyruvic acid2 and the production of energy via the TCA cycle. Secondary metabolism regards the production of metabolites that are not used in energy production for example penicillin from Penicillium chrysogenum. In this case the metabolite is being utilized as a defence mechanism against other microorganisms in the environment. In essence Penicillium chrysogenum can kill off the competition to allow itself to propagate efficiently. It should be noted that these secondary metabolites are only produced in times of stress when resources are low and the organism must produce these compounds to kill off its competitors to allow it to survive.

MEDIA FORMULATION:

Lactose: 1%

Calcium Carbonate: 1%

Cornsteep Liquor: 8.5%

Glucose: 1%

Phenyl acetic acid: 0.5g

Sodium hydrogen phosphate: 0.4%

Antifoaming Agent: Vegetable oil

FERMENTATION

To begin the fermentation process, a number of these spores will be introduced into a small (normally 250-500ml) conical flask where it will be incubated for several days. At this stage, explosive growth is the most desired parameter and as such the medium in the flask will contain high amounts of easily utilisable carbon and nitrogen sources, such as starch and corn-steep liquor. At this stage, the spores will begin to revive and form vegetative cells. Temperature is normally maintained at 23-280C and pH at ~6.5, although there may be some changes made to facilitate optimum growth. The flask will often have baffles in it and be on a shaking apparatus to improve oxygen diffusion in the flask.

Once the overall conditions for growth have been established and there is a viable vegetative culture active inside the flask, it will be transferred to a 1 or 2 litre bench-top reactor. This reactor will be fitted with a number of instruments to allow the culture to be better observed than it was in the shake flask. Typical parameters observed include pH, temperature, and stirrer speed and dissolved oxygen concentration. This allows tweaking of the process to occur and difficulties to be examined. For example, there may not be enough oxygen getting to the culture and hence it will be oxygen starved. At this point, the cells should be showing filamentous morphology, as this is preferred for penicillin production. As before, cell growth is priority at this stage. At this stage, growth will continue as before, however, there are often sudden changes or loss in performance. This can be due to changes in the morphology of the culture (Penicillium chrysogenum is a filamentous fungi and hence pseudoplastic) that may or may not be correctable.

At this stage the medium being added to the reactor will change. Carbon and nitrogen will be added sparingly alongside precursor molecules for penicillin fed-batch style. Another note is that the presence of penicillin in the reactor is itself inhibitory to the production of penicillin. Therefore, we must have an efficient method for the removal of this product and to maintain constant volume in the reactor. Other systems, such as cooling water supply, must also be considered. If all goes well we should have penicillin ready for downstream processing. From here it can be refined and packaged for marketing and distribution to a global market.

References:

1. Hare, T; White, L / penicillin production

2.http://nobelprize.org/medicine/educational/penicillin/readmore.html

PHOTOSYSTEM I & II; RED DROP EFFECT

2011-12-05T08:14:00.001-08:00

RED DROP EFFECT:

Wavelengths beyond 700nm are apparently of insufficient energy to drive any part of photosynthesis. So a huge drop in efficiency has been noticed at 700nm. This phenomenon is called as RED DROP EFFECT. In other words there is a sharp decrease in quantum yield at wavelengths greater than 680nm. This decrease in quantum yield takes place in the red part of the spectrum. The number of oxygen molecules released per light quanta absorbed is called as quantum yield of photosynthesis. This effect was first of all noticed by Robert Emerson of Illinois University. Later on Emerson and his group observed that if chlorella plants are given the inefficient far red light and red light of shorter wavelengths in alternate fashion, the quantum yields were greater than could be expected from adding the rates found when either colour was provided alone. This synergistic effect or enhancement is known as EEE or Emerson Enhancement Effect. This was the first good evidence that there are two photo systems; one absorbs far red light and other red light and both of them must operate to drive photosynthesis most effectively.

PHOTOSYSTEMS I & II: COMPOSITION, LOCATION AND FUNCTIONS IN THYLAKOIDS:

The two photo systems can be separated from thylakoids by PAGE.

Major green bands shows PS I which contains chl a, small amounts of chl b , some beta carotenes. One of the chl a molecule is made somehow special by its chemical environment so that it absorbs light near 700nm so it is called as P700 which is the reaction centre for PS I and to which surrounding carotenes and chlorophyll molecules in that photosystem transfer their energy. At least 2 iron containing proteins similar to ferredoxin are also present in which each of four iron atoms in each protein is bound to 2 sulfur atoms; these are called as Fe-S proteins. The Fe-S proteins are primary electron acceptors for PS I. Only one of the 4 iron atoms present can accept electrons and as a result Fe ³⁺ will be reduced to Fe^2+.Subsequently Fe²⁺ is reoxidised to Fe³⁺during electron transport pathway.

PS II also contains chl a, chl b . the eraction centre is P 680. The primary electron acceptor is colorless chl a that lacks Mg^2+. This molecule is called as pheophytin; abbreviated as pheo. Associated with pheo is quinone which is abbreviated as Q because of its ability to quench fluorescence of P680 by accepting its excited electron. PS II also contains one or more proteins containing bound manganese. It is believed that 4 Mn²⁺are bound to one or more proteins and one cl^- bridges two Mn²⁺ together.

Apart from two photosystems 2 LHCs (light harvesting complexes) are also present; one of which functions with PS I and other functions with PS II. Their function is to harvest light energy by absorbing it and transferring it to proper photosystem, where it eventually reaches to P680 pr P700.

To solve the problem of cooperation between 2 Photosystems because of their distant locations two mobile electron carriers are also present. These are PQ (plastoquinone) and PC (plastocyanin). PC is copper containing pigment which is bound loosely to inside of thylakoid membranes next to channel. When its copper becomes reduced from Cu²⁺to Cu⁺¹by PS II, it can move along the membrane carrying an electron to PS I where it is reoxidised to Cu²⁺ form. it then shuttles back to PS II and picks up still another electron. Another carrier system is a group of Quinones called PQs that moves laterally and vertically within the fluid membranes. PQs carry 2 electrons and two protons from PS II to PS I.

Cooperation of 2 PSs also require more electron transport systems. Another complex of proteins are cyt b₆_, cyt f and cyt _b3 and Fe-S protein called ferredoxin. Fd transfers electrons from other Fe-S proteins of PS I directly to NADP+ completing the electron transport process.

A final component of thylakoids essential for the photophosphorylation is ATPase or CF complex. This complex either hydrolyzes ATP to ADP and Pi. Or synthesize ATP from Pi and ADP by photophosphorylation. So ATP synthesis is strongly favoured by electron transport and electron transport is favoured by photophosphorylation, so CF couples the two processes together.

CITRIC ACID PRODUCTION

2011-12-05T03:59:00.001-08:00

CITRIC ACID PRODUCTION

The first ever commercial production of citric acid was launched in UK by Sturage Company by JOHN & EDMUND; 1826

In 1880; Citric acid was first synthesised from glycerol

In 1893; Wehmer observed occurrence of citric acid as a microbial product by using penicillium.

In 1922; Millard recorded accumulation of citric Acid In culture of Aspergillus niger under condition of nutrition deficiency.

In 1923; Pfizer began fermentation based process in USA

PRODUCTION

1. Fermentation: A. niger is the choice for production of citric acid for several decades. Large number of other microbes such as P.luteum, P.cirinum, pichia spp. Have also been used. Fermentation can be carried out by any of following processes:

a) KOJI PROCESS (solid state fermentation): it’s a Japanese process in which special strains of A.niger are used with solid substrate such as sweet potato starch. Mold is used to which wheat bran was substituted. The pH of bran was adjusted between 4–5 and additional moisture is picked up during steaming so as to get water content of mash around 70 – 80%. After cooling the bran to 30 – 60^oCthe mass is inoculated with KOJI which was made by a special strain of A.niger. Since bran contains starch which on saccharification produces citric acid by amylase of A.niger. Bran after inoculation is spread in trays to a depth of 3 – 5 cm and kept for incubation at 25-30^oC. After 5 – 8 days koji is harvested and citric acid is extracted.

b) Liquid Surface Culture Process: in this case aluminium or stainless steel shallow pans or trays are used. Sterilized medium contains molasses and salts. Fermentation is usually carried out by blowing spores of A.niger over the surface of the solution for 5-6days. Spore germination occurs within 24 hours and a white mycelium grows over the surface of the solution. After 8-10days of inoculation liquid can be drained off and citric acid can be extracted from the mycelia mat.

c) Submerged Culture Process: this method is quite economical. In this case A. japonicus (black mold) is slowly bubbled in a stream of air through a culture solution. Since organism shows subsurface growth and produces Citric acid in culture solution the yields are inferior in comparison to liquid surface culture fermentation.

Referencing a Web Page

2011-12-04T19:19:00.001-08:00

Referencing a web page

When referencing something you have found on the web you need to distinguish what you are referring to as the internet is made up of a vast range of material from journal articles to personal and organisational websites. Below is a list of information you can include:

Author/Editor or Organisation, Year the site was published or last updated, Title of work - main title and subtitle (screen heading/sub-heading), Online address or location within database - full address (URL or DOI), Date you looked at the information, the access date.

You can also include other identifying features such as a page or screen reference, paragraph or line number or perhaps a labelled section or part of a table or graph.

Type of medium - for example online database, online bulletin board.

Publisher and place of publication - for example documents on portable databases, which organisation has prepared the materials and where they are located.

Name of database.

Organisational website: following is the example for referencing a website:

National Trust (2011) Planning for the people. Available at: http://www.nationaltrust.org.uk/main/w-chl/wcountryside_environment/w-planning-landing.htm (Accessed: 20 September 2011).

Referencing BOOKS (print/online)HARVARD STYLE

2011-12-04T18:37:00.001-08:00

This article is for those students who struggle for referencing; i have assembled various types of referencing in different posts under different headings. This is Harvard style of referencing. I'm sure you want to learn it because you don't want to be the victim of plagiarism.

List of references

At the end of your essay, place a list of the references you have cited in the text. Arrange this in alphabetical order of authors' surnames, and chronologically (earliest publication date first) for each author, where more than one work by that author is cited. The author's surname is placed first, followed by initials or first name, and then the year of publication is given.

Books (print and online)

Type	Examples
One author	Cole, GHA 1991, Thermal power cycles, Edward Arnold, London. Series titles and edition statements (for editions other than the first) should be included. Goldsworthy, J 2010, Parliamentary sovereignty: contemporary debates, Cambridge studies in constitutional law, Cambridge University Press, Cambridge. Abbott, HP 2008, The Cambridge introduction to narrative, 2nd edn, Cambridge University Press, Cambridge.
Two or more authors	List all authors in the list of references. See the second part of this guide for how to cite in-text. Douglas, M & Watson, C 1984, Networking, Macmillan, London. Flexer, RW, Baer, RM, Luft, P & Simmons, TJ 2008, Transition planning for secondary students with disabilities, 3rd edn, Pearson, Upper Saddle River, New Jersey.
Two or more books in one year by the same author	List in alphabetical order by title. King, P 1984a, Power in Australia, UQP, St. Lucia. ------- 1984b, Solar power, Macmillan, Melbourne.
Edited books	If the role of an editor (or compiler, reviser or translator) is of primary importance, list the work under those names. Use abbreviations such as ed., eds, trans., rev., comp. and comps. Long, PE (ed.) 1991, A collection of current views on nuclear safety, Penguin, Harmondsworth. Ahdar, R & Aroney, N (eds) 2010, Shari'a in the West, Oxford University Press, Oxford.
Chapters in edited books	Callaghan, J 2010, 'Singing teaching as a profession', in S Harrison (ed.), Perspectives on teaching singing: Australian vocal pedagogues sing their stories, Australian Academic Press, Bowen Hills, Queensland. Shachar, A 2010, 'State, religion, and the family: the new dilemmas of multicultural accommodation', in R Ahdar & N Aroney (eds), Shari'a in the West, Oxford Unversity Press, Oxford.
Editions	The edition (if other than the first edition) is included after the main title. Morton, JS 1984, Wind power: an overview, 2nd edn, Melbourne University Press, Melbourne.
Part of a series	The series title is included after the main title. Muller, R & Turner, JR 2010, Project-oriented leadership, Advances in project management, Gower, Farnham, England. Editions go after the series title. Corrigan, T 2010, A short guide to writing about film, The short guide series from Pearson Longman, 7th edn, Longman, New York.
Anonymous (no author or editor given)	Start with the title. The eliciting of frank answers 1955, Engineering Publications, Florida.
Conference paper	Trump, A 1986, 'Power play', Proceedings of the third annual conference, International Society of Power Engineers, Houston, Texas, pp. 40-51.
Page numbers	Occasionally, it may be necessary to cite page numbers for books. If so, present the numbers as the final item of the citation as in the example above (e.g. p. 10, pp. 19-25, pp. 21-6, pp. 21, 31-5).
Acknowledging editors, compilers, revisers or translators	If the author's role remains of primary importance, editors, compilers, revisers or translators can also be acknowledged. Use abbreviations such as ed., eds, trans., rev., comp. and comps. Tolstoy, L 1930, What is art? and essays on art, trans. A Maude, Oxford University Press, London. Mayakovsky, V 1942, Mayakovsky and his poetry, comp. H Marshall, Pilot Press, London.
Corporate authors	The jurisdiction is not usually given for government agencies but is indicated by the place of publication. Department of Energy 1980, Projections of energy needs, HMSO, London. Office of the Aboriginal Land Commissioner 2001, Urapunga land claim no. 159, Parliamentary paper, Aboriginal and Torres Strait Islander Commission, Canberra. Xerox Corporation 1988, Xerox publishing standards: a manual of style and design, Watson-Guptil, New York. Parent bodies precede subdivisions. World Association of Veterinary Anatomists. International Committee on Avian Anatomical Nomenclature 1979, Nomina anatomica avium: an annotated anatomical dictionary of birds, Academic Press, London.
Online books	Author Year (of creation or last revision), Title, edition/version (if applicable), name and place of the sponsor of the source (publisher, place), viewed Day Month Year,<URL either full location details or just the main site details>. McClain, M & Roth JD 1999, Schaum's quick guide to writing great essays, McGraw-Hill, New York, viewed 17 January 2005, <http://ezproxy.usq.edu.au/login?url=http://site.ebrary.com/lib/unisouthernqld/Doc?id=5002145>. Fitzgerald, FS 1920, This side of paradise, Scribner, New York, viewed 18 January 2005, <http://www.bartleby.com/115/>.
Chapters in an online books	Author Year (of creation or last revision), 'Chapter title', in book editor(s) (ed.), Book title, name and place of the sponsor of the source (publisher, place), viewed Day Month Year, <URL either full location details or just the main site details>. Gould, SJ 2000, 'More things in Heaven and Earth', in H Rose & S Rose (eds), Alas, poor Darwin: arguments against evolutionary psychology, Harmony Books, NewYork, viewed 17 January 2005, <http://ezproxy.usq.edu.au/login?url=http://site.ebrary.com/lib/unisouthernqld/Doc?id=10015543>.

Time for fun

2011-12-02T17:57:00.001-08:00

And this one is for all those who really think that metabolism is not for them! they find it so hard to remember those complex pathways and cycles!!!

but i am sure you would love this Kreb's Cycle!!!!
;)

L-Lysine Production

2011-12-02T06:34:00.001-08:00

L-Lysine Fermentation

Out of 20 naturally occurring amino acids, L- lysine is one of 9 essential amino acids and commercially important amino acids. It is mainly used as feed additive in the animal feed industry; mixed with various common livestock such as cereals which do not contain sufficient levels of L-Lysine for the livestock’ nutritional requirements, in especially monogastric animals like broilers, poultry and swine and as a supplement for humans and improving the feed quality by increasing absorption of other amino acids.

L-Lysine can be produced by chemical or biochemical method; whichever is more economic. Gram+ve cyanobacteria strains like Corynebacterium glutamicum, Brevibacterium flavum are used for industrial production.

Fermentation Medium:

Apart from physical parameters like pH, Agitation and aeration rate and temperature; media composition is very important factor.

The seed culture to be prepared includes:

Glucose: 20g

Peptone: 10g

Meat extract: 5g

Sodium chloride: 2.5g in 1 litre of tap water

Seed culture obtained is reinoculated for 2^nd seed culture in media containing:

Molasses: 200g

Soy protein hydrolysate 18g in 1L tap H₂O

Above culture is reinoculated with B.flavum

Acetate is used as C source

After obtaining first and second media production media is used which includes:

Cornsteep liquor

Ammonium sulphate

Glycerol

CaCO₃

Incubation for 72 hours at 28 degrees

Recovery:

Fraction of lysine fermentation broth is obtained by any suitable, Methods such as Ultrafiltration or Centrifugation. In order to overcome difficulties of high viscosity in culture broth; filterability can be improved by adding a mineral acid like conc. H₂SO₄ and then heat the culture broth at 100degrees for at least 5 minutes. The resulting product is L lysine.

Random

2011-12-02T05:49:00.001-08:00

Apparently i do have a BLOG which i think is waiting for me to write !! But feeling so exhausted with this cold and fever. So i apologize to my students with whom i have promised for notes. Sorry Guys i will be back soon..
Wish you luck for the forthcoming exams.
And do let me know how did you find today's 4 Lectures in a row!!! I am sure you must be saturated enough!!

Have a Happy Learning.
And while you wait for my next post listen to this (a motivational song)
Hope you'll like it!
See you Soon.

Michaelis Menton Equation

2011-11-22T07:11:00.000-08:00

ENZYME KINETICS

The Michaelis Menton Equation: a generalized theory of enzyme action was formulated by Leonor Michaelis and Maud Menton in 1913. The derivation starts with a basic step involving formation and breakdown of the ES complex.

The overall reaction is:

k₁k₂

E + S ES E + P

k_-1

the initial velocity V₀can be determined by the breakdown of ES complex into product which is give by:

V₀= k₂ [ES] Eq No. 1

Since it is not easy to measure [ES] experimentally we should figure out an alternative expression of [ES]. So , we will consider [E_t], that denotes for total enzyme concentration.

Free or unbound enzyme can be represented by:

[E_t] – [ES]

The rate of formation and breakdown of ES can be determined by:

Rate of ES formation = k₁ ([E_t] – [ES])[S]

Rate of ES breakdown = k_-1[ES] + k₂[ES]

At the steady state rate of [ES] formation will be equal to ES breakdown so above equation can be written as:

k₁ ([E_t] – [ES])[S] = k_-1[ES] + k₂[ES]

To solve the above equation multiply the left side and simplify the right side:

k₁[E_t][S] - k₁[ES][S] = (k-_{1 +}k₂)[ES]

add the term k₁[ES][S] to both sides of the equation:

k₁[E_t][S] = (k₁[S] + k_-1 + k₂)[ES]

and then solve the equation for [ES]:

[ES] = [E_t][S]

[S] + (k₂+ k_-1)/k₁

The term (k₂+ k_-1)/k₁ is defined as Michaelis constant K_m

Substitute k_m into above equation:

[ES] = [E_t][S]

[S] + K_m

Now V₀can be expressed in terms of [ES] by substituting above equation into equation no.1:

V_{0 =} k₂[E_t][S]

[S] + K_m

Since maximum velocity occurs when enzyme is saturated with [ES] = [E_t] so V_max can be defined as k₂[E_t] so substitute the value of V₀into above equation:

V_{0 =} V_max[S]

[S] + K_m

The above equation is called as Michaelis Menton equation.

A numerical relationship exists in the Michaelis menton equation when V₀ is exactly one half of V_{max .}then:

V_max/ 2 = V_max[S]

[S] + K_m

Divide above equation by V_max we get:

½ = [S] / K_m + [S]

Solving for K_m we get K_m₊[S] = 2 [S],

Or k_m = [S] , when V₀ = ½ V_max

Transformation of Michaelis Menton equation: Double Reciprocal plot

V_{0 =} V_max[S]

[S] + K_m

Take the reciprocal of above equation:

1/V₀ = K_m + [S] / V_max[S]

Separate the components of numerator on the R.H.S of the equation and after simplification we get:

1/V₀ = K_m+ [S]

V_max[S] V_max

This equation is known as double reciprocal plot or Lineweaver Burk equation.

ENZYME INHIBITION

2011-11-22T05:40:00.000-08:00

Enzyme Inhibition

Enzyme inhibitors are the agents that interfere with the catalysis and slow down or even halt the reactions. There are 2 broad classes of enzyme inhibitors:

1. Reversible

2. Irreversible

Reversible inhibition: is characterized by a rapid dissociation of the enzyme inhibitor complex. Reversible inhibition can be:

Ø Competitive

Ø Uncompetitive

Ø Mixed / non competitive

Competitive Inhibition: In this type of inhibition a competitive inhibitor competes with the substrate for an active site of enzyme; as a result inhibitor occupies the active site and prevents the interaction of substrate with the enzyme. The competitive inhibitors are the compounds having similarity with substrate and thus they combine with enzyme to form EI (enzyme inhibitor) complex.

This theory can be better justified by the example in case of medical science; in which the therapy is based upon the competition at the active site and is used to treat patients who ingest a solvent, methanol which is usually found in the gas line antifreeze. The enzyme alcohol dehydrogenase found in our liver converts methanol to formaldehyde and results in damage to the tissues and in severe cases it causes blindness. The reason behind this blindness is that eyes are quite sensitive to formaldehyde.

The medical therapy here is to give intravenous infusion of ethanol to the patients because ethanol competes effectively with the methanol as an alternative substrate for the enzyme alcohol dehydrogenase. In other words ethanol acts as a competitive inhibitor to ethanol and the effect of ethanol can be nullified as its concentration decrease over time as the dehydrogenase enzyme converts ethanol into acetaldehyde. So intravenous infusion should be given at a rate that maintains a controlled concentration in the blood stream for several hours. This will slow down the production of formaldehyde and ultimately kidneys will excrete out the methanol harmlessly in the urine.

Uncompetitive inhibition: can be distinguished by the fact that inhibitor binds only to the enzyme substrate complex. This type of inhibition cannot be overcome by addition of more substrates.

E + S ES E + P

ESI complex

UNCOMPETITIVE INHIBITION

Mixed inhibition: the inhibitor will bind at a site distinct from the substrate active site but it will bind to either ES or E

Non competitive inhibition: the inhibitor and substrate can bind simultaneously to an enzyme molecule at different binding sites. This inhibition cannot be overcome by increasing the substrate concentration.

Both mixed and uncompetitive can be observed only for the enzymes with 2 or more substrates.

Irreversible inhibition: here the inhibitors will covalently bind to the enzyme and provides an alternative approach: they will modify the functional groups which can then be identified. Basically irreversible inhibition is important to determine what functional groups are required for enzymic activity and X-ray crystallography is the best approach. Irreversible inhibitors can be divided into 2 categories:

Suicide inhibitors: which are modified substrates that provide the most specific means to modify an enzyme active site. The inhibitors bind to the enzyme as substrates. The catalytic mechanism then generates intermediate that inactivates the enzyme through covalent modification. The fact that enzyme participates in its own irreversible inhibition; that’s why it is called as suicide inhibitor.

Affinity labels: are molecules that are structurally similar to the substrates for the enzyme and that covalently bind to the active site residues. Thus they are specific for the enzyme active site.

2011-11-20T03:17:00.000-08:00

PHOTOSYNTHESIS

Photosynthesis is a mechanism in which complex organic substances are synthesised from the inorganic substances or in other words it is a oxidation – reduction process in which water molecules are oxidised to form oxygen and carbon dioxide molecules are reduced to form sugars (carbohydrates). This reduction of CO₂ into sugars requires an energy source like ATP and NADPH (assimilatory powers). This reduction process takes place in dark conditions while production of assimilatory powers takes place in light. So there are 2 phases that occurs during photosynthesis.

Light Dependent Phase: This phase requires light so it light dependent and it is also best known as HILL Reaction after the name of its discoverer.

Light Independent Phase: This phase does not require light so it is called as DARK Reaction or BLACKMAN’s Reaction (after the name of its discoverer).

MECHANISM OF ABSORPTION OF LIGHT:

When a visible photon of light with a wavelength between 380nm and 780nm strikes the chlorophyll molecule it releases an electron from chlorophyll to an outer molecular orbital. This state of chlorophyll molecule is called as excited or an activated state. Usually the normal state of an atom or molecule is called as Ground state or Singlet state (S₀) in which the electrons are present in the even number and paired state. The excited chlorophyll molecule shows four states:

Singlet state first (S₁)

Singlet state second (S₂)

Triplet state first (T₁₎

Triplet state second (T₂)

So S₁ state would be the one when a red light photon strikes a chlorophyll molecule which becomes photo excited and an electron will be released from its ground molecular orbital to the outer molecular orbital. This state is unstable state as it has half life period of only 10^-9s and it produces two molecular orbitals each having one electron.

S₂ state will be produced in the same way as the S₀; the only difference is that this time blue light photon will photo excite the chlorophyll molecule and release electron into outer MO. The electron is raised more higher than the S₁state because blue light photon possesses more energy than red light photons. This state also produces 2 MO’s and is unstable with a half life period of 10_-9 s.

Since S₁ and S₂states both are unstable they are converted into S₀ state by releasing energy through some processes like heat, phosphorescence and fluorescence. The S₁ state is converted in to S₀state by releasing energy in the form of heat. This is called as fluorescence.

But all of the energy is not lost as fluorescence; still some of energy is left which is being utilised to drive photosynthetic reactions. The S₂state is first converted into S₁state by releasing small amount of energy and when S₁state loses energy it is converted into 2 interconvertible states called as T₁ and T₂ states. T₁ state is then converted in to S₀ state by loosing small amount of energy. This phenomenon is known as phosphorescence.

ABSORPTION SPECTRUM

It can be defined as the amount of the light of different wavelengths absorbed by the pigment. if the light of different wavelengths is passed through the extracted chlorophyll the absorption of each wavelength can be measured by spectrophotometer. And when this absorption is plotted the resulting plot we get is called as absorption spectra. Different pigments absorb different wavelength of light. For instance, the absorption spectra of chl a is in blue and red region. Other lights like yellow green and orange are absorbed only slightly. That’s why chlorophyll is not green because it absorbs green but actually it reflects and transmits green. The exact position of the peaks in the spectra depends upon the solvent used for the extraction of pigments. Chl a shows max absorption at 662nm in red region and 430nm in blue region. While Chl b shows max absorption peak at 644 nm in red region and 455nm in blue region.

Figure shows absorption spectra of chl a and chl b : vertical axis has absorption and horizontal axis is wavelength in nm.

In next post we will be doing action spectra and mechanism of photosynthesis!!!!!!

ENZYMES

2011-11-19T20:19:00.000-08:00

ENZYMES

Enzymes are the substances present in the cell in the minute amounts and capable of speeding up chemical reactions which are associated with life processes; so any impairment of enzymic activity is evident by any change in the cell which could be death as well!!! So it is not wrong to say that any substance that have unique capacity of speeding up a chemical reaction along with accelerating the velocity of reaction without necessarily initiating it is called as CATALYST and enzyme duly qualify to fit into this property.

All enzymes are produced in the cell but some of them would function in the cellular environment and some will be secreted through cell wall. On this basis we have got two types of enzymes: the former ones are Intracellular enzymes and the latter ones are extracellular enzymes. Intracellular enzymes perform catabolic reactions and provide energy required by the cell. Extracellular enzymes make necessary changes on the nutrients in the medium to allow them to enter the cell.

Properties of Enzymes

Enzymes are proteinaceous in nature and therefore possess properties specific to the proteins i.e. they are non dialyzable and easily denatured by heat.

A complete enzyme is a Holoenzyme which is composed of a protein part and non protein part (organic molecule). The protein portion is referred to as Apoenzyme. The organic molecule is referred to as Coenzyme. In some cases non protein portion of an enzyme can be metal. In fact many enzymes require the addition of metal ions in order to be activated. these metal ions function in combination with the enzyme protein and they are regarded as cofactors.

In my next post i will be adding up some more notes for the inhibition & kinetics.

BEER (Schematic Representation)

2011-11-19T05:15:00.000-08:00

BEER PRODUCTION

2011-11-19T04:23:00.000-08:00

THE VERSATILE MICROORGANISMS

Latter part of the nineteenth century can be considered the beginning of industrial food microbiology. Once it was established that certain yeast grown under certain conditions produced beer and that certain bacteria could spoil the beer; then brewers were able to understand the microbiological role and were in a position to control the quality of their products. Microorganisms have proved their versatility by exhibiting their special qualities and their role in not only in the food industry but in brewing industry as well.

We will begin with some non dairy fermentation like alcoholic beverages and vinegar.

Beer production:

Beer is an undistilled beverage produced from fermentation of barley malt by yeast especially Sacccharomyces crevisiae and S. carsibergenesis. Generally materials rich in starch like rice, wheat and maize are also added to increase the amount of fermentable sugars. They are called as ADJUNCTS.

Beer production involves four main steps:

1. MALTING

2. MASHING

3. SACCHARIFICATION

4. FERMENTATION

It’s always better to explain any industrial fermentation schematically as it gives a better view of the whole process and from examination point of view; it leaves better impact. I would suggest the schematic view but if you are comfortable with the paragraph explanations then even its perfect!!!

i have posted schematic self explanatory sketch for beer production in next post !!!

Have a great learning and let me know how you find it!!