Swine flu - from a biological viewpoint

There are three genera of Influenza viruses that cause human flu. They are classified as A, B and type C. Of the three genera of influenza viruses , Influenzavirus A and C also cause influenza in pigs too.Type A is common and the influenza virus C is rare in pigs. Within Influenza virus A and Influenza virus C, the strains found in pigs and humans are largely distinct from eachother.

Normally, Swine influenza is caused by influenza A subtypes H1N1, H1N2, H3N1, H3N2 and H2N3. Among them, H1N1, H3N2, and H1N2 are the most common influenza A virus subtypes in pigs. But the 2009 flu outbreak is due to a new strain of infuenza (designated H1N1), not previously reported in pigs.

The mixing of the genetic material of two similar viruses that are infecting the same cell is called the reassortment. According to the initial description, the new virus has been made by the reassortment of at least four strains of influenza A virus subtype H1N1, including one strain endemic in humans, one endemic in birds, and two endemic in swine. Subsequent analysis suggested it was a reassortment of two strains of Swine Influenza Viruses.^]Although initial reports identified the new strain as swine influenza, its origin is still not confirmed.

The direct contact between infected and uninfected animals is the main route of transmission of swine flu between pigs. Airborne transmission is also an important means of infection. People who work with poultry and swine, has a high risk of getting the virus. But, this strain (2009 outbreak) became an epidemic as it transfers from human to human through coughing or sneezing.

Fever, lethargy, sneezing, coughing, difficulty breathing and decreased appetite, weight loss and poor growth are the main symptoms of the disease in pigs. But the mortality is usually low (around 1-4%). In humans, symptoms include fever, cough, sore throat, body aches, headache, chills and fatigue. Unlike in earlier occations, diarrhea and vomiting are also main symptoms in the 2009 outbreak.

The identification of the disease has 3 steps. First, Infuenza virus A is identified. If positive, then search for the H1N1 strain. The new strain identification is the last step which can be done only in main laboratories and which takes around two days. But, when the viral genome is sequenced, a one step identification can be done through the designing of a Real Time PCR kit, which would greatly simplify the identification process. I am hoping to write more on this later.

Garlic for the prevention of blood clotting

The compound Allin naturally occurs in Garlic. When the garlic clove is chopped, Allin converts into Allicin with the action of an enzyme. allicin shows the antibacterial & antifungal effects . But when cooked, as allicin decomposes, diallile sufide is made, which has much lower antibacterial & antifungal effects.

After chopping the garlic clove, when it is dissolved in a solvent like eddible oil, an unsaturated disulfide is made by binding three Allicin molecules together. This compound is known as Ajoene. Ajoene also can be found naturally in Garlic bulbs.

Ajoene has anticlotting properties. So it prevents platelets in the blood from forming blood clotts. This reduces the potential of forming heart disease & strokes. Another very important thing is that it is effective in inhibiting the growth of tumor cells. This is done by targetting the microtubule cytoskeleton of such cells. Also it shows antioxidant effects by inhibiting the release of superoxidents. And as it has antimicrobial activities, Ajoene is used in Yeast infections.

Amino acid sequencing in proteins from the N terminal

The determination of amino acid sequence in proteins is known as protein sequencing. First of all, the protein should be extracted from the tissue & should separate the protein. before analyzing the amino acid sequence, should determine whether the protein contains more than one polypeptide chain. As the number of polypeptide chains is equal to the number of N terminal a.a. residues, we determine the no. of N terminal a.a. residues per molecule of protein. If the polypeptide chains have no covalent cross linkages, they can be separated by altering PH, 8M Urea/6M Guanidium HCl, high salt concentration. But if the chains are covalently cross linked by disulfide bonds, commonly they are cleaved by reducing the disulfide bond to sulfhydryl groups with mercaptoethanol. Then check the purity by using a method like polyacrylamide gel electrophoresis.

Now complete hydrolysis is done either by acid hydrolysis or by alkaline hydrolysis. In the acid hydrolysis, excess 6N HCl is added in a sealed evacuated tube at 110-120 C for 24-72h. In the alkaline hydrolysis, add 5N Ba(OH)2 under reflux for 18-24h.

Identification of N terminal amino acids -
The first useful method for this was described by Sanger. He used Fluorodinitrobenzene for this. Free unprotonated alpha amino group of peptides react with this & forms a yellow coloured derivative. Now subject to acid hydrolysis with 6N HCl. Then all the peptide bonds hydrolyses, but the bond between DNFB & alpha amino group of N terminal amino acid is stable. Then this labelled residue is separated from other amino acids by chromatography.

Another common method is Edman's method. Here, Phenyl isothiocyanate is used to cleave N terminal a.a. from peptide without disrupting other amino acids. It binds with the free amino group of a peptide to yeild the corresponding phenylthiocarbamoyl peptide. Then treat with anhydrous acid. Then the N terminal a.a. splits off as a phenylthiocarbamoyl a.a. Then it is crystallized separated & identified usually by gas liquid chromatography. The great advantage of this method is that it does not disturb the rest of the peptide chain after the removal of the N terminal a.a.

Lippincott's Illustrated Reviews : Biochemistry

Today I bought the Lippincott's Biochemistry book (4th edition), as I am reading for a Biochemistry M.Sc. It covers all the sections in Metabolism. It contains very clear coloured figures in Lipid metabolism, Nitrogen metabolism & also in Intermediary metabolism. And also the book gives a very good idea about the genetic information. The main thing is that, the book has been written in a simple way that anyone can understand. Because of that, I recomend this book for those who are interested in Biochemistry, specially in Metabolism.

Rational drug design

Most of the drugs are discovered by chance observations. With the development of Science, large scale screening experiments were done for drug targets (receptors) using a large number of different compounds.

To be effective, a drug must be bound with its targeted receptor. Unlike the traditional way, in the rational drug design, a drug is designed considering its receptor structure or one of its natural ligands. RDD involves the use of three-dimensional information about biomolecules obtained from such techniques as x-ray crystallography and NMR spectroscopy. This is also known as structure based drug design.

There are databases containing the structures of many different chemical compounds. Using the developed software, computer can identify what are the molecules that show higher affinities with the discovered structure of the receptor. If such a molecule was not discovered, there are programmes that can build molecules having the ability to interact with the receptor. If not, there are some other programmes that can identify molecules having similar properties to the ligands that interact with the receptor. When those are identified, they are tested in the laboratory. As this method reduces the large scale screening, it decreases the expense.