A Butterfly and Biotechnology

Dear readers, I apologize that I stopped writing since last year. I don't have any great excuse other than poor planning. I was lost on my way to understand marine biology. As you might be knowing, I switched field, moved from my focus over bacteria and human disease related studies to climate change and marine biology. However, my research focus continues to be in molecular biology. Long story short, I was learning all about climate change, ocean acidification, ocean, marine animals in the past year. I even learnt how to spawn and culture oysters. How cool is it? Not cool?! Well, I think it is cool!  I can setup mini Ocean acidification systems which mimics the future acidified ocean conditions; I even gained some plumbing related skills. This was totally a new experience and I thoroughly enjoyed it. However, I had a tough summer in a rural fishing village in China, learning how to grow oysters from the Chinese oyster farmers (for those who do not know what I am doing: I ...

Hi there! (am using Whatsapp) :D When I started writing this, I wanted to start with a "Hi" and suddenly, the famous Whatsapp status came into my mind! :P See, am really addicted to Whatsapp nowadays, changing DP and Status often. Oof, I should stop writing whatsapp status and start writing here. (This is NO ADvertisement for Whatsapp :P) In the last post, I said that I'm in the USA doing research and now, am back in India after successfully completing the internship! Yaaai, back home, back home! It feels good when you are in home, yes, am happy to be home. But, sometimes, its good to visit places and learn new things, leaving home. Let's come to the purpose of this post now! In this post, am gonna share few things I learnt from my internship. I was basically cloning different fusion proteins and was doing invitro degradation studies of those cloned proteins using western blots. I've done cloning before, when I was doing my under graduation (UG), but,...

I don't know why, but, I really love this guy! :P Yes, he is PCR! You ask me anything, like, what technique we can use for introducing mutation? what for diagnosis? I'll answer PCR for all! :P Let me talk about him for sometime here. PCR (Polymerase Chain Reaction) is used for amplifying any gene from a given sample using Taq polymerase, dNTPs, Primers and buffers. After PCR the amplified product or amplification is generally checked by running an Agarose gel electrophoresis. But, in case of Real Time PCR there is no need for running gels as the progress of the PCR is monitored online with the help of fluorophores. Generally SYBR Green dye, Taqman or molecular beacon probes are used for Real Time PCR. In SYBR Green method, the fluorophore binds with the double stranded DNA and produces fluorescence, and hence as the amplification increases, fluorescence increases, but the fluorophore has no specificity and hence, even if the amplified product is not the product of your inter...

It's been a long time, since I wrote a post here. Finally, final year of my course and so very busy :) with books! And now, got time to share with you. As you know already (don't know?, then get to know :P ), I use to have favorite subjects in each semester, third semester it was microbiology, then in fourth semester, it was cell biology, fifth was molecular biology, sixth was genetic engineering and now i'm in seventh semester, but, you know what, I don't have a favorite subject!!! Don't worry that I lost interest, instead, I got 3 favorite subjects - Immunology, Animal biotechnology and Plant Biotechnology! It's awesome this time to have more than one favorite subject and here I'm gonna tell you something about, cre-lox system which is most widely used for making modifications (mostly deletions). These modifications can be done at a specific tissue alone by using a tissue specific promoter i.e., you can selectively knock out a particular gene in partic...

Let it be any disease, ranging from a fever (which is the symptom of many diseases) to HIV, diagnosis at an early stage is very important for giving specific treatment.Whenever I go to a doctor, he asks me things like, stomach pain, fever, body pain, head ache, running nose, throat pain etc., then, he checks pulse, then he uses his stethoscope, he then gives all the possible antibiotics! Yes, really, this happens in most cases. Then, if my problem is not fixing up in a week, he'll ask me to take a blood test, this, that, and, all! Nothing wrong in this, because he can't ask everyone coming to him to take blood test at the very first sitting, then, no one will visit him back saying he sucks out blood all the time! But, it is okay to have a blood test after a week, but, not after a month! Diagnosing a disease after it had reached a severe stage is comparatively less significant than diagnosing at an early stage. So, how to diagnose? Antigen - Antibody! Antigen and Antibody ...

Hi, dear readers, friends, it's been a long time, I wrote here. Sorry for that, was a bit busy in lab! And, you can be happy because of the fact that I was busy, as I got lots of experience to share with you! Let us first start with SDS PAGE! SDS PAGE - Sodium Dodecyl sulphate - Poly Acrylamide Gel Electrophoresis! This SDS PAGE is done for separating proteins based on their molecular weight. It is a widely used technique and it is very useful for having an idea about the expression of your protein of interest. Principle: The name SDS PAGE comes from the fact that this method uses SDS for making your protein uniformly negatively charged and of course, the gel is prepared using poly acrylamide. Why to make the protein negatively charged? Because, here our interest is to separate proteins based only on their molecular weight, but not based on charge and all proteins are not negatively charged like DNA (which is separated based on size using Agarose Gel electrophoresis ). SDS is ...

Oral cancer refers to cancer in any part of your mouth like tongue, lips, palate etc., Cancer may be due to various reasons like irritation due to continuous alcohol consumption, smoking, poor oral hygiene etc., And it can also happen due to Human Papilloma Virus (HPV). Human Papilloma Virus is a type of non enveloped virus (Papilloma) that can infect humans. They are classified generally as "High Risk" and "Low Risk" types. The high risk type HPV 16 is found to cause oro-pharyngeal cancer. Diagnosis: Generally biopsy is done where a small part of your tumor is removed and observed under microscope. The biopsy can be just cutting a small portion or it can also be done using brush for collecting the cells. After confirming the abnormality using this microscopic observation, further analysis is done for finding out the type of HPV which caused the oral cancer or to find whether the cancer is just because of alcohol/smoking. This further analysis can be d...

Southern blotting is used for finding specific DNA sequence from a DNA sample by using the combination of techniques like  gel electrophoresis, capillary electrophoresis and hybridization. The DNA from the gel (after gel electrophoresis)is transferred to a nitrocellulose membrane and hybridization analysis is done for finding out the sequence of our interest using a probe) Let us discuss here the steps involved in doing Southern blotting. The steps are 1) Preparation of Sample 2) Restriction of the Sample 3) Gel Electrophoresis 4) Pre-treatment of the gel 5) Blotting 6) Hybridization 1) Preparation of Sample: (plant/animal/bacterial) For tissue or blood samples the DNA could be obtained by treating with SDS (Sodium dodecyl Sulphate) If we are going to have the DNA from a bacterial sample, there are separate protocols for extracting genomic DNA and pDNA . For extracting DNA from plants, CTAB (cetyltrimethyl ammonium bromide) is used. This CTAB binds with the DNA and h...

Hi, Today I'm going to share something about TB! TB - Tuberculosis is generally caused by Mycobacterium tuberculosis.  The most common symptom of TB is "non -stop" cough! They say, many people in India are "carrier" of the bacteria, but not the disease! Oh God! if you are in India, better go and check for this bacteria! The possibility of the spread of the disease could be due to unhygienic conditions! You spit in public places? you sneeze? cough? No problem, you can sneeze or cough, but be careful! Careful coughing? careful sneezing? yes, you might spread the population this mycobacterium you are carrying (you need not have TB), so, be careful in sneezing and coughing! Okay, let us come to the point, I started typing this with a view of giving an overview about "the diagnosis of Tuberculosis". The most common test used for checking TB is "Tuberculin Skin Test". Let me explain you how this is done! Tuberculin Skin Test! Let us firs...

E.coli VS Plants! As an undergraduate of Biotechnology, I know about cloning . I know about cloning a gene which codes for a human protein into a bacterial cell, E.coli, most times. I also know about producing transgenic plant varieties. But, I don't know about cloning a human gene into plant! I came to know about cloning a human gene into plant and producing the protein in plants from the workshop session of AVIDADHAM'13. Let me explain something about this! As you may know, eukaryotic gene has both introns and exons. So cloning a eukaryotic gene into a prokaryote will have lots of problem like splicing and post translational modification. Generally for cloning eukaryotic gene into a prokaryote like E.coli, we do follow bottom up approach where we use mRNA to synthesise cDNA, to remove the noncoding introns. But, even if we remove the introns there will be problems with post translational modification. So, to avoid this, we are cloning our gene from human into pla...

Hi, Wish you a very happy day! Let all you researches result only in success! J You know, I’m learning cloning, wow, rhyming it is, learning – cloning! Like this rhythm, cloning is also fun! Yes, fun, interesting! Let me share with you, what I know about cloning. The first step of any cloning experiment would be selecting a vector. Now, I’m learning cloning using plasmid as a vector. So, you have to choose a vector for cloning at first. Vector is nothing; it’s just a plasmid DNA into which we can incorporate our gene of interest and transform the vector into a host which will produce the protein coded by our gene of interest. Vector need not be only p-DNA, viruses could also be used as vector. But, here, we are going to have an overview of cloning using Plasmid vector. Okay, we had selected the vector, let us assume. What next? We have to look at our gene of interest now. We have to get the sequence of our gene of interest – it’s available in databases lik...

We all know that we can cut and engineer our DNA or DNA of any other organism. But, so far the methods used for DNA cutting are not precise. Available techniques: By the older method, the genes are added into the cell and they get inserted into the genome of the cell in a random manner. This can’t be used when our aim is to engineer the DNA at a specific site and here we can’t also replace the already existing gene with our gene. There is homologous recombination method, but unfortunately natural recombination won’t occur in cells that easily! There are also methods which use Zinc fingers for delivering nucleases which cuts the DNA, but, this is really hard, because nuclease can’t target every possible DNA sequence. This is costly too. TALENs – Transcription Activator Like Effector Nucleases – cut the DNA at specific location. But, what to do, this is also costly! Our new method Here, we are going to use the already  existing proteins of bacteria...

We all love sweets, isn’t it? From a cute baby who had just started feeling and enjoying the tastes to 100 year old people, love sweets! Oh, I could hear you, yes, Diabetic patients can’t enjoy sweets. But, they too love to have sweets. Even, my father is diabetic and he uses to eat sweets hiding from my mom! Okay, what for that sweet love, you are asking? Nothing wrong in that, but, if you are crazy about the bottled drinks, then, I’m sorry, you must start worrying! L Aspartame – is an artificial sweetener which is used in most of the bottled drinks. And, that is an approved artificial sweetener by FDA (US Food and Drug Administration – which tests and approves all food and drug items before they are marketed) “It is approved by FDA, then, why we must worry?”, is this your next question? Let me answer you! Aspartame is formed using two aminoacids – L-Phenyl alanine and L aspartate. This when broken down during metabolism in our body produces – phenylalanine and hence ...

In the previous post, GM Mosquitoes #1   we had seen about the GM mosquitoes used for curing malaria. Now, we are gonna see about the GM mosquitoes designed for eradicating mosquitoes population! Aedes aegypti is the mosquito species which spreads Dengue. Nowadays, people are suffering severely because of this Dengue. In most cases it just leaves with mild fever. But, in some cases, Dengue is deadly! So, to get rid of this great dengue nuisance, scientists had found a solution - GM mosquitoes! We had seen that in the case of eradication of malaria by GM mosquitoes that scientists had made the mosquitoes resistant to malaria causing protist, but, here in this case of dengue the genetic modification is different. Dengue! In the case of dengue, male mosquitoes are made sterile and when they mate with the wild type female mosquitoes, their young ones are made unviable i.e they die before reaching adult stage. So, this reduces the population of mosquitoes by the death of ...

You are troubled at the mid-night? Your days are affected due to the lack of sound sleep? I can understand; The "mosquitoes", they are responsible for all this. We can bear with them if they are just biting and sucking a drop of blood, but, never, when they are injecting us with something like a "doctor", that too, which is never going to cure the disease like doctor's injection, but, going to give us disease. Mosquito bats, liquids :( even with the help of these things, we are getting malaria, dengue, chikungunya :( :( Scientists had found a solution for this greatest problem of our night!(nowadays daytime too) GM mosquitoes, these genetically modified species are resistant to diseases like malaria.  MALARIA! How malaria generally spreads! As we all know, its because of mosquitoes, especially the female Anopheles mosquito which gets the virus when it sucks blood from an infected animal/human. Half of the life cycle of the Plasmodium speci...

Hi, Wish you a good time :) Molecular biology! I was taught about "cot value analysis" in my molecular biology class. Here, you could read something, which I know about cot value. Cot (C not (zero) t) value analysis: This analysis uses the DNA denaturation and renaturation kinetics. This is used for measuring the repetitive DNA sequence in a given DNA sample. This analysis has application like separating repetitive sequences from mixture of DNA sample. Okay, let us discuss the procedure now. Note: Cot value = (C zero) * (Time) * (constant representing the effect of cation in the buffer on renaturation) where, c zero -> DNA concentration (mol/l) T - Renaturation time (sec) Procedure: Denature the DNA sample by heating Cool and renature the sample, note renaturing extent (as cot value) at particular temperatures until a particular cot value is reached. Now, dilute this sample with sodium phosphate buffer- SPB (0.03M - at this buffer concentration the DNA bind...

Cancer! As you may know,  cancer is uncontrolled multiplication of cells. There are several reasons for this uncontrolled multiplication of  cells like mutations due to UV exposure or exposure to certain chemicals, even genetic defects, excessive alcohol consumption or smoking (kindly, avoid smoking or alcohol consumption). Still there are several reasons you could quote as "cancer causing". There are different types of cancer based on the part of the body affected like lung cancer, lung cancer, blood cancer etc., Huge number of people all over the world are suffering from cancer, it's a deadly disease, it has no preventive measures and moreover, there is no real cure for cancer, only treatment methods are available! Here, we are going to discuss about the possibility of using magnets in curing cancer. When I read about usage of super magnets in treating breast cancer just by hanging the super magnet in a necklace which hangs over the breast of the patients (!...