A Butterfly and Biotechnology

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 (!...

Hi, Didn't read the previous perl posts? Go here,  perl  #1   #2   #3   #4 ) In the previous post of perl programming, we learnt how to search an aminoacid in a protein sequence. Now, we are going to look at a program by which the "start and stop codons" in a protein sequence could be easily identified. Here, we go, Program to identify start and stop codons easily:  print "enter a file containing Dna sequence\n"; $dnafile=<>; chomp($dnafile); unless(open(DNAFILENAME,$dnafile)) { print "file not found\n"; exit; } $dna=<DNAFILENAME>; $dna=join("",$dna); $dna=~s/\s//g; $dna=uc($dna); $dna=~tr/T/U/; print "The mrna is:\t",$dna,"\n"; my(%code)= ( 'AUG'=>'Start', 'UGA'=>'Stop', 'UAA'=>'Stop', 'UAG'=>'Stop', ); for($i=0;$i<(length($dna)-2);$i+=3) { $codon=substr($dna,$i,3); if($codon=~AUG) { $out.=$code{$cod...

Hi, This is semester exam time! All the very best for the people who are gonna write their exams. Are you interested very much in science? Looking for a fellowship? This is exclusively for Indian students - not for foreign students! (Sorry). This is not only for biology students, but, also for Physics, Chemistry, Mathematics, Engineering and earth and planetary science students. Then, this is a great chance for you. Apply for the Indian Academy of Sciences  (IAS)- Summer Research Fellowship Programme  - You could find all the details "here" You could Register here  and the recommendation letter format could be found  here  ! This is for both students and teachers. While registering online, you might get doubts like, "where to select the list of guides" - The list of guides is provided in the application form - as detail number "14" Scroll down the application, you could find the link for selecting the guides. You can check the details like...

Hi, We started learning perl programs in our last post. For viewing previous posts, use the links ( perl #1 #2  #3 ) Today I'm gonna give you a program for searching a specific amino acid in a protein sequence.You can easily understand the logic by yourself. Here we go, Program for searching an amino acid in a protein sequence: print "enter a protein file\n"; $proteinfile=<>; chomp($proteinfile); unless(open(PROTEINFILE,$proteinfile)) { print "file not found\n"; exit; } $protein=<PROTEINFILE>; $protein=join("",$protein); $protein=~s/\s//g; $protein=uc($protein); print "The sequence is",$protein,"\n"; $a=A; $position=0; for($i=0;$i<length($protein);$i=$position+1) { $position=index($protein,$a,$i); if($position=~-1) { last; } print $position+1,"\t"; } print "- the position(s) in which alanine is found\n"; exit; The output for the above program will be like this. Try executing!  H...

Hi, You read the first two posts about perl? Missed? Don't worry, go and read here ( perl #1 #2 ) From today, we can learn few programs that would help biology students! Ya, as a biotechnology student I use perl programs for dealing with DNA , RNA and Proteins. So, I know just something about perl (very limited) for processing sequences! Okay, let's learn some basic programs. Program to convert DNA sequence to protein sequence: print "enter a dna sequence file\n"; $dnafile=<>; chomp($dnafile); unless(open(DNAFILENAME,$dnafile)) { print "file not found\n"; } $dnafile=<DNAFILENAME>; $dna=join("",$dnafile); $dna=~s/\s//g; $dna=uc($dna); print "DNA seq. is\n",$dna; $dna=~tr/T/U/; print "mRNA seq. is\n", $dna,"\n"; my(%genetic_code)= ( 'UUU'=>'F', 'UUC'=>'F', 'UUG'=>'L', 'UUA'=>'L', ...

Hi, Yesterday we learnt about installing perl in windows (Didn't read yesterday's post? check here Perl programming #1  ) and how to “print” using perl! Today, let’s start with the basics, how to get input using perl? To get a text file from user using perl: Just it is very simple, type as follows, $variable=<STDIN>; This will get the file name. This also works in perl, $variable=<>; No need to give STDIN! Just the open and closed angular brackets are itself considered as standard input. Then, always give chomp after the standard input, this chomp is nothing but “chop” which chops the “enter” à new line character i.e., whenever you give an input, you press “enter” which will be considered as a new line character. In order to remove that new line character, chomp must be given. How to use chomp? Use as follows, $variable=<>; chomp($variable); Simple, this chops the new line character from your input. Let us l...

Perl is a programming language. This is a powerful language which has features similar "C". This is generally used for text processing. "Perl" is not an acronym officially, but, it has got backronyms(may be invented with a false etymology)  in use such as "Practical Extraction and Reporting Language". In Biotechnology, this Perl is used generally for processing text data of DNA sequences and converting them to mRNA or searching for a specific pattern in a protein sequence etc., I'm gonna write a series "Perl programming #1, #2, #3 etc.. with simple programs and explanations. Wanna learn perl with me? Let's begin from today. I'm sure, atleast you will get to know the Basics of perl. You can learn a programming language, of course, free of cost, with in a weak!!! What you need for perl programming? PERL and UNIX: If you work in UNIX, you need not install perl, just  go to terminal, and you could create a perl file just by typing as ...

Hi, DNA computing, this is a topic in which my professor asked me and my friend  to give a lecture. We gave our best and here you can find a summary of our lecture. DNA computing: It's computing with the use of DNA, in stead of the normal microprocessors used. Why DNA or cells or biological molecules for computation? I could give you three major reasons: 1) Large storage capacity 2) High parallelism 3) Speed Large Storage capacity : DNA could store large information comparing the normal storage devices used like CDs. If we store the information in DNA in CDs and arranga it like a thread. That thread could round the Earth by 374 times!!!! Can you imagine the capcity of DNA now? High parallelism:  DNA could process in several ways parellely. Speed:  All biological reactions happen with in seconds. So, using biological molecules can increase the speed of computing to a greater extent. Okay, but, how biological molecules could be used f...

Hi, During the last practical exams I shared my experience. (Read here) I shared certain questions with answers which the examiner asked me during the practicals. Even this time, I'm going to share a few questions and answers with you. Here we go, This time I had 2 lab exam (Practicals), number one - Bio informatics and two - Molecular biology. Let us start with the Bio informatics lab. Bio informatics:   In this Bio info practicals, we were provided with two exercises - one must be done using various bio info tools such as Clustal W, T-coffee, BLAST P, BLAST-N, PHYLIP etc., The other exercise is PERL programming! :( :'(  The first exercise using tools is very simple, but, I find the programming, let it be any programming, it's very difficult :'( Even in the model practicals, I couldn't debug the program :( So, I worked really hard to learn the PERL! I was working with my lap for a whole day. And atlast, I got good confidence that I could write my own pro...

Hi, Agarose gel electrophoresis In the previous post I explained how to quantify DNA, and now we can find the molecular weight of that extracted DNA. But, how? Simple, you need to run an agarose gel! Preparation of agarose gel: Agarose gel must be prepared based on the DNA we are going to run. For example: if you are going to run Genomic DNA, you must use 0.6%gel, for plasmid DNA, you must use 0.8% gel, for PCR(Polymerase chain reaction) sample, you must use 1.2% gel. You may ask, why three different % of gels? The answer for your question is: Genomic DNA will be bulkier than pDNA - so, we must use a gel with less percentage, so that the pore size will be greater and the genomic DNA can move easily. In case of PCR sample, the gene amplified won't be bulky, so, it moves fast, very fast in low percent gel, that's why to have an optimum speed we use a higher percentage of gel comparatively. And, when our aim is to separate two sequences with relatively equal size...

Hi, I explained the principle behind the extraction of pDNA in my last post. Extracted the DNA, what next? Let us quantify the DNA extracted. How to quantify? Very simple, all you need is Spectrophotometer. Just take 1 microliter of your DNA extract in an eppendorf, make it upto 500 microliter with nanopure water. (else 1000, or any desired volume) mix it well Now, put this into a quartz cuvette (0.5ml), measure the O.D value at 260 nm. Use blank as nano pure water. Note: The path length of the cuvette must be 1cm. Okay, we got the O.D value now, how to get the concentration of your DNA? It's very simple, do the following calculation. If your O.D. Value is 1, then, the concentration of your DNA sample is 50 microgram/ml so, now, if your concentration = obtained O.D.( let it be 0.5) * 50 microgram/ml * Dilution factor How to calculate the dilution factor?  Simple! here your dilution factor is 500/1 i.e., 500 micro liter contains 1 micro liter of DNA, you can calcu...