Monday, March 27, 2017

Gel Electrophoresis

Gel Electrophoresis
Principle and Applications
Dr. Aditya Arya, Ms. Shikha Jain

Date of publication: 28 Mar 2017
Electrophoresis is the movement of particles dispersed in a fluid, under the influence of an electric field which has uniform spatial distribution. The electrophoresis is principally based on electrokinetic phenomenon which was observed for the first time by Ferdinand Frederic Reuss in 1807. It is the basis for a number of analytical techniques used in chemistry for separating molecules by size, charge, or binding affinity. Electrophoresis of positively charged particles (cations) is known as cataphoresis, while electrophoresis of negatively charged particles (anions) is known as anaphoresis. Electrophoresis is a technique used in laboratories in order to separate macromolecules based on size. The technique applies a negative charge so proteins move towards a positive charge. In electrophoresis molecules are separated on the basis of their charge and molecular weight. Infact, the charge is responsible for creating a pull and molecular weight creates a drag across the matrix that creates differences in the mobility of molecules. In broad terms, electrophoresis may be grouped into two sub types a. Zone electrophoresis and b. Moving Boundary electrophoresis


Tuesday, March 21, 2017

Analysis of Biochemistry Section in CSIR -NET (2011- 2016)

Analysis of CSIR-NET Biochemistry Questions (2011- 2016)
Dr. Aditya Arya*
Date of publication: 21 Mar 2017

Question paper has a very defined and set pattern of questions and weightage of each unit is well maintained in the paper. Part A has most of the aptitude questions involving basic Physics, Chemistry, Biology and mathematics. Section B and C has questions from the defined syllabus. It has been observed in the past years the questions are often arranged in the order of units prescribed in the syllabus. As Biochemistry is the first unit of the syllabus, the question from biochemistry section are found in the beginning of section B and Section C. Questions in section B are often memory based and require fewer efforts while questions of C part may involve technical details and experimental observations and therefore need a better comprehension.  Biochemistry per se is equally important as other units and has defined set of questions that encompass, about 3-4 questions (generally, question no 21- 25) each year in part B and 4-5 question each year in part C (Generally Q 71- 76). However, some questions from the 13th Unit that involve techniques are often related to basic concepts of biochemistry and thereby increasing the questions from this subjects and causing variable trend across years. 

Sunday, February 5, 2017

Biochemistry Practice Questions

Biochemistry Practice Problems
Compilation from Various Internet Sources
Posted on 5 Feb 2017

Check for more updates in Future

DOWNLOAD 1: Atomic Structure and Chemical Bonding 
DOWNLOAD 2: Mole concept and concentration terms 
DOWNLOAD 3: pH and Buffers 
DOWNLOAD 4: Bioenergetics 

Monday, January 9, 2017

Basics of Microarray

Basics of Microarray
Edited by: Dr. Aditya Arya*
Date of publication: 11 Jan 2017

Microarray is a hybridization of a nucleic acid sample (target) to a very large set of oligonucleotide probes, which are attached to a solid support, to determine the sequence or to detect variations in a gene sequence or expression or for gene mapping.  Several competing technologies for microarray probe implementation have emerged. Affymetrix (name of the company) pioneered this field with by using in situ synthesized oligonucleotides as probes and by designing microarrays in silico, thereby obviating the need for the management of clone libraries. Later two more major companies named Agilent and Illumina begun their microarray platforms based on slightly different strategies.  DNA microarrays can be used to detect DNA (as in comparative genomic hybridization), or detect RNA (most commonly as cDNA after reverse transcription) that may or may not be translated into proteins. The process of measuring gene expression via cDNA is called expression analysis or expression profiling. Microarray technology has two major applications: Gene Expression Analysis and Genetic Variation Analysis.

This Quick note provides a comprehensive understanding of microarray technique for especially for undergraduate students. However, for the researchers who intend to carry out actual microarray experiments, must consult further readings of this text.

Wednesday, December 28, 2016

Polymerase Chain Reaction

Dr. Aditya Arya, Dr. Amit Kumar and Ms Jayanti Jha
Date of publication: 30 Dec 2016

Polymerase chain reaction (PCR) is one of the most important tools in molecular biology which allows amplification of nucleic acid sequences in vitro through repetitive cycles. PCR can replicate any specific region of DNA billions fold in few hours. The PCR machine is also called as thermocycler. This Quick Note describes variants (including most modern classes of PCR called digital PCR)

Saturday, November 12, 2016

Principles of Microscopy
Aditya Arya, PhD

Date of publication: 13 Nov 2016

Microscopic techniques are critical to several research domains including biology, Physics and Chemistry and even in clinical diagnosis. Apart from an essential tool in research, microscopes have become a teaching a learning companion for both students and teachers. Since the inventions of first microscope by Hans and Zacharias Janssen in 1590, microscopes have evolved a lot both in terms of improved resolution and magnification. The best microscopes today can have a resolution of less than 1 angstrom and a magnification of over 1 million, while our eyes cannot resolve two dots at a distance lesser than 0.2 mm. Increasing resolution and magnification has created enormous opportunities in research and wider scope of application. Now, microscopes are used in clinical diagnosis, molecular and cell biology studies, nano-material research and even determination of structure of bio molecules.

Microscopy is the technical field of using microscopes to view objects and areas of objects that cannot be seen with the naked eye (objects that are not within the resolution range of the normal eye). There are three well-known branches of microscopy: optical, electron, and scanning probe microscopy.

In this Quick note, we will be discussing about basic principles and types of common microscopic techniques and their application in Life Science Research.

Sunday, November 6, 2016

In situ Hybridization Techniques from Ish… to Shish….

Dr. Aditya Arya

Date of publication: 6 Nov 2016

Among various other biochemical and molecular techniques, in situ hybridization techniques have their own importance especially due to its ability to detect a molecular change directly at its site of occurrence. In situ hybridization was developed by Joseph G. Gall and Mary-Lou Pardue in 1969. In situ hybridization  is a type of hybridization of target DNA or RNA with  a labeled complementary DNA, RNA or modified nucleic acids strand (commonly known as probe) to localize a specific DNA or RNA sequence in a portion or section of tissue (in situ), or, if the tissue is small enough (e.g., plant seeds, Drosophila embryos), in the entire tissue (whole mount ISH), in cells, and in circulating tumor cells (CTCs) etc. Originally, the detection of hybridization was based on radioactive nucleotides and detection of radioactivity, however the with the advent of highly specific and sensitive fluorophore it is now possible to tag probes with fluorophore and therefore the technique is now popular as Florescent in situ hybridization of FISH.  In this Quick note a description about the principle, its variants and applications are provided. 

Saturday, October 22, 2016

A Guide for Choosing M.Sc. program in Life Sciences is finally released..

Must read for all B.Sc. life Science students aspiring to do M.Sc. in Life Sciences

This book is intended for many students who wonder what next after their BSc in biological sciences. As a stepwise guide, this will also serve as a self counselling tool to the students. In the past decade, It was common tradition in Indian education system that most of the student and of course their parents train their students to prepare for medical or engineering exams, and in case not selected in medical exams they often seek the basic biology courses such as BSc followed by MSc, without even known the scope and opportunities in this segment of educational qualification. The trends are however changing and students as well as parents are become aware by emerging trends in print and digital media and students are orienting themselves towards non-conventional vocational courses or conventional non-tradition courses for MSc.  The lack of awareness of suitable courses or the opportunities prevents the young talent from being groomed and thus results in poor employability. A prospective doctor becomes a teacher, a prospective teacher joins a marketing expert in industries and in neither of the cases individuals becomes successful. This book is an attempt to guide young students to groom their talent by reaching the suitable place and also knowing the prospective path of their professional life.  
This book contain several chapters which describe about the importance of MSc course and guide students to make a choice between various programs. Also, this book provides comprehensive details about a number of courses and institutions offering MSc programs in biological sciences. A separate chapter has been added on how to prepare for MSc entrance exams and opportunities outside India,


Wednesday, September 28, 2016

Writing an Effective Research Proposal/ Write-up 

Dr. Aditya Arya
Date of Publication: 28th Sep 2016

Research proposals and write up are very important for entrance in some of the premiere Institutes of India such as TIFR (Tata Institute of Fundamental research) as well as for various MS programs abroad. As a matter of fact most of the students in Indian universities (except premiere Institutes) are not exposed to hardcore research and have hands on learning experience on limited techniques and seldom perform a research based project. Some of the summer training programs such as Indian Academies Summer Fellowship (IAS) provides opportunity to Masters Students to undergo research oriented training and experience scientific procedures. Usually, the purpose of asking for such research proposals or write ups from the students, is to determine the scientific aptitude, level of technical skills and interest of the candidate to determine the suitability for specific position or course. 

Based on the increasing demand from the students and several queries, this articles was prepared, Any comments or suggestions may be made at the comment option below or further queries may be sent to 

EXTENDED and UPDATED on Oct 3, 2016

Tuesday, September 20, 2016

Hand Written Notes

Dr. Aditya Arya 
20 Sep 2016 [last updated on 16 March 2017]

I am glad to share with you scanned copy of my handwritten notes (made during undergraduate /Postgraduate studies) on various topics (1000+ pages). Based on the request from various students (5000+ students used the photocopies of these notes in Jiwaji University colleges in last 10 years).  I am now making them available publicly for academic purpose. These may be helpful for both, MSc. entrance exams as well as university exams. These notes are very basic and you may need to add more to this if preparing higher exams like CSIR-NET JRF etc.  Please note that, these notes are being distributed free of cost, anyone making commercial use of this content shall be treated under law. 

Bachelor's Notes: Prepared as per the prescribed syllabus of the Jiwaji University, Gwalior (MP) from 2006- 2008. 





Saturday, August 20, 2016

The Protein Folding Problem: Anfinsen hypothesis and Levinthal paradox

Dr. Aditya Arya, Dr. Amit Kumar
Date of publication: 21 Aug 2016

We all know that proteins fold spontaneously on keeping them in suitable aqueous environment. However, there are some deeper questions which we must know about protein folding that, what are the models of proteins folding? Which route does a protein follow while folding? And how protein folding does not defy the second law of thermodynamics despite of the fact the randomness of protein itself is reduced on folding? We would also understand two famous hypothesis put forth by Levinthal and Anfinsen and various probability based question arising about the protein structure. . Infact the work of Anfinsen was recognized globally and he was awarded Nobel Prize in chemistry in the year 1972. Finally this note will end with a few practice MCQs based on the two key concepts.
There have been a number of questions in MSc entrances including JNU, IISc and TIFR on anfinsen hypothesis and levinthal paradox. 

Sunday, July 24, 2016

Illustrated Summary of Metabolism 
Dr. Aditya Arya
Date of publication: 24.07.2016

Metabolic processes are so complicated and it is difficult to understand them especially when we observe the individualistic approach. In biochemistry, It is equally important to have a bird eye's view on overall metabolism of various bio molecules to get a clear idea of what is happening to food that we eat. How it is digested, transported and utilised in the body. Liver is central to all metabolic processes and the functions of liver are regulated under the tight control of nervous system and hormonal system. Here in this post I present you an illustrated view of the overall process. This is a PDF (non-printable) documents only intended for digital reading. These illustrations are closely related to classroom lectures, so students may also visit the you tube channel to view some of the related classroom lectures on Biochemistry to recall the content (click to visit channel)., This content is adopted from Concise Biochemistry - by Aditya Arya. Hope this will help in enhancing the understanding of the topic. 

Thursday, June 9, 2016

Proteolytic Enzyme: Basic information and cleavage rules

Dr. Aditya Arya
Date of publication: 10 June 2016

Cleavage pattern obtained from proteolytic enzymes are commonly used to determine the sequence of small proteins or peptides.  Most of the proteolytic enzymes are capable of cleaving the protein at specific positions. Cleaving a protein with specific enzyme and then analysing the fragments may help in the determination of the order of amino acids by simple logical reasoning.   In this quick note we will understand how to solve such questions and also a detailed view cleavage rules. Additionally, we will also understand the problem solving skills based on the cleavage rules. Concluding remarks include commercial applications of proteases. This note has been prepared by content provided by global experts in the field of proteins (European Molecular Biology Laboratory and Swiss Bioinformatics Institute).  

NOTE: Past years trends of CSIR-NET exam and other nationwide competitive exams have shown frequent usage of these rule in questions. The question might appear very difficult and cannot be solved if we do not know the cleavage rules.  Most of books and online solved papers have not provided any details or solutions of such questions and this is Exclusive content prepared by us. Hope this will help in your preparation. 

Sunday, June 5, 2016


Understanding the fact that enzymology is one the key areas of many competitive exams and there is a lot of confusion over various type of regulation, we are providing you free access to one of the chapter (a few pages deleted) of our brand new "Concise Biochemistry" book which is further supported by a video lecture by author on the same topic. All the previously asked questions have been solved at the end of the chapter. 

Hope it will help in your last minute preparation. Good Luck.

CLICK here to download enzyme regulation chapter 

CLICK here to watch the video lecture on the same topic

Wednesday, April 20, 2016

Flow cytometry: Principle and Applications
Dr. Aditya Arya, Dr. Amit Kumar

Date of publication: 22.04.2016

Flow cytometry is one of the most powerful technique for the research as well as clinical diagnosis that simultaneously measures and then analyzes multiple physical characteristics of single particles (often cells) by forcing them to flow in a fluid stream and analysing through a beam of light. The properties measured include a particle’s relative size, relative granularity or internal complexity and relative fluorescence intensity.  These characteristics are determined using  an orchestered optical and electronic system that records how the cell or particle scatters incident laser light and emits fluorescence.  This technology has applications in a number of fields, including molecular biology, pathology, immunology, plant biology and marine biology. It has broad application in medicine (especially in transplantation, hematology, tumor immunology and chemotherapy, prenatal diagnosis, genetics and sperm sorting for sex preselection). Also, it is extensively used in research for the detection of DNA damage, caspase cleavage and apoptosis. The articles will provide a basic information on principle and data representation in flow cytometry. 

Additionally, if you are interested in knowing the workflow of FACSCalibure (a signle laser flow cytometer from BD) you may like the following workflow (especially for researchers).