Biology Is Love

  Facts and information about Bioinformatics especially for DBT-JRF:  [Part -2] These notes are only for the students who are not interested in Bioinformatics but want to solve and memorize the common questions in DBT-JRF.  These are just the random facts, prepared from analyzed PYQs. The following are handwritten notes. If you face any problems please let us know in the comment section. 

 Facts and information about Bioinformatics especially for DBT-JRF:  [Part -1] These notes are only for the students who are not interested in Bioinformatics but want to solve and memorize the common questions in DBT-JRF.   DOT BLOT: Pairwise sequence similarity   Protein database: Try to recall the names and the subcategories.   E- value:  BLAST: Have a look at the difference between local and global alignment.  If a nucleotide sequence encoding a protein is known and a homologous protein to be identified, --> the best analysis tool is BLASTx. Read the following:  Substitution Matrix: [Along with PAM and BLOSUM] These notes are based on the PYQs.  Similarity search:

 Crabtree effect: The name is given by an English Biochemist Herbert Grace Crabtree.  This effect is referred to as the production of ethanol in aerobic conditions rather than biomass by yeast cells at high external glucose concentrations through the TCA cycle.  This is basically the decrease in the rate of electron transport due to the mass action of the elevated phosphorylation ratio.  Warburg effect: This effect is referred to as an increase in the rate of glucose uptake and the production of lactate in aerobic conditions. The discoverer of this effect,  Warburg hypothesized that this effect is mainly due to the dysfunctional mitochondria, observed in the tumor cells, predominantly found in the cancer developmental cells.  The Crabtree-Warburg effect interprets that the avoidance of a decrease in ATP is observed in those conditions where higher glucose uptake is found than the downstream processing capability of the second phase of the glycolysis. 

The following suggestions for Biology (HS-2024- Bengali version) are hand-written. If any kind of problems arise, please let us know in the comment section.   All the best!!!!!!!!!

  MTT Assay Principle : The MTT assay provides a readout of cell viability & growth that works by measuring cell metabolic activity. The yellow tetrazolium MTT (3-(4, 5-dimethyl thiazolyl-2)-2, 5-diphenyltetrazolium bromide) is reduced by the metabolically active cells, by the action of dehydrogenase enzymes, to produce reducing equivalents such as NADH and NADPH. The resulting intracellular purple formazan can be solubilized and quantified by spectrophotometric means at 570nm. MTT is sensitive to light. This assay should be performed in the dark. The MTT assay measures,  cellular metabolic activity as an indicator of cell viability, proliferation and cytotoxicity.

The Basic steps of the cell-reviving process   1)   Cryopreserved Cells [with DMSO (Dimethyl sulfoxide)] were collected from the -80°C. 2)  Then the cells were thawed rapidly in the water bath at 37 °C for 30-45 sec to protect the cells from DMSO. 3)  The cells were transferred into a 15 ml falcon which already contains 6 ml of media [DMEM (Dulbecco’s Modified Eagle Medium) + 10% FBS (Foetal Bovine Serum) + 1X penicillin-streptomycin solution]. 4)  The centrifugation was performed at 1100 rpm for 5 minutes. 5)  The Supernatant was discarded in the beaker containing a small amount of bleach and water.  The pellet was collected. 6) T he pellet was washed with media to remove the trace of DMSO. 7)  The cells are resuspended in 1 ml of media.   8)  The cells were transferred to the T-25 flask which already contains 4 ml of media.  9)  Finally, the cells were observed under the microscope and kept in the incubator at 37°...

 Process of lactation/lactogenesis - Souti Das To provide milk to neonates, at the end of pregnancy around the time when the young is born, the mammary glands undergo a process that initiates milk secretion, called lactogenesis. The human mammary gland is composed of about 20 lobes, each with an excretory lactiferous duct that opens at the nipple. Loves, in turn, are composed of several lobules, which contains secretory structures called alveoli, and the terminal portions of the ducts. The epithelia of the alveoli and ducts are composed of apical luminal ductal or alveolar cells and a myoepithelial cell layer on the basal side of the epithelium. Myoepithelial cells are stellate, smooth muscle-like cells, and contraction of these cells in response to oxytocin expel milk from the lumina of the alveoli and ducts. Source: White and Porterfield  4th Edition     Lactogenesis has two main phases. The initiation phase (Lactogenesis I) is characterized by increased express...

Mechanism of Release Of Ovum (OVULATION) - Souti Das  During the 1st 5 months of development, a finite number of primordial follicles form in the fetal ovary, these follicles contain an oocyte surrounded by follicular cells. These primordial follicles arrests at 1st meiotic division till puberty and then they further undergo development and become primary follicles.                                       During the early primary follicular stage, follicular cells are cuboidal and Zona Pellucida appears as a thin band of glycoprotein that separates oocyte and follicular cells. In the late follicular stage, follicular cells proliferate into a stratified epithelium known as Zona Granulosa . During the secondary follicular stage, proteoglycan riched antrum appears in the Grannulosa layer. Cell layers in the Zona Grannulosa increase and thereby Zona Pellucida gets thickened. In this sta...

  CLONING VECTORS AND EXPRESSION VECTORS -Devlina Sarkar What is called a Vector?    In biology, a vector is any vehicle , often a virus or a plasmid that is used to ferry a desired DNA sequence into a host cell as part of a molecular cloning procedure.  What are Cloning vectors? A cloning vector is a vector that propagates the DNA we're interested in, in the organism we've chosen to propagate it in, to get clones of our gene of interest. Elements , a cloning vector must have: 1. Origin of replication - The specific sequence of nucleotide in a DNA, which acts, as the origin of the replication process is known as ORI . The foreign DNA starts replicating along with the host cell when it is integrated or connected to this sequence. 2. Multiple Cloning Sites(MCS) - An MCS contains many unique restriction sites to choose from, so compatible restriction enzymes(such as EcoRI,HinDIII etc) can be used on both the vector and the insert. 3. Selectable Markers- ...

  INTRODUCTION TO RECOMBINANT DNA TECHNOLOGY(RDT) - Devlina Sarkar v What is Recombinant DNA technology ? RDT is a series of procedures that is used to join together (recombine) DNA segments from different organisms and inserting it into a host organism to produce new genetic combinations. v What is called Recombinant DNA ? Recombinant DNA (rDNA) is   m olecules  of  DNA  from two different species that are inserted into a host organism to produce new genetic combinations that are of value to science, medicine, agriculture, and industry. Recombinant DNA in a living organism was first achieved in 1973 by  Herbert Boyer , of the University of California at San Francisco, and  Stanley Cohen , at Stanford University , who used   E. coli  restriction enzymes to insert foreign DNA into plasmids. v What is the basic use of RDT? Using RDT we can get a huge no of copies/clones of a particular gene or DNA(cloning) by usi...

  ANAMMOX - Nandini Das Anammox is an abbreviation for anaerobic ammonium oxidation , is a globally important microbial process of the nitrogen cycle.

Fertilization In Sea Urchin - Malay Nayak 1.        What is sea urchin? ·          Spiny water animal ·          Phylum ECHINODERMATA ·          Roughly spherical sea animal Sea Urchin   2. Why Sea Urchin ? The cell-surface events that take place during fertilization have been studied most extensively in sea urchins, members of the phylum Echinodermata . ·    Sea urchin gametes are easy to collect, ·    fertilization occurs outside the animal body. ·    As a result, researchers can observe fertilization and subsequent development simply by combining eggs and sperm in seawater in the laboratory.