added more blogposts

wiki/blogposts/cellcompetency.md

+---
+title:  Cell Competency
+author: Gunisha Aggarwal
+date: 20 September 2024
+---
+
+Competency refers to the cell's potential of taking [DNA](#) fragments from the environment to the inside of the cell. 
+
+This process is found naturally in many bacterial species. The **natural competence** helps to uptake DNA from surroundings and incorporate it in the cell's own genome, which will allow it to get [transformed](#). Sometimes a fragment can be uptaken and only used for nutritional purposes without it getting attached to the genome. Frederick Griffith discovered the process in *Streptococcus pneumoniae.* It differs from artificial competence in being genetically encoded. Also, the regulation of natural competence is dependent on multiple genes.
+
+There is another process referred to as **artificial competence** where the cells are artificially made competent by certain ways. This is done to aid in [cloning](#), that is, so as to incorporate genetic segments of interest into the genetic material of the host cell.
+
+For transformation to take place we require the DNA to pass the outer and inner cell membrane. There are various physical and chemical ways of doing it. DNA is **hydrophilic** and hence cannot pass cell membrane. Thus, top achieve competence, small pores are artificially induced in the cell surface which allow its internalisation.
+
+There are various ways of making a cell competent.
+
+### Chemical Methods
+Bacteria like *E.coli* when soaked in salt solutions achieve competence. Mandel and Higa in 1970 discovered that when treated with an ice cold solution of calcium chloride followed by brief heating at 37/42 °C, bacteria can be [transfected](#) with bacteriophage λ DNA. Similar methods were used for competency later on for plasmid DNA transformation in cells like *E. coli.*
+
+Ice cold salt solutions like calcium and magnesium chloride accompanied by **heat shock** (immediate increase of temperature, which creates thermal instability and increases the permeability) are most commonly used to create small pores and this membrane permeabilisation helps in DNA uptake. The salt with divalent positively charged ions neutralise the negative charge on DNA, which reduces the repulsive forces to an extent which brings the DNA near the cell surface. Subsequenly, by heat shock, pores are created that allows the DNA to enter in the cell.
+ 
+### Physical Methods
+
+#### (a) Electroporation
+This method uses a high voltage electrical pulse to create transient pores in the membrane. When cells are supplied with an electric shock, the membrane orientation arranges itself in such a way that a gap is created. These gaps or small transient pores allow for DNA uptake. Here, the cell's own material can be also lost. Also. the pores are transient, which  means they form for a very small duration of time.
+#### (b) Freeze - thaw method
+This technique is least uses rapid freezing and thawing. Cells are rapidly frozen in liquid nitrogen or kept at -80°C and then rapidly thawed at 37°C. This physically disrupts the cell membrane.
+ 
+Competent cells are very important in research in the field of molecular biology and other related fields. It is a very crucial technique for manipulating the genetic material for achieving targeted results and scientific advancements.
+ 
+#### References
+1. Sambrook J, Russel D. Molecular Cloning: A Laboratory Manual. 3rd edition. Vol. 1. New York, NY, USA: Cold Spring Harbor Laboratory Press; 2001.
+2. Blokesch, M. (2016). Natural competence for transformation. Current Biology, 26(21), R1126-R1130.

wiki/blogposts/clickchem.md

+---
+title:   What is Click Chemistry? 
+author:  Devansh Jhawar 
+date:  29 September 2024 
+---
+
+The ‘click’ in click chemistry is intended to convey that sense of satisfaction you receive when you put Lego pieces together. In fact, the story goes that the term was coined by Jan Dueser, the wife of **K. Barry Sharpless**, the American chemist who was recently awarded the [Nobel prize](#) for his work in click reactions. Jan found the simplicity of click reactions similar to clicking Lego blocks together. 
+
+Click reactions:
+1. Have high yield and purity.
+2. Produce minimal waste/toxic products and next to no byproducts.
+3. Have elementary/mild reaction conditions and are simple to perform.
+4. Have fast kinetics.
+5. Are highly selective and specific, i.e. are mutually [orthogonal](#) (specific components of the reactants react in the presence of many other functional groups without affecting them).
+
+The ‘cream and the crop of click chemistry’ is undoubtedly the **Copper(I)-catalysed azide-alkyne cycloaddition (CuAAC).** For this, we will first need to understand cycloaddition reactions.
+
+A **cycloaddition** reaction is the formation of cyclic compounds (a cyclic adduct - a direct combination of molecular species without any loss of atoms) when multiple unsaturated molecules (having double or triple bonds) come together and are joined by sigma-bonds (single bonds). Linearly connected multiple-bonded molecules form sigma bonds at the terminals to form cyclic compounds. A cycloaddition generally results in a decrease in bond multiplicity - that is, the overall number of electron pairs shared between two atoms.In simple words, the double/triple bonds ‘convert’ into single bonds at the terminals to form a ring. The illustration given below should provide a fair idea.
+
+To get to know click reactions better, let us look at the gold standard of click reactions - CuAAC and then compare it with its contemporary **Huisgen 1,3-Dipolar Cycloaddition** (non-catalysed) to understand what qualifies as a click reaction, and what does not.
+ 
+The CuACC reaction transforms an organic azide and a terminal alkyne exclusively into a triazole. A triazole consists of a five-membered ring with two carbon atoms and three nitrogen atoms. More specifically, the product is a **1,4-disubstituted 1,2,3-triazole. **
+
+Let’s compare the non-catalysed Huisgen 1,3-dipolar cycloaddition (henceforth referred to as HDC) with the copper-catalyzed variant, CuAAC - to understand why one is a click reaction and the other isn’t. 
+
+1. Right off the bat, HDC forms two isomers, whereas CuACC yields a single product. A click reaction is highly specific and yields a high-purity product with no other byproducts. The formation of a single product eliminates the need for further purification in the case of CuACC. 
+2. HDC requires high temperatures (sometimes above 100°C) to proceed. These conditions limit the reaction’s applicability with heat-sensitive substrates. CuACC occurs under mild conditions like room temperature, which increases the sensitivity of the reaction to certain other molecules.
+3. Talking about sensitivity, the CuACC has a wide range of tolerance for functional groups. For example, the presence of carboxyl, amino, hydroxyl, etc. functional groups does not interfere with the reaction, making it a lot more versatile than HDC.
+3. The uncatalysed reaction is slow, often taking hours or even days to achieve completion, whereas CuACC is extremely fast and essentially irreversible, and is usually complete within minutes.
+
+Basically, click reactions are just better, and all other reactions have a skill issue when compared with click reactions.

wiki/blogposts/clicknobel.md

+---
+title:  Why Click Chemistry Won the Nobel
+author: Chandana Valaboju
+date: 30 September 2024
+---
+
+Picture this: it's the 1990s. Scientists are trying to figure out a way to make compounds and materials easily without resorting to highly specific reaction mechanisms, catalysts and reagents. Why? Well, the more specific it is, the more difficult, costly and time consuming it would become. A chemist named **K. Barry Sharpless** figured that it would be beneficial to somehow come up with a streamlined process, where each compound could be made using a limited set of highly robust and efficient reactions. He suggested a bunch of reactions (click reactions), out of which [1,3-dipolar cycloaddition](#) reaction between azides and alkynes turned out to be the most potent as of now. 
+
+However, the reaction itself was difficult to achieve. The rates were low at ambient temperature (which is undesirable), and azides are often explosive in nature, which discouraged industrial companies to produce it. This changed when **Morten Meldal** and **Christian W. Tornoe** discovered that active copper-species can be used as a catalyst, which increased the reaction rate by upto 10^7 times! 
+
+Copper is a toxic substance for human beings, and hence another hurdle arose for cycloaddition click reaction to be carried out in human beings. Enter **Carolyn R. Bertozzi**, who devised a new way to initiate it - SPAAC (strain-promoted azide-alkyne cycloaddition), that is, [copper free click chemistry](#). Bertozzi and her team showed that SPAAC reaction involving a substituted cyclooctyne structure (cyclooctyne, by itself, is heavily strained) and azides proceeded as expected (without the use of copper). Now, the reaction has been fine-tuned to be used in living creatures. 
+
+The joint effort of all these people created something which can very much be [used](#) by human beings and improve their lives, which fetched them the **Nobel Prize in Chemistry** in 2022.  
+
+#### References: 
+1. Olof Ramstrom. (2022, October 5). Scientific Background on the Nobel Prize in Chemistry 2022, CLICK CHEMISTRY AND BIOORTHOGONAL CHEMISTRY. The Nobel Committee for Chemistry 
\ No newline at end of file

wiki/blogposts/clickuses.md

+---
+title:  Uses of Click Chemistry
+author: Chandana Valaboju
+date: 30 September 2024
+---
+
+The click reaction mechanism is simple, with minimum reaction conditions, reagents and catalysts. This is essential for the usage of it in human beings, so that that doesn’t get in the way of the body’s usual chemical reactions ([bio-orthogonality](#)). Since groups like azides and alkynes are not normally found in biological molecules, the reaction becomes highly selective. This makes it an attractive choice. 
+
+Applications include (based on modifying functional biomolecules):
+
+1. **Drugs:** A research team has shown that click chemistry can be used to inhibit HIV-1-PR, an enzyme that supports the HIV virus and causes AIDS. 
+
+2. **Nucleic Acid Labelling:** Advantageous when applied for the in vitro and in vivo study of cell cycle kinetics, DNA and RNA synthesis, and cellular proliferation. 
+
+3. **Radiochemistry:** It aids in the development of highly effective in vivo targeting methods, easy labeling of peptides and proteins. 
+
+4. **Materials Science:** Since it is compatible with many functional groups, there really is no limit to where it can be used. For instance, hydrogels were developed for use in tissue engineering using click chemistry. 
+
+#### References:
+1. Zihau Xu, Kaitlin M. Bratlie. (2018, May 26). Click Chemistry and Material Selection for in Situ Fabrication of Hydrogels in Tissue Engineering Applications. ACS Publications. 
+2. Jan-Philip Meyer, Pierre Adumeau, Jason S. Lewis, Brian M. Zeglis. (2016, October 27). Click Chemistry and Radiochemistry: The First 10 years. ACS Publications. 
+3. Mukesh M. Mugdal, Nagaraju Birudukota, Mayur A. Doke. (2018, July 19). Applications of Click Chemistry in the Development of HIV Protease Inhibitors. National Library of Medicine.  
+4. Nicolo Zuin Fantoni, Afaf H. El-Sagheer, Tom Brown. (2021, January 14). A Hitchhiker’s Guide to Click-Chemistry with Nucleic Acids. ACS Publications. 
+5. Olof Ramstrom. (2022, October 5). Scientific Background on the Nobel Prize in Chemistry 2022, CLICK CHEMISTRY AND BIOORTHOGONAL CHEMISTRY. The Nobel Committee for Chemistry 
\ No newline at end of file

wiki/blogposts/cloningvec.md

+---
+title:  Cloning Vector
+author: Mihir Kapse
+date: 5 September 2024
+---
+
+A **cloning vector** is like a transportation vehicle. It helps to put foreign [DNA](#) into a microbe, mainly for [cloning](#) (that is, replication). A cloning vector is a small piece of DNA that can be stably maintained in an organism, and into which a foreign DNA fragment can be inserted for cloning purposes. However, it does not perform cloning on its own -- it requires the DNA replication machinery of the host. It just acts as a carrier.
+
+In 1973, Cohen and Boyer made a significant breakthrough by developing the first cloning vector, a [plasmid](#) (aA DNA molecule generally present in bacteria that can replicate independently of the genomic DNA). 
+
+First, a fragment of DNA from a foreign microbe is cut using a [restriction enzyme](#). The foreign DNA fragment is then joined with the vector DNA through the process of [molecular ligation](#), often using the enzyme DNA ligase.  The **recombinant vector** (foreign DNA + vector DNA) is then introduced into the host cell. If the host cell accepts the recombinant DNA, the replication process of DNA starts producing multiple clones of the foreign DNA with itself. The cells that successfully performed cloning are screened and separated from the group. 
+
+A cloning vector has some key features:
+1. **Cloning Site:** Every cloning vector has few to many sites for foreign DNA to be conveniently inserted into them. 
+2. **[Selectable Marker:](#)** Cloning vectors, when processed through molecular ligation, may or may not get ligated. It's a desired feature that cloning vectors have a selectable marker, so that later on they can be separated from the ones that are not ligated.
+3. **Reporter gene:** The reporter gene is not present in all cloning vectors. They are helpful in the process of screening cells that have successfully performed cloning from the entire batch.
+
+In 1983, Jack Szostak and Andrew Murray opened new doors by developing artificial chromosomes (particularly, **Yeast Artificial Chromosomes (YAC)**). Later on in the mid-late 1990s, Human Artificial Chromosomes (HAC) were developed. Artificial chromosomes are special because they can be used for cloning large fragments of DNA (up to 1 million pairs).
+
+Presently, we know a large number of cloning vectors. However, not all can be used for a specific process. A cloning vector is chosen based on various factors: size of the insert, the **copy number** (number of copies of the plasmid present per cell, which determines how much the gene will be replicated) and cloning method. Some of the common cloning vectors we work with are bacteriophages, plasmids, cosmids, and artificial chromosomes.
+
+Some of the important applications of cloning vectors are in:
+1. Gene Cloning
+2. Gene Expression Studies
+3. [Genetic engineering](#)
+4. DNA sequencing (YAC for Human Genome Project)
+5. Vaccine development
+
+
+#### References:
+
+1. A Preston, Choosing a cloning vector, Humana Press, 2003
+2. Kouprina N, Earnshaw WC, Masumoto H, Larionov V, A new generation of human artificial chromosomes for functional genomics and gene therapy, Cellular and Molecular Life Sciences, April 2013

wiki/blogposts/cufreeclick.md

+---
+title:  Copper-Free Click Chemistry
+author: Vidhi Chauhan
+date: 1 October 2024
+---
+
+### Copper in Biological Systems
+Copper is a trace mineral found in all body tissues. It Is required for the formation of red blood cells, iron absorption, neuron and immune function. It is also required as a cofactor for many enzymes, called cuproenzymes.
+
+### Copper Toxicity
+Copper as a toxic metal affects the liver mainly. It usually results in the development of liver cirrhosis, and damage to organs such as the kidneys, the heart and the brain. When consumed through food, copper intoxicated food stuff can cause the development of acute gastrointestinal symptoms. Copper toxicity is also linked to Alzheimer’s disease, where free copper levels have been found to rise.
+
+### Copper Free Click Chemistry
+Copper free [click chemistry](#) encompasses [bioorthogonal reactions](#) that do not use toxic copper catalysts and proceed at lower activation barriers. Bioorthogonal reactions are reactions which occur inside biological systems without interfering with the local reactions.
+
+It is based on Wittig's copper free click reaction. It is a reaction between cyclooctyne and phenyl azide to produce a single product, a triazole, in an extremely fast reaction. The reaction moves forward due to the **ring strain** in the cyclooctyne. Ring strain refers to the instability arising due to differences in bond angles. The ideal bond angle for an alkyne is 180 degree, but cyclooctyne has an angle of 160 degree, which causes strain. Other derivatives of cyclooctyne that are used for copper free chemistry are OCT, MOFO (monofluorinated cyclooctyne), DIFO (difluorinated cyclooctyne) and MFCO (monofluorosubstituted cyclooctyne).
+
+### Applications
+Copper free click chemistry is used for labeling biomolecules in *live laboratory mice*. Mice are the model organism for understanding human biological systems due the similarities in their biology. It was successfully used to label molecules called azidosugars without any damage to tissues like intestines, heart and liver of the mice, due to copper toxicity. Particularly, copper free click chemistry presents a good option for facilitating clicking in Alzheimer's prone or Alzheimer's afflicted systems.
+
+#### References
+1. Pamela V. Changa,1, Jennifer A. Preschera,1, Ellen M. Slettena , Jeremy M. Baskina , Isaac A. Millera , Nicholas J. Agarda , Anderson Loa , and Carolyn R. Bertozzi *Copper-free click chemistry in living animals*
+2. Lisa M. Gaetke, Ching Kuang Chow *Copper toxicity, oxidative stress, and antioxidant nutrients*
+3. Jeremy M. Baskin; Jennifer A. Prescher; Scott T. Laughlin; Nicholas J. Agard; Pamela V. Chang; Isaac A. Miller; Anderson Lo; Julian A. Codelli; Carolyn R. Bertozzi (2007). *"Copper-free click chemistry for dynamic in vivo imaging".* Proceedings of the National Academy of Sciences.
+4. Rostovtsev, VV, Green, LG, Fokin, VV, Sharpless, KB. (2002) *Angew. Chem..* 114, 2596.
+5. Akeroyd N. (2010) *Click chemistry for the preparation of advanced macromolecular architectures* Stellenbosch University.

wiki/blogposts/enzymes.md

+---
+title:  Enzymes
+author: Vidhi Chauhan
+date: 5 September 2024
+---
+
+<p align = “center”>
+*Without enzymes, biochemical reactions would simply not occur fast enough for life to exist. Enzymes are what allow life to be as feasible as it is today.*
+/p>
+
+Enzymes are catalysts that work in biological systems. **Catalysts** are substances that speed up reactions by lowering their activation energy (energy that a reactant must possess for the reaction to proceed). Enzymes speed up biochemical reactions. They are mostly proteins, but some RNA also show catalytic capacity — these are called ribozymes.
+
+How do enzymes work? The essence lies in the structure of each enzyme. Every enzyme is shaped to fit a specific reactant of a specific reaction. This reactant is called a **substrate**. The enzyme then changes the structure of this attached substrate, which changes the pathway of the reaction in a way that activation energy decreases. The earlier consensus was that enzymes have a “lock and key” model – the enzymes are rigid and attach to the substrate like a key fitting in a lock. But 60 years ago, the biochemist **Daniel Koshland** proposed the “induced fit” model – the enzymes change their shape for better attachment to their respective substrates.
+
+Enzymes work in a very specific pH and temperature range. Any change in the environment can lead to the enzyme becoming **denatured** – the shape of the enzyme gets distorted, sometimes irreversibly.
+
+The enzymes are classified using a four level classification system. Each enzyme has a code consisting of four numbers separated by periods, each number corresponding to a level in the system. This code is called the **Enzyme Commission Number** (EC Number). The first level consists of seven major enzyme classes, which are:
+
+1. **Oxidoreductases:** These catalyse the transfer of electrons, hydrogen or oxygen from one substance to another. These reactions are called oxidation reactions
+2. **Transferases:** These catalyse the transfer of functional groups (part of a molecule that has a characteristic chemistry). For example, kinases transfer the phosphate group from one molecule to another. This process is called phosphorylation.
+3. **Hydrolases:** These catalyse the cleavage of substances in the presence of water.
+4. **Lyases:** These catalyse the cleavage of substances without water.
+5. **Isomerases:** These catalyse isomerisation processes. Isomerisation refers to the change in the arrangement of atoms in a molecule.
+6. **Ligases:** These catalyse the combination of two substances and the formation of new bonds. For instance, DNA ligase combines two [DNA](#) strands and is used in the replication and repair of DNA.
+7. **Translocases:** These catalyse the transfer of substances across membranes.
+
+An interesting class of enzymes called **polymerases** help in DNA replication. They are involved in a process called **[Polymerase Chain Reaction](#)** (PCR). They are different from ligases in that they can join two single [nucleotides](#) together, while ligases can only join longer polynucleotide strands.
+
+#### References
+1. Britannica, T. Editors of Encyclopaedia (2023, March 20). polyvinylidene chloride. Encyclopedia Britannica. 
+2. Dagmar Ringe, Gregory A. Petsko, How Enzymes Work. *Science Volume 320* (2018)
+3. Moss GP. "Recommendations of the Nomenclature Committee". *International Union of Biochemistry and Molecular Biology on the Nomenclature and Classification of Enzymes by the Reactions they Catalyse*.
+

wiki/blogposts/gelelectro.md

+---
+title:  Agarose Gel Electrophoresis
+author: Aarav Ghate
+date: 1 October 2024
+---
+
+**Electrophoresis** is a technique used to separate [DNA](#), [RNA](#) or [protein](#) molecules based on their size, using an electric current. **Agarose Gel Electrophoresis** uses agarose, a component of agar, as a matrix to filter nucleic acids based on their size. The matrix is made of supercoiled agarose molecules arranged in a three dimensional structure, which has pores and channels for the proteins to pass. 
+
+Initially, agarose powder is dissolved in a suitable medium and heated to just below boiling point. The liquid is placed in an appropriate cast and allowed to solidify. The matrix is held together by hydrogen bonds, and liquifies once again if heated. 
+
+DNA and RNA carry a negative charge due to the phosphate groups that form their backbone. The samples are placed into wells (holes in the agarose gel) and begin to move towards the positive terminal when a voltage is applied across the gel. Dyes may be placed along with the sample to monitor its progress (called tracking dyes, such as **bromophenol blue**) and loading buffers may be used to increase the density (so that the sample sinks to the bottom of the well). 
+
+Smaller molecules travel faster in the gel because of **sieving** through the pores in agarose, so after applying voltage for some time, a gradient is seen from the largest molecules to the smallest molecules. Eventually, the molecules separate into groups called **bands** depending on their size. These DNA in these bands may be separated by cutting, liquefying the agarose gel and then purifying the sample. 
+
+Since nucleic acids cannot be viewed with the naked eye, dyes like methylene blue may be added to view the bands. However the most commonly used technique is the incorporation of **ethidium bromide** in the sample. Ethidium bromide forms a complex with the nucleic acids and fluoresces under UV light. The sample is stained and placed under a UV light with a higher intensity of fluorescence indicating a larger amount of DNA in that band. 
+
+Agarose Gel Electrophoresis has many applications ranging from separation of DNA fragments by size, to analyzing the products of PCR. 
+
+#### References:
+
+1. Jeppsson JO, Laurell CB, Franzén B, Agarose Gel Electrophoresis, Clinical Chemistry, (1979)
+2. Lee PY, Costumbrado J, Hsu CY, Kim YH, Agarose gel electrophoresis for the separation of DNA fragments, Journal of Visualized Experiments (2012). 
+

wiki/blogposts/geneticcode.md

+---
+title: Genetic Code
+author: Chandana Valaboju
+date: 3 September 2024
+---
+
+The genetic code refers to the sequence of instructions contained in a [gene](#). The instructions aid in forming [peptide bonds](#) between corresponding [amino acids](#), which later fold to give proteins. The flow of information happens from DNA to mRNA to proteins. This is called the [Central Dogma of Molecular Biology](#).
+
+The information is stored in DNA by the sequence in which nucleotide bases are arranged. After [transcription](#) of DNA, the mRNA formed moves to the ribosomes. A combination of three nucleotide bases together is called a **codons** and corresponds to a particular amino acid. [tRNA](#) (transfer RNA) binds to each codon and brings the corresponding amino acid along with it, during the process of [translation](#). 
+
+There are 64 possible codon sequences, out of which 61 correspond to an amino acid and the other three are stop codons (UAA, UAG, UGA), which don’t get translated and signal the end of the translation process. The AUG codon has a dual purpose – it codes for methionine and acts as an initiator codon, that is, it signals the beginning of translation.
+
+The genetic code is said to be **degenerate**, because a single amino acid can be coded for by more than one codon. The genetic code is nearly **universal** for all organisms, with only rare variations ever detected (like in some mitochondrial codons and some protozoans).
+
+The genetic code, outlining which codon corresponds to which amino acid, is given below.
+
+#### References:
+
+1. James D Watson, Tania Baker, Stephen Bell, Alexander Gann, Michael Levine, Richard Losick, Molecular Biology of the Gene, India: Affiliated East West Press, 2024
+2. Koji Tamura. (2016, Aug 25). The Genetic Code: Francis Crick’s Legacy and Beyond. National Library of Medicine.

wiki/blogposts/geneticengg.md

+---
+title: Genetic Engineering and Bioethics
+author: Creetika Dahal
+date: 1 September 2024
+---
+
+Genetic engineering involves designing and modifying sequences of genomes. This technology was born in 1927 when nonspecific changes in *Drosophila* DNA were recorded after radiation exposure. The modern era of genetic engineering surfaced after researchers showed that when a segment of DNA was introduced into a cell, it could be integrated into the pre-existing genome to enable specific changes in the cell. Subsequently, leaps and bounds have been achieved in refining, building upon and discovering new techniques and practices.
+
+The foundations of genetic engineering were laid with [Recombinant DNA](#) technology and the use of [plasmids](#) as [cloning vectors](#) and the ability to cut DNA at specific sites using [restriction enzymes](#). Today, genetic engineering may involve changing a single base pair (A-T or C-G), deleting a region of DNA, or adding a new segment of DNA. Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated protein 9 (Cas9) is one such technology that can easily correct erroneous genes and also turn selective genes ‘on’ and ‘off’. Researchers can use proteins and guide RNA to cut DNA at very specific sites to add/disable genes. In 2020, it won the Nobel prize in biology. 
+
+Most gene editing technologies involve molecules that recognise and bind to specific DNA sequences, allowing researchers to use custom molecules to affect genetic changes on any gene. There are also subtler, more long-term methods of widespread gene editing over an entire group or population.
+
+The ethics of genetic engineering is a slippery slope, but it must be walked on during a proper evaluation of the topic. With the first successful transformation of a human cell by adding genomic DNA having been achieved in 1962, we have had a long time to think about the consequences of our actions. Changes that can be artificially induced in a cell reach far and wide, and it is difficult to draw clear ethical boundaries. There have been instances of experiments being considered ‘dubious’, most involving some alteration in the human genome. It appears to be a general public consensus that genetic editing against disease and disability is acceptable, while enhancements –such as athletic ability and intelligence, or for altering physical characteristics, such as eye colour and height are frowned upon. There is also a long-standing issue debate about [Dual-Use Research of Concern (DURC)](#) - that is, research that is intended to provide a clear benefit but could easily be misapplied to do harm.  
+
+Certain guidelines like the Nuremberg Code and Ethical Principles for Medical Research Involving Human Subjects (The Declaration of Helsinki) have been proposed, with the latter being adapted by the World Health Organisation (WHO) for its member countries to adhere to. These materials are very important because it is important to not regard the entire practice as evil and misdirected. The potential of genetic engineering in medicine, agriculture and technology is immense. Greater efficiency in selective plant breeding, increased resistance to disease, companion species, and reduction of agricultural pollution, are a few of the widespread advantages that can be brought about through conscious use of genetic editing. While the imperative ethical debates continue, progress must also show in the practical applications of genetic engineering as a viable technology for good. 
+
+#### References
+
+1. Khalil, A.M. The genome editing revolution: review. *J Genet Eng Biotechnol 18, 68* (2020).
+2. Mike Smith. (08/28/2024). *Genetic Engineering*. National Human Genome Research Institute. 
+3. Tamura, R., & Toda, M. (2020). Historic Overview of Genetic Engineering Technologies for Human Gene Therapy. *Neurologia medico-chirurgica*, 60(10), 483–491.
+4. Rothschild J. (2020). Ethical considerations of gene editing and genetic selection. *Journal of general and family medicine*, 21(3), 37–47.
+5. Ormandy, E. H., Dale, J., & Griffin, G. (2011). Genetic engineering of animals: ethical issues, including welfare concerns. *The Canadian veterinary journal = La revue vétérinaire canadienne*, 52(5), 544–550.
+

wiki/blogposts/immunostaining.md

+---
+title: Immunostaining
+author: Palak Raisinghani
+date: 3 September 2024
+---
+
+**Immunostaining** is a diagnostic process. It is used by pathologists to detect the presence of certain antigens present in sample of blood, bone marrow or tissue. It is widely used to diagnose infections, cancers, and other conditions.
+
+**Antigens** are certain proteins or amino acid sequences, that are present on the surfaces of various body cells and foreign particulate objects entering the body. They are like markers telling the immune cells whether an object is foreign or not. The immune system generates **antibodies** highly specific for a certain antigen. They are shaped in such a way that they only lock on the antigens that they target. In simple words, an antigen is anything to which an antibody is generated.
+
+The antigen has small sites on it which bind to the receptors of the antibodies - these are called **epitopes.** Epitoes are also referred to as antigenic determinants. These are the parts of antibodies that detect and bind to the epitopes of antigens.
+
+The same principle of antigen-antibody interaction is used in immunostaining, except that here the antibodies are introduced into the sample externally (and not produced by the body). They bind to the target antigen only. 
+The antibodies used in this process are linked to an enzyme or fluorophore. The conjugated enzymes are reacted further with a substrate, eventually forming a coloured or chemiluminescent product. Fluorophores are chemicals that absorb and emit energy in a predictable fashion. This eventually makes the antibodies easy to spot under the microscope. Pathologists interpret the slide and determine whether a target antigen is present or absent thus completing the diagnosis.
+ 
+Immunostaining has emerged as a commonly used and valuable technique in diagnosis. However, some disadvantages are associated with the application of this technique. Immunostaining encompasses a few different methods:
+1. **Immunohistochemistry:** the antibodies bound to the antigens are stained with dyes or enzymes and this is placed on a glass slide that is evaluated under the microscope.
+2. **Flow cytometry:** the antibodies are stained, and a laser is used to analyses the sample and sort all the cells on by one into different categories.
+3. **Immuno-electron microscopy:** antibodies are linked to nanoparticles of gold. Gold is visible as dark flecks under an electron microscope; thus, it is easy to examine the sample.
+
+Immunostaining methods are extensively used in **protein Purification,** that is, a the process of separation of certain target protein from a mixture of other molecules/cells/tissues or whole organisms. Protein purification is a highly researched field as the process is often crucial in diagnosis of infections. 
+
+Immunostaining can be used to investigate the presence or absence of a certain protein, its distribution in a tissue and across regions and parts of a cell. Once the different proteins in a sample have been separated by [SDS-PAGE](#) and [Western Blotting](#), the band corresponding to the protein is often identified using immunostaining. Antibodies against the protein of interest, conjugated with an enzyme or fluorophore (as before), are used for this purpose. 
+
+#### References
+1. Idleburg, C., Lorenz, M. R., DeLassus, E. N., Scheller, E. L., & Veis, D. J. (2021). Immunostaining of Skeletal Tissues. Methods in molecular biology (Clifton, N.J.), 2221, 261–273.
+2. Binch, A., Snuggs, J., & Le Maitre, C. L. (2020). Immunohistochemical analysis of protein expression in formalin fixed paraffin embedded human intervertebral disc tissues. JOR spine, 3(3), e1098.
+3. Maity, B., Sheff, D., & Fisher, R. A. (2013). Immunostaining: detection of signaling protein location in tissues, cells and subcellular compartments. Methods in cell biology, 113, 81–105.
+
+
+
+
+

wiki/blogposts/misfoldedprot.md

+---
+title:  Protein Folding and Misfolded Proteins
+author: Ritik Ravichandran
+date: 29 August 2024
+---
+
+Proteins are made up of building blocks called [amino acids](#). When these amino are strung up together in different ways, we get different proteins. This level of organisation is known as the **primary structure** of the protein.
+
+This sequence of amino acids then usually assumes one of two structures. 
+1. A highly coiled slinky like structure known as an **alpha helix**. 
+2. A sheet like structure known as a **beta sheet**. 
+This is known as the secondary structure of the protein. 
+
+These secondary structures then fold to form compact functional structures. Depending on the function they have to perform, they assume a specific 3D structure. It is this **tertiary structure** that determines the biological function of the protein. The specific shape allows the protein to interact with other molecules, perform catalytic functions, or provide structural support. It is also important to understand that a **misfolding** resulting in an erroneous tertiary structure can lead to many diseases.
+
+Protein-folding research began before we knew about diseases caused by protein misfolding. Before 1972, it was believed that infectious diseases were caused by viruses and bacteria. Stanley Prusiner’s research on Creutzfeldt-Jakob disease revealed that misfolded proteins, known as **prions**, could also be responsible for disease. This discovery changed our understanding of many conditions, showing that protein misfolding is also involved in diseases like Alzheimer’s, Parkinson’s, Huntington’s, and type II diabetes.
+
+What's amazing is that proteins can self-assemble spontaneously and reversibly into their unique native three-dimensional structure under suitable physiological conditions. Here, “spontaneous” means that no external energy source such as ATP hydrolysis is required. This led scientists to believe that it was the amino acid sequence that dictated the way that the protein would fold. In other words, all the information required for a protein to adopt the correct three-dimensional conformation is provided by its amino acid sequence!
+
+In order to make sure that these proteins fold correctly , our body produces another protein called **chaperone proteins**. Chaperone proteins, also known as molecular chaperones, are proteins that help other proteins fold into their native conformations.
+
+The protein folding problem is something scientists have been working on for years. But what is it? For decades, scientists have tried to find a method to reliably determine a protein’s structure from its sequence of amino acids alone. This grand scientific challenge is known as the protein-folding problem.
+
+**AlphaFold,** a breakthrough AI software, has been able to make remarkable progress in this area. With AlphaFold we are now able to predict the 3D structure of proteins from their amino acid sequence. 
+
+But how has AlphaFold managed to crack the problem that took scientists decades -- in just 4 years? The answer lies in the sheer magnitude of data that AlphaFold can assimilate and process. AlphaFold was taught by showing it the sequences and structures of around 100,000 known proteins. AlphaFold is helping to accelerate research in many fields, including: disease treatment, breaking down single-use plastics, and finding new malaria vaccines.
+
+In essence, understanding protein folding helps us see how proteins do their job and what happens when they don’t. This insight is crucial for understanding and treating diseases caused by misfolded proteins. 
+
+#### References:
+1. Cooper GM. The Cell: A Molecular Approach. 2nd edition. Sunderland (MA): Sinauer Associates; 2000. Protein Folding and Processing.
+2. Dobson, C. M. Protein folding and misfolding. Nature 426, 884–890 (2003) 
+3. Dobson, C. M. Protein misfolding diseases: Getting out of shape. Nature 418, 729–730 (2002) 
+4. Jumper, J., Evans, R., Pritzel, A. et al. Highly accurate protein structure prediction with AlphaFold. Nature 596, 583–589 (2021)

wiki/blogposts/ndd.md

+---
+title: Neurodegenerative Diseases (NDDs)
+author: Ishwari Bhattacharya
+date: 1 October 2024
+---
+
+### Introduction 
+
+Regeneration is one of nature’s most captivating feats. 
+
+It's a testament to the resilience and adaptability of life. A planarian worm (eg. *Taenia solium* (pork tapeworm)), can be cut into many pieces and each piece will regrow into a full worm within about two weeks. Although the regenerative capacity in human beings is limited, it plays a significant role in our everyday lives. 
+
+Ironically, the most important and intricate cells of our body, the nerve cells or [neurons](#) have very limited regenerative capacity. **Neuroregeneration** is defined as the regrowth or repair of nervous tissues,cells or cell products. Neuroregenerative mechanisms may include generation of new neurons, glia, axons, myelin, or synapses. Neuroregeneration differs between the peripheral nervous system (PNS) and the central nervous system (CNS) (that is, the brain and spinal cord) with regards to the functional mechanisms involved, especially in the extent and speed of repair. Unlike a peripheral nervous system (everything apart from the brain and spinal cord) injury, injury to the central nervous system is not followed by extensive regeneration. 
+
+**Neurodegeneration** is defined as a complex process that causes death of neurons in the brain and spinal cord, resulting in damage and dysfunction. Chronic neurodegeneration leads to **neurodegenerative diseases**, a condition that damages and destroys parts of our nervous system over time, especially our brain. These conditions are permanent and incurable. 
+
+The most common NDDs include Alzheimer’s disease, Parkinson’s disease, prion disease, Amyotrophic lateral sclerosis (ALS), motor neuron disease, Huntington’s disease, spinal muscular atrophy, and spinocerebellar ataxia. 
+
+### Common causes and symptoms of NDDs 
+
+Some neurodegenerative diseases have a single cause that healthcare providers can identify. But in many cases, this isn't the case. Instead, research shows that multiple factors probably contribute to neurodegenerative diseases, which may even be undetectable. 
+
+So far, experts have generalized some possible causes or risk factors, like: 
+
+1. **Age:** These conditions have strong ties to age. The older you are, the greater your chances of developing one. Some degenerative brain diseases can start earlier in life, but this is less common. 
+2. **Genetics:** Many neurodegenerative diseases have strong ties to family history. That’s often because of specific mutations you can inherit that increase your risk. Spontaneous mutations can also happen, and sometimes a combination of genes plays a role. 
+3. **Environment:** Our environment can be a major factor in developing these conditions. for example, lower vitamin D levels, which are more common the farther you live from the Earth’s equator, have links to dementia-type diseases 
+4. **Medical history:** Some neurodegenerative conditions can either happen because of specific medical events or can get worse because of them. Some examples include cancer, certain types of infections, if you've had head injuries and more. 
+5. **Habits, routines and choices:** daily lifestyle, use and abuse of drugs and hallucinogens and an overall unhealthy life can very likely lead to such conditions. 
+
+The symptoms of neurodegenerative diseases can vary widely, even among people with the same condition. There are a few reasons for this. Firstly, each person’s brain is unique. No two brains form or work in exactly the same way. That means the same condition can still affect two people differently. Further, neurodegenerative diseases happen for many different reasons. The possible causes can vary widely for these conditions, even among conditions of the same type. The symptoms depend the parts of your brain or nervous system affected.
+
+### Alzheimer’s Disease 
+
+Alzheimer's disease is alarmingly prevalent and has a significant impact globally.Over 55 million people worldwide are living with dementia and Alzheimer's disease contributes to 60-70% of these cases. Alzheimer's disease is a significant cause of morbidity and mortality among the elderly in India.      While exact statistics on Alzheimer's as a cause of death can vary, it is known to be one of the            leading causes of dementia, which affects over 1 million individuals in the country. 
+
+# Symptoms 
+
+The most common early symptom is difficulty in remembering recent events. As the disease advances, symptoms can include  problems with language, disorientation (including easily getting lost), mood swings, loss of motivation,self-neglect, and behavioral issues. As a person's condition declines, they often withdraw from family and society. Gradually, bodily functions are lost, ultimately leading to death. Although the speed of progression can vary, the average life expectancy following diagnosis is three to twelve years. 
+
+# Causes 
+
+The cause for most Alzheimer's cases is still mostly unknown, except for 1–2% of cases where deterministic genetic differences have been identified. Several competing hypotheses attempt to explain the underlying cause; the most predominant hypothesis is the **amyloid beta (Aβ) hypothesis.**
+
+When abnormal amounts of amyloid beta (Aβ) protein accumulate extracellularly as **amyloid plaques and tau proteins**, or inside the cell as neurofibrillary tangles in the brain, it affects our brain's neuronal functioning and connectivity, resulting in a progressive loss of brain function. This altered protein clearance ability is age-related, regulated by brain cholesterol, and associated with other neurodegenerative diseases. 
+
+# Pathophysiology 
+
+Alzheimer's disease is characterized by loss of neurons and synapses in the cerebral cortex and certain subcortical regions. This loss results in gross wasting away of the affected regions, including degeneration in the temporal lobe and parietal lobe, and parts of the frontal cortex and cingulate gyrus. 
+
+Upon postpartum inspection of the brain of the affected patients, both Aβ plaques and neurofibrillary tangles(NFTs) are clearly visible in microscopy especially in the hippocampus. However, Alzheimer's disease may occur without neurofibrillary tangles in the neocortex. 
+
+Aβ plaques  are dense, mostly insoluble deposits of beta-amyloid peptide and cellular material outside and around neurons. Neurofibrillary tangles (NFTs) are aggregates of the **microtubule-associated protein (MAP) tau** which has become **hyperphosphorylated** (excessive and unnatural addition of phosphate groups) and accumulate inside the cells themselves. 
+
+However, recent studies show that beta-amyloid protein deposition starts decades before the first clinical symptoms. Furthermore, based on the assessment of the distribution of neurofibrillary tangles (NFTs), subtypes of Alzheimer's disease - for example hippocampal sparing, typical or limbic-pre dominant -- have been proposed, arguing for further subclassification of AD. 
+
+In summary, for the current neuropathological diagnosis of Alzheimer's disease , based on the recommendation of the National Institute on Aging-Alzheimer’s Association, an ‘ABC’ score, for the description of Alzheimer's disease induced neuropathological change, has been adopted.  
+
+1. **Score A** for ‘amyloid’: incorporates the phases of Aβ deposition. 
+2. **Score B** for ‘Braak’: integrates stages of tau-positive neurofibrillary degeneration. 
+3. **Score C** for ‘CERAD’: credits the extent of appearance of argyrophilic neuritic plaques. 
+
+The ABC score put together classifies the neuropathological changes by the disease into 4 levels: not, low, intermediate or high. 
+
+#### References
+
+1. Lamptey RN, Chaulagain B, Trivedi R, Gothwal A, Layek B, Singh J; A Review of the Common Neurodegenerative Disorders: Current Therapeutic Approaches and the Potential Role of Nanotherapeutics; Int J Mol Sci; February 2022
+2. Patow, Gustavo; Escrichs, Anira; Ritter, Petra; Deco, Gustavo; Whole-Brain Dynamics Disruptions in the Progression of Alzheimer's Disease: Understanding the Influence of Amyloid-Beta and Tau"; bioRxiv; March 2024
+3. Erkkinen, Michael G.; Kim, Mee-Ohk; Geschwind, Michael D. Clinical Neurology and Epidemiology of the Major Neurodegenerative Diseases. Cold Spring Harbor Perspectives in Biology. April 2018
\ No newline at end of file

wiki/blogposts/pcr.md

+---
+title: Polymerase Chain Reaction
+author: Mukta Khanolkar
+date: 31 August 2024
+---
+
+**Polymerase Chain Reaction (PCR)** is a process used to [replicate](#) or ‘amplify’ genes of interest. It repeats a cycle multiple times to produce a large number of [DNA](#)/[RNA](#) copies. It is a rapid automatic process with high specificity. PCR is particularly useful when working with small quantities of DNA samples, to avoid risking the whole sample in the experiment in case it fails. Thus, any synthetic biology experiment working with DNA relies heavily on PCR. It is no surprise that Kary Mullis was awarded the Nobel Prize in 1993 in recognition of his invention of PCR.
+
+The PCR setup consists of a reaction mixture containing the desired DNA segment, nucleotides, primers, necessary enzymes and more in a device called a **‘thermal cycler’.**
+
+PCR makes use of the enzyme [DNA polymerase](#) to replicate DNA. Since it is difficult for the enzyme to initiate replication *de novo*, PCR makes use of **primers,** which are short sequences of DNA complementary to the gene we are trying to amplify. Once the primers bind to the correct site on DNA, DNA polymerase can extend the primers and facilitate replication.
+
+A single PCR cycle involves the following steps:
+1. **Denaturation:** The DNA segment is heated to high temperatures (94-98°C) to separate its two strands.
+2. **Annealing:** The strands are cooled down to 48-72°C. This allows primer molecules present in the reaction mixture to bind with them.
+3.  **Extension:** DNA polymerase adds complementary nucleotides to the single strands of DNA. Thus, two copies of DNA are obtained at the end of the cycle.
+
+With each cycle, the number of DNA copies doubles – that is, it exponentially increases (2n after n cycles). One cycle takes around three minutes. Thus, a billion gene replicas can be produced in a few hours. After amplification, the DNA obtained is purified and then used for other processes.
+
+Fun fact: PCR uses a special type of polymerase called Taq polymerase which is functional even at the high temperatures of the thermal cycler (while normal human enzymes would get denatured). It is isolated from the bacterium *Thermus aquaticus*.
+
+#### References:
+1. Khehra N, Padda IS, Swift CJ. Polymerase Chain Reaction (PCR) [Updated 2023 Mar 6]. Treasure Island (FL): StatPearls Publishing; 2024 Jan-.
\ No newline at end of file

wiki/blogposts/plasmiddnaiso.md

+---
+title:  Plasmid DNA Isolation
+author: Gunisha Aggarwal
+date: 31 August 2024
+---
+
+### Isolation of DNA
+
+Friedrich Miescher, a Swiss physician, isolated [DNA](#) for the first time. Isolation of DNA is the most crucial method of molecular biology. Without it, downstream molecular analysis is not possible. It is the starting point of any experiment. 
+
+DNA can be isolated from any biological material such as cells, tissues and viruses. Isolated DNA should have good quantity and quality as it should be pure means free of contamination like that of RNA and proteins.
+DNA isolation can be done by using organic, non-organic and adsorption methods.
+
+### Isolation of Plasmid DNA
+
+[Plasmids](#) are small circular extrachromosomal DNA molecules present mostly in bacteria. These are present inside the cell but are physically separated from chromosomal DNA, and can replicate independently. While chromosomal or genomic DNA is large and mainly codes for all the necessary genetic information, plasmids are smaller in size and contain certain genes that confer various properties to the host like antibiotic resistance.
+
+Plasmid isolation is a very important molecular process for [gene cloning](#), gene expression analysis, sequencing and mutagenesis. Isolation and purification of plasmids consists of four steps:
+
+1. **Growth of bacterial culture:** Plasmids are isolated from bacterial cultures. These are inoculated with bacterial colonies picked from a cultured agar plate. The culture is grown and aliquots of these are used for plasmid DNA isolation.	
+2. **Harvesting of cells:** It can be achieved by techniques like filtration or centrifugation.
+3. **Lysis of cells:** Harvested cells are lysed by using certain reagents like non-ionic or ionic detergents, organic solvents, alkali and heat.
+4. **Purification of Plasmid DNA:** After lysis plasmid DNA obtained is always contaminated with RNA and chromosomal DNA. So, it should be in purified form.
+
+An **alkaline lysis using sodium dodecyl sulphate (SDS)**, a strong anionic detergent at high pH opens the cell wall, denatures chromosomal DNA and proteins. So, it releases plasmid DNA in the solution. This alkaline solution breaks the base pairing. The question arises that then plasmid DNA should also get disrupted in such a case. It happens that the strands of plasmid DNA that are closed circular in shape are unable to separate from each other as they are topologically intertwined, due to which plasmid DNA does not get disrupted.
+
+### References:
+1. Sambrook J, Russel D. Molecular Cloning: A Laboratory Manual. 3rd edition. Vol. 1. New York, NY, USA: Cold Spring Harbor Laboratory Press; 2001.
+2. Brown, TA. (2010). Gene Cloning and DNA Analysis, An Introduction. 6th edition. (6th ed.) John Wiley &; Sons Ltd.
+3. Tan, S. C., & Yiap, B. C. (2009). DNA, RNA, and protein extraction: the past and the present. BioMed Research International, 2009(1), 574398.

wiki/blogposts/proteinopathies.md

+---
+title:  Proteinopathies
+author: Aarav Ghate
+date: 1 October 2024
+---
+
+[Neurodegenerative diseases (NDDs)](#) are characterised by progressive deterioration of parts of the nervous system, such as the neurons, their synapses or glial cells. In some NDDs, this may be caused by deposition of proteins in the nervous system. In particular, when a protein misfolding leads to its deposition, it is called a **proteinopathy.**
+
+Since proteins are long polymers, they form characteristic three dimensional structures in order to remain compact. This is known as [protein folding](#). Generally, a protein will spontaneously fold into a structure that is the least energetic thermodynamically. This particular structure allows parts of the protein to interact with other molecules and receptors in the cell.  
+
+However, in certain cases, there may be two structures that are vastly different structurally, but have comparable energies. While one structure is the native one in the body and has a particular function, the other may be useless or even toxic. The body has developed molecules known as **‘chaperones’**, which bind to the proteins and allow them to fold only in the correct structure by inhibiting the pathway that forms alternative, unwanted  structure. However, given the large number of proteins present in the body, some still misfold due to random chance and form linear or fibrillar aggregates known as amyloid deposits. 
+
+A formation of **amyloid deposits** (due to misfolding of amyloid beta protein) in the nervous system leads to proteinopathies, such as Alzheimer’s Disease, Huntington’s Disease and Parkinson’s Disease. In some cases, the misfolding of one protein may catalyse misfolding of other proteins surrounding it, leading to a feedback loop. Prion diseases are proteinopathies that spread via ‘infectious’ proteins. These diseases are caused by toxic protein deposits which convert neighbouring proteins to toxic conformations. The risk of being affected by proteinopathies increases significantly with age, perhaps due to an increased frequency of misfolded protein aggregates. 
+
+Treatment strategies for proteinopathies involve preventing the formation of further aggregates by targeting proteins that are specific to a disease (for example, beta-amyloid protein in Alzheimer’s). Drugs that inhibit accumulation and promote chaperone expression could be potential treatments in the future. Vaccines which act against aggregation may also play a significant role. 
+
+#### References:
+1. Reynaud, E. Protein Misfolding and Degenerative Diseases. Nature Education, (2010).
+2. Kovacs GG, Molecular Pathology of Neurodegenerative Diseases: Principles and Practice, J Clinical Path, (2019) 
+

wiki/blogposts/restrictionenz.md

+---
+title:  Restriction Enzymes
+author: Mihir Kapse
+date: 29 August 2024
+---
+
+Restriction enzymes, often called restriction endonucleases, are a class of [enzymes](#) (biological catalysts present in living organisms) that play a vital role in the defence mechanism of bacteria and archaea - and are used by [synthetic biologists](#) in [Recombinant DNA](#) technology. 
+
+The term ‘restriction enzyme’ originates from studying bacterial virus phage 𝜆 (the virus that attacks *E. coli*). They are thought to have likely evolved from a common ancestor and became widespread via horizontal gene transfer. The way they were discovered was basically through their functionality.
+
+When a virus (specifically, a bacteriophage) attacks a bacterium, it inserts foreign [DNA](#) into the cell. Restriction enzymes cut this DNA into multiple fragments, making it less harmful. 
+
+How does the restriction enzyme know where it should cut? Each restriction enzyme is designed such that it recognises and cuts only a unique DNA sequence. This unique sequence is known as a **recognition site**. These are characterised by 4-8 bases which are generally a palindrome (Example: GTAATG) or a mirror-palindrome (DNA sequences where a segment of nucleotides read the same forward and backwards on both strands, Example: GATATC-CTATAG (complementary base pairing)). For example, the EcoRI (from E.coli bacteria) enzyme recognises the GAATTC base pair sequence, the Alul (from A. luteus) enzyme recognises the AGCT base pair sequence, and the Haell (from H. aegyptius) enzyme recognises the GGCC base pair sequence.
+
+There is the possibility that similar base pair sequences exist in the bacterial DNA also. Bacteria use the **methylase enzyme** to add methyl groups to their DNA to prevent the restriction enzyme from cutting its own DNA.
+
+How do we use Restriction Enzymes? It has various applications. 
+1. **Recombinant DNA Technology:** DNA fragments are cut from various sources using restriction enzymes and joined with other DNA sequences using [DNA ligase](#) to make new artificial DNA.
+2. **Modular DNA Assembly:** In processes like gene cloning and construction, restriction enzymes are used to assemble multiple DNA fragments in a predefined order. 
+3. **Site-Directed Mutagenesis:** Scientists use restriction enzymes to make specific cuts and study the effects of these changes on gene function and regulations.
+
+Presently, we know more than 3600 restriction enzymes from 250 different species. Researchers have been successful in studying over 3000 of these in detail and have commercialised 800 of these. We don’t know what the future holds for us. Someday, we might even be able to make artificial restriction enzymes that could be used for novel purposes, by manipulating the target site to suit our purposes. The possibilities are infinite!
+
+#### References: 
+1. Roberts RJ, Restriction and modification enzymes and their recognition sequences, Science Direct, Jan 1980
+2. Roberts RJ, Restriction endonucleases, CRC Critical Reviews in Biochemistry, 1976
+3. Roberts RJ, How restriction enzymes became the workhorses of molecular biology, Proceedings of the National Academy of Sciences of the United States of America, 2005

wiki/blogposts/rna.md

+---
+title: RNA
+author: Mihir Kapse
+date: 1 October 2024
+---
+
+In any living cell, there are mainly two types of nucleic acids – [DNA](#) and [RNA](#). RNA (ribonucleic acid) is a polymeric biomolecule which is essential for most biological functions, either by performing the function itself or by acting as a template to produce proteins. It is a biopolymer of **nucleotides.** These nucleotides may be made up of four different types of nitrogenous bases - adenine, guanine, cytosine and uracil (in DNA, thymine is present instead of uracil), that is, A G C and U.
+
+In 1910, Phoebus Levene distinguished between [DNA](#) and RNA. He identified that RNA contains ribose sugar, while DNA contains deoxyribose. He also discovered the aforementioned difference in nitrogenous bases present in the nucleotides. 
+
+Thereafter, it was discovered that there are actually three different types of RNA – namely messenger RNA (mRNA), ribosomal RNA (rRNA), and transfer RNA (tRNA). They are distinguished based on the functions they perform. All RNA molecules are synthesized from a DNA template through a process called [transcription](#).
+
+1. **mRNA (messenger RNA):** As the name suggests, it is messenger molecule. It acts as a carrier of genetic information for a protein sequence from DNA to [ribosomes](#), the protein factory of cell. Each sequence of three nucleotides in mRNA is called a **codon**. A specific type of amino acid corresponds to particular codon. This is known as the [genetic code](#).
+
+2. **tRNA (transfer RNA):** tRNA is a small biopolymer with about 70-80 nucleotides. Each tRNA has an **anticodon** region that is complementary to the mRNA’s codon. The anticodon part pairs up with the codon part of mDNA during the process of [translation](#), and also binds to the amino acid corresponding to the codon. The main function of tRNA is to act as an **adapter molecule** and help translate the genetic code of mRNA into the sequence of amino acids that make up the protein. 
+
+3. **rRNA: (ribosomal RNA):** It is a catalytic RNA, and constitutes a large portion of a ribosome. It hosts the translation process between tRNA and mRNA, within the ribosome.
+
+Initially, it was thought that RNA could not be used for any therapeutic purposes due to its short half-life. However, with advances in technology, we are now able to stabilize RNA molecules, opening doors to its various applications in therapeutics. RNA-based vaccines are on the rise today, which are easier to produce than traditional vaccines.
+
+

wiki/blogposts/selectablemarker.md

+---
+title: Selectable Markers
+author: Mukta Khanolkar
+date: 30 September 2024
+---
+
+Once cells are [transformed](#) by inserting the gene of interest, they need to be separated for further procedures. To do so, the [cloning vector](#) is designed to contain certain genes. These genes, called **‘selectable markers’**, often give transformed cells the ability to survive in conditions where **non-transformants** (cells which have not taken up the plasmid) or **non-recombinants** (cells which have a self-ligated [plasmid](#), which does not contain the gene of interest) struggle to grow. For example, resistance genes make transformants resistant to antibiotics, herbicides and other toxic agents.
+
+Separating transformed cells on the basis of this newly acquired ability is called ‘positive selection’. Since untransformed cells did not integrate selectable markers into their DNA, they are rid of and this is called ‘negative selection’.
+
+Some of the most popular selectable markers are antibiotic resistance genes. Bacteria like *Escherichia coli* have always been favored for biotechnological uses. Hence, it is no surprise that antibiotic resistance is used to identify transformants from non-transformants. The NPT-II gene (neomycin phosphotransferase II) confers resistance to bacteria against the antibiotics kanamycin and neomycin.
+
+How exactly does this process of selection of transformants work? Consider the famous **pBR322 plasmid,** designed by Bolivar and Rodriguez (hence the name pBR322). It contains ampicillin and tetracycline resistance genes. If the gene of interest is inserted in the region of, say, tetracycline resistance, the recombinants will only be resistant to ampicillin - because the tetracycline resistance gene gets interrupted. This is called **insertional inactivation**. 
+
+In the antibiotic-based screening approach, the recombinants are grown on an ampicillin-containing master plate. A replica of the colony is created using a nitrocellulose membrane. This is transferred to a medium containing both ampicillin and tetracycline. This process is called replica plating. Only the non-recombinants grow (as the recombinants have lost tetracycline resistance, and the non-transformants do not have ampicillin resistance as they lack pBR322). 
+
+Thus, the transformed colonies can be selected by comparing the master and replica plates.
+
+Fun fact! It would be a concern if these modified organisms transferred this resistance to normal cells. Hence, selectable markers are sometimes removed in subsequent generations by a process named **‘excision’.**
+
+#### References:
+1. Screening Methods in Recombinant DNA Technology; Danaher Life Sciences Library
+2. Genetically Modified Food/Organism: M. Rabiei, S. Sardari; Encyclopedia of Toxicology (Third Edition), 2014
+3. Bt Crops; Mahmood-ur-Rahman et al.; Emerging Technologies and Management of Crop Stress Tolerance, Volume 1, 2014
+4. Breeding Genetics and Biotechnology; H.D. Jones; Encyclopedia of Applied Plant Sciences (Second Edition), 2017
+5. Tissue Culture and Genetic Transformation in Sorghum bicolor; D. Balakrishna et al.; Breeding Sorghum for Diverse End Uses, 2019

wiki/blogposts/tauopathies.md

+---
+title:  Tauopathies
+author: Aarav Ghate
+date: 1 October 2024
+---
+
+**Tauopathies** are a kind of neurodegenerative Disease (NDD) and a subclass of [proteinopathies](#). They are characterised by the [misfolding](#) of the tau protein, which leads to aggregates of abnormal tau which manifest as [neurofibrillary tangles](#).
+
+Tau are microtubule associated proteins that are responsible for stabilisation of these tubules, which is important for axonal growth. Neuronal microtubules form the cytoskeleton of neurons, and are important in neuronal migration and differentiation. Tau undergoes phosphorylation at specific sites in order to bind with the microtubules as well as for other functions. However, in some cases the tau may get **hyperphosphorylated** which leads to abnormal interactions with microtubules as well as other tau proteins. A positive tau-tau interaction leads to the formation of aggregates known as neurofibrillary tangles.
+
+**Neurofibrillary tangles (NFTs)** are known largely as a biomarker for Alzheimer’s Disease, however they develop in other tauopathies as well. In Alzheimer’s, the tau protein gets hyperphosphorylated (and is called p-Tau), and subsequently forms neurofibrillary tangles and paired helical filaments. These hamper axonal functions and lead to the degeneration of neurons. Interestingly, factors released by the presence of [beta-amyloid aggregates](#) (another biomarker of Alzheimer’s) may trigger p-Tau hyperphosphorylation and misfolding. The presence of beta-amyloid greatly impacts the neuron to neuron transport of the misfolded p-Tau protein. Hence, NFTs and p-Tau proteins are considered key biomarkers for Alzheimer’s, the most common among the tauopathies.
+
+Treatment of tauopathies focuses on decreasing protein aggregation and neurofibrillary tangles. The use of [aptamers](#) to bind to sites on the p-Tau protein in order to prevent phosphorylation is also being studied. 
+
+#### References:
+
+1. Govindaraju, T, Alzheimer’s Disease, Royal Society of Chemistry, (2022).
+2. Wang, Y. Mandelkow, E. Tau in Physiology and Pathology, Nature Reviews, (2016)
+3. Johnson, G. Stoothoff, W., Tau Phosphorylation, Journal of Cell Science, (2004)