The CRISPR Codex: Decoding Gene Editing with Syed Muiz

Chapter 1 of The CRISPR Codex:

CRISPR-Cas Technology – A Simplified Guide

by Syed Muiz for BioVerse

 

Welcome to The CRISPR Codex – a science series focused on the powerful gene editing tool called CRISPR. In this first part, I'll make the foundation by talking about how CRISPR was discovered and how it works  and how it’s being used in real-life genetic engineering.

CRISPR-Cas systems are a built-in immune system found in bacteria and other simple organisms. It is highly diverse adaptive & specific (I'll explain this later in this series) microbial immune system used by most archaea (~90%) and many eubacteria (~40%) to protect thmselves from invading viruses and plasmids. At first it found as a strange DNA pattern in E. coli bacteria back in the 1980s and its now become one of the most powerful tools in genetic engineering. These system allow the cell to recognize and distinguish incoming 'foreign' DNA from 'self' DNA. CRISPR-Cas system consist of two general parts: CRISPRs (Clustered Regularly Inter-spaced Short Palindromic Repeats) and Cas (CRISPR-associated) protein. CRISPER-Cas consist highly conserved short repeated sequences separated by similarly sized short spacers sequences and they are unique sequences originating from viral or plasmid DNA. A spacer works like a memory cell in our immune system or like how a vaccine trains our body, it stores a viral DNA sample so the bacteria can recognize and fight that same virus in the future. By adding new spacers in their genome, bacteria able to recognize new matching viral DNA or plasmid genomes. The size of CRISPR repeats and spacers varies between 23 to 47 bp and 21 to 72 bp, respectively. The bacterial genome contain more then one locus and they are highly diverse and hypervariable spacer sequences, even between closely related strains. 

Another feature associated with CRISPR loci is the presence of a conserved sequence, called the Leader. It sits just upstream of the CRISPR array, in the direction where transcription begins. This Leader sequence acts like a starting signal, helping in the proper transcription of CRISPR RNAs (crRNAs). It also plays a role in guiding the integration of new spacers, making sure they're always added to the same end, like how new files always go on top in a stack. CRISPER activity requires a set of CRISPR-associated (cas) genes, which are usually found closely to the CRISPER and that code for cas protein essential to the immune response. These cas proteins perform a variety of functions, including DNA cleavage, RNA processing, and interacting with other CRISPR components. Different types of cas proteins, like Cas9, Cas12, and others, are used for specific tasks within the CRISPR system. In CRISPR-Cas systems currently being grouped into two classes, six types, and over 30 subtypes.

Overview of Medication Classification

Overview of Medication Classification

 

We all takes medicines some time with the prescription of a Doctor and sometime, just go to the medical store and purchase medicine with our incomplete knowledge because in general we have good experience of taking medicine in our life. According to National Library Of Medicine "7 billion people on Earth is exposed to 14,000 prescription medicines across a lifetime" (taking medicine without prescription is unethical and dangerous). However, proper use of medications requires not just knowledge of the drug itself but an understanding of its mechanism of action, therapeutic value, side effects, interactions with other drugs, and how it aligns with the specific needs of a patient. Despite this complexity, many individuals, especially those outside the medical profession, are often unaware of the significance of these considerations. In this article-Overview of Medication Classification we will explore the key aspects of medications, their classifications, function, and why the necessity of a doctor's prescription cannot be ignore. My aim is to provide a clear, accessible guide to empower individuals to make informed decisions about their health and understand the rationale behind prescribed treatments. And lay a foundation for those readers who are unfamiliar with pharmacology.

Types & Classification of Medicines

Medicines are categorized by their origin and use. By origin, Natural Medicines come directly from plants, animals, or microbes, such as morphine (from opium) or penicillin (from fungi). While Synthetic Drugs are fully lab-created, like aspirin, and Semi Synthetic ones  are like amoxicillin, modify natural compounds. And Biologicals, such as insulin or monoclonal antibodies that are derived or extracted from living systems through advanced biotechnology.
And by use, Preventive Medicines include vaccines and prophylactic drugs to stop diseases before they occur. Curative medicines, like antibiotics and antivirals, treat and eliminate infections. Symptomatic medicines, such as analgesics and antipyretics, manage pain and fever without addressing the root cause. and lastly Supportive medicines, like supplements, IV fluids(Intravenous fluids)....etc. That helps in enhance recovery or maintain health. While the pharmacological classification is a complex and time consuming topic but straightforwardly, we can mainly classify them according to their approach- 

A. Traditional Classification

• By Therapeutic Use: Groups medicines based on the condition they treat (e.g., antihypertensives, antidiabetics).
• By Mechanism of Action(MOA): Based on the physiological pathway affected (e.g., enzyme inhibitors, receptor blockers).
• By Chemical Structure: E.g., beta-lactams, benzodiazepines.
• By Route of Administration: Oral, parenteral, topical, inhalational.

B. Modern and Interdisciplinary Approaches

• Pharmacological Targets: Drugs categorized by the molecular targets they act upon (e.g., ion channels, G-protein-coupled receptors).
• Systems Biology Approach: Medicines grouped based on their effect on specific biological networks or pathways.
• Epigenetic-Based Classification: Emerging fields classify drugs based on their impact on gene expression (e.g., histone deacetylase inhibitors).

The Framework of Medications

Medications, we are all familiar with this term, and for some extent their usage also. But we often don't know about how they work and their framework which is very crucial to know, not only for medical professionals but also patient to ensure their safe and effective use. Medications are categorized in various ways to facilitate their use in healthcare settings.Without going deeper, The most prominent methods of classification include grouping them by their chemical structure, mechanism of action, therapeutic use, and generation. Each classification system serves a distinct purpose, yet together, they form a cohesive system which aids medical professionals in selecting the appropriate medication for a patient. In biology, we all study classification of animals, and similarly this branch has its own classification and taxonomy. When we study Pharmacalogical classification we saw some similarity in both frameworks, we can understand this concept with my biological analogy (While pharmacological taxonomy don’t correspond directly to biological taxonomy, but for the sake of understanding I made a loose analogy)

• Kingdom: Medicine (e.g., pharmaceuticals).
• Phylum: Therapeutic class (e.g., antihistamines).
• Class: Mechanism of action (e.g., H1 receptor blockers).
• Order: Subclassifications (e.g., first vs. second-generation antihistamines).
• Family: Chemical structure similarities.
• Genus and Species: Individual drugs (e.g., cetirizine, loratadine).

1. Chemical Structure Classification

The chemical structure of a drug is one of the most fundamental ways to classify it. Drugs that share a similar chemical backbone are grouped into families. For example, beta-lactam antibiotics—such as penicillins, cephalosporins, and carbapenems, share a same characteristic chemical structure called the beta-lactam ring, which is central to their antimicrobial properties. And this is most importent thing to Understand the structure to helps and predict the drug's behavior in the body and its potential side effects and its therapeutic applications. Imagine a chemical structure as the "skeleton" of a species. Just as closely related species share similar skeletal structures (e.g., mammals with vertebrae), drugs within the same chemical family share a structural framework that defines their function and interactions.

• Beta-lactams: Antibiotics containing a beta-lactam ring (e.g., penicillins, cephalosporins).
• Benzodiazepines: Sedatives and anxiolytics (e.g., diazepam, lorazepam).
• Sulfonamides: Antimicrobials derived from sulfonic acid (e.g., sulfamethoxazole).

2. Mechanism of Action (MOA) Classification

Drugs are also classified by their mechanism of action—how they interact with the body to produce therapeutic effects. For example, antihistamines like cetirizine and loratadine block H1 receptors, which are responsible for allergic reactions such as sneezing, itching, and swelling. By preventing histamine from binding to these receptors, these medications alleviate allergic symptoms. Similarly, beta-blockers like propranolol work by inhibiting beta-adrenergic receptors, reducing heart rate and blood pressure, which helps manage hypertension and heart-related conditions. The mechanism of action can be likened to the "behavioral role" of an organism in an ecosystem. Just as a predator regulates prey populations to maintain ecological balance, a drug targets specific molecules or pathways to restore physiological equilibrium. some are-

• Receptor Agonists: Stimulate receptors (e.g., beta-agonists like salbutamol).
• Receptor Antagonists: Block receptors (e.g., beta-blockers like propranolol).
• Enzyme Inhibitors: Inhibit specific enzymes (e.g., ACE inhibitors like enalapril).
• Ion Channel Modulators: Affect ion channels (e.g., calcium channel blockers like amlodipine).

3. Therapeutic Use

Another common way to classify medications is by their therapeutic use that is, the conditions they are designed to treat. For example, analgesics such as paracetamol (acetaminophen) and ibuprofen relieve pain. Antibiotics like amoxicillin and ciprofloxacin combat bacterial infections, while antipyretics such as acetaminophen reduce fever. By understanding a drug’s therapeutic purpose, a doctors can match the right medication to a patient’s condition. Therapeutic use is ulike to the ecological niche of a species. Just as a specific organism fulfills a unique role in its habitat (e.g., bees as pollinators), each drug is tailored to address a particular medical condition or symptoms.

• Antipyretics: Reduce fever (e.g., paracetamol).
• Analgesics: Relieve pain (e.g., ibuprofen, morphine).
• Antibiotics: Treat bacterial infections (e.g., penicillin, azithromycin).
• Antivirals: Treat viral infections (e.g., oseltamivir for influenza).
• Antifungals: Treat fungal infections (e.g., fluconazole).
• Antihypertensives: Control high blood pressure (e.g., losartan, atenolol).
• Antidiabetics: Manage diabetes (e.g., insulin, metformin).

4. Generational Classification 

Generations are not universally applied across all drugs but are used to represent evolutionary improvement within a drug class. This is particularly true for antihistamines and antibiotics. For example, first-generation antihistamines (e.g., diphenhydramine) cross the blood-brain barrier, causing sedation and drowsiness. In contrast, second-generation antihistamines (e.g., loratadine, cetirizine) are designed to be non-sedating, offering allergy relief without drowsiness. Similarly, with antibiotics, first-generation cephalosporins target a narrower range of bacteria, while later generations provide broader-spectrum coverage to combat resistant strains. Generational classification resembles the well known evolutionary timeline of species. Just as organisms adapt and diversify to survive changing environments, drug generations evolve to improve efficacy, reduce side effects, and overcome resistance.

• First-Generation Drugs: Original compounds with basic therapeutic effects (e.g., penicillin).
• Second-Generation Drugs: Improved versions with enhanced efficacy or fewer side effects (e.g., cephalosporins).
• Third-Generation Drugs: Further optimized for specific diseases or targets (e.g., biologics, precision medicine).

Antibiotics: Penicillin (1st generation), Cephalosporins (2nd generation), Carbapenems (3rd generation), and advanced beta-lactams (4th/5th generation).
Antipsychotics: Typical antipsychotics (1st generation, e.g., haloperidol) vs. Atypical antipsychotics (2nd generation, e.g., risperidone).
Antihistamines: Sedative (1st generation, e.g., diphenhydramine) vs. Non-sedative (2nd generation, e.g., loratadine). 

The Concept of Drug Families

In pharmacology, a drug family consists of medications sharing common characteristics, such as chemical structure, mechanism of action, or therapeutic effects. For example, antihistamines, regardless of generation, are grouped together because they all block histamine receptors. This classification is grounded in their physiological effects and therapeutic indications rather than superficial similarities. When doctors prescribe levocetirizine (a second-generation antihistamine) and montelukast (a leukotriene receptor antagonist) together for allergic rhinitis, they are combining two drugs from different families to enhance therapeutic efficacy. Levocetirizine targets histamine receptors, while montelukast blocks leukotrienes involved in allergic responses. This combination provides comprehensive symptom relief. Although, fexofenadine belongs to a distinct antihistamine family due to its non-sedating properties and differing receptor activity. Drug families can be compared to taxonomic groupings in biology. Just as species are grouped into families based on there shared traits (e.g., Canidae for dogs, wolves, and foxes), drugs are categorized into families based on shared characteristics like structure and function as well.

The Role of Doctor Prescriptions

The epistemology of medicine revolves around integrating scientific knowledge, empirical evidence, and patient specific factors into decision making. that's why a doctor’s prescription isn’t just a piece of paper, it’s the backbone of proper treatment. It ensures the right medication with the correct dosage and reaches the right patient while factoring in everything from their health to other medications they’re already using. A Dr analyses all that things and then make a Decision. Because this isn’t just about routine it’s about precision and safety.

1. Pharmacodynamics(PK) and Pharmacokinetics(PD)

When prescribing a drug, two major aspects come into play Pharmacodynamics and Pharmacokinetics. Pharmacodynamics is, what the drug does to the body (ADME - Absorption, Distribution, Metabolism, Excretion). and Pharmacokinetics is, what the body does to the drug (mechanism of action, dose-response relationships). . Doctors don’t prescribe medications randomly or just based on there mechanism, they select drugs for prescription having these things in mind; how the drug will act, what side effects it might cause, and how the body will absorb, break down, and eliminate it(ADME). Misjudging this could mean anything from a missed cure to a toxic reaction.

2. Safety Profile and Side Effects

Not every patients are the same. Their age, weight, gender, genetics, and medical history shape how they’ll respond to a drug. For example, if someone has liver issues, certain medications can build up in the body, leading to harm. Similarly, combining multiple medications can trigger dangerous drug interactions. Think of anticoagulants like warfarin—combine them with common pain relievers like NSAIDs, and the risk of bleeding. A doctor has all these things in mind and after processing all these things,he made a decision for prescription. Similarly every drug has its risks, Some are mild and others can be life-altering. Take opioids as an example they’re excellent for managing severe pain but come with addiction risks, that can’t be ignored. This is why doctors tread carefully, prescribing such drugs only when absolutely necessary and under strict monitoring.

The Dangers of Self Medication

Self medication might seem harmless but-it’s playing with fire. Without medical guidance, you’re not just guessing at what might help, you’re risking misdiagnosis, overdosing, or serious side effects. And the worse part is, masking symptoms with random medication can delay proper diagnosis. Imagine someone with a bacterial infection taking cold medicine to suppress symptoms. They might feel better temporarily but leave the infection untreated, letting it worsen in the background.

Conclusion

The field of pharmacology is vast and there is a lot more to understand, but as this article is just an overview of medication classification, I tried to make it as concise as possible. But I believe that after reading this article, you will get an idea about simple classifications, categorizations, generations of drugs, and their types. Also, we are now on the same page regarding why medications, while powerful tools for managing health, are highly dependent on the knowledge and judgment of healthcare providers. A doctor’s prescription is based on a careful consideration of the patient’s condition, the drug’s mechanism of action, potential interactions, and safety profile. That's why we should not take medicines on our own. Lastly, by understanding the basic principles of medication classification, mechanisms, and the role of a doctor’s guidance, we can make informed decisions about our health and better appreciate the importance of professional healthcare.

References:

1. Food and Drugs Administration (.gov)

2. Drug class

3. Drug Class And Medical Classification-Very Well healthcare.com

4. National Library of Medicine

Basic information about new Omicron Variant of Corona Virus.

omicron variant of corona virus

we know that covid 19 has a wreaked havoc all over the world and it is become the most dangerous pandemic of this century. It has taken many lives across the world but we also know that we are about to experience a new threat in the coming days which is omicron variant of covid 19 (B.1.1.529) which is also known as "The Variant Of Concern". No, one knows where omicron first emerges. But it was first identified in Botswana, South Africa and then now it has been detected in many other countries including India, Australia, England, France, Germany, Canada, Denmark, Austria, Belgium, Hong Kong, Israel, Italy, Netherlands, Portugal and Scotland. The recent reports show that this variant has spread to 38 countries around the world. But let me make this thing clear , no specific information has been received about  this omicron variant but all we know is that information has been gathered it by "WHO". Its symptoms are mild like Headache, fatigue, body pain, scratchy throat without cough but in this case there is no loss of smell or loss of taste occur. And mostly males in the age group between 20-30s are infected by this omicron variant.

My main motive is to educate about this virus to those people who are not aware of the field of science or those students who are studying in any field other then science. So for I am trying to use such words which can be understood by the people of all classes and fields. These things are little bit  complicated. So basically the virus is made up with two components Protein and Nucleic acid. protein is the coat of the virus and nucleic acid is the genetic component of the virus. Nucleic acids can be RNA or DNA but in case of corona virus it is the RNA. If we look the structure of omicron virus we see many spike or spring loop like structure on the outer surface of virus which is actually are amino acids, (Because amino acids join together and make proteins) and these structure are called spike protein. Basically the spike protein is a highly glycosylated and large type 1 transmembrane fusion protein that is made up of 1160 to 1400 amino acids, depending upon the type of virus, I'm not going that deep...... but these things are basics for understand the virus. and with the help of these spike protein virus attaches the host cells and then enters the host cells (in this case the human's nose and  mouth cells are the host cells) and takes possession of it and start infecting the cell. and then virus starts making many copies of itself ....as a result of which the person becomes ill.

Now why this variant is called  "The Variant Of Concern" according to The WHO and the CDC, there are some special points which are highlighted about this-

1). Increased transmission.    

2). Increased severity of illness.

3). Decreased efficacy to drugs.

4). Decreased efficacy to vaccines.

These 4 points of characteristics have arisen due to "Mutations" in this virus. So basically when the virus acquires small changes in genetic materials we called this "Mutation". And whenever the virus mutated, it becomes a new variant of itself. The Alpha variant has 23 mutations compared with the original Wuhan strain. The Beta variant has some other mutations in which it has 8 distinct mutations that may effect  how the virus binds to cells. Similarly The Gama variant is closely related to Beta variant but this variant carries 8 additional sequence changes mutation. The Delta variant has several important mutations with 8 new mutations. The Eta variant carries some of the same mutations seen in the Alpha variant and 4 other additional mutation. And The Iota variant has 3 different mutations. The Kappa variant has some 7-8 new mutations. after this The Lambda variant has another 7 new mutations. And The Mu variant also has some mutations those are found in beta variant and some other mutation. And now finally, The new Omicron variant have more than 30 mutation. So you can now understand why this one is more dangerous then older variants or versions of the corona virus .Because of this heavy mutation in this omicron variant that only reason why the WHO and CDC is calling this as a "Variant Of Concern"

WHY DO WE AFRAID...?

Fear as described by Google is an unpleasant emotion caused by the belief that something or some one is dangerous and its like cause harm.Most of the fears that we actually have are just contemplative thoughts that we are thinking too often it's fear, some fear is some big unknowable scary thing .Most of people  generally when they are young,being afraid of the dark as well as with some other fear,like of Ghosts,Monsters or other spooky,creepy and weird things.And as we get older we might not use that sort of explanation anymore,but these irrational fears still stick around us.

Researches say that there are way to fight those fears too,the way we usually fear is a well understood part of psychology.Most of the time its through classical conditioning.we have an automatic reactions,like imagine a person who's expert in bike riding but then suddenly it becomes an accident or think a person who's generally cool with his/her pet animal like dog..... but then,dog bites him/her and he/she has to go to the hospital that would make anybody frighten.Then in consequence, the neutral stimulus becomes a conditional stimulus , which gives us the same automatic reaction which I was already mentioned.In another words ,after that experience that person is more likely to be afraid when she/he sees a dog or that who got accident is more likely to be afraid when he/she again ride a bike.This type of things generally called PHOBIA,The PHOBIA is an extreme stage of fear there are many types.Here some examples :-

1. Musophobia : Fear of rats.
2. Cynophobia : Fear of dogs.
3. Arachnophobia / Ophidiophobia : Fear of spider and snakes.
4. Mysophobia :Fear of germs.
5. Trypanophobia : Fear of needles and injections.
6. Haemophobia : Fear of blood.
7. Acrophobia : Fear of height.
8. Astrophobia : Fear of thunder or lighting.
9. Pteromerhanophobia : Fear of flying.
10. Dentophobia : Fear of dentists.
11. Glosophobia : Fear of social situations / public speaking (AKA Social Anxiety Disorder).
12. Thanatophobia /Necrophobia :Fear of death or dead things.
13. Coulrophobia / Pediophobia : Fear of clown or joker / dolls.
14. Agoraphobia / Claustrophobia : Fear of closed or open space.
15. HEXUKASIAI-HEXEKONTA-HEXAPHOBIA : Fear of repetition of number six.
16. Hippotomonstroesquipedaliophobia :Fear of long words. 
17. Gnosophobia : Fear of knowledge.
18. Emelophobia : Fear of vomit.
19. Carantophobia : Fear of cancer.
20. Gamophobia : Fear of wedding.

Researches has found that conditioned responses are probably linked with ''Amygdala'', that`s a brain part that active when we are afraid or have a lot of excitement & anger so conditioned fear kind of make sense they are based on something that happened to us.But these facts not enough for us because we wanna be smarter then other.So the question is why it's happen ? and what the science behind the fear.Let's find out....!

In animals, fear caused imbalance between excitement and sense of control.whereas,human have contextual brain if individual think's experience as ''too real'' an extreme fear response can overcome the sense of control over the situation.Here is a chain reaction in the brain that starts with a stressful stimulus and ends with release of chemicals that can cause a raising heart beat or blood pressure and fast breathing this type of motion stimulates several parts of our brain such as the Sensory Cortex, Thalamus, Hypothalamus , Amygdala and Hippocampus now the question is how it works in our brain ?.Well.......2B layer of the "Superior Colliculus" receives visual information from "Parasol Ganglion Cells" in the Retina through "Magnocellular Cells".Now further process occur in two parts or in other words it has two potential pathways which depends on the type of visual process or in another words it's depends on what are you see or experience .
 The first part called "Mental Low Road",in this part of process, First sensory information down to the amygdala .The Amygdala processes the memory and emotional reactions from the stimulus and attempts to protect us by continuing this process forwarding the data to Hypothalamus.The Hypothalamus activates the "FIGHT-OR-FLIGHT" response, or "FOF-action" for short. And the second part of this process called "Mental High Road", this is similar situation like mental low road but now in this part of reaction one more part of brain participates named Hippocampus .This almond shaped part tries to form some sort of context by asking question like ''What the mean of this or have I saw this type of thing or have I heard this sound or .....etc,'' it's depends on the situation .And when we have sure that we are safe and now in this situation nothing is dangerous or harmful.The hippocampus send a message to the Amygdala that there is no pitfall or threat, the Amygdala send message to Hypothalamus to turn off the FOF- action.

An Overview of Trees Social System

This drawing made by my little sister SYEDA KULSUM FATEMAH HANAFI

As we know that plants and trees are also a living things like us and other animals. Human have own language to communicate .....even animal have there own language and gesture to communicate to each other as well as plants can talking,trading and waging war to each other.On this topic many scientists research on it.Over thirty years period forest scientists revealed that trees have some amazing social skills trees can actually talk to each other.And this is not just a basic or simple communication either,they have an impressively large vocabulary.In forest there are hundreds of conversation happening right below to the ground but we can't hear a single word because trees don't communicate via speech,vocal or gestures......but they communicate through electrical impulses, just like the human nervous system.

Underneath the soil a tree's  roots spread horizontally.Roots are spread as far wide as the tree is tall.
As they grow...they intertwine and connect with the roots of all the other trees that surround it.
not only can a tree send electrical signal or impulse to  its direct neighbors but by relaying messages trees can talk to each other that are many tree apart this interconnected network of root,the system  has been nicknamed "WOOD WIDE WEB"
in another words we can also say that......the forest is one single organism.Basically in this system fungi and mycorrhiza do a very important role.The fungi connecting themselves into this hidden social networking system or simply we can say "the root-based social network" and provide nutrients and receive sugars.But recently scientists found there connection deeper then first thought,When trees get low on certain elements,which they use to grow such as Carbon,Sulphor and Phosphorus they send a request out into the WOOD WIDE WEB.The closest tree that has same enough amount of that elements,helps the another one by sharing required element.But the question is how do they share the nutrients ? 
The answer is that by plugging into the fungi in the network,tree can share resources and trees also carry physical elements all around,if they notice a particular tree is not getting enough sun light they slowly reconfigure their branches to let the extra light.They may even disconnect their roots from rotten or dead tree.They can count the passing days and keep track of how many warm or cold days there are throughout the summer and spring each years.They have personalities, there are both types of trees,good and bad tree.
Good trees helps there neighbors trees,plants and other organism. Whereas,Bad trees steal nutrients from other trees and plants.They even have wars some trees like Black Walnuts

BLACK WALNUT

spread toxins through network and harm or kills their rivals, either some trees like Peach and Oak protects there own even parents trees will helps there young ones by passing and sharing some nutrients for good growth.In this sense we can also say,that trees have ability to recognize and And they can understand the difference between themselves and others.