InSilico Codex

InSilico Codex My page uncovers biomedical discoveries, events, and inventions with insights from peer-reviewed journals.

Helpful at the university level explanations on how science and tech are working to secure the future of human health.

11/23/2025

1/ 🧬 Immune Athero is coming

LDL is largely solved for rich health systems. PCSK9s, inclisiran, gene editing soon.

Yet patients with LDL at 40 still infarct.

The next wave treats the artery as an immune organ, not a plumbing problem.

That is the immune atherosclerosis trade

A thread 🧵

MicroRNAs & Gene Regulation 🧬‼️MicroRNAs (miRNAs) are small, non-coding RNA molecules that play a central role in post-t...
11/23/2025

MicroRNAs & Gene Regulation 🧬‼️

MicroRNAs (miRNAs) are small, non-coding RNA molecules that play a central role in post-transcriptional gene regulation, influencing whether genes are expressed, suppressed, or silenced.

🔹 How miRNAs Are Formed

1. Transcription
Primary microRNAs (pri-miRNAs) are first transcribed from genomic DNA.

2. Nuclear Processing :Drosha
The Drosha-associated complex trims pri-miRNAs, releasing a short hairpin precursor known as pre-miRNA.

3. Cytoplasmic Processing : Dicer
Pre-miRNA is transported to the cytoplasm, where Dicer cleaves it to produce a mature miRNA (~21–25 nucleotides).

4. RISC Assembly
The double-stranded miRNA binds Argonaute (Ago2), which removes one strand and forms the RISC (RNA-induced silencing complex).

5. Gene Silencing
RISC recognizes target mRNAs through full or partial sequence complementarity, leading to:

⏩ mRNA degradation, or

⏩ Translation inhibition

🔹 miRNAs & Cancer 📌

Many miRNAs influence tumor biology by either:
🔸Suppressing cancer development (tumor-suppressive miRNAs), or
🔸 Promoting malignancy (oncomiRs)

Mutations in Dicer or other miRNA-processing proteins have been linked to cancer progression.
Additionally, tumor-specific miRNA expression patterns are now used as diagnostic and classification tools, similar to mRNA expression profiling.

🔬 From Gene to Protein: The Elegant Journey of Gene ExpressionThe flow of genetic information inside a cell is a masterp...
11/23/2025

🔬 From Gene to Protein: The Elegant Journey of Gene Expression

The flow of genetic information inside a cell is a masterpiece of precision, regulation, and timing. Every protein we rely on whether for growth, immunity, or cellular repair emerges from a finely tuned multistep process known as gene expression. Here’s how this biological orchestra unfolds:

1️⃣ Regulation of Transcription – The Decision Point
Gene expression begins long before any RNA is made. Enhancers act like “green signals,” boosting transcription, while repressors serve as “red lights,” preventing unwanted activity. Together, they guide RNA Polymerase II to the promoter region, deciding when and how strongly a gene should be expressed.

2️⃣ Transcription – Writing the First Draft
Once activated, RNA Polymerase II synthesizes pre-mRNA—a raw, unrefined transcript. This is the cell’s first draft of the genetic message.

3️⃣ Pre-mRNA Processing – Refining the Message
Before leaving the nucleus, the pre-mRNA undergoes critical editing steps:
✔️ 5’ Capping protects the transcript
✔️ Splicing removes introns and connects useful exons
✔️ Poly-A tail addition ensures stability
These modifications transform pre-mRNA into a mature, translation-ready message.

4️⃣ Translation – Converting Code Into Function
Ribosomes read the mature mRNA like a blueprint, assembling amino acids into a polypeptide chain. This is where the genetic code becomes something tangible—a functional protein.

5️⃣ Post-Translational Modifications – Fine-Tuning Function
Newly formed proteins undergo essential modifications such as phosphorylation and glycosylation, which determine their activity, folding, signaling behavior, and cellular location.

6️⃣ Protein Degradation – Quality Control & Homeostasis
Finally, damaged or unneeded proteins are dismantled by the proteasome, ensuring cellular quality control and maintaining protein balance.

✨ In essence, gene expression is not just a biological process—it’s a high-precision regulatory network that ensures every cell produces the right protein, at the right time, and in the right amount.

Indications for Dialysis (AEIOU)A – Acidosis • Severe metabolic acidosis (usually pH < 7.1) • Not responding to medical ...
11/23/2025

Indications for Dialysis (AEIOU)

A – Acidosis
• Severe metabolic acidosis (usually pH < 7.1)
• Not responding to medical therapy (e.g., bicarbonate)
E – Electrolytes
• Severe hyperkalemia (usually K⁺ > 6.5 mmol/L or with ECG changes)
• Refractory to medical treatment (insulin, calcium, bicarbonate)

I – Intoxications
Dialyzable toxins include:
• Ethylene glycol
• Methanol
• Lithium
• Salicylates (aspirin)
• Theophylline
• Barbiturates

(These substances are removed effectively by hemodialysis.)

O – Overload
• Refractory fluid overload
• Pulmonary edema not responding to diuretics (furosemide)
• Causing respiratory distress or hypoxia

U – Uremia

Symptoms of severe uremia such as:
• Pericarditis (uremic pericarditis)
• Encephalopathy (confusion, seizures)
• Uncontrolled bleeding (platelet dysfunction)
• Severe nausea/vomiting, anorexia

Other Indications
• Severe acute kidney injury (AKI) with rising creatinine and oliguria/anuria
• GFR < 10 mL/min (chronic kidney disease, stage 5), or

𝐂𝐞𝐧𝐭𝐫𝐢𝐟𝐮𝐠𝐚𝐭𝐢𝐨𝐧 𝐨𝐟 𝐁𝐥𝐨𝐨𝐝 𝐂𝐨𝐦𝐩𝐨𝐧𝐞𝐧𝐭𝐬⁣Centrifugation is a laboratory technique used to separate the components of whole blo...
11/20/2025

𝐂𝐞𝐧𝐭𝐫𝐢𝐟𝐮𝐠𝐚𝐭𝐢𝐨𝐧 𝐨𝐟 𝐁𝐥𝐨𝐨𝐝 𝐂𝐨𝐦𝐩𝐨𝐧𝐞𝐧𝐭𝐬⁣
Centrifugation is a laboratory technique used to separate the components of whole blood based on their density by spinning the sample at high speed. When whole blood is placed in a centrifuge, its components form distinct layers:⁣

𝟏. 𝐏𝐥𝐚𝐬𝐦𝐚 𝐚𝐧𝐝 𝐏𝐥𝐚𝐭𝐞𝐥𝐞𝐭𝐬 (𝐓𝐨𝐩 𝐋𝐚𝐲𝐞𝐫 – 𝟓𝟓%)⁣
Color: Pale yellow⁣
Composition: Water, proteins, hormones, nutrients, waste products⁣
Platelets: Small cell fragments involved in blood clotting⁣
Reason for position: Least dense, so they rise to the top⁣

𝟐. 𝐖𝐡𝐢𝐭𝐞 𝐁𝐥𝐨𝐨𝐝 𝐂𝐞𝐥𝐥𝐬 (𝐌𝐢𝐝𝐝𝐥𝐞 𝐋𝐚𝐲𝐞𝐫 – 𝐁𝐮𝐟𝐟𝐲 𝐂𝐨𝐚𝐭)⁣
Color: Thin whitish layer⁣
Composition: Leukocytes (neutrophils, lymphocytes, monocytes, eosinophils, basophils)⁣
Function: Defense and immunity⁣
Reason for position: Intermediate density⁣

𝟑. 𝐑𝐞𝐝 𝐁𝐥𝐨𝐨𝐝 𝐂𝐞𝐥𝐥𝐬 (𝐁𝐨𝐭𝐭𝐨𝐦 𝐋𝐚𝐲𝐞𝐫 – 𝟒𝟓%)⁣
Color: Red⁣
Function: Transport oxygen and carbon dioxide⁣
Reason for position: Most dense, so they settle at the bottom⁣
Why Centrifugation is Important?⁣
Helps isolate plasma for diagnostic tests⁣
Separates RBCs for transfusion⁣
Allows examination of specific blood components⁣
Essential for hematology and clinical laboratory procedures⁣

سائٹیکا وہ حالت ہے جس میں درد سائٹک نَس کے راستے پر پھیلتا ہے۔ یہ نَس کمر کے نچلے حصے سے شروع ہو کر کولہے سے گزرتی ہوئی ...
11/20/2025

سائٹیکا وہ حالت ہے جس میں درد سائٹک نَس کے راستے پر پھیلتا ہے۔ یہ نَس کمر کے نچلے حصے سے شروع ہو کر کولہے سے گزرتی ہوئی ٹانگ کے پچھلے حصے تک جاتی ہے۔ یہ درد عموماً نَس کی جلن، سوزش یا دباؤ کی وجہ سے ہوتا ہے، جو اکثر ہرنی ایٹڈ ڈِسک، اسپائنل اسٹی نوسس یا پٹھوں کی سختی سے پیدا ہوتا ہے۔ سائٹیکا میں مبتلا افراد کو کمر کے نچلے حصے، کولہے اور ٹانگ میں تیز، چبھتا ہوا درد محسوس ہو سکتا ہے۔ اکثر اوقات ٹانگ میں سن ہونا، جھنجھناہٹ یا کمزوری بھی محسوس ہوتی ہے۔ لمبے وقت تک بیٹھنا علامات کو مزید خراب کر دیتا ہے، جبکہ کچھ لوگوں کو ٹانگ میں جلن یا بجلی کے جھٹکے جیسا درد بھی محسوس ہوتا ہے۔

سائٹیکا کا مؤثر علاج مناسب دیکھ بھال، ورزش اور طرزِ زندگی میں تبدیلیوں کے ذریعے کیا جا سکتا ہے۔ دستی تھراپی (Manual Therapy) پٹھوں کی کھنچاؤ کو کم کرنے میں مدد دیتی ہے، جبکہ McKenzie exercises ریڑھ کی ہڈی کی سیدھ بہتر بناتی ہیں۔ Nerve gliding تکنیکیں نَس پر دباؤ کم کرنے میں مددگار ہوتی ہیں۔ کور مضبوط کرنے والی ورزشیں طویل مدت میں ریڑھ کی ہڈی کو سپورٹ فراہم کرتی ہیں۔ گرم یا ٹھنڈی پیکنگ سوزش اور پٹھوں کے کھچاؤ کو کم کرنے میں مفید ہو سکتی ہے۔ مریضوں کو چاہیے کہ وہ طویل بیٹھنے، زیادہ وزن اٹھانے اور ہائی امپیکٹ سرگرمیوں سے اجتناب کریں۔ مناسب علاج اور مستقل مزاجی سے زیادہ تر لوگ درد میں واضح کمی اور بہتر حرکت حاصل کر سکتے ہیں۔

Whole-Genome Shotgun Sequencing — Key Concepts 🧬‼️Whole-genome shotgun sequencing works by breaking the genome into frag...
11/20/2025

Whole-Genome Shotgun Sequencing — Key Concepts 🧬‼️

Whole-genome shotgun sequencing works by breaking the genome into fragments, sequencing them, and using computational overlaps to reconstruct long genomic regions.
However, repetitive DNA makes full chromosome assembly difficult when only short fragments are used.

⏩ 1. Plasmid Shotgun Sequencing (Short Inserts)

🔹Genomic DNA is fragmented into 500–1000 bp pieces.

🔹Inserts are sequenced randomly and assembled using overlaps.

📌 Limitation:
Short reads cannot bridge repetitive elements (e.g., transposons).
➡️ Results in many small contigs that cannot form complete chromosomes.

⏩ 2. BAC Shotgun Sequencing (Large Inserts + Paired Ends)

🔹Uses BACs (Bacterial Artificial Chromosomes) containing large genomic fragments (200–300 kb).

🔹Only the paired ends (~1000 bp from each side) are sequenced.

These paired-end reads provide long-range linking information across repetitive regions.
➡️ Allows assembly of large contigs that span entire chromosomes.

⏩ 3. Why BAC Paired-End Reads Are Critical

🔹Both end reads originate from the same large fragment.

🔹This anchors contigs on the genome even when repetitive sequences intervene.

🔹Enabled chromosome-level assemblies in major projects such as the Human Genome Project.

🔬 Short reads alone → cannot assemble across repetitive DNA
🔬 Large BAC paired-end reads → allow full chromosome assembly

📚MedChemExpress Digest |  Triple-negative Breast Cancer 🔬Triple-negative breast cancer ( ) is an aggressive and heteroge...
11/20/2025

📚MedChemExpress Digest | Triple-negative Breast Cancer

🔬Triple-negative breast cancer ( ) is an aggressive and heterogeneous subtype defined by the absence of ER, PR, and HER2. Its lack of actionable therapeutic targets contributes to the poorest prognosis among subtypes.
💡As a result, endocrine and HER2-targeted therapies offer limited benefit, making chemotherapy, immunotherapy, and emerging targeted agents the current mainstays of treatment.
📌TNBC comprises several molecular subtypes—each with distinct biology and clinical behavior:
· Basal-like
· Mesenchymal (M)
· Immunomodulatory (IM)
· Luminal Androgen Receptor (LAR)

🔍Understanding these subtypes is key to improving treatment decisions and developing more precise therapeutic approaches for TNBC.

𝐒𝐚𝐥𝐦𝐨𝐧𝐞𝐥𝐥𝐚 𝐓𝐲𝐩𝐡𝐢 𝐯𝐬. 𝐒𝐚𝐥𝐦𝐨𝐧𝐞𝐥𝐥𝐚 𝐏𝐚𝐫𝐚𝐭𝐲𝐩𝐡𝐢 ⁣⁣How They Appear on XLD Agar & Key Characteristics⁣⁣⁣⁣Understanding the pheno...
11/20/2025

𝐒𝐚𝐥𝐦𝐨𝐧𝐞𝐥𝐥𝐚 𝐓𝐲𝐩𝐡𝐢 𝐯𝐬. 𝐒𝐚𝐥𝐦𝐨𝐧𝐞𝐥𝐥𝐚 𝐏𝐚𝐫𝐚𝐭𝐲𝐩𝐡𝐢 ⁣⁣

How They Appear on XLD Agar & Key Characteristics⁣⁣
⁣⁣
Understanding the phenotypic differences between Salmonella Typhi and Salmonella Paratyphi is essential for accurate identification in clinical microbiology. Both organisms behave differently on Xylose Lysine Deoxycholate (XLD) agar, a selective and differential medium widely used for isolating enteric pathogens.⁣⁣
⁣⁣
𝐂𝐨𝐥𝐨𝐧𝐲 𝐀𝐩𝐩𝐞𝐚𝐫𝐚𝐧𝐜𝐞 𝐨𝐧 𝐗𝐋𝐃 𝐀𝐠𝐚𝐫⁣⁣
⁣⁣
🔹 𝘚𝘢𝘭𝘮𝘰𝘯𝘦𝘭𝘭𝘢 𝘛𝘺𝘱𝘩𝘪⁣⁣
⁣⁣
➤ Produces black-centered colonies due to H₂S production⁣⁣
⁣⁣
➤ Initially red colonies turn darker as H₂S accumulates⁣⁣
⁣⁣
➤ Xylose is weakly fermented, but lysine decarboxylation restores alkalinity → red colonies with black centers⁣⁣
⁣⁣
⁣⁣
🔹 𝘚𝘢𝘭𝘮𝘰𝘯𝘦𝘭𝘭𝘢 𝘗𝘢𝘳𝘢𝘵𝘺𝘱𝘩𝘪⁣⁣
⁣⁣
➤ Typically forms red or pink, translucent colonies⁣⁣
⁣⁣
➤ Does NOT produce H₂S (except some rare strains)⁣⁣
⁣⁣
➤ Appears lighter compared to S. Typhi⁣⁣
⁣⁣
➤ Fermentation pattern is similar but without the H₂S-associated blackening⁣⁣
⁣⁣
⁣⁣
𝐊𝐞𝐲 𝐁𝐢𝐨𝐜𝐡𝐞𝐦𝐢𝐜𝐚𝐥 𝐂𝐡𝐚𝐫𝐚𝐜𝐭𝐞𝐫𝐢𝐬𝐭𝐢𝐜𝐬⁣⁣
⁣⁣
➤ Feature - 𝘚. 𝘛𝘺𝘱𝘩𝘪 ⁣⁣
⁣⁣
𝐇₂𝐒 𝐏𝐫𝐨𝐝𝐮𝐜𝐭𝐢𝐨𝐧 - Positive ⁣⁣
𝐌𝐨𝐭𝐢𝐥𝐢𝐭𝐲 - Motile ⁣⁣
𝐕𝐢 𝐀𝐧𝐭𝐢𝐠𝐞𝐧 - Present (major virulence factor) ⁣⁣
𝐏𝐚𝐭𝐡𝐨𝐠𝐞𝐧𝐢𝐜𝐢𝐭𝐲 - Causes Typhoid Fever ⁣⁣
⁣⁣
➤ Feature - 𝘚. 𝘗𝘢𝘳𝘢𝘵𝘺𝘱𝘩𝘪⁣⁣
⁣⁣
𝐇₂𝐒 𝐏𝐫𝐨𝐝𝐮𝐜𝐭𝐢𝐨𝐧 - Negative⁣⁣
𝐌𝐨𝐭𝐢𝐥𝐢𝐭𝐲 - Motile ⁣⁣
𝐕𝐢 𝐀𝐧𝐭𝐢𝐠𝐞𝐧 - Absent⁣⁣
𝐏𝐚𝐭𝐡𝐨𝐠𝐞𝐧𝐢𝐜𝐢𝐭𝐲 - Causes Paratyphoid Fever (A, B, C)⁣⁣
⁣⁣
𝐂𝐥𝐢𝐧𝐢𝐜𝐚𝐥 𝐑𝐞𝐥𝐞𝐯𝐚𝐧𝐜𝐞⁣⁣
⁣⁣
➤ Both organisms are transmitted via the f***l–oral route.⁣⁣
⁣⁣
➤ Early identification on selective media like XLD agar helps in timely diagnosis, outbreak tracking, and targeted antimicrobial therapy.⁣⁣
⁣⁣
➤ Visual cues such as H₂S production are often the first hints for differentiating these two human-adapted pathogens.⁣⁣
⁣⁣

The ECG Pocket Code—Your Fastest Way to Read Any ECG!Struggling with ECG interpretation? Here’s a simple pocket code tha...
11/20/2025

The ECG Pocket Code—Your Fastest Way to Read Any ECG!

Struggling with ECG interpretation?

Here’s a simple pocket code that makes every ECG easy — even under pressure.
📘 Knowledge (Body)
A good ECG reading depends on a structured, consistent approach.
Use this quick pocket code every time:
ECG P-O-C-K-E-T Code
P — Patient
Check name, age, clinical history, symptoms.
O — Overall Rhythm
Regular or irregular? Sinus or non-sinus?
C — Calibration & Check
Paper speed 25mm/s, amplitude 10mm/mV, artefacts?
K — Key Intervals
PR, QRS, QT — normal or prolonged?
E — Emergencies
Look for STEMI, VT, heart block, hyperkalemia signs.
T — Technical Review
Lead placement, missing leads, baseline wander.

This one code improves accuracy, confidence, and speed, especially for students, technologists, and residents.

🧫 E. coli – Basic Details1️⃣ IntroductionEscherichia coli (E. coli) is a Gram-negative, rod-shaped, facultative anaerobi...
11/18/2025

🧫 E. coli – Basic Details

1️⃣ Introduction

Escherichia coli (E. coli) is a Gram-negative, rod-shaped, facultative anaerobic bacterium commonly found in the intestines of humans and warm-blooded animals.

Most strains are harmless, but some can cause infections.

2️⃣ Scientific Classification

Domain: Bacteria

Family: Enterobacteriaceae

Genus: Escherichia

Species: E. coli

3️⃣ Morphology

Shape: Rod-shaped (bacilli)

Gram Reaction: Gram-negative (pink)

Size: 1–3 µm long

Motility: Mostly motile (peritrichous flagella)

Spores: Non-spore forming

Capsule: Some strains may have capsules

4️⃣ Cultural Characteristics

Growth Requirements

Temperature: Optimum 35–37°C

pH: 6.5–7.5

Atmosphere: Facultative anaerobe (grows with or without oxygen)

Growth on Media

Nutrient Agar: Smooth, circular, cream-colored colonies

MacConkey Agar:

Pink colonies = lactose fermenter

EMB Agar:

Metallic green sheen (typical of E. coli)

TSA: Good growth

5️⃣ Biochemical Characteristics

E. coli is biochemically distinctive:

Test Result

Indole Positive
Methyl Red Positive
Voges-Proskauer Negative
Citrate Negative
Oxidase Negative
Catalase Positive
Lactose Fermentation Positive
Gelatin Hydrolysis Negative

IMViC pattern: ++--

6️⃣ Pathogenic Strains (Types)

Some harmful variants include:

EHEC – Enterohaemorrhagic (e.g., O157:H7)

ETEC – Enterotoxigenic

EPEC – Enteropathogenic

EIEC – Enteroinvasive

EAEC – Enteroaggregative

Harmless (normal flora) strains exist too.

7️⃣ Symptoms of Pathogenic E. coli (Medical)

Diarrhea

Abdominal cramps

Fever

Vomiting
(Depends on strain)

8️⃣ Importance in Microbiology Lab

Why E. coli is important in pharmaceuticals?

Used as a indicator organism for f***l contamination.

Used in method suitability test (USP , ).

Used in growth promotion test (GPT) for media.

Used to validate:

Water system

Environmental monitoring

Sterility test

9️⃣ Antibiotic Sensitivity

Non-pathogenic strains usually sensitive to:

Ampicillin

Gentamicin

Ciprofloxacin

Tetracycline

Pathogenic strains may show resistance.

10️⃣ Safety Classification

Biosafety Level: BSL-1 (harmless strains)

Pathogenic strains: BSL-2

11️⃣ Storage of Culture

As per USP/GLP:

Maintain stock at 2–8°C for short term

For long term: –20°C or –80°C in glycerol

🔬 Decoding the Molecular World: The Enduring Legacy of Blotting TechniquesThe image below beautifully summarizes the fou...
11/18/2025

🔬 Decoding the Molecular World: The Enduring Legacy of Blotting Techniques
The image below beautifully summarizes the foundational blotting techniques that have shaped molecular biology. More than just lab procedures, Southern, Northern, and Western blots are still critical for validating discoveries and diagnosing diseases in ways other methods can't.
The Blotting Family: Origins & Core Principles
At their heart, all blotting techniques involve separating biomolecules, transferring them to a membrane, and then detecting specific targets. It's a testament to their elegance that these methods, developed decades ago, remain central to modern research.
* Southern Blot (DNA - Edwin Southern, 1975): The pioneer! This technique allows us to pinpoint specific DNA sequences within complex samples. Did you know it was crucial in the early days of DNA fingerprinting and still plays a role in diagnosing specific large-scale genomic rearrangements that can be missed by sequencing?
* Northern Blot (RNA - Alwine, Kemp & Stark, 1977): Named in humor, this method is essential for understanding gene expression by detecting specific RNA transcripts. It's particularly powerful for analyzing RNA splice variants and even quantifying tiny microRNAs, offering a quantitative edge.
* Western Blot (Protein - Towbin, Staehelin & Gordon, 1979): The workhorse of protein analysis! Using antibodies, it identifies and quantifies specific proteins. Beyond basic detection, it's indispensable for validating antibody specificity and studying complex post-translational modifications like phosphorylation, which dictate protein function.
Why They Remain Indispensable: Modern Relevance
Their continued relevance stems from their:
* Unrivaled Specificity & Sensitivity: Providing direct, unambiguous evidence that complements high-throughput data.
* Critical Clinical Diagnostics: The Western Blot is still a confirmatory test for HIV infection, and Southern Blots are vital for diagnosing specific genetic disorders (e.g., Fragile X syndrome) and specific cancers.
* In-depth Protein Characterization: Offering a precise view of protein size, abundance, and modification in a specific biological context.
These techniques are not just historical artifacts; they are dynamic tools continually being refined with digital imaging and faster transfer methods, proving their irreplaceable role in scientific discovery and clinical care.
What's one surprising or unexpected insight you've gained from using blotting techniques in your work? Share your experience!

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