The Coming Of The Great Psychic

VIVA LA BIOENGINEERING

• Network Analysis in Precision Medicine VOLUME THREE NOVEMBER 2023

The Coming of the Great Psychic

Think about it!

VIT Bhopal Design by: Anushka Jena (21BOE10039)

EDITOR’S NOTE We’re back with the third issue of Viva La BioEngineering. In this issue, we delve deeper into the future of Biology when integrated with the superpowers of Artificial Intelligence. The creation of the Great Psychic can predict the consequence of every single change in your body. What started as small interventions like fit bits and pulse oximeters, will soon become precise simulations of every individual’s internal environment.

A future where your proximity to cancer can be detected without a Biopsy, a future where it will be known specifically which pathway in your body has malfunctioned, and which treatment would work best for you, as a unique individual. This Great Psychic no longer belongs to the land of magic, imagination, and fantasy, but it will soon be the reality of the future. This is the futuristic land of Systems Biology In this issue, we will also be giving you a sneak peek into all the exciting activities, The Bioengineering Club, has been engaging in, since the last issue. I hope this magazine will remain worth your time!

Divya Maria Thomas Chief Editor

CONTENTS 4

WAR AND PEACE Invasive and Non-invasive Methods of Diagnosis A Step towards Peace -Sharanya Vishnubhatla (22BOE10060)

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PREREQUISITES TO THIS FUTURE: DATA COLLECTION How is data collected for cancer diagnosis using bio-markers?

What data would we require to map the entire human body?

-Shradhay Chaturvedi (21BOE10042)

12

MATHEMATICAL SIMULATION IN BIOSCIENCES A passing trend or an exciting new technology in Diagnostics -Eshita Mukherjee (22BOE10088)

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NETWORK ANALYSIS FOR PREDICTIVE HEALTHCARE: A NEW PARADIGM -Shatakshi Malviya (21BOE10008)

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WHAT WE HAVE BEEN UPTO? -Akriti Singh (22BOE10106)

Design by: Anushka Jena (21BOE10039) Photos by: Aditya Binukumar (21BOE10055)

WRITTEN BY SHARANYA VISHNUBHATLA. PHOTOS BY ADITYA BINUKUMAR.

WAR AND PEACE Did you know that in the not-so-distant past, before the development of the hair-clip-like gadget that we all refer to as a pulse oximeter, healthcare experts had to rely on a quick and painful test called a blood gas test to determine the level of oxygen in the blood? A need would be inserted into the artery, and measurement of the extracted blood was to be done within the next 10 minutes for high accuracy.

Not only was this dangerous, but it also lacked efficiency.

However, oximeters have changed the game.

According to Yale Medicine, “A small, electronic device called a pulse oximeter is clipped onto a part of the body, usually a fingertip. The device emits light that passes through the fingernail, skin, tissue, and blood. On the other side of the finger, a sensor detects and measures the amount of light that passes through the finger without getting absorbed by the tissue and blood. Using that measurement, the device calculates the oxygen saturation of the blood.”

What does this tell us? Could it truly be a possibility for us to understand the human body, without invading it and waging great wars every other month?

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Invasive and Non-invasive Methods of Diagnosis: What are they?

There are two major types of diagnostic testing, viz. Invasive and Non-Invasive.

The former is done by gaining access to the body through an incision, cut, or a natural opening like nostrils, throat, or genital holes, while the latter is done by simple screening methods including but not limited to X-rays, CT scans, and an Ultrasound.

Often when there is a need to administer any medicinal product to a target area, it is preferred to as an ‘invasive procedure’ and has to be done by the need for an invasive one.

But if our methods of diagnosis are invasive, and it is found that the individual is not diseased, then we unnecessarily expose them to infections from dermatological openings, painful probing, health complications, and discomfort. And if declared diseased, we are exposing them twice.

Therefore, for the benefit of our patients, the future of disease diagnosis has to go towards the direction of least invasiveness.

Effect of Human foxp2 on Mice A study found that mice carrying the Human Foxp2 gene were capable of a broader range of vocalization and better at repetitive behavior like solving mazes than their wild counterparts.

WRITTEN BY SHARANYA VISHNUBHATLA. PHOTO BY ADITYA BINUKUMAR.

a skilled operator. Simply put, a non-invasive diagnosis determines

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WRITTEN BY SHARANYA VISHNUBHATLA.. PHOTOS BY ADITYA BINUKUMAR.

A Small Step towards Peace Let’s

consider

sampling (CVS), where cells

amniocentesis, the widely

of

known

for

extracted and tested, is the

diagnosis of abnormalities

NIPT test. Known as the

in a fetus. Here, a sample of

Non-Invasive

the amniotic fluid is taken

Testing

to

taking a blood sample from

method

analyze

chromosomal

the

placenta

are

Prenatal

test,

it

involves

alignment, any mutations

the

present, etc. It’s typically

woman’s blood is known to

used to screen for Down’s

contain fragments of fetal

Syndrome,

DNA,

Edward’s

mother.

and

A

pregnant

this

in

turn

tests

to

Syndrome, and other major

undergoes

diseases.

determine

However, since it involves

abnormalities.

inserting an instrument into

While extracting a vial of

the uterus, it is dangerous

blood

for

the

is

any

still

considered

fetus

and

‘invasive’ per se, it does not

for

the

involve

uncomfortable

inserting

any

mother. An up-and-coming

instrument into the uterus,

alternative

thereby

for

reducing

any

amniocentesis or

chances of harm to the

chorionic villus

fetus.

Lightweight alternative to Cas9 A CRISPR-based enzyme enAsCas12f has matched the effectivity of Cas9 but at one-third of its size. The enzyme was derived using deep mutational scanning and structural analysis on unmutated AsCas12f.

6

a picture of human cell anatomy

Imagine

Prerequisites to non-invasive this future: Data seamlessly Collection

where sensors

a world

integrate into daily life,

Data

continuously monitoring

fundamental

vital signs, biomarkers,

invasive diagnostics as it

and

enables

healthcare

professionals

to

physiological

collection for

is non-

parameters

through

wearables

like

informed decisions, detect

smart

health issues early, tailor

smartwatches, clothing, lenses.

and This

contact

treatments,

and

make

advance

medical research. It plays a

data collection ensures

pivotal role in improving

early detection of health

patient care, outcomes, and

issues, providing alerts

the

for even the smallest

healthcare systems.

overall

efficiency

of

bodily changes.

Engineered Bacteria works with CAR-T Cells to End Tumours: Synthetic biologists at Columbia Engineering have engineered tumor-colonizing E.coli probiotics that help in CAR T-cell immunotherapy against solid tumors. The probiotics achieve this by tagging the tumor using synthetic antigens.

WRITTEN BY SHRADHAY C, SHATAKSHI M. PHOTO BY ADITYA BINUKUMAR

real-time

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PHOTOS BY ADITYA BINUKUMAR

A picture of connections seen in neocortex of a mouse brain

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Mini Spotlight!

How is data collected for cancer diagnosis using biomarkers?

Cancer diagnosis via biomarkers entails collecting and analyzing diverse data types to pinpoint molecular

or

genetic

changes

linked to cancer. The process includes

sample

collection,

processing, genetic analysis (like DNA sequencing), RNA analysis, proteomic

analysis

(e.g.,

mass

spectrometry), epigenetic analysis imaging, pathological examination, data

integration

using

bioinformatics, validation in larger patient

cohorts,

application. validated

for

and

clinical

Biomarkers

are

diagnostic

and

prognostic value, ultimately aiding cancer

diagnosis

and

patient

management. This comprehensive approach allows for the detection and characterization of cancerbased

on

specific

molecular

signatures and genetic alterations.

founded 'The Thought Emporium,' merging

Biology

Nanotechnology

and

after

leaving

Carleton University. His YouTube channel began in high school, showcasing simplifying

projects scientific

and

concepts.

Notable feats include using AAV to cure

lactose

intolerance

and

engineering yeast for spider silk and carotene. He built a DIY magnetron, and a radio telescope, and pursued a rat neuron-based processor. His instructional videos span

genetic

engineering

to

nuclear physics. Atkin also hosts 'Whose gene is it anyways?' where he educates on plasmid vectors through creative demos. His work promotes

scientific

exploration

and accessible education.

WRITTEN BY SHRADHAY CHATURVEDI. PHOTO BY ADITYA BINUKUMAR.

(e.g., DNA methylation), medical

Canadian biohacker Justin Atkin

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What data would we require to map the entire h Mapping every single reaction that could occur in the human body, is not an easy task. It would require us to feed the model with immense data, that will be personalized to the individual.

Here are some of the types of experimental data that would be needed:

Structural Data

Proteomic Data Comprehensive proteomic data to determine the presence, abundance, and post-translational modifications of proteins in different cell types and tissues.

Enzyme Kinetics

Cellular Localization Dat

Structural information for proteins, enzymes, and metabolites to understand how they interact and catalyze reactions.

Metabolomic Data Metabolomic data detailing the concentration and flux of small molecules (metabolites) in various cellular and tissue environments.

Detailed kinetic parameters for enzymes involved in metabolic reactions, including substrate affinity (Km), maximum reaction rate (Vmax), and inhibition constants.

Biochem Assays Physiological Data Data on physiological parameters, such as pH, temperature, and ion concentrations, that affect reaction rates.

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Knowledge of the subcellular localization proteins and enzymes within cells.

Assays to activities, concentra rates unde conditions

A picture of a Microarray or sequencing chip

human body?

ta

Environmental Data

Pathway Data

Data on external factors, such as dietary intake and exposure to toxins, which influence metabolism.

Information about metabolic pathways, including enzyme-substrate relationships, regulatory mechanisms, and metabolic fluxes.

Experimental Conditions

n of

to measure enzyme es, metabolite ntrations, and reaction nder different ons.

Data on protein-protein interactions to understand how proteins in metabolic pathways may interact and influence each other.

Disease-Specific Data Disease-related data, such as mutations, gene expression changes, and metabolic alterations associated with various diseases.

Genomic Data Sequencing data for the entire human genome and possibly individual genomes to account for genetic variation.

Information about gene expression levels in different tissues and under various conditions.

WRITTEN BY SHRADHAY CHATURVEDI. PHOTO BY ADITYA BINUKUMAR.

emical s

Protein-Protein Interaction Data

Information about experimental conditions, including cell culture conditions, tissue-specific conditions, and perturbations (e.g., drug treatments or genetic modifications).

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WRITTEN BY ESHITA MUKHERJEE |CHIEF EQUITY OFFICER| . PHOTOS BY ADITYA BINUKUMAR.

MATHEMATICAL SIMULATION IN BIOSCIENCES A passing trend or an exciting new technology in Diagnostics?

Once we collect the data required, it's time to build the models that we can feed our data to.

Modeling biological systems uses computer simulations of biological systems, to analyze and visualize complex connections of cellular processes, and to create accurate real-time models of its response to environmental and internal stimuli, for example, model cancer cells to find weaknesses in their signaling pathways.

Recently, dynamic mathematical models in biology have become a trend.

Besides the Michaelis–Menten model, the Hodgkin–Huxley, and the Lotka– Volterra model, the emergence and widespread recognition of the importance of simulation in biology is a recent phenomenon.

This is definitely the future of accurate and non-invasive healthcare: Dassault Systémes is applying this technology to realistically simulate the heart, in the “Living Heart Project”.

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Pictures of brain scans of mice involved in Blue Brain Project

NETWORK ANALYSIS FOR PREDICTIVE HEALTHCARE: A NEW PARADIGM Network analysis takes this personalization to the next level.

Continuously monitoring multiple organ systems and their provides personalized health risk insights, factoring in genetics, lifestyle, and the environment for tailored healthcare advice.

Network analysis refers to the application of network theory and techniques to analyze and interpret complex patterns of interactions or relationships between various biological, physiological, or healthrelated elements or variables.

The power of network analysis lies in its ability to detect deviations from normal health parameters early. When the AI algorithms identify anomalies or predict potential health issues, they trigger alerts. These alerts can be sent to healthcare providers, caregivers, or directly to the individual, prompting them to take proactive measures.

WRITTEN BY SHATAKSHI MALVIYA. PHOTO BY ADITYA BINUKUMAR.

interactions through mathematical models, this system

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WRITTEN BY SHATAKSHI MALVIYA. PHOTOS BY ADITYA BINUKUMAR.

One of the most promising aspects of network analysis is its predictive power. As the system continually gathers data on various organ systems, it can predict the onset of diseases or malfunctions. For instance: Cardiovascular Health: By monitoring heart rate, blood pressure, and arterial health, the system can predict the risk of heart disease or stroke.

Respiratory Health: Continuous monitoring of lung function and oxygen levels can detect early signs of respiratory diseases like asthma or chronic obstructive pulmonary disease (COPD).

Metabolic Health: Changes in glucose levels, insulin sensitivity, and dietary habits can be analyzed to predict the risk of diabetes or metabolic syndrome.

Neurological Health: Monitoring brain activity and sleep patterns can help predict neurodegenerative diseases like Alzheimer's or identify sleep disorders.

Immune System: Continuous monitoring of immune markers can predict susceptibility to infections and autoimmune diseases.

Network analysis for predictive healthcare is not just a vision for the future; it's a promising reality on the horizon. As technology continues to advance, the dream of predictive healthcare may become commonplace, ushering in a new era of proactive and personalized medicine for all.

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CROSSWORD ACROSS: 3. branch of biology involving the application of computers and computer science to the understanding and modeling of the structures and processes of life 5. process of cell identification and cell selection, and subsequent separation of the different cell species 6. the process by which the information encoded in a gene is turned into a function DOWN: 1. the process by which cells communicate with other cells within their body or with the external environment 3. study of the complete set of proteins expressed by an organism 4. study of human genes and chromosomes ANSWERS: 1. CELLSIGNALING 2. PROTEOMICS

3. COMPUTATIONALBIOLOGY 4. GENOMICS

5. CELLSORTING 6. GENEEXPRESSION

What have we been upto?

We’ve been bustling around like little bees, actively building our hive. Our entire leadership crew has changed. With tears in our eyes, we bid adieu to the Great visionaries and founders of our club, as they welcomed us aboard this Battleship.

The new members had their debut, with the BIO EXPO' 23: an event where we took the Students of VIT Bhopal on an expedition, investigating unseen life on the surfaces of the earth, and uncovering the hidden microbial world, through hands-onon-workshops. deep dive into the world of medical writing with the help of Dr. Smita Srivastava.

And without any rest, on the 21st of October, we have the Next Gen Networking event, where we conducted the initiation ceremony for the 23 Batch Bioengineering Newbies, to give them a sneak peak of what's on the other side of the bridge

MADE BY AKRITI SINGH

After that, on the 14th of October, they took a

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VOLUME THREE OCTOBER 2023

Innovation and Inventions at the intersection of Biology and Engineering

VIT BHOPAL

Viva la bioengineering