BIOLOGY FOR ENGINEERS

DR. SHILPA SIVASHANKAR

DEPARTMENT OF BIOTECHNOLOGY
ACHARYA INSTITUTE OF TECHNOLOGY
E MAIL – SSHILPA@ACHARYA.AC.IN
 MODULE 4
TRENDS IN BIOENGINEERING (QUALITATIVE): 5
(QUALITATIVE):
BIOPRINTING TECHNIQUES AND MATERIALS, 3D PRINTING OF EAR, BONE AND SKIN. 3D PRINTED
FOODS. ELECTRICAL TONGUE AND ELECTRICAL NOSE IN FOOD SCIENCE, DNA ORIGAMI AND
BIOCOMPUTING, BIOIMAGING AND ARTIFICIAL INTELLIGENCE FOR DISEASE DIAGNOSIS. SELF-
HEALING BIOCONCRETE (BASED ON BACILLUS SPORES, CALCIUM LACTATE NUTRIENTS AND
BIOMINERALIZATION PROCESSES) AND BIOREMEDIATION AND BIOMINING VIA MICROBIAL SURFACE
ADSORPTION (REMOVAL OF HEAVY METALS LIKE LEAD, CADMIUM, MERCURY, ARSENIC).
DNA ORIGAMI AND BIOCOMPUTING:
INTRODUCTION:

• DNA nanotechnology, especially DNA origami technology, has been useful in the bottom-up
fabrication of well-defined nanostructures ranging from tens of nanometers to sub-
micrometers.
• We highlight applications of origami structures in
• nanofabrication, nano photonics and nanoelectronics, catalysis, computation, molecular
machines,
• bioimaging, drug delivery and biophysics.
• Challenges for the field, including size limits, stability issues and the scale of production, and
discuss their possible solutions
• Outlook on next-generation DNA origami techniques that will allow in vivo synthesis and
multiscale manufacturing.
• DNA origami
• Nanoscale folding of DNA to create arbitrary two- and
three-dimensional shapes at the nanoscale.
• The specificity of the interactions between complementary
base pairs makes DNA a useful construction material,
through design of its base sequences.
• DNA is a well- understood material that is suitable for
creating scaffolds that hold other molecules in place or to
create structures all on its own.
• The current method of DNA origami was developed by
Paul Rothemund at the California Institute of Technology.
• The process involves the folding of a long single strand of
viral DNA (typically the 7,249 bp genomic DNA of M13
bacteriophage) aided by multiple smaller "staple" strands.
• These shorter strands bind the longer in various places,
resulting in the formation of a pre-defined two- or three-
dimensional shape.
• Examples include a smiley face and a coarse map of China
and the Americas, along with many three-dimensional
structures such as cubes.
To produce a desired shape, images are drawn with a raster fill of a single long DNA molecule.

computer program that calculates the placement of individual staple strands.

staple binds to a specific region of the DNA template

The DNA is mixed, then heated and cooled. As the DNA cools, the various staples pull the long strand into the
desired shape.

Designs are directly observable via several methods, including electron microscopy, atomic force microscopy,
or fluorescence microscopy when DNA is coupled to fluorescent materials.
GAS EXCHANGE MECHANISMS:
• Air enters the body through the mouth or nose and quickly moves to the pharynx or throat. From there, it passes
through the larynx, or voice box, and enters the trachea.
• The trachea is a strong tube that contains rings of cartilage that prevent it from collapsing. Within the lungs,
the trachea branches into a left and right bronchus. These further divide into smaller and smaller branches
called bronchioles. The smallest bronchioles end in tiny air sacs. These are called alveoli.
• They inflate when a person inhales and deflate when a person exhales. During gas exchange oxygen moves
from the lungs to the bloodstream. At the same time, carbon dioxide passes from the blood to the lungs. This
happens in the lungs between the alveoli and a network of tiny blood vessels called capillaries, which are
located in the walls of the alveoli.
 SPIROMETRY

• Spirometry uses a machine called a spirometer. A spirometer is a

medical device that consists of a mouthpiece and a tube. They
connect to a machine that measures your airflow.
• It is the most common of the pulmonary function tests. It measures
lung function, specifically the amount and/or speed of air that can
be inhaled and exhaled
• And used to diagnose asthma, chronic obstructive pulmonary
disease (COPD) and other conditions that affect breathing.
Requirements of an acceptable spirometer are:
• Spirometers must be able to accumulate volume for ≥15 s.
• The measuring volume should be ≥8 L (body temperature and pressure, saturated).
• The accuracy of reading should be at least ±3% (or ±0.05 L) with flows from 0–14 L per s.
• The total resistance to airflow at 14 L per s should be <1.5 cmH2O per L per s (<0.15 kPa per L per s).
COPD:
Chronic obstructive pulmonary disease (COPD) is a chronic inflammatory lung disease that causes obstructed airflow from the
lungs. Symptoms include breathing difficulty, cough, mucus (sputum) production, and wheezing. It's typically caused by long-
term exposure to irritating gases or particulate matter, most often from cigarette smoke. People with COPD are at increased
risk of developing heart disease, lung cancer, and a variety of other conditions.
Emphysema and chronic bronchitis are the two most common conditions that contribute to COPD. These two conditions
usually occur together and can vary in severity among individuals with COPD.
Symptoms
COPD symptoms often don't appear until significant lung damage has occurred, and they usually worsen over time, particularly
if smoking exposure continues.
Signs and symptoms of COPD may include:
* Shortness of breath, especially during physical activities
* Wheezing
* Chest tightness
* A chronic cough that may produce mucus (sputum) that may be clear, white, yellow, or greenish
* Frequent respiratory infections
* Lack of energy
* Unintended weight loss (in later stages)
* Swelling in ankles, feet, or legs
Tests may include:
* Lung (pulmonary) function tests.
* Chest X-ray.
* CT scan.
* Arterial blood gas analysis.
* Laboratory tests.
 VENTILATORS

A ventilator is a device that supports or takes over the breathing process, pumping air into the
lungs.
Types of ventilator
• Face mask ventilators
• Mechanical ventilators
• Manual resuscitator bags
• Tracheostomy ventilators
FACE MASK VENTILATOR

• It is a noninvasive method of supporting the breathing

and oxygen levels.
• The mask fits over the nose and mouth while air blows
into the airways and lungs.
Mechanical ventilator
These are machines that take over the breathing process
entirely . It work via a tube in a person’s throat, pumping
air into the lungs and transporting carbon dioxide away.
 MANUAL RESUSCITATOR BAGS

• These are pieces of equipment that allow person to

control the airflow of their ventilator with their hands.
• These devices consist of an empty bag or bladder that
a person squeezes to pump air into the lungs.

Tracheostomy ventilator
• A tracheostomy is a procedure where a doctor creates
an opening in the windpipe and inserts a tube, which
allows air to flow in and out. This enables a person to
breathe without using their nose or mouth.
KIDNEY AS FILTRATION SYSTEM
INTRODUCTION:
Kidneys remove wastes and extra fluid from the body. Kidneys also remove acid that is produced by the cells of the
body and maintain a healthy balance of water, salts, and minerals—such as sodium, calcium, phosphorus, and
potassium—in the blood. Without this balance, nerves, muscles, and other tissues in the body may not work
normally.
Kidneys also make hormones that help
* Control blood pressure.
* Make red blood cells NIH external link.
* Keeps bones strong and healthy.
ARCHITECTURE:
The kidneys are two bean-shaped organs, each about the size of a fist. They are located just below the rib cage, one
on each side of the spine. Healthy kidneys filter about a half cup of blood every minute, removing wastes and extra
water to make urine. The urine flows from the kidneys to the bladder through two thin tubes of muscle called ureters,
one on each side of the bladder. Your bladder stores urine. Kidneys, ureters, and bladder are part of your urinary tract
MECHANISM OF FILTRATION:
• Each kidney is made up of about a million filtering units called nephrons. Each nephron includes a filter, called the
glomerulus, and a tubule. The nephrons work through a two-step process: the glomerulus filters blood, and the
tubule returns needed substances to your blood and removes wastes.
• Each nephron has a glomerulus to filter your blood and a tubule that returns needed substances to your blood and
pulls out additional wastes. Wastes and extra water become urine.
The glomerulus filters your blood
• As blood flows into each nephron, it enters a cluster of tiny blood vessels—the glomerulus. The thin walls of the
glomerulus allow smaller molecules, wastes, and fluid—mostly water—to pass into the tubule. Larger molecules,
such as proteins and blood cells, stay in the blood vessel. The tubule returns needed substances to your blood and
removes wastes.
How does blood flow through my kidneys?
• Blood flows into the kidney through the renal artery. This large blood vessel branches into
smaller and smaller blood vessels until the blood reaches the nephrons. In the nephron, blood
is filtered by the tiny blood vessels of the glomeruli and then flows out of the kidney through
the renal vein.
• Blood circulates through your kidneys many times a day. In a single day, kidneys filter about
150 quarts of blood. Most of the water and other substances that filter through your glomeruli
are returned to the blood by the tubules. Only 1 to 2 quarts become urine.
• When the kidney doesn't function properly, Chronic kidney disease occurs when a disease or
condition impairs kidney function, causing kidney damage to worsen over several months or
years
CKD:
Chronic kidney disease includes conditions that damage your kidneys and decrease their ability to keep you healthy by filtering
wastes from your blood. If kidney disease worsens, wastes can build to high levels in your blood and make you feel sick. You
may develop complications like
* high blood pressure
* anemia (low blood count)
* weak bones
* poor nutritional health
* nerve damage
SYMPTOMS:
People with CKD may not feel ill or notice any symptoms. The only way to find out for sure if you have CKD is through specific
blood and urine tests. These tests include the measurement of both the creatinine level in the blood and the protein in the urine.
TREATMENT:
Depending on the cause, some types of kidney disease can be treated. Often, though, chronic kidney disease has no cure.
Treatment usually consists of measures to help control signs and symptoms, reduce complications, and slow the progression of
the disease. If your kidneys become severely damaged, you might need treatment for end-stage kidney disease.
DIALYSIS:
Dialysis is a procedure to remove waste products and excess fluid from the blood when the kidneys stop working properly. It
often involves diverting blood to a machine to be cleaned.
There are 2 main types of dialysis:
* Haemodialysis involves diverting blood into an external machine, where it's filtered before being returned to the body
* Peritoneal dialysis involves pumping dialysis fluid into the space inside your abdomen (tummy) to draw out waste products
from the blood passing through vessels lining the inside of the abdomen
MUSCULAR AND SKELETAL SYSTEM AS SCAFFOLDS:
Skeletal muscle architecture is one of the most important properties that determine a muscle’s force and excursion capability. In
the current review, basic architectural terms first are reviewed, and then specific examples relevant to upper extremity anatomy
are presented. Specific examples of anatomic considerations required for surgical reconstruction after radial nerve palsy also are
detailed

Muscle architecture is the physical arrangement of at the macroscopic

muscle fibres level that determines muscle’s mechanical function. There
are several different muscle architecture types including: parallel,
pennate and hydrostats. Force production and gearing vary depending
on the different muscle parameters such as muscle length, fiber length,
pennation angle, and the physical cross sectional area.

There are two main types of muscle architecture

• Parallel
• Pennate
Parallel
The parallel muscle architecture is found in muscles where the fibers
are parallel to the force-generating axis. These muscles are often used
for fast or extensive movements and can be measured by the anatomical
cross-sectional area (ACSA).
MECHANISM:
The nervous system (your body’s command center) controls your voluntary muscle movements. Voluntary muscles are ones you
control intentionally. Some involve large muscle groups to do activities like jumping. Others use smaller movements, like
pushing a button.
Movements happen when:
Our nervous system (brain and nerves) sends a message to activate your skeletal (voluntary) muscles. Our muscle fibers contract
(tense up) in response to the message. When the muscle activates or bunches up, it pulls on the tendon. Tendons attach muscles
to bones. The tendon pulls the bone, making it move. To relax the muscle, your nervous system sends another message. It
triggers the muscles to relax or deactivate. The relaxed muscle releases tension, moving the bone to a resting position.
Hundreds of conditions can cause problems with the musculoskeletal system. They can affect the way you move, speak and
interact with the world. Some of the most common causes of musculoskeletal pain and movement problems are:
* Aging
* Arthritis
* Back problems
* Cancer
* Congenital abnormalities
* Injuries
* Osteoporosis
* Muscular dystrophy
Everyone has pain in their muscles and joints from time to time. One of the most common musculoskeletal conditions is
Osteoporosis. More than 60% of people in the United States have Osteoporosis at some point in their lives. Arthritis is also very
common. More than 54 million adults in the U.S. have Muscular dystrophy. Most people recover from these disorders without
long-term health problems.
BIO-ENGINEERING SOLUTIONS FOR MUSCULAR DYSTROPHY AND OSTEOPOROSIS
• Awareness is increasing that bone morbidity due to osteoporosis is a major complication of Duchenne muscular dystrophy (DMD) and its
treatment and that it requires monitoring for early diagnosis and intervention to prevent clinically important sequelae.
• The traditional method of fabricating 3D muscle constructs first developed more than 25 years ago involves casting myogenic cells within a
cylindrically shaped collagen-I gel that is anchored at the ends to porous felts. In this system, cell-mediated gel compaction and remodeling
result in the generation of uniaxial passive stress within the gel, which, in turn, promotes the fusion of myoblasts into myotubes and also
myotube alignment.
• Alternatively, myoblasts, or mixtures of myogenic precursors and fibroblasts, can be cultured on laminin- or hydrogel-coated dishes until
spontaneous contractions of formed myotubes detach the entire cell layer, allowing it to self-assemble into a cylindrical tissue construct
attached at the ends to premade suture anchors.
• Although cell alignment within 3D constructs is not required for the formation of contractile myotubes, it increases fusion efficiency while
passive stress promotes both cell survival and myogenesis. In addition to collagen I, different natural hydrogels and their chemically modified
derivatives can support the 3D growth and fusion of myogenic cells; the most functional results have been achieved using fibrin-based gels.
Carefully optimizing the composition of the fibrin gel to enhance cell-matrix interactions as well as optimizing the starting cell population to
improve myogenic fusion and SC maintenance and providing dynamic culture conditions to improve cell survival and maturation have
enabled rodent skeletal muscle tissues to be engineered with contractile properties comparable to those of native muscle (e.g., twitch and
tetanus-force amplitudes)