21BE45 | BIOLOGY FOR ENGINEERS | SEARCH CREATORS.

Subject Code:21BE45

Subject : BIOLOGY FOR ENGINEERS

Hanumanthu

Dep. Of CSE

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Module 5
TRENDS IN BIOENGINEERING
(QUALITATIVE):

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Module – 5

TRENDS IN BIOENGINEERING (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:

Biological materials are self-assembled with near-atomic precision in living

cells, whereas synthetic 3D structures generally lack such precision and
controllability. Recently, 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. In this
Primer, we summarize the methodologies of DNA origami technology, including
origami design, synthesis, functionalization and characterization. We highlight
applications of origami structures in nanofabrication, nano photonics and
nanoelectronics, catalysis, computation, molecular machines, bioimaging, drug
delivery and biophysics. We identify challenges for the field, including size
limits, stability issues and the scale of production, and discuss their possible

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solutions. We further provide an outlook on next-generation DNA origami

techniques that will allow in vivo synthesis and multiscale manufacturing.

DNA origami is the 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 wellunderstood 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. This design is then fed into a computer program that calculates
the placement of individual staple strands. Each staple binds to a specific region
of the DNA template, and thus due to Watson-Crick base pairing, the necessary
sequences of all staple strands are known and displayed. The DNA is mixed, then
heated and cooled. As the DNA cools, the various staples pull the long strand into

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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.

Bottom-up self-assembly methods are considered promising alternatives that

offer cheap, parallel synthesis of nanostructures under relatively mild conditions.

Since the creation of this method, software was developed to assist the process
using CAD software. This allows researchers to use a computer to determine the
way to create the correct staples needed to form a certain shape. One such
software called caDNAno is an open source software for creating such structures
from DNA. The use of software has not only increased the ease of the process but
has also drastically reduced the errors made by manual calculations.

Applications:
Many potential applications have been suggested in literature, including enzyme
immobilization, drug delivery systems, and nanotechnological self-assembly of
materials. Though DNA is not the natural choice for building active structures for
nanorobotic applications, due to its lack of structural and catalytic versatility,
several papers have examined the possibility of molecular walkers on origami
and switches for algorithmic computing. The following paragraphs list some of
the reported applications conducted in the laboratories with clinical potential.

Long strands of DNA are folded into a complex scaffold of staple strands having
200–300 nucleotides. This leads to formation of a complex structure that has
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characteristic features because of their nanoscale dimensions. These DNA

nanostrustures are known to still be in their preliminary developmental stages,
since key domains, such as their biocompatibility and physiochemical
characterizations are yet to be established. However, theoretically, DNA origami
has the immense potential to contribute significantly in a wide range of fields,
such as diagnosis and drug delivery. Cancer therapy and diagnosis is one such
potential domain where DNA origami showed significant anticancer efficacy and
may contribute immensely.

BIOCOMPUTING:

A computer that uses components of biological origin (such as molecules of

DNA) instead of electrical components. The device is rudimentary—it can only
perform basic high-school-level math problems.

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In the quest to understand and model the healthy or sick human body, re searchers
and medical doctors are utilizing more and more quantitative tools and
techniques. This trend is pushing the envelope of a new field we call Biomedical
Computing, as an exciting frontier among signal processing, pattern recognition,
optimization, nonlinear dynamics, computer science and biology, chemistry and
medicine.

Computing process which use synthesized biological components to store and

manipulate data analogous to processes in the human body. The result is small,
faster computing processes that operates with great accuracy. Main component
used is DNA. The main application is in disease prediction and disease diagnosis.

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BIOIMAGING AND ARTIFICIAL INTELLIGENCE FOR DISEASE

DIAGNOSIS:

1) BIOIMAGING:

Bioimaging is a noninvasive process of visualizing biological activity in a

specific period. It does not inhibit the various life processes such as movement,
respiration, etc., and it helps to report the 3D structure of specimens apart from
inferencing physically. It is helpful in connecting the observation of subcellular
structures and all the tissues in the multicellular organisms.

The imaging of biological samples, or bioimaging, plays a key role in current life
science research, enabling scientists to analyze molecules, cells and tissues from
a range of living systems.

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Nanoparticle fluorescence imaging has been used in gene detection, protein

analysis, enzyme activity evaluation, element tracing, cell tracking, early stage
disease diagnosis, tumor related research, and monitoring real time therapeutic
effects.

Bioimaging spans the observation of subcellular structures and entire cells over
tissues up to entire multicellular organisms. Among others, it uses light,
fluorescence, electrons, ultrasound, X-ray, magnetic resonance and positrons as
sources for imaging.

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2) ARTIFICIAL INTELLIGENCE IN DISEASE DIAGNOSIS:

Artificial intelligence can assist providers in a variety of patient care and

intelligent health systems. Artificial intelligence techniques ranging from
machine learning to deep learning are prevalent in healthcare for disease
diagnosis, drug discovery, and patient risk identification. Numerous medical data
sources are required to perfectly diagnose diseases using artificial intelligence
techniques, such as ultrasound, magnetic resonance imaging, mammography,
genomics, computed tomography scan, etc. Furthermore, artificial intelligence
primarily enhanced the infirmary experience and sped up preparing patients to
continue their rehabilitation at home.

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Detecting any irresistible ailment is nearly an afterward movement and

forestalling its spread requires ongoing data and examination. Hence, acting
rapidly with accurate data tosses a significant effect on the lives of individuals
around the globe socially and financially (Minaee et al. 2020). The best thing
about applying AI in health care is to improve from gathering and processing
valuable data to programming surgeon robots.

AI describes the capability of a machine to study the way a human learns, e.g.,
through image identification and detecting pattern in a problematic situation. AI
in health care alters how information gets composed, analysed, and developed for
patient care.

System planning is the fundamental abstract design of the system. It includes the
framework’s views, the course of action of the framework, and how the
framework carries on underneath clear conditions. A solid grip of the framework
design can help the client realize the limits and boundaries of the said framework.
In pre-preparing, real-world information requires upkeep and pre-preparing
before being taken care of by the calculation. Because of the justifiable
explanation, real-world data regularly contains mistakes regarding the utilized
measures yet cannot practice such blunders. Accordingly, information pre-
preparing takes this crude information, cycles it, eliminates errors, and spares it
an extra examination. Information experiences a progression of steps during pre-
handling: Information is purged by various strategies in information cleaning.
These strategies involve gathering information, such as filling the information
spaces that are left clear or decreasing information, such as the disposal of

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commas or other obscure characters. In information osmosis, the information is

joined from a combination of sources.

The information is then amended for any blend of mistakes, and they are quickly
taken care of. Information Alteration: Data in this progression is standardized,
which depends upon the given calculation. Information standardization can be
executed utilizing several ways. This progression is obligatory in most
information mining calculations, as the information wants to be as perfect as
possible. Information is then mutual and developed.

SELF HEALING BIOCONCRETE:

Bio-concrete is a self-healing form of concrete designed to repair its own cracks.

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To heal cracks in the concrete, Jonkers chose bacteria (Bacillus pseudo?rmus and
B. cohnii), that are able to produce limestone on a biological basis. The positive
side-effect of this property: the bacteria consume oxygen, which in turn prevents
the internal corrosion of reinforced concrete. However, the bacteria do not pose
a risk to human health, since they can only survive under the alkaline conditions
inside the concrete. Based on these findings, Jonkers and his team of researchers
developed three different bacterial concrete mixtures: self-healing concrete,
repair mortar, and a liquid repair system.

In self-healing concrete, bacterial content is integrated during construction, while

the repair mortar and liquid system only come into play when acute damage has
occurred on concrete elements. Self-healing concrete is the most complex of the
three variants. Bacterial spores are encapsulated within two-to four-millimeter
wide clay pellets and added to the cement mix with separate nitrogen,
phosphorous and a nutrient agent. This innovative approach ensures that bacteria
can remain dormant in the concrete for up to 200 years. Contact with nutrients
occurs only if water penetrates into a crack – and not while mixing cement. This
variant is well-suited for structures that are exposed to weathering, as well as
points that are difficult to access for repair workers. Thus, the need for expensive
and complex manual repairs is eliminated.

Self-healing concrete is nothing but concrete which can retain itself to the original
state when it is subjected to cracks." Bio-concrete is a material that will
biologically produce minerals like limestone with the help of bacteria present in
it, which will heal cracks that appear on the concrete surfaces.Bacterial self-

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healing is an innovative technology allowing repairing open micro-cracks in

concrete by CaCO3 precipitation. This bio-technology improves the durability of
the structure. In this paper, peptone, yeast extract and Bacillus Subtilis were
added as microbial adjuvant in concrete mix design.

Rahbar predicts self-healing concrete could extend the life of a structure from 20
years, for example, to 80 years. Other research into creating self-healing concrete
has focused on adding microbes and Bacillus megaterium, a spore-forming
bacteria that produces an enzyme that is expelled into the concrete mix.

The healing agent consisting of B. cohnii spores, calcium lactate and yeast extract
immobilized in light-weight aggregates was also combined with cement, fly ash,
limestone powder,PVA fibers,water in a repair mortar.

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BIOREMEDIATION AND BIO MINING VIA MICROBIAL SURFACE

ADSORPTION:

1) BIOREMEDIATION:

Bioremediation is a biotechnical process, which abates or cleans up

contamination. It is a type of waste management technique which involves the
use of organisms to remove or utilize the pollutants from a polluted area. Types
of Bioremediation

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Bioremediation is of three types –

1) Biostimulation:

As the name suggests, the bacteria is stimulated to initiate the process. The
contaminated soil is first mixed with special nutrients substances including other
vital components either in the form of liquid or gas. It stimulates the growth of
microbes thus resulting in efficient and quick removal of contaminants by
microbes and other bacterias.

2) Bioaugmentation:

At times, there are certain sites where microorganisms are required to extract the
contaminants. For example – municipal wastewater. In these special cases, the
process of bioaugmentation is used. There’s only one major drawback in this
process. It almost becomes impossible to control the growth of microorganisms
in the process of removing the contaminant.

3) Intrinsic Bioremediation:

The process of intrinsic bioremediation is most effective in the soil and water
because of these two biomes which always have a high probability of being full
of contaminants and toxins. The process of intrinsic bioremediation is mostly
used in underground places like underground petroleum tanks. In such place, it is
difficult to detect a leakage and contaminants and toxins can find their way to
enter through these leaks and contaminate the petrol. Thus, only microorganisms
can remove the toxins and clean the tanks.

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Bioremediation helps clean up water sources, create healthier soil, and improve
air quality around the globe. But unlike excavation-based remediation processes,
which can be disruptive, bioremediation is less intrusive and can facilitate
remediation of environmental impacts without damaging delicate ecosystems.

Immobilization of microbial cells and enzymes by adsorption takes place through

their physical interaction with the surface of water-insoluble carriers. This
method, commonly used in bioremediation processes, is quick, simple, eco-
friendly and cost-effective.

Microorganisms are utilized in bioremediation because of their ability to degrade

environmental pollutants due to their metabolism via biochemical pathways
related to the organism’s activity and growth.

2) BIOMINING:

Biomining is the process of using microorganisms (microbes) to extract metals

of economic interest from rock ores or mine waste. Biomining techniques may
also be used to clean up sites that have been polluted with metals.

Valuable metals are commonly bound up in solid minerals. Some microbes can
oxidize those metals, allowing them to dissolve in water. This is the basic process
behind most biomining, which is used for metals that can be more easily
recovered when dissolved than from the solid rocks. A different biomining
technique, for metals which are not dissolved by the microbes, uses microbes to

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break down the surrounding minerals, making it easier to recover the metal of
interest directly from the remaining rock.

Most current biomining operations target valuable metals like copper, uranium,
nickel, and gold that are commonly found in sulfidic (sulfur-bearing) minerals.
Microbes are especially good at oxidizing sulfidic minerals, converting metals
like iron and copper into forms that can dissolve more easily. Other metals, like
gold, are not directly dissolved by this microbial process, but are made more
accessible to traditional mining techniques because the minerals surrounding
these metals are dissolved and removed by microbial processes. When the metal
of interest is directly dissolved, the biomining process is called “bioleaching,”
and when the metal of interest is made more accessible or “enriched” in the
material left behind, it is called “biooxidation.” Both processes involve microbial
reactions that can happen anywhere the microbes, rocks, and necessary nutrients,
like oxygen, occur together.

Bioleaching (or biomining) is a process in mining and biohydrometallurgy

(natural processes of interactions between microbes and minerals) that extracts
valuable metals from a low-grade ore with the help of microorganisms such as
bacteria or archaea.

Instead of separating the metal from the pyrite with high temperatures or
pressures, biomining uses microbes from the Acidthiobacillus and Leptospirillum
genera to do the job.

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A) Heavy metal ions adsorption process; the metal ions of wastewater adhere

to the surface of nanoporous adsorbents, which has a high surface area due
to its porosity. The adsorption process could be selective for one or more
metals than others. The regeneration process could be achieved using a
desorbing agent.

B) Various modification techniques (i.e., nitrogenation, oxidation, and

sulfuration) are used to functionalize carbon with different functional

groups. Functionalization enhances adsorption capacity and stability.

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Module-05

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