Biotechnology and Its
Applications in Sciences and Medicine
Since the days of independence of
Malaya, medical officers have always been given permanent appointments.
However, beginning in 2016, the Malaysian government enforced the contract
appointment policy for house officers due to a lack of permanent medical officer
positions available due to far too many doctors graduating. Since then,
thousands of doctors are employed on contract without a permanent job in
government service. Since the purpose of any study is to find employment to
sustain ourselves and to support our families later, we need to find a more
suitable and less competitive course to take after leaving school. This is our
main purpose of education. Of course, we can pursue multiple courses just to
acquire a wide spectrum of knowledge for academic purposes once we have secured
a job on graduation if we wish. But the basic degree or diploma course we enrol
should be one that can secure us a comfortable job and nothing more than this.
What then are other options that
are available in the areas of science or medicine where there is better scope
for employment?
Some years ago, I was having a
social dinner at the Lake Club in Kuala Lumpur organized by the Malaysian
Senior Scientists Association (MSSA) where I was a member. Sitting beside me on
the same table were two high profile medical personalities, one was Toh Puan Dato’ Seri Hjh. Dr Aishah Ong,
and another sitting on the same table on my left was Tan Sri Dr Jegathesan
Manikavasagam who was then the Director of the Institute for Medical Research
where I was also working until I retired. Toh Puan Dato’ Seri Hjh. Dr
Aishah Ong was the Chairman of the Board of Directors for the University
Teaching Hospital until 1986. She was also a member of the University Malaya’s
Council from 1987 until 1996 (before the university’s corporatisation) and then
became a member of the Board of Directors for University of Malaya (after the
corporatisation) from February 1997 to February 2003. From February 2003 until
2008, she was appointed as the Pro-Chancellor of the University of Malaya, the
first woman to be appointed to the post. Besides that, she was appointed as a
member of the Directors Council for the International Medical College from 1991
until 1998 and from 2001 to February 2003, she was appointed as a council
member for International Medical University (IMU) after the college earned its
university status.
As both of them were very familiar
with medical education and are also members of MSSA, I struck up a conversation
with both of them on the scope of studying medicine in this country since
thousands of medical graduates landed up as contract doctors in
government service and were left without permanent jobs.
Tan Sri Dr Jagathesan told me
medical doctors who were on contract basis in government service who went
into private practice instead too found difficulty in employment since over
500 private clinics nationwide were forced to close down due to very high
expenses of running them with very few patients, with most patients seeking
treatment in government clinics and government hospitals as treatment there is
free-of-charge despite long wait and overcrowding. He told me the practice of
medicine is now a very competitive field with far too many doctors in the
country.
Toh Puan Dr Dato’ Seri Hjh. Dr
Aishah Ong also agreed that there were too many medical graduates then.
I then asked Tan Sri Dr Jagathesan
since there was a wide avenue of other studies that were open wide to students
other than medicine what then would be the best course to choose to secure a
permanent job?
Tan Sri Dr Jega’s opinion that
biotechnology would be the best even though he is a medical doctor who later specialized
in bacteriology and pathology. As both of them are medical doctors they too
think the same. He told me there are too many biotech companies with too many
vacancies for employment with few graduates in biotech companies.
Then just a few days ago, in an
article on “Endless Possibilities with Science” from a local university
published in the New Straits Times on Friday, 19 April 2024 they wrote about a
3-year degree course in biotechnology, molecular biology that gives ample
opportunities for employment in both government and the private sectors.
I thought about this area of
science since I too have undergone a few months postgraduate training in
biotechnology and its application in medical research when I was working at the
Institute for Medical Research (IMR). That was sometime in the 1980’s as one of
my in-service courses with the Ministry of Health at IMR. It was part of the
ASEAN countries technical collaboration courses conducted for senior medical
researchers and senior medical officers in government service at the IMR.
However, the lecturers who conducted the course came not from ASEAN countries,
but from the UK, France, Switzerland and other European countries.
In that course, I found molecular
biology and molecular medicine entwined with biotechnology, technically quite
challenging to understand initially but interesting, thanks to my already
strong background in biology, chemistry, especially in analytical chemistry,
medicine, microbiology, statistics, food quality control and in evolutionary
biology.
Since I read about the 3-Year BSc
course in biotechnology offered by a local university and my own exposure in
this area, I decided to write an article here on the science of DNA and how
this is applied in a very vast area of sciences for employment for younger
generations.
As this area of science is
immensely huge, I shall briefly run through biotechnology; how various branches
of sciences and medicine are linked directly or indirectly to
biotechnology. In other words, the branches of disciplines of sciences
needed to be read together directly or indirectly with biotechnology.
Biotechnology is a field that
merges biology with technology to create products and processes aimed at
improving various aspects of life, including healthcare, agriculture, industry,
and the environment. It involves the manipulation of living organisms or their
components to develop useful products and applications.
Branches or related disciplines
that are often studied alongside biotechnology include:
- Molecular Biology: Understanding the
fundamental processes of living organisms at the molecular level is
crucial in biotechnology. This includes studying DNA, RNA, proteins, and
their interactions. Molecular biology is a branch of biology that focuses
on the study of biological processes at the molecular level, particularly
the structure and function of biomolecules such as DNA, RNA, and proteins.
It investigates how these molecules interact and regulate cellular
processes such as replication, transcription, translation, and gene
expression. Molecular biology provides the foundation for understanding
the genetic basis of diseases, as well as the development of molecular
techniques and tools used in various fields, including biotechnology,
genetics, and medicine. Molecular biology can exist and progress as a
field on its own without direct reliance on biotechnology. However,
biotechnology frequently utilizes molecular biology techniques and
principles for various applications, such as genetic engineering, gene
editing, and molecular diagnostics.
- Molecular Medicine: Molecular medicine
is a multidisciplinary field that seeks to understand the molecular
mechanisms of diseases and develop targeted therapies based on this
understanding. It applies principles and techniques from molecular
biology, genetics, biochemistry, and other disciplines to diagnose, treat,
and prevent diseases at the molecular level. Molecular medicine and
molecular biology are closely related fields, but they have distinct
focuses and objectives.
The goal of molecular medicine is
to develop personalized and precise treatments that are tailored to individual
patients' genetic makeup and the molecular characteristics of their diseases.
This field encompasses areas such as pharmacogenomics, gene therapy, molecular
diagnostics, and targeted drug delivery.
While molecular medicine
specifically applies molecular biology principles to understand and treat
diseases, molecular biology is a broader field that encompasses the study of
molecular processes in various biological contexts beyond just medical applications.
- Genetics: Knowledge of genetics is essential
for manipulating the genetic material of organisms, such as gene editing
and genetic engineering. Similar to molecular biology, genetics is a
standalone field that doesn't require biotechnology but often collaborates
with it. Biotechnology applications like genetic engineering heavily rely
on genetic principles, but genetics itself encompasses broader studies of
heredity, variation, and gene function.
- Biochemistry: Biochemical processes within
living organisms are central to biotechnology applications. This includes
the study of enzymes, metabolism, and cellular processes. Biochemistry,
the study of chemical processes within and relating to living organisms,
has numerous applications in biotechnology, particularly in understanding
cellular processes and developing biotechnological products. However,
biochemistry is a distinct field that can exist independently.
5. Pharmacology:
Biotechnology has revolutionized the pharmaceutical industry, with applications
ranging from the development of new drugs to personalized medicine. Pharmacology
focuses on the study of drugs and their effects on biological systems. While
biotechnology has revolutionized aspects of pharmacology, particularly in drug
development and personalized medicine, pharmacology as a discipline predates
modern biotechnology and can function independently.
- Microbiology is another field that can
stand on its own but frequently intersects with biotechnology, especially
in areas such as industrial microbiology (e.g., fermentation processes),
environmental microbiology (e.g., bioremediation), and microbial
biotechnology (e.g., production of pharmaceuticals). Microorganisms play a
significant role in biotechnology, whether it's for producing
pharmaceuticals, fermenting food and beverages, or cleaning up
environmental pollutants.
- Bioprocess Engineering: This field focuses
on designing and optimizing processes for the large-scale production of
biotechnological products, such as vaccines, antibiotics, and biofuels. Bioprocess
engineering is a specialized field within chemical engineering that
focuses on designing and optimizing processes for biotechnological
applications. While it heavily relies on biotechnology principles, it is a
distinct discipline within engineering.
- Bioinformatics: With the vast amounts of
biological data generated in biotechnology research, bioinformatics is
crucial for organizing, analysing, and interpreting this data using
computational tools and techniques. Bioinformatics, which
involves the application of computer science and statistical techniques to
biological data, is closely intertwined with biotechnology, particularly
in managing and analysing large datasets generated by biotechnological
experiments. However, bioinformatics can also be applied in fields beyond
biotechnology, such as evolutionary biology and drug discovery.
- Chemical Engineering: Understanding
principles of chemical engineering is vital for scaling up
biotechnological processes from lab-scale to industrial production. Chemical
engineering is a broad discipline that encompasses various industries,
including biotechnology. While biotechnological processes are a
significant part of chemical engineering, the field as a whole is not
exclusively dependent on biotechnology.
- Environmental Science: Biotechnology offers
solutions for environmental problems, such as bioremediation of polluted
sites, wastewater treatment, and sustainable agriculture practices. Environmental
science incorporates knowledge from various disciplines, including
biology, chemistry, and ecology, to understand environmental systems.
Biotechnology plays a role in environmental science through applications
such as bioremediation, but it is not a prerequisite for the field.
- Ethics and Regulation: Given the ethical
considerations and regulatory frameworks surrounding biotechnology,
studying ethics and law related to biotechnology is crucial for
understanding its societal implications and ensuring responsible
innovation.
One thing common when studying
biotechnology is to understand deoxyribonucleic acid (abbreviated DNA), the
molecule that carries genetic information for the development and functioning
of an organism. DNA is used in various applications such as in biotechnology,
molecular medicine, agriculture, research, drug industry, etc. For practical
applications into all the branches of biological sciences mentioned above, we
shall start with DNA extraction, shall we? That would be more practical in this
discussion, an area of study I too underwent when I worked at the Institute for
Medical Research as part of my in-service postdoctoral training. They are
briefly discussed:
The extraction of DNA: The
isolation of DNA from a biological sample is a fundamental step in many
molecular biology techniques, including DNA sequencing. It involves isolating
DNA from cells or tissues while minimizing contamination and degradation.
Here's a general overview of how samples are collected, and DNA extraction
typically done:
- Sample Collection: The first step is to collect the
sample containing the cells or tissues from which DNA will be extracted.
This could be blood, saliva, buccal swabs, tissue biopsies, plant
material, or microbial cultures, depending on the source of DNA needed.
- Cell Lysis: The collected sample is then subjected
to cell lysis, which involves breaking open the cell membranes to release the
cellular contents, including DNA. This can be achieved through mechanical
disruption (e.g., grinding, blending), enzymatic digestion (e.g., using
proteases to degrade proteins), or chemical lysis (e.g., using detergents
to disrupt cell membranes).
- Removal of Proteins and Lipids: Once the cells are
lysed, the mixture typically contains a complex mixture of DNA, proteins,
lipids, and other cellular components. To isolate the DNA, it's necessary
to remove these contaminants. This is often done through proteinase
digestion to degrade proteins and the addition of organic solvents or
detergents to remove lipids.
- DNA Purification: After removing proteins and
lipids, the DNA is typically purified using methods such as precipitation
with alcohol or extraction with organic solvents. These methods separate
DNA from other cellular components based on their solubility properties.
5.
DNA Resuspension: The purified DNA is then resuspended in a suitable buffer or
solvent to stabilize it and make it suitable downstream.
There are also several other
methods used to extract DNA samples from various sources, such as blood,
saliva, tissue, or hair. Here are some common techniques:
1.
Phenol-Chloroform Extraction: This method involves breaking open cells using a
detergent solution, followed by separating DNA from other cellular components
using phenol and chloroform.
2.
Chelex Extraction: Chelex resin binds to metal ions, allowing DNA to be
released from cells when heated. This method is often used for extracting DNA
from blood or saliva samples.
3.
Spin Column Extraction: In this method, DNA binds to a membrane within a spin
column while contaminants are washed away. Finally, the purified DNA is eluted
from the column.
4.
Salting Out: This technique uses a high concentration of salt to precipitate
DNA from a solution. The DNA can then be collected by centrifugation.
5.
Silica-Based Extraction: Silica can bind DNA in the presence of certain
solutions. DNA is then washed and eluted from the silica, resulting in purified
DNA.
6.
Magnetic Bead Extraction: Magnetic beads coated with molecules that bind DNA
are used to isolate DNA from a sample. The beads are then separated from the
solution using a magnet, and the DNA is eluted.
7.
Organic Extraction: Organic solvents such as ethanol or isopropanol, are used
to precipitate DNA from a solution. The DNA can then be collected by
centrifugation.
Each method has its advantages and
is suited to different sample types and downstream applications. The choice of
extraction method depends on factors such as the sample type, the amount of DNA
required, and the downstream applications.
I remember the term “Southern blot
technique” when I was doing my postgraduate training in biotechnology at the
Institute for Medical Research where I was working.
The Southern blot is a laboratory
technique used to detect specific DNA sequences in a sample of DNA. It involves
several steps:
DNA Digestion: The DNA sample is
cut into smaller fragments using restriction enzymes.
Gel Electrophoresis: The fragmented
DNA is then separated based on size using gel electrophoresis. The DNA
fragments are loaded into wells in an agarose gel and subjected to an electric
field, causing them to migrate through the gel.
Denaturation and Transfer: The DNA
fragments are denatured (separated into single strands) and then transferred
from the gel onto a membrane, typically made of nitrocellulose or nylon.
Hybridization:
The membrane-bound DNA is then
exposed to a labelled DNA probe, which is a single-stranded DNA molecule
complementary to the sequence of interest. The probe hybridizes (binds) to its
complementary sequence on the membrane.
Detection:
The location of the probe-bound DNA
is visualized using autoradiography or other detection methods, depending on
the labelling of the probe.
The Southern blot technique is
named after its inventor, Edwin Southern, and it's commonly used in molecular
biology laboratories for various applications such as identifying specific
genes, detecting gene rearrangements, and analysing DNA methylation patterns.
It used to be a time when the
extraction and analysis of DNA was very time consuming. I remember it took us
two days using an ultra-centrifuge overnight to spin down a half-done blood or
tissue sample. Even for ordinary chemical analysis which I did for my MSc
degree in food analysis and food quality control, we use only an ordinary
centrifuge to spin down the precipitate for only 10 -15 minutes in an
analytical sample.
However, the time required for DNA
extraction and centrifuging can vary depending on factors such as the type of
sample, the extraction method used, and the level of purification required.
Often a very high-speed ultracentrifuge is used. In some cases, DNA extraction
can be completed in as little as 30 minutes, while more complex samples or
extraction methods may take several hours or even days to complete.
A simple DNA extraction from
bacterial cultures using a commercial DNA extraction kit might take around 30
minutes to an hour, while extracting DNA from a tissue biopsy using traditional
phenol-chloroform extraction methods might take several hours due to additional
steps and purification procedures involved. Additionally, high-throughput
automated DNA extraction systems can process multiple samples simultaneously,
reducing the overall extraction time for large-scale projects.
Amplification:
The next step once the DNA is
extracted is amplification. But what is amplification of DNA, how is this done
and its purpose?
DNA amplification is a technique
used to make multiple copies of a specific segment of DNA. This process is
essential for various applications in molecular biology, genetics, forensics,
medical diagnostics, and biotechnology. The most common method for DNA
amplification is the polymerase chain reaction (PCR).
Here's how PCR works:
- Denaturation: The DNA sample containing the target
sequence is heated to around 95°C to break the hydrogen bonds between the
two strands, resulting in the separation of the double-stranded DNA into
two single strands.
- Annealing: The sample is cooled to a lower
temperature, typically around 50-65°C, allowing primers (short DNA
sequences complementary to regions flanking the target sequence) to bind
to the single-stranded DNA template.
- Extension: The temperature is raised to around
72°C, the optimal temperature for DNA polymerase activity. DNA polymerase
enzyme synthesizes new DNA strands by adding nucleotides complementary to
the template strand, starting from the primers. This process extends the
primers, creating copies of the target sequence.
These three steps constitute one
cycle of PCR. The cycle is then repeated multiple times (usually 20-40 cycles),
resulting in exponential amplification of the target DNA sequence. After each
cycle, the number of DNA copies approximately doubles, leading to millions or
even billions of copies of the target sequence within a relatively short
period.
Amplification in the context of DNA
sequencing refers to the process of making multiple copies of a specific DNA
fragment. This is typically done using a technique called polymerase chain
reaction (PCR), which is widely used in molecular biology and genetics. In PCR,
a DNA template is repeatedly heated and cooled in the presence of DNA
polymerase enzymes and specific primers, which are short DNA sequences that
flank the target region to be amplified. Each cycle of heating and cooling
doubles the number of DNA molecules, resulting in exponential amplification of
the target sequence. Amplification is crucial in DNA sequencing because it
generates sufficient quantities of DNA for analysis, especially when starting
with limited or degraded samples.
DNA Sequencing:
Our next step in DNA analysis
is sequencing. A lot of lay people have heard of DNA sequencing. But what is
meant by sequencing? How is it done and for what purpose is sequencing?
DNA sequencing is the process of
determining the exact order of nucleotides (adenine, guanine, cytosine, and
thymine) within a DNA molecule. The sequence of these nucleotides forms the
genetic code that dictates the structure and function of an organism. DNA
sequencing is done using various methods, each with its own speed and accuracy.
Massively parallel high-throughput
long or short-read DNA sequencing and computing:
Massively parallel
high-throughput DNA sequencing refers to modern sequencing technologies that
allow for the simultaneous sequencing of millions of DNA fragments in a single
experiment. This is in contrast to earlier sequencing methods, such as Sanger
sequencing, which sequenced one DNA fragment at a time. High-throughput
sequencing techniques enable researchers to sequence entire genomes,
transcriptomes, or metagenomes rapidly and cost-effectively.
There are two main approaches to
high-throughput DNA sequencing:
- Short-read sequencing: Also known as
next-generation sequencing (NGS), short-read sequencing platforms generate
short DNA fragments (usually 100-300 base pairs) and sequence them in
parallel. Examples of short-read sequencing platforms include Illumina sequencing
and Ion Torrent sequencing. Short-read sequencing is well-suited for
applications such as whole-genome sequencing, exome sequencing, RNA
sequencing (RNA-Seq), and ChIP sequencing (ChIP-Seq).
- Long-read sequencing: Long-read sequencing
technologies produce much longer DNA reads (thousands to tens of thousands
of base pairs) compared to short-read sequencing. This allows for the
sequencing of complex genomic regions, such as repetitive sequences,
structural variants, and full-length transcripts, which are often
difficult to resolve with short-read sequencing. Examples of long-read
sequencing platforms include Pacific Biosciences (PacBio) sequencing and
Oxford Nanopore sequencing.
Massively parallel high-throughput
sequencing generates vast amounts of sequencing data, which must be processed
and analysed using computational methods. This involves tasks such as base
calling (converting raw signal data to DNA sequences), read alignment (mapping
DNA reads to a reference genome or transcriptome), variant calling (identifying
genetic variations), and downstream analysis (e.g., gene expression analysis,
pathway analysis). High-performance computing systems and bioinformatics
algorithms are essential for handling and analysing the large volumes of
sequencing data generated by high-throughput sequencing platforms.
Here are some commonly used methods
and their approximate speeds:
Sanger Sequencing:
This method involves
chain-termination sequencing using dideoxy nucleotides (ddNTPs). It's
considered the traditional method. It typically takes hours to days to sequence
a single DNA fragment. We shall discuss the Sanger sequencing process and its
purposes shortly.
Next-Generation Sequencing
(NGS):
Illumina Sequencing: Utilizes
reversible terminators and fluorescently labelled nucleotides. It can sequence
millions to billions of DNA fragments simultaneously. Depending on the platform
and the length of the reads, sequencing can take from a few hours to several
days.
Ion Torrent Sequencing:
Measures pH changes as nucleotides
are incorporated. It can produce results in a matter of hours, depending on the
sequencing depth.
454 Pyrosequencing: Measures the
release of pyrophosphate upon nucleotide incorporation. It's faster than Sanger
sequencing but slower than Illumina. It typically takes hours to days for
sequencing.
Single-Molecule Sequencing:
Pacific Biosciences (PacBio):
Utilizes zero-mode waveguides to observe DNA polymerase activity in real-time.
It can produce long reads but is slower compared to Illumina. Sequencing
typically takes several hours to days.
Nanopore Sequencing:
Passes DNA through a protein
nanopore, measuring changes in electrical current as individual bases pass
through. It's relatively fast and can provide real-time sequencing results in
minutes to hours.
The speed of DNA sequencing depends
on factors such as the method used, the length of the DNA fragments being
sequenced, the depth of coverage required, and the specific equipment and
protocols being used. Advances in technology continue to improve the speed and
efficiency of DNA sequencing methods.
There are several methods for DNA
sequencing, but the most commonly used technique is called Sanger sequencing,
developed by Frederick Sanger in the 1970s.
Here is a simplified explanation of
the Sanger sequencing process and its applications:
- DNA Extraction: First, DNA is extracted from the
cells of interest, whether they be from a human, animal, plant, or
microorganism.
- DNA Amplification: Since the amount of DNA obtained
from extraction may be minuscule, it needs to be amplified through a
process called polymerase chain reaction (PCR). PCR uses special enzymes
to make multiple copies of the DNA segment of interest. The purpose of DNA
amplification is manifold:
- Research: PCR allows researchers to study specific
genes or DNA sequences of interest, enabling various genetic and molecular
studies.
- Diagnosis: PCR is widely used in clinical
diagnostics to detect the presence of pathogens (such as viruses and
bacteria), genetic disorders, and cancer biomarkers.
- Forensics: PCR is utilized in forensic science to
amplify small amounts of DNA found at crime scenes, enabling DNA profiling
and identification of suspects.
- Genetic Engineering: PCR is a crucial tool in
genetic engineering techniques like gene cloning, site-directed
mutagenesis, and DNA sequencing.
- Biotechnology: PCR plays a vital role in
biotechnological applications such as DNA sequencing, gene expression
analysis, and recombinant DNA technology.
- Overall, DNA amplification techniques like PCR have
revolutionized biological and medical research, providing powerful tools
for studying and manipulating DNA.
- Preparation of DNA Fragments: The amplified DNA is
then fragmented into smaller pieces.
- DNA Sequencing Reaction: Each fragment is mixed
with a primer, DNA polymerase, and a mixture of nucleotides, including
some special nucleotides called dideoxynucleosides (ddNTPs), which
terminate DNA synthesis when incorporated into the growing DNA strand.
- Separation of DNA Fragments: The DNA fragments are
then separated based on their size using a technique called gel
electrophoresis. An electric field is applied to the gel, causing the DNA
fragments to migrate through it. Shorter fragments move faster than longer
ones.
- Detection: As the DNA fragments migrate through the
gel, they pass by a detector that records the fluorescent signal emitted
by each nucleotide as it is incorporated into the growing DNA strand.
- Data Analysis: The fluorescent signals are then
analysed to determine the sequence of nucleotides in each DNA fragment.
The purpose of DNA sequencing is
manifold:
- Genetic Research: DNA sequencing is fundamental to
understanding the genetic basis of diseases, traits, and evolutionary
relationships. It helps researchers identify genetic variations associated
with diseases, study gene expression patterns, and trace the evolutionary
history of species.
- Medical Diagnosis and Treatment: DNA sequencing is
increasingly used in clinical settings to diagnose genetic disorders,
predict disease risk, and tailor treatments to individual patients based
on their genetic makeup (known as precision medicine).
- Drug Development: Understanding the genetic basis
of diseases enables the development of targeted therapies and drugs. DNA
sequencing is used to identify drug targets, study drug efficacy, and
predict patient responses to treatment.
- Agriculture and Biotechnology: DNA sequencing is
used in agriculture to breed crops with desirable traits, improve
livestock health and productivity, and develop genetically modified
organisms (GMOs) with enhanced characteristics such as pest resistance or
higher nutrient content.
- Forensic Analysis: DNA sequencing is employed in
forensic science to identify individuals, establish familial
relationships, and solve crimes by analysing DNA evidence left at crime
scenes.
Overall, DNA sequencing has
revolutionized biological and medical research, leading to profound
advancements in our understanding of genetics and its applications across
various fields.
Bioinformatics:
Bioinformatics is an
interdisciplinary field that combines biology, computer science, mathematics,
and statistics to analyse and interpret biological data, particularly large
datasets generated by modern molecular biology techniques. At its core, bioinformatics
aims to develop computational methods and tools to understand biological
processes at the molecular level, especially focusing on DNA, RNA, and protein
sequences, structures, and functions.
In the context of molecular biology
and DNA, bioinformatics plays a crucial role in analysing DNA sequences,
identifying genes, understanding genetic variation (including mutations),
predicting protein structures and functions, and studying the interactions
between biomolecules. By applying computational algorithms and techniques,
bioinformatics enables researchers to extract meaningful information from vast
amounts of genomic and proteomic data.
Some applications of bioinformatics
include:
- Genome Sequencing and Annotation: Bioinformatics
tools are used to assemble, annotate, and analyse genomes, providing
insights into the organization and function of genes within an organism's
DNA.
- Functional Genomics: Bioinformatics methods help
researchers understand how genes interact with each other and with
environmental factors to regulate biological processes.
- Comparative Genomics: By comparing DNA sequences
across different species, bioinformatics can reveal evolutionary
relationships, identify conserved regions, and uncover genetic
adaptations.
- Structural Biology: Bioinformatics tools are used
to predict and analyse the three-dimensional structures of proteins and
nucleic acids, providing insights into their functions and interactions.
- Phylogenetics: Bioinformatics methods are employed
to reconstruct evolutionary trees, elucidating the relationships between
different species based on their genetic similarities and differences.
Bioinformatics is closely related
to computer science because it relies heavily on computational techniques,
algorithms, and software tools to process, analyse, and visualize biological
data. Computer science provides the foundation for developing efficient
algorithms for sequence alignment, database management, data mining, machine
learning, and other computational tasks essential to bioinformatics research.
Additionally, advances in computer hardware and software have significantly
accelerated the analysis of biological data, enabling researchers to tackle
complex biological questions on a scale that was not feasible before.
Mutation:
Having explained all the above,
sometimes a pathogenic organism mutates. What exactly is mutation that most
people hear about during the Covid-19 pandemic but could not quite
understand. They spoke about the coronavirus or other pathogenic organisms
mutating to defy treatment due to drug resistance or a vaccine, but they have
only some vague ideas. What then is mutation, and what causes it? Once a
virus or a pathogenic bacterium mutates into another form, we need to sequence
the mutated variant or even a new strain all over again.
Mutation is a fundamental process
in genetics whereby there is a change in the DNA sequence. This change can
involve alterations to individual nucleotides (the building blocks of DNA),
such as substitutions, insertions, or deletions, as well as larger rearrangements
of DNA segments. Mutation involves alterations to the sequence of nucleotides
in the DNA chain. This can occur through various mechanisms, including errors
during DNA replication, exposure to certain chemicals or radiation, or through
genetic recombination. The result is a modification in the genetic code, which
can lead to different traits or characteristics in organisms.
DNA analysis applied in
medicine:
DNA analysis plays a crucial
role in various aspects of medicine, contributing to diagnosis, treatment, and
prevention of diseases. Here are several key applications:
- Genetic Testing: DNA analysis is used to identify
genetic variations associated with inherited diseases, susceptibility to
certain conditions, and drug responses. This information helps in
diagnosing genetic disorders, predicting disease risk, and personalizing
treatment plans.
- Diagnostic Testing: DNA analysis is employed to
detect pathogens directly from patient samples, aiding in the diagnosis of
infectious diseases. Techniques such as PCR (Polymerase Chain Reaction)
and DNA sequencing are used to identify bacteria, viruses, and parasites.
- Cancer Diagnosis and Prognosis: DNA analysis is
used to identify genetic mutations associated with cancer. Techniques like
next-generation sequencing (NGS) are used to analyse tumour DNA for
mutations that can guide treatment decisions and predict prognosis.
- Pharmacogenomics: DNA analysis helps in
understanding how genetic variations affect an individual's response to
medications. Pharmacogenomic testing can identify genetic factors
influencing drug metabolism, efficacy, and adverse reactions, enabling
personalized medication selection and dosing.
- Prenatal Screening and Diagnosis: DNA analysis is
used for prenatal screening and diagnosis of genetic disorders in
foetuses. Techniques like amniocentesis and chorionic villus sampling
(CVS) analyse foetal DNA obtained from amniotic fluid or placental tissue
to assess genetic abnormalities.
- Forensic Medicine: DNA analysis is employed in
forensic investigations to identify individuals, establish biological
relationships, and solve crimes. DNA profiling techniques, such as short
tandem repeat (STR) analysis, are used to compare DNA samples obtained
from crime scenes to those of suspects or victims.
- Infectious Disease Outbreak Tracking: DNA analysis
helps in tracking the spread of infectious diseases and identifying the
source of outbreaks. By sequencing the genomes of pathogens, researchers
can trace transmission patterns and develop strategies for containment and
control.
- Gene Therapy: DNA analysis contributes to the
development and optimization of gene therapy approaches for treating
genetic disorders. By understanding the genetic basis of diseases,
researchers can design targeted gene therapies to correct or modulate disease-causing
genetic mutations.
These are just a few examples of
how DNA analysis is applied in medicine. As technology advances and our
understanding of genetics deepens, DNA analysis continues to play an
increasingly important role in various aspects of healthcare.
How is DNA analysis applied in
forensic science?
This is another area I am familiar
with, having completed a postdoctoral course in Forensic Science from the
University of Cambridge just before the Covid-19 outbreak in January 2020.
Very briefly explained, DNA
analysis is a fundamental tool in forensic science, playing a critical role in
criminal investigations, identification of human remains, and establishing
biological relationships. Here's how DNA analysis is applied in forensic
science:
- Crime Scene Investigations: DNA analysis is used to
identify and analyse biological evidence left at crime scenes, such as
bloodstains, saliva, semen, and hair follicles. Forensic scientists
collect these samples and extract DNA to create DNA profiles of potential
suspects or victims.
- DNA Profiling: Forensic DNA analysis involves
creating DNA profiles, which are unique genetic fingerprints of
individuals. Techniques such as short tandem repeat (STR) analysis are
commonly used to analyse specific regions of the DNA that vary between individuals.
By comparing DNA profiles obtained from crime scene evidence to profiles
in DNA databases or suspects, forensic scientists can link individuals to
crimes or exclude suspects.
- Cold Case Investigations: DNA analysis is
instrumental in re-examining cold cases where DNA evidence was collected
but remained unsolved. Advances in DNA analysis techniques, such as
improved sensitivity and the ability to analyse degraded samples, allow
forensic scientists to revisit old evidence and potentially identify
perpetrators.
- Identification of Human Remains: DNA analysis is
used to identify human remains in cases of mass disasters, natural
disasters, or criminal acts. By comparing DNA samples from the remains to
reference samples from relatives or missing persons, forensic scientists
can establish positive identifications.
- Establishing Biological Relationships: DNA analysis
helps establish biological relationships in cases involving paternity
disputes, child custody, immigration, and familial searches. By comparing
the DNA profiles of individuals, forensic scientists can determine
familial relationships with a high degree of accuracy.
- Exoneration of Wrongfully Convicted Individuals:
DNA analysis has been instrumental in exonerating individuals who have
been wrongfully convicted of crimes. DNA testing of biological evidence,
often stored for years, can provide conclusive evidence of innocence and
lead to the release of innocent individuals.
- Crime Scene Reconstruction: DNA analysis, combined
with other forensic evidence, such as fingerprints, bloodstains, and
ballistics, helps reconstruct the sequence of events at crime scenes. This
information assists investigators in understanding how a crime occurred
and identifying suspects.
- Wildlife Forensics: DNA analysis is also applied in
wildlife forensic investigations to identify species, individual animals,
and trace the origins of illegal wildlife products, such as ivory, fur, or
exotic meats.
In forensic science and in crime
investigation entomology is also involved.
Entomology, the study of insects,
plays a crucial role in crime investigation, particularly in estimating the
postmortem interval (PMI) and assisting in the determination of various aspects
of a crime scene. Here's how entomology aids in crime investigation:
- Postmortem Interval Estimation: Insect colonization
patterns on a corpse can provide valuable information about the time since
death. Forensic entomologists study the succession of insects that
colonize a body after death, as well as their developmental stages, to
estimate the postmortem interval. Different insect species have distinct
life cycles and behaviours, allowing entomologists to correlate the
presence of certain insects with specific stages of decomposition and
thereby estimate how long the body has been deceased.
- Location of Death: Insect evidence collected from a
crime scene can help determine where the death occurred. By analysing the
types of insects found on a body or at a crime scene and comparing them to
local insect populations, entomologists can infer whether the body was
moved after death or if certain activities took place in specific
locations.
- Movement of the Body: Insect activity can also
indicate postmortem movement of a body. For example, if insects associated
with a particular habitat are found on a body in a different location, it
may suggest that the body was transported there after death.
- Toxicological Analysis: Some insects, particularly
blowflies, can accumulate toxins or drugs from decomposing tissues.
Analysing the chemical composition of insect larvae or pupae found on a
body can provide valuable information about any substances present in the
body at the time of death.
- Entomological Evidence: Insect evidence can serve
as valuable physical evidence in criminal investigations. Insect remains,
such as eggs, larvae, or pupae, found on a body or at a crime scene can be
collected and analysed for species identification and developmental stage.
This evidence can corroborate other findings and help establish the
circumstances surrounding a crime.
- Environmental Conditions: Insect activity is
influenced by environmental factors such as temperature, humidity, and
weather conditions. By considering these factors along with insect
evidence, entomologists can refine their estimations of the postmortem interval
and provide more accurate assessments of the circumstances surrounding a
death.
Overall, entomological evidence
provides valuable insights into the timeline, location, and conditions
surrounding a death, contributing to the investigation and resolution of
criminal cases. Overall, DNA analysis is a powerful tool in forensic science, providing
valuable evidence for criminal investigations, victim identification, and
justice system integrity.
Molecular Biology:
What about molecular biology? What
does it entail in the study of molecular biology and the scope of the study in
medicine or other areas of sciences? Molecular biology is a branch of biology
that focuses on the study of biological processes at the molecular level,
particularly the interactions between various systems of a cell, including the
interactions between DNA, RNA, proteins, and their biosynthesis. It encompasses
a wide range of topics such as the structure and function of biomolecules,
genetic regulation, gene expression, DNA replication, and the molecular basis
of diseases.
In the study of molecular biology,
researchers use techniques and methodologies from various disciplines such as
genetics, biochemistry, and biophysics to investigate how biological molecules
interact and contribute to the functioning of cells and organisms. This may
involve experiments conducted in vitro (in a laboratory setting) or in vivo
(within living organisms).
The scope of molecular biology in
medicine is vast and crucial. It underpins our understanding of various
diseases at the molecular level, including cancer, genetic disorders,
infectious diseases, and neurodegenerative diseases. By elucidating the molecular
mechanisms underlying these conditions, molecular biologists can develop novel
diagnostic tools, therapeutic interventions, and personalized medicine
approaches.
Furthermore, molecular biology has
applications beyond medicine, extending into various areas of science and
technology. For example, in agriculture, molecular biology techniques are used
to improve crop yield, develop genetically modified organisms (GMOs), and
enhance pest resistance. In environmental science, molecular biology helps in
understanding microbial communities, bioremediation processes, and monitoring
ecosystem health. Additionally, molecular biology plays a crucial role in
biotechnology, pharmaceuticals, and forensic science, among other fields,
driving innovation and advancements in these areas.
Damage to DNA:
However, whether biotechnology is
applied in medicine or in forensic science, DNA can be damaged by boiling or
prolonged exposure to high temperatures. It can also be damaged by
boiling, heating left over a very long period DNA is a delicate molecule that
can be denatured or degraded by heat. When DNA is heated, the hydrogen bonds
holding the double helix structure together can break, causing the DNA strands
to separate (denature). Additionally, prolonged exposure to heat can lead to
chemical changes in the DNA molecule, such as hydrolysis of the phosphodiester
bonds that link the nucleotides together.
However, the extent of damage
depends on factors such as the temperature, duration of exposure, and the
presence of stabilizing agents. For example, while boiling DNA in water can
cause extensive damage, DNA in some organisms, like certain thermophilic bacteria,
is naturally resistant to high temperatures.
In laboratory settings, DNA samples
are typically handled with care to minimize damage. Heat can be used
intentionally to denature DNA for certain applications, such as PCR (Polymerase
Chain Reaction), where the DNA strands need to be separated to initiate
replication. However, for most applications, including DNA extraction and
storage, it's important to avoid excessive heating to preserve the integrity of
the DNA molecule.
Employment Opportunities:
A graduate student studying
biotechnology has a wide range of employment opportunities across various
sectors, including academia, industry, government, and healthcare. Here are
some potential career paths for graduates with expertise in DNA biotechnology:
- Research Scientist: Many graduates find employment
as research scientists in academic institutions, research laboratories,
biotechnology companies, or government agencies. They may conduct basic or
applied research in areas such as genetics, genomics, molecular biology,
bioinformatics, or drug development.
- Biotechnology Industry: The biotechnology industry
offers numerous career opportunities for graduates with expertise in DNA
biotechnology. They may work in pharmaceutical companies, biotech
startups, or companies specializing in DNA sequencing, diagnostics,
genetic engineering, or personalized medicine.
- Clinical Laboratory Scientist: Graduates with a
background in DNA biotechnology can pursue careers as clinical laboratory
scientists or clinical geneticists in hospitals, diagnostic laboratories,
or healthcare organizations. They may perform genetic testing, analyse DNA
samples for diagnostic purposes, or provide genetic counselling to
patients.
- Bioinformatics Specialist: With the increasing
reliance on computational analysis in genomics and molecular biology,
there is a growing demand for bioinformatics specialists who can analyse
and interpret large-scale DNA sequencing data. Graduates with expertise in
both DNA biotechnology and bioinformatics may find employment in academia,
research institutions, pharmaceutical companies, or biotech startups.
- Quality Control/Assurance Specialist: In industries
involved in DNA sequencing, diagnostics, or biopharmaceuticals, graduates
can work as quality control or quality assurance specialists to ensure
that products meet regulatory standards and quality requirements. They may
perform quality control testing, develop quality assurance protocols, or
conduct regulatory compliance audits.
- Product Development Specialist: Graduates can work
in product development roles in biotechnology companies, where they may be
involved in developing new DNA sequencing technologies, diagnostic assays,
genetic tests, or biopharmaceutical products. They may contribute to
product design, optimization, validation, and commercialization processes.
Science Communication/Outreach:
Some graduates may choose to pursue careers in science communication,
education, or outreach, where they can use their expertise in DNA biotechnology
to engage with the public, communicate scientific concepts, and promote scientific
literacy. They may work as science writers, educators, science journalists, or
outreach coordinators in museums, science centres, nonprofit organizations, or
media outlets.
Overall, the employment prospects
for graduate students studying DNA biotechnology are diverse and promising,
with opportunities for career advancement and specialization in various fields
related to genetics, genomics, and in molecular biology.
This greatly contrasts to solely
studying medicine. A medical doctor is not trained or qualified to do any
other job other than to treat the sick. He cannot even go into medical research
unless he has a higher scientific degree such as a Master of Science, or a
Doctorate degree (PhD) as he needs to publish papers in scientific journals
which is highly challenging, and this is really tough.
These are just a few examples of
disciplines that intersect with biotechnology. Depending on specific
applications or areas of interest within biotechnology, other fields like
immunology, nanotechnology, and ecology may also be relevant.
Biotechnology often intersects with
and draws upon various branches of science, although not all of these branches
require biotechnology to function or progress independently.
So, while biotechnology interfaces
with and benefits from these branches of science, they are not inherently
reliant on biotechnology for their existence or advancement.
However, we shall not discuss this
article any further as they are such a vast area of sciences.
(A 7,208 worded essay in 33 pages)
