Applications of Biotechnology in Sciences and Medicine

 

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:

1. 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.
2. 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.

3. 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.
4. 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.

6. 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.
7. 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.
8. 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.
9. 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.
10. 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.
11. 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:

1. 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.
2. 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).
3. 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.
4. 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:

1. 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.
2. 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.
3. 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:

1. 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).
2. 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:

1. DNA Extraction: First, DNA is extracted from the cells of interest, whether they be from a human, animal, plant, or microorganism.
2. 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:
3. Research: PCR allows researchers to study specific genes or DNA sequences of interest, enabling various genetic and molecular studies.
4. Diagnosis: PCR is widely used in clinical diagnostics to detect the presence of pathogens (such as viruses and bacteria), genetic disorders, and cancer biomarkers.
5. Forensics: PCR is utilized in forensic science to amplify small amounts of DNA found at crime scenes, enabling DNA profiling and identification of suspects.
6. Genetic Engineering: PCR is a crucial tool in genetic engineering techniques like gene cloning, site-directed mutagenesis, and DNA sequencing.
7. Biotechnology: PCR plays a vital role in biotechnological applications such as DNA sequencing, gene expression analysis, and recombinant DNA technology.
8. Overall, DNA amplification techniques like PCR have revolutionized biological and medical research, providing powerful tools for studying and manipulating DNA.
9. Preparation of DNA Fragments: The amplified DNA is then fragmented into smaller pieces.
10. 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.
11. 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.
12. 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.
13. 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:

1. 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.
2. 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).
3. 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.
4. 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.
5. 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:

1. 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.
2. Functional Genomics: Bioinformatics methods help researchers understand how genes interact with each other and with environmental factors to regulate biological processes.
3. Comparative Genomics: By comparing DNA sequences across different species, bioinformatics can reveal evolutionary relationships, identify conserved regions, and uncover genetic adaptations.
4. 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.
5. 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:

1. 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.
2. 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.
3. 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.
4. 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.
5. 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.
6. 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.
7. 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.
8. 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:

1. 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.
2. 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.
3. 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.
4. 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.
5. 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.
6. 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.
7. 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.
8. 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:

1. 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.
2. 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.
3. 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.
4. 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.
5. 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.
6. 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:

1. 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.
2. 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.
3. 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.
4. 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.
5. 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.
6. 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.

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