CHAPTER ONE

1.0 EXECUTIVE SUMMARY

Student Industrial Work Experience Scheme (SIWES) commenced March 15
2021 and ended August 15 2021 at Molecular and Simulation center, Abaiyamedi
Off Ilawe Road Ado Ekiti State
To achieve the aim in which the program (SIWES) was designed, at MOLS
AND SIMS, I discovered a lot about Computational and Molecular experiments
and research. This report comprises of what I learnt at MOLS AND SIMS,
practical challenges faced and theoretical principles learnt during the six month
SIWES program.
Bioinformatics tools and software play a great role in the drug discovery and
drug development, technologies like molecular docking results in faster and easier
drug discovery process. The nature and activities of Genes are studied at the
Molecular level as well as the effect of various foreign substances such as drugs.
The aim is to find a cure to life threatening diseases especially those that are
common in Africa. The Centre’s mandate is drawn out of two key historical events;
first, the rapid expansion of knowledge space in clinical diseases especially within
Africa and second, the robust application of computational techniques in medicine.

1.1 INTRODUCTION
The students Industrial Work Experience scheme (SIWES) was designed and
jointly put in place by the Federal government, Industrial training Fund (ITF),
tertiary institutions and other agencies like National University Commission
(NUC), National Polytechnic council for college of education.
It is a program established in the year 1973 under the National Development
Plan Decree 47, as provided and maintained the decree under the umbrella of
Industrial Training Fund with the main aim of preparing and helping students of
tertiary institution to obtain exposure on practical fields with respect to their
profession. Through this exposure, students are expected to have better
understanding of their profession and develop practical skill in addition to their
theoretical skills which they got from there institution.
Oyedele, (1990) states that work experience is an educational program in
which students participate in work activities while attending school. It is a
compulsory six (6) months practical training that students must undertake as part
of the requirement for the award of Bachelor of Science (B.Sc.) Degree in
Biochemistry at Adekunle Ajasin University, Akungba-Akoko, Ondo State. Since
no study is complete without the practical experiences, the interaction of practical
knowledge with the theoretical bases is necessary. Parties involved in the
completion of the program includes: Tertiary Institution, Employers, Students and
National Universities Commission.
This very report is a progressive report of my six-month industrial training at
Molecular And Simulation Center, Abaiyamedi Ado Ekiti State.

1.2 Objective of SIWES.

There are various positive reasons why the Student Industrial Work Experience
Scheme was funded; some of the reasons are listed below.
• To provide an avenue/medium in Nigerian Universities for students to
acquire industrial skills and practical experience in their course of study.

• To build a relationship between the institution and the organization or

industry where students are attached.
• To enlist and strengthen employer involvement in the entire educational
process of preparing University and other tertiary institution undergraduates
for employments in industries.

• To expose students to work methods and technique in handling equipments

that may not be available in Universities.
• To give organizations, industries and establishments a chance to impact
students.
• To provide opportunity for students to apply their knowledge in real work
situations.
• To create an avenue for students to know the specific area they will focus on
in their field of study.

1.3 Objective of Report

The general objective of the report is to relate the major skills and experience
acquired at Molecular and Simulation Center during my Six (6) month
industrial training.

However, the specific objectives are:

• To show the history and other important information about my place of

industrial attachment.
• To give a detailed description of work done.
• To show some skills developed and techniques learnt.
• To discuss some practical challenges faced at work.
• To show some theoretical principles learnt during the programme.
• To write the specific contributions I made to the company.
• To discuss the future of the business within the Nigeria economy.
• To discuss relevance of industrial training exercise to my course of study.
 CHAPTER TWO
NATURE OF BUSINESS/LITERATURE REVIEW OF INDUSTRY
2.0 History of Company
The Molecular And Similation Center (MOLS AND SIMS) Ado Ekiti State,
Nigeria, was esthablished in the year 2018. It was established to conduct research,
gather data, and disseminate technological information on matters relating to drug
development, using cutting-edge scientific methods.
The Centre’s mandate is drawn out of two key historil events; first, the rapid
expansion of knowledge space in clinical diseases especially within Africa and
second, the robust application of computational techniques in medicine. MOLS
AND SIMS therefore leverages on computational techniques to research clinical
ailments common in Africa.
For efficiency, MOLS AND SIMS is divided into five semi-autonomous Units;
• Software research and Development Unit

• Molecular Simulation and Drug Design Unit

• Natural Product Innovation Unit

• Patent application and Entrepreneurial Unit

• Drug Testing Unit

 Software research and Development Unit is developing several in-house
software for computational Biology, Molecular Simulation and Drug Design Unit
is using the software for drug development, Natural Product Innovation Unit is
developing a repository of African plants with therapeutic potentials and
identifying their active components and cognate cellular targets in diseases, Drug
Testing Unit develops disease models for testing our synthetic drug candidates or
natural products for clinical efficacies and safety; while our Patent application and
Entrepreneurial Unit is involved in technology transfer and manpower training.

2.1 VISION AND MISSION STATEMENT

2.1.1 VISION
A Centre committed to the conservation of the rich Genetic Resources of the
nation, with a view to enhancing drug design, research and medicine.
2.1.2 MISSION
Molecular and Simulation center mission is to rapidly expand the knowledge space
in clinical diseases especially within Africa, and also to apply computational
techniques in medicine.
2.2 Management Structure
The Molecular and Similation Center is divided into the following basic
departments and sections.
1. Molecular biology section
2. Bioinformatics section
3. Animal testing section
Molecular biology: This is the study of gene structure and functions at the
molecular level to understand the molecular basis of hereditary, genetic variation
and the expression patterns of genes. It studies the flow of information from DNA
to RNA to protein.
Bioinformatics: This is the application of computer technology to the
management of biological information. It is an interdisciplinary research field that
combines biology, computer science and statistics into a broad based field that
impacts biology, biochemistry etc.
Animal testing: This is a unit that deals with the caring, grouping and feeding of
experimental animals such as rat, mice, etc. for laboratory work.
Figure 1: Organogram of the Centre for Bio-computing and Drug
Development
2.3 Organizational Structure.

Senior Researcher
Research Assistant
Staffs
Trainees

2.4 Market/ Service Situation of CBDD

The Centre, MOLS AND SIMS, has been mandated to perform the following
functions:
• Exploration, collection, identification, storage and conservation of gene
expression in plants, animals and microbes.
• Acquisition, maintenance, utilization, exchange and dissemination of
information on genetic materials of plants, animals and microbes.
• National coordination of genetic resource programme and sustainable
utilization.
• Fostering relationship with other national satellite genetic research centers
located in other universities, research institutes, polytechnics as well as other
international organization and centers on programmes concerning genetic
research and biotechnology application.

2.5 Economic Environment in Which MOLS AND SIMS Operates

 It is an established fact that the success and sustainability of any business
depends on the economic environment in which it operates. If an organization
functions and performs well, the economic environment has greatly influenced it.
To execute the mandate effectively and ensure proper running of activities within
the organization, MOLS AND SIMS collaborates with indigenous and international
research institutes, universities and biotechnological companies abroad (Inqaba
Biotech). Considering the location of MOLS AND SIMS, it is one of the very few
research institutes in the area.

CHAPTER THREE

3.0 Bioinformatics

Bioinformatics is an interdisciplinary field that develops methods and

software tool for understanding biological data. As an interdisciplinary field of
science, bioinformatics combines computer science, Biology, Mathematics and
engineering to analyze and interpret biological data.
Bioinformatics is a tool for providing insight into the structures of molecular
biology-that part of biology that studies the properties of DNA, RNA and proteins.
In particular, bioinformatics deals with the task of understanding information
chemically encoded into life that controls the structural processes ongoing in all
living organisms. Bioinformatics is usually concerned with applying statistical and
computational methods to analysis of data determined from sequenced DNA and/or
RNA or the simulation of protein-protein interactions and how this can help us
understand the evolution of proteins and their connections with similar proteins in
other organisms.(Santos et al 2003)
Bioinformatics tools aid in the comparison of genetic and genomic data and
more generally in the understanding of evolutionary aspects of molecular biology.
At a more integrative level, it helps analyze and catalogue the biological pathways
and networks that are an important part of systems biology. In structural biology, it
aids in the simulation and modelling of DNA (Sim et al., 2012).

3.1.1 Structural Bioinformatics

Plate 1: Ribbon diagram of a Protein

Protein structure prediction is another important application of
bioinformatics. The amino acid sequence of a protein and the so called primary
structure can be easily determined from the sequence on the gene that code for it.
Knowledge of this structure is vital in understanding the function of the protein.
Structural information is usually classified as one of secondary, tertiary and
quaternary structure. A viable general solution to such predictions remains an open
problem; most efforts have so far been directed towards heuristics that work most
of the time. Dawson et al (2016).
One of the key ideas in bioinformatics is the notion of homology. In the genomic
branch of bioinformatics, homology is used to predict the function of a gene: if the
sequence of gene A, whose function is known, is homologous to the sequence of
gene B, whose function is unknown, one could intefer that B may share A’s
function. In the structural branch of bioinformatics, homology is used to determine
which parts of protein are important in structure formation and interaction with
other proteins. In a technique called homology modeling, this information is used
to predict the structure of a protein once the structure of a homologous protein is
known. This currently remains the only way to predict protein structures reliably

3.1.2 In-Silico Drug Design

In-silico methods help in identifying drug targets via bioinformatics tools.
They can also be used to analyze the target structures for possible binding/active
sites, generate candidate molecules, check for their drug likeness, dock these
molecules with the target, rank them according to their binding affinities, further
optimize the molecules to improve binding characteristics. This method is
important to any experiment work in biochemistry, biotechnology, and the likes. It
gives the work a focus, reduce the cause of finances.
The use of computers and computational methods permeates all aspects of
drug discovery today and forms the core of structure-based drug design. High-
performance computing, data management software and internet are facilitating the
access of huge amount of data generated and transforming the massive complex
biological data into workable knowledge in modern day drug discovery process.
The use of complementary experimental and informatics techniques increases the
chance of success in many stages of the discovery process, from the identification
of novel targets and elucidation of their functions to the discovery and
development of lead compounds with desired properties. Computational tools offer
the advantage of delivering new drug candidates more quickly and at a lower cost.

3.1.3 List of computer-aided drug design (CADD), software, databases and

web services
These tools are classified according to their application field, trying to cover
the whole drug design pipeline.

Databases
ProteinDataBank (PDB)
ChEMBl
ZincDatabase

Chemical structure representations

pymol
marvinSketch
ChemDraw

Moleculae modelling
Amber
SwissSideChain
SwissParam

Docking
Schrodinger
Autodock
Pymol

3.1.4 Molecular docking

In the field of molecular modeling, docking is a method which predicts the

preferred orientation of one molecule to a second when bound to each other to
form a stable complex (lengauer t et al), this process therefore requires the protein
and ligand(s) be downloaded from their respective databases.
 Place 2: Diagram of a Protein complex
Molecular docking is one of the most frequently used methods in structure-based
drug design, due to its ability to predict the binding-conformation of small
molecule ligands to the appropriate target binding site. Characterization of the
binding behavior plays an important role in rational design of drugs as well as to
elucidate fundamental biochemical processes.(Kitchen DBet al)Molecular docking
path is as follows:
• Understand the biochemistry of the disease/detect the molecular bases for
disease.
• Identify the target receptor responsible.
• Model the target receptor.
• Create a file for the receptors.
• Download phytochemical present in the plant of interest.
• Create a library of phytochemicals.
• Prepare the receptor using Pymol.
• Prepare the ligands using the terminal.
• Dock using any type of the molecular docking software.
3.1.5 Docking score
Docking programs generate a large number of potential ligand poses, most scoring
functions are physics-based molecular mechanics force fields that estimate the
energy of the pose within the binding site (Murco MA et al1995).
Docking score for example could be in this form below:
Table 1: Ligands and Docking Score
Ligands Docking
score
Adipic acid , 2-decyl isobutyl ester -6.8
Cholest-4-ene, 3 beta - -5.1
(methoxymethoxy)
 Glycidol stearate -4.9
Levo-Menthyloxyacetic acid -7
3-bromo-2-propynyl palmitate -4.9
2,4-Decadienal, (E,E) -4.1
Cyclopentadecanone, 2-hydroxy -4.9
2 - (3-hydroxybutyl) cyclooctanone -6.2
1-ethyladamantane -6.2
2-dodecenal -4.9
9-Eicosene, [E] -6.2
Hexestrol -4.1
Oleoyl chloride -4.9
Cholesterol -6.2
Didodecyl phthalate -5.1

The best docking score therefore is the one with the highest negative value.
3.2 Molecular Biology
Molecular Biology concerns the molecular basis of biological activity between
biomolecules in the various systems of a cell, including the interaction between
DNA, RNA, and Proteins and their biosynthesis, as well as the regulation of these
interactions (Alberts et al., 2016).
Researchers in Molecular Biology use specific techniques native to
Molecular Biology but increasingly combine these with techniques and ideals from
genetics and Biochemistry. Biochemistry is the study of the chemical substances
and vital processes occurring in live organisms. Biochemists focus heavily on the
role, function and structure of biomolecules. The study of the chemistry behind
biological processes and the synthesis of biological active molecules are examples
of Biochemistry (Berg et al., 2016).
Molecular Biology is the study of Molecular underpinnings of the processes
of replication, transcription, translation, and cell function. The central Dogma of
Molecular Biology where genetic material is transcribed into RNA and then
translated to protein, despite being an oversimplified picture of Molecular Biology,
still provides a good starting point for understanding the field.
Much of Molecular Biology is quantitative, and recently much work has
been done at its interface with Computer science in bioinformatics and
Computational biology. In the early 2000s, the study of gene structure and
function, molecular genetics, has been among the most prominent sub-fields of
molecular biology. Increasingly many other areas of biology focus on molecules,
either directly studying interactions in their own right such as in cell biology and
developmental biology, or directly, where molecular techniques are used to infer
historical attributes of population or species, as in fields in evolutionary biology
such as population genetics and phylogenetic.
Organized into this report, explains molecular interactions and therefore fall
within the purview of molecular biology. The discussion on the chemical structure
of proteins and nucleic acids, the physicochemical techniques in measuring
molecular size and shape, the mechanism of enzymatic reactions, the functions of
DNA and RNA, and the mechanism of phase transition in polynucleotides.
Deoxyribonucleic acid (DNA) is the molecule which carries the genetic
instructions for almost every living thing. Its unique chemistry not only allows this
information to be copied and passed on to an organism’s descendent, it also allows
scientists opportunities to investigate and manipulate an organism at a molecular
level. As a result, molecular biology techniques are at the forefront of most cutting
edge scientific research. In this report you will discover a number of commonly
used molecular biology techniques involving DNA.

3.2.1 Common Molecular Biology Techniques

Below is a list of various Molecular Technique/steps involved in Molecular
biology.
3.2.2 Rearing of experimental animals
In researching human disease, model organisms allow for better understanding the
disease process without the added risk of harming an actual human. The specie
chosen will usually meet a determined taxonomic equivalent to humans, so as to
react to disease or its treatment in a way that resembles human physiology as
needed. The mouse has since been used as a model organism and is associated with
many important biological discoveries of the 20 th and 21st centuries (Yarri et al.,
2005).When researchers look for an organism to use in their studies, they look for
several traits. Among these are size, generation time, accessibility, manipulation,
genetics, conservation of mechanics etc. Rats and mice are commonly used and
other rodents which are used are: guinea Pig, hamsters, and gerbils.

3.2.3 Testing the Experimental Animals

This is a short list of tests carried out on experimental animals.
• Mutagenicity and Carcinogenicity: mutagenic and carcinogenicity tests
examine potential genetic effects from pharmaceuticals, industrial
chemicals, and consumer products, classifying the chemicals for cell
mutations and carcinogens. Rats and mice are commonly used in these
studies and dissected afterwards for the organs that are required to be
harvested for examination.

• Metabolic Toxicity: some chemicals and drugs are essentially nontoxic

but become hazardous once ingested and metabolized by the body. These
animals are made to ingest the chemical substance which is being tested,
for given period of time after which they are dissected and require organs
are harvested for examination.

• Phytochemical Testing: chemical extract from plants which are known to

cure diseases is mixed with the feed for the experimental animals these
chemical extracts most times are from already known plants which are
used locally as concoctions taken by humans and at times, new plants are
tested. After feeding or intubating the animals with the extracts for a
given period of time they are dissected and required organs are harvested
for examination.
 Plate 3: A dissecting set.

3.2.4 RNA Extraction

Organs collected from experimental animals are placed into already labeled
eppendorf tubes which contain reagents. The reagent into which the organs are
placed is determined by the type of experiment. Formalin, Normal saline or Trisol
are reagents which are usually used. RNases are ubiquitous enzymes which
degrade RNA, trizol reagent inactivates endogenous RNases in samples. The blood
of the experimental animals are sometimes collected for hematology, this depend
on the nature of experiment.

3.2.5 Homogenization
The collected organs are placed
into the thermocycler to undergo 25cycles for 10 minutes at 50 degrees centigrade
after which they are homogenized, either manually or with the use of a
homogenizing machine. Homogenization is done to obtain a fine substance
required to further the experiment. Homogenization of samples lysis cells, disrupt
cells and dissolve cell components in trizol.

Plate 4: PCR Thermocycler

3.2.6 Addition of Chemical Substances: after homogenization a flash

centrifugation is done for the fine substance obtained from homogenization to
settle at the base of the eppendorf tube.

• 100 microliters of Snap Kit is added into the samples and they are
homoginized and boiled for 10 minute before centrifuged for
30minutes at 10,000 revolutions per minute. The centrifugation is to
enhance the partitioning of the homogenized organs to RNA and
Debris of the sample. RNA stays at the upper layer, Debris at the
base. RNA which is at the upper layer is extracted with a micro pipette
into newly labelled eppendorf tubes.
• Into the extracted RNA, 50 microliters of Isoamylpropanolis
dispensed, to precipitate the RNA. To mix, the eppendorf tubes
should be inverted. This is then incubated (placed inside the
refrigerator) at -20°C for at least 1 hour. (RNA precipitate is often
invisible before centrifugation but make a gel-like pellet on the side
and bottom of the tube). After 1 hour the RNA would have formed
white crystals at the base of the tube. The solution at the top
 (Isoamypropanol) is decanted leaving the RNA crystals behind. This
is centrifuge at 3000rpm for 20 min at 4°C to pellet the RNA. The
supernatant solution is carefully removed.
• To the RNA crystals left, 50 microliters of 70% ethanol is dispensed
to wash off the RNA pellets (crystals) and any traces of
Isoamypropanol which might still be present. This is carried out by
vortexing. Ethanol residual are removed with a fine-tipped pipette
and the pellets are air dried for 1 to 5 min. It should not dry
completely so that the solubility of the pellets will not decrease.
• 50 microliters of nuclease free water is aspirated into the RNA
crystals with a micropipette.

• REVERSE TRANSCRIPTION (RT-PCR)

As the name suggested reverse transcriptase, it means we have a template RNA,
and from the RNA we will produce DNA segment. The RNA single strand is
amplified to a double stranded DNA with the aid of the reverse transcriptase.
The starting template for a PCR reaction can be DNA or RNA. DNA is usually the
appropriate template for studying the genome of the cell or tissue (as in inherited
genetic diseases, somatic mutation in a tumor, or somatic rearrangement in
lymphocytes) and for the detection of DNA viruses. For information on gene
expression in a cell or tissue or the presence of genomic RNA in a retrovirus such
as HIV, RNA is the appropriate template. RNA can be better than genomic DNA
for detecting structural changes in long genes, since amplifying the spliced RNA
transcript instead of the genomic sequence greatly reduces the length of DNA to be
handled without losing any of the coding regions where clinically significant
deletions may be expected. RT-PCR combines cDNA synthesis from RNA
templates with PCR to provide a rapid, sensitive method for analyzing gene
expression. RT-PCR is used to detect or quantify the expression of mRNA, often
from a small concentration of target RNA. The template for RT-PCR can be total
RNA or selected RNA. (Robert et al., 2003)
RT reactions can be primed with:
1. Random primers
 2. dNTPs (dinucleotidetriphosphates)
3. Nuclease free water
4. Reverse transcriptase buffer
5. Reverse transcriptase.
After mixing the above reagents in the appropriate quantities, a specific quantity of
this cocktail is added to the RNA samples. Then, the samples are transferred to a
PCR thermocycler at 420C for 4hrs for the purpose of reverse transcription i.e
conversion from RNA to its complementary DNA (cDNA). Other than this, after
adding the cocktail to the RNA samples, the samples can be left overnight at room
temperature, for the same purpose.
RT-PCR can be carried out either in two-step or one-step formats. In two-step RT-
PCR, each step is performed under optimal conditions. cDNA synthesis is
performed first in RT buffer and one tenth of the reaction is removed for PCR. In
one-step RT-PCR, reverse transcription and PCR take place sequentially in a single
tube under conditions optimized for both RT and PCR.

• Polymerase Chain Reaction (PCR)

This is one of the most important technique used in molecular biology and is
basically used to copy DNA. PCR allows a single DNA sequence to be amplified
into millions of DNA molecules. Polymerase chain reaction is an extremely
versatile technique for copying DNA. In brief, PCR allows specific DNA sequence
to be copied or modified in predetermined ways. The reaction is extremely
powerful and under perfect conditions could amplify 1 DNA molecule to become
1.07 Billion molecules in less than 2 hours. The PCR technique can be used to
introduce restriction enzyme sites to ends of DNA molecules, or to mutate
particular bases of DNA, the latter is a method referred to as site-directed
mutagenesis. PCR can also be used to determine whether a particular DNA
fragment is found in a cDNA library. PCR has many variations, like reverse
transcription PCR (RT-PCR) for amplification of RNA, and more recently,
quantitative PCR which allow for quantitative measurement of DNA or RNA
molecules.
Typically, PCR consists of a series of 20-40 repeated temperature changes, called
cycles, with each cycle commonly consisting of 2-3 discrete temperature steps,
usually three. The cycling is often preceded by a single temperature step at a high
temperature (> 900 C), and followed by one hold at the end for final product
extension or brief storage. The temperature used and the length of time they are
applied in each cycle depend on a variety of parameters. These include the enzyme
used for DNA synthesis, the concentration of divalent ions and dNTPs in the
reaction, and the melting temperature of the primers (Rychlik et al., 1990).

Plate 7: PCR tubes.

CYCLING PROCDURE
• Initialization Step: (only required for DNA polymerases that require heat
activation by hot-start PCR (Sharkey et al.,1994) This step consists of
heating the reaction to a temperature of 94-96 0 C (or 980 C if extremely
thermostable polymerase is used), which is held for 1-9 minutes.

• Denaturation Step: this step is the first regular cycling event and consists of
heating the reaction to 94-980 C. It causes DNA melting of the DNA template
by disrupting the hydrogen bonds between complementary bases, yielding
single-stranded DNA molecule.

• Annealing Step: the reaction temperature is lowered to 50-65 0C for 20-40

seconds allowing annealing of the primers to the single stranded DNA
template. This temperature must be low enough to allow for hybridization of
the primer to the strand, but high enough for the hybridization to be specific,
i.e. the primer should only bind to imperfectly. If it is too high, the primer
might not bind.
 • Extension/Elongation Step: The temperature at this step depends on the
DNA polymerase used; Taq polymerase has its optimum activity temperature
at 75-800 C, (Chein et al., 1976) and commonly a temperature of 720C is
used with this enzyme. At this step the DNA polymerase synthesizes a new
DNA strand complementary to the DNA template strand by adding dNTPs
that are complementary to the template in 5 1 to 31 direction, condensing the
51 -phosphate group of the dNTPs with the 3 1-hydroxyl group at the end of
the nascent (extending) DNA strand. The extension time depends both on the
DNA polymerase used and on the length of the DNA fragment to amplify.
As a rule-of-thumb, at its optimum temperature, the DNA polymerase
polymerizes a thousand bases per minute. Under optimum conditions, i.e., if
there are no limitations due to limiting substrates or reagents, at each
extension step, the amount of DNA target is doubled, leading to exponential
(geometric) amplification of the specific DNA fragment.

The process of denaturation, annealing and elongation constitute of one

cycle. Multiple cycles are required to amplify DNA. The formula used to
calculate the number of DNA copies formed after a given # of cycles
repeated is, 2^# of cycles. (Lawyer et al., 1993).

• Final elongation: This single step is occasionally performed at a

temperature of 70-740 C(this is the temperature needed for optimal
activity for most polymerases used in PCR) for 5-15 minutes after the
last PCR cycle to ensure that any remaining single-stranded DNA is
fully extended.
• Final hold: This step at 4-150C for an indefinite time may be
employed for short-term storage of the reaction.
The PCR process can be divided into three stages;
• Exponential Amplification: At every cycle, the amount of product is
 doubled (assuming 100% reaction efficiency). The reaction is very sensitive:
only minute quantities of DNA must be present.
• Leveling Off Stage: The reaction slows as the DNA polymerase loses
activity and as consumption of reagents such as dNTPs and primers causes
them to become limiting.
• Plateau: No more product accumulates due to exhaustion of reagents and
enzyme.
DNA absorbance can be taken if need with the use of a spectrophotometer.

Figure 2: Polymerase Chain Reaction

• Gel Electrophoresis
To check whether the PCR generated the anticipated DNA fragment
(sometimes referred to as the amplier or amplicon), agarose gel electrophoresis is
employed for size separation of the PCR products. The size(s) of PCR products is
determined by comparison with DNA ladder (a molecular weight marker), which
contains DNA fragments of known size, run on the gel alongside the PCR
products.
Agarose gel is a three-dimensional matrix formed of helical agarose molecules in
super-coiled bundles that are aggregated into three-dimensional structures with
channels and pores through which biomolecules can pass. The gel is prepared by
dissolving the agarose powder in an appropriate buffer, such as TAE or TBE, to be
used in electrophoresis. The agarose is dispersed in the buffer before heating it to
near-boiling point, but avoid boiling. The Ethidium Bromide may be added to the
agarose solution before it gels, or the DNA gel may be stained later after
electrophoresis. The melted agarose is allowed to cool sufficiently before pouring
the solution into a cast as the cast may wrap or crack if the agarose solution is too
hot. A comb is placed in the cast to create wells for loading sample, and the gel
should be completely set before use.
The concentration of gel affects the resolution of DNA separation. For a standard
agarose gel electrophoresis, a 0.8% gives good separation or resolution of large 5-
10kb DNA fragments, while 2% gel gives good resolution for small 0.2-1kb
fragments. 1% gels is often used for a standard electrophoresis. The concentration
is measured in weight of agarose over volume of buffer used (g/ml). High
percentage gels are often brittle and may not set evenly, while low percentage gels
(0.1-0.2%) are fragile and not easy to handle. Low-melting-point (LMP) agarose
gels are also more fragile than normal agarose gel. Low-melting point agarose may
be used on its own or simultaneously with standard agarose for the separation and
isolation of DNA. (Fotard et al., 1991).
3.2.11 Loading in Samples and Running Of Agarose Gel
Once the gel has set (solidified), the comb and stopper is removed, leaving wells
where DNA samples can be loaded. Loading buffer is mixed with the DNA sample
before the mixture is loaded into the wells.

Plate 8: A micropipette
Once solidified, the agarose gel is placed into the gel box. It contains a high
percentage of glycerol, so it increases the density of your DNA sample causing it to
settle at the bottom of the gel well, instead of diffusing in the (Electrophoresis
unit). The gel box is filled with 1× TAE (or TBE) until the gel is covered. A
molecular weight ladder is loaded into the first lane of the gel. When loading the
samples into the well a positive pressure should be maintained on the sample to
prevent bubbles or buffer from entering the tip of the pipette. The very top of the
tip of the pipette will be into the buffer just above the well. Very slowly and
steadily, the sample is then pushed out and watched as it fills the well. After the
entire sample is unloaded, the pipettor is pushed to the second stop and carefully
raising the pipette straight out of the buffer. The samples are carefully loaded into
the additional wells of the gel. The gel is run at 80-150 V until the dye line is
approximately 75-80% of the way down the gel.
Black is negative, red is positive. (The DNA is negatively charged and will run
towards the positive electrode.)
A typical run time is about 1-15 hours, depending on the gel concentration and
voltage.
The power supply is turned off and the electrodes are disconnected from the power
source, and then the gel is carefully removed from the gel box. If EtBr was not
added to the gel and buffer, the gel is placed into a container filled with 100ml of
TAE running buffer and 5microliters of EtBr, it is placed on a rocker for 20-30
minutes, EtBr solution is replaced with water and destain for 5 minutes.

Plate 9: Electrophoresis Set Up

Visualization of RNA Samples: Using any device that has UV light, such as a
spectrophotometer, the DNA fragment is visualized.
When using a UV light, the skin should be protected by wearing safety goggles or
a face shield, gloves and a lab coat. If the DNA will be purified for later use, a long
wave length UV should be used and this should be exposed for as little time as
possible to minimize damage to the DNA.

Plate 7: A Photophoresis Machine

Analyzing gels
Using the DNA ladder in the first lane as a guide (the manufacturer’s instruction
will tell the size of each band), the bands gotten in the sample lane can be
interpreted to determine if the resulting DNA bands that are seen are expected or
not.
 CHAPTER FOUR

4.0 Skills Developed and Techniques Learnt

The Student Industrial Work Experience scheme held at Molecular And Similation
Center gave me the opportunity to:

• Develop research skill in medical laboratory.

• Develop skills use in the disinfection and sterilization of the laboratory

equipment.

• Develop skills used in handling laboratory machine and equipment used for
Molecular experiments. E.g. the Centrifuge, PCR machine, Electrophoretic
tank, Photophoresis, etc.

• Develop working relationship with students and staff of the company.

• Learnt the use of Software and online databases for computational

experiments at the Biocomputing unit.

• Learnt the skills used in writing research papers for publication.

• Learnt action of various chemical substances and reagents used for

molecular experiment.

• Learnt how to prepare different solutions and reagents E.g. TBE buffer (1,
0.5), TAE buffer, EDTA, H2O2 buffer.

• Learnt activities carried out at the animal test unit such as intubation of
experimental animals and preparation of feed for experiments

4.1 Practical Challenges Faced At Work

 • During my first few days at the Molecular and Simulation Center, I had
challenges in handling laboratory equipment and machines used for
Molecular experiment.
• Laboratory scientists had a great challenge of trust for industrial training
students to work in sensitive section of the laboratory thus, denying me the
opportunity of handling sensitive experiments which I felt I could handle.
• At first it seems tedious to know which reagent and chemical substance
which is to be used to carry out specific experiment and the result which will
be obtained after each experiment.
• Difficulty in creating a library of phytochemicals.
• Difficulty in using software and online data base used for experiments in the
Biocomputing unit. E.g. Schrodinger, Pymol, Chembl etc.
• Inadequate power supply.
• The problem of getting the exact volume of required reagents during the
preparation of cocktail.
• Shortage of distill and deionized water and some chemical substance used
for experiment sometimes.
• I encountered challenges while intubating experimental animals.

4.2 Theoretical Principles Learnt During the Program

Listed below are the theoretical principles learnt during my six months of SIWES.
• Centrifuge involves the principle of sedimentation where the acceleration at
centripetal force causes denser substance to separate out along the radial
direction to the bottom of the eppendorf tube.
• 100% Ethanol is not safe for sanitizing because it evaporates faster and may
not really kill the microorganism, it is being used for. Therefore, 70%
 Ethanol must be added to 30% of distill water in order to reduce the rate of
evaporation of the Ethanol and thus increase its effect on the organism.
• With bioengineering, new plants can be developed which contain higher
levels of phytochemicals.
• At the Molecular and Simulation Center various machines are used for
Molecular experiment one of which is the Photophoresis machine and I
discovered that it functions with UV light.

4.3 Specific Contributions Made to the Center

The specific contributions made to the Centre during my SIWES programme
include the following:
• I participated actively in all experiments, research work carried out in both
Biocomputing and Molecular laboratory and I gave ideas that helped the
work.
• Cleaning of animal house and taking care of experimental animals.
• Preparation of Distil and Deionized water used for Molecular experiments.
• Making a list of new primers used for molecular experiments.

4.4 THE FUTURE OF THE BUSINESS WITHIN THE NIGERIAN

ECONOMY
The major objective of the Molecular and Simulation Center, Ado Ekiti
state is to find a cure for ailments and diseases causing health challenges in our
world today. Each day various new diseases spring up and the need to find a cure
for these is on a rise. Humans will forever have a need for good health, this shows
that the services rendered by the Molecular and Simulation Center will always be
needed and asked
To execute the mandate effectively and ensure proper running of activities within
the organization, MOLS AND SIMS collaborates with indigenous and international
research institutes, universities and biotechnological companies abroad (Inqaba
Biotech) to make the work carried out in the laboratory more effective.
Considering the location of MOLS AND SIMS, it is one of the very few research
company in the area.
The services rendered by the Molecular And Simulation Center gives an assurance
of an excellent future in the World of Research, Molecular Experiments and
Bioinformatics.
4.5 Relevance of Industrial Training Experience Gained to the Course of
Study
At the Molecular and Simulation Center where I was attached during my six
months of SIWES, I learnt and carried out Molecular and Computational
experiments. Biochemistry is the study of the chemical substances and vital
processes occurring in living organisms. Biochemists focus heavily on the role,
function and structure of biomolecules.
Molecular Biology concerns the molecular basis of biological activity between
biomolecules in the various systems of a cell, including the interaction between
DNA, RNA, and proteins and their biosynthesis, as well as the regulation of these
interactions (Albert et al., 2016).

CHAPTER FIVE
5.0 GLOSSARY OF WORDS
• Ez vision: this is used as an anti-gel or post-run stain to visualize DNA in
agarose gels, it allows instant visualization.
• Eppendorf tubes: these are tubes of different sizes and shapes in which
samples are placed into during experiments.
• Down regulation: a process by which a cell decreases the quantity of a
cellular component, such as RNA or Protein.
• Up regulation: an increase in the number of receptors on the surface of
 target cells, making the cells more sensitive to a hormone or other agent.
• Ethidium Bromide: this is an intercalating agent commonly used as a
fluorescent tag (nucleic acid stain) in molecular biology laboratories for
techniques such as agarose gel electrophoresis.
• Biuret solution: a liquid mixture of Potassium hydroxide and copper sulfate
used to detect protein and peptide in human urine.
• Ablation Experiment: an experiment designed to produce an animal
deficient in one or a few cell types in order to study cell lineage or cell
function.
• Hematology: it is the science or study of blood, blood-forming organs and
blood diseases.
• Chembl: a manually curated chemical database of bioactive molecules with
drug-like properties.
• Beta-actin: this is an ubiquitously expressed and highly conserved 42kD
cytoplasmic protein involved in cell motility.
• VEGFR: Vascular endothelia growth factor. A signal protein produced by
cells that stimulate vasculogenesis and angiogenesis.
• TBE: Tris borate EDTA. This is a buffer solution containing a mixture of Tri
base, boric acid and EDTA.
• EDTA: Ethylenediaminetetraacetic acid. It is a synthetic amino acid and
chelating agent for divalent metals.
• Cdk: Cylin dependent kinase, a family of protein kinase involved in
regulating transcription, m RNA processing and differentiation of nerve
cells.
• Catenation: This is the ability of an element to form linkage with same
elements.
• Pose: This is one of Marvin icons which helps to choose the number of
docking scores to be shown after docking.
• CHEMSPIDER: A chemical structure database providing fast access to
over 50 million structures, properties and associated information.
• Desalting: This occurs when buffer salts and other small molecules are
removed from a sample in exchange for water.
• Marvin Sketch: This is the software which is used to sketch structures of
chemicals and compounds.

5.1 RECOMMENDATION
 The Student Industrial Work Experience Scheme is a Scheme that should be
encouraged, it’s has benefited students a lot, countless things are learnt during the
period of six or four months, depending on the tertiary institution. It equip students
to face life outside their campuses and to learn to shoulder responsibilities. Due to
its various benefits, this scheme should be improved because improving it has a
great positive impact on the lives of students.
Listed below are ways this scheme can be improved:

• Rules binding the activities of students in their places of attachment should

be introduced and sent to directors of the establishment this will gear
students to be punctual at work and responsible.
• School based supervisors should keep contact of industry based supervisors
during site visit to foster good relationship between the department and the
organization. This will help students who seek IT placement in the future.
• The school should set up a committee that will collaborate effectively with a
wide network of industry and organization, so that instead of student going
about seeking placement they will rather be posted to organizations and
industries of interest relevant to their courses of study.
• On the logbooks provision for printed images should be made, there are
some images which cannot be drawn like the structures of chemicals, ligands
and proteins.
• Tertiary institutions should monitor the activity of students in their places of
attachment and good steps should be taken when a student gets into an
organization with nothing to add to his/her knowledge.
• During visitation students should be asked to perform few experiments
he/his has learnt, this will be a good prove of knowledge acquisition, since
that’s the main reason for the scheme.

5.2 CONCLUSION
These six months of SIWES has really broadened my knowledge of
Biochemistry. It has opened my eyes to new and interesting areas in the field.
During this period I worked at the Molecular Biology and Biocomputing units, I
got exposed to various experiments carried out and before SIWES ended I could
carry out all experiments with little or no supervision by the director of the Center.
New grounds are being broken in science every day, I was introduced to various
new development in science worldwide I had an interesting and eye opening
experience.
The world battle with diseases every day, working at the Molecular and Simulation
Center has given me the joy that the war against these diseases can be won. I can
operate machines used for Molecular experiments and I can carry out some
Biocomputational experiments effectively and independently.
I shouldered responsibilities and I got exposed to what is expected in a work
place setting. It is a great privilege for me to practice what I have being taught in
class and all I have read in Biochemistry text books.
I learnt a lot and I have found Biochemistry a very interesting course to
study and I have discovered it is one of the solutions to the health challenges we
face in our world today.

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