CSC 443 - BIOINFORMATICS
INTRODUCTION TO BIOINFORMATICS
Bioinformatics is the application of computational techniques to analyze the
information associated with biomolecules on a large-scale. It has now firmly
established itself as a discipline in molecular biology, and encompasses a wide
range of subject areas from structural biology, and genomics to gene expression
studies.
Molecular Bio – informatics: bioinformatics is conceptualizing biology in terms
of molecules (in the sense of physical chemistry) and applying "informatics
techniques" (derived from disciplines such as applied mathematics, computer
science and statistics) to understand and organize the information associated
with these molecules, on a large scale. In short, bioinformatics is a management
information system for molecular biology and has many practical applications.
Bioinformatics is the application of mathematical, statistical and computing
methods to solve biological problems. Bioinformatics has the ability to impact
the traditional wet-lab approaches in several significant fields. The major impact
is on data: acquisition, storage, retrieval, analysis and interpretation of biological
data which is aimed at solving biological problems. Bioinformatics differs from
a related field known as Computational Biology. Bioinformatics involves
sequence, structural and functional analysis of genes and genomes and their
corresponding products. Meanwhile, Computational Biology encompasses all
biological areas that involve computation.
"Bioinformatics" is defined as:
"A field of science that uses computers, databases,
mathematics, and statistics to collect, store,
organize, and analyze large amounts of biological,
medical, and health information."
The collection, storage, organization, and analysis of biological data allow
researchers and practitioners to make data-driven decisions, advance
medical knowledge, improve patient care, and ultimately enhance public
health outcomes.
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In Vitro, In Vivo and In Silico Experiments
In Bioinformatics, there are three broad categories of experiments that
researchers conduct to test a hypothesis. These include: in vitro studies,
in vivo studies, and in silico studies. Let's explore these topics briefly.
Differences between In Vitro, In Vivo and In Silico Assays in
Preclinical Research
How to choose which type of experiment is best-suited for my
research?
In Vitro Experiments
"In vitro" means "in glass." In vitro studies are conducted outside of a living
organism, typically in a laboratory setting. Scientists use cells, tissues, or
isolated parts of an organism to investigate biological phenomena. It
involves experiments performed in test tubes, petri dishes, or other
artificial environments. For example, researchers may study the effects of
a drug on cells grown in a lab to understand its potential benefits or side
effects. In vitro studies provide controlled conditions and allow scientists
to observe specific interactions or processes in a simplified manner.
In Vivo Experiments
"In vivo" means "within the living." In vivo studies involve experiments
conducted within a living organism, such as animals or humans.
Researchers administer substances, treatments, or interventions to the
organism and observe the effects on the entire system. These studies aim
to understand how a substance or treatment behaves within a biological
system and how it may affect overall health, physiology, or behavior. For
instance, scientists may test a new drug on animals to determine its
efficacy and safety before moving to human trials. In vivo studies provide
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a more comprehensive understanding of how interventions interact with
living organisms.
In Silico Experiments
"In silico" refers to computer simulations or modeling. In silico studies
involve using computer-based methods to simulate and analyze biological
systems, processes, or phenomena. Researchers input relevant data,
such as molecular structures or physiological parameters, into computer
models or algorithms. These models can help predict or simulate various
aspects of biological processes, drug interactions, or disease progression.
For example, scientists might create a computer model of a virus to study
its behavior and test different strategies to combat it. In silico studies offer
a cost-effective and efficient way to explore a wide range of scenarios and
make predictions without the need for extensive experimental work.
What are in silico assays?
In silico studies are biological experiments carried out entirely on a computer, or via
a computer simulation. As such, they are by far the newest of the three research
methods (the first took place in 1989). Although in silico studies represent a relatively
new way of research and are not replicates of living organisms, these studies have
already contributed notably to biomedical research and drug discovery. For example,
a 2009 study used software emulations to predict how certain drugs already on the
market could treat drug-resistant strains of tuberculosis. Thus, they can contribute to
the research field by providing a cost-effective and scalable method.
There is a variety of in silico techniques:
• Bacterial sequencing techniques – These methods have been developed to identify
bacteria through bacterial DNA and RNA sequencing. The most commonly used is
polymerase chain reaction (PCR).
• Molecular modeling – The science of representing molecular structures numerically and
simulating their behavior with the equations of quantum and classical physics.
• Whole-cell simulations – These refer to computer models of cellular behavior.
More recently, artificial intelligence technologies are also gaining prominence along
the whole target discovery process. Deep and machine learning tools allow
researchers to automate and extract more meaningful information from experimental
outputs, in order to generate models and build complex networks by integrating
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different data sources. Ultimately, these technologies greatly speed up the extraction
process of potential therapeutic targets. However, results should be further validated
through the exploitation of experimental methodologies (in vitro and in vivo).
What are in vitro assays?
In vitro (Latin for within the glass) assays take place in a controlled environment, in a
petri dish or test tube, outside of a living organism. They refer to work done with
microorganisms as well as with cells, tissues, or other biological components that
have been removed from the living organisms of interest. These approaches are
suitable for cellular and molecular studies, such as for understanding signal
transduction or cellular signaling pathways.
In vitro studies provide invaluable advantages: are cost-effective, time-efficient, and
do not require animal use. They allow more rapid development of new treatments,
since many drugs can be studied at one time, and only those that appear to be
efficacious go on to later stages. That’s why they are often the first step in the drug
discovery process, although results obtained with these approaches need further
confirmation with in vivo experiments.
Despite in vitro studies’ conveniences, one major shortcoming is that they fail to
replicate the precise cellular conditions and natural functioning of a whole organism.
For these reasons, in vitro studies may lead to results that do not correspond to what
happens within a living organism. For example, in the last few years in vitro studies
were used to research microorganisms, but they failed to model the competition and
interaction of microbes that take place in the human body. Thus, the causal
relationship between microbes and chronic diseases was overlooked. Additionally,
knowledge about the role of pathogens in disease was gained by testing only well-
known and easy-to-culture microbes. However, recent estimates are that less than
2% of bacteria can be characterized through in vitro techniques.
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What are in vivo assays?
In vivo (Latin for “within the living”) experiments are conducted with a whole, living
organism, as opposed to a partial or dead organism. In vivo preclinical studies
consist of animal testing and are the previous stage to clinical trials in humans.
As they occur within the organism, the results of in vivo studies are considered more
reliable or more relevant than those of in vitro studies. In vivo studies are better
suited for observing the overall effects of an experiment on a living subject, where
interactions, compensations, metabolism, and distribution contribute to the final
observable effect. Thus, these studies enable researchers to better understand
disease pathology, which makes them invaluable for biomedical research.
Historically, in vivo animal studies mainly used mammalian mouse or rat models, but
regulations such as the 3Rs of research have led to an increase in alternative
models such as zebrafish.
The principles of the 3Rs (Replacement, Reduction and
Refinement) were developed over 50 years ago providing a
framework for performing more humane animal research.
Types of Data: Qualitative and Quantitative Data
Next, let's explore the two main types of data encountered in
bioinformatics: qualitative and quantitative. Understanding these data
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types is important because they are essential components of the scientific
method used in biomedical research.
Qualitative data refers to non-numerical information that describes
characteristics or attributes. For example, it could involve identifying the
presence or absence of a specific genetic variant or assigning species
names, and taxonomic classifications.
Quantitative data, on the other hand, involve numerical measurements
or counts. This includes data obtained from techniques like high-
throughput sequencing or microarray analysis. Examples include gene
expression levels, protein abundance, or sequence similarity scores.
Aims of Bioinformatics
The aims of bioinformatics are threefold.
The first aim, at its simplest bioinformatics organizes data in a way that allows
researchers to access existing information and to submit new entries as they are
produced, for example, the Protein Data Bank for 3D macromolecular structures.
While data-curation is an essential task, the information stored in these databases
is essentially useless until analyzed. Thus the purpose of bioinformatics extends
much further.
The second aim is to develop tools and resources that aid in the analysis of data.
For example, having sequenced a particular protein, it is of interest to compare it
with previously characterized sequences. This needs more than just a simple text-
based search and programs such as FASTA and BLAST must consider what
comprises a biologically significant match. Development of such resources
dictates expertise in computational theory as well as a thorough understanding of
biology.
The third aim is to use these tools to analyze the data and interpret the results in
a biologically meaningful manner. Traditionally, biological studies examined
individual systems in detail, and frequently compared them with a few that are
related.
In bioinformatics, we can now conduct global analyses of all the available data
with the aim of uncovering common principles that apply across many systems
and highlight novel features.
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Biological databases
Biological data are complex, exception-ridden, vast and incomplete. Therefore
several databases has been created and interpreted to ensure unambiguous results.
A collection of biological data arranged in computer readable form that enhances
the speed of search and retrieval and convenient to use is called biological
database. A good database must have updated information.
Importance of biological database
A range of information like biological sequences, structures, binding sites,
metabolic interactions, molecular action, functional relationships, protein
families, motifs and homologous can be retrieved by using biological databases.
The main purpose of a biological database is to store and manage biological data
and information in computer readable forms.
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Primary database vs. secondary database
•A primary database contains only sequence or structural information.
•The database derived from the analysis or treatment of primary data are
secondary database. It is very important for interfering protein function.
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Examples of some primary biological database
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Examples of Some Secondary Biological Database
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Accession Number
This is a unique identifier to a GenBank sequence record. The
typical format is 1-2 letters followed by 4-6 digits. Here are a few
fictitious though syntactically correct examples: AG123456,
BF43251.
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CENTRAL DOGMA OF MOLECULAR BIOLOGY
Central dogma - The central dogma of molecular biology is a theory
stating that genetic information flows only in one direction, from DNA,
to RNA, to protein, or RNA directly to protein.
What are the 3 processes of central dogma?
The three processes of the central dogma are DNA replication,
transcription, and translation. During DNA replication, DNA is copied to
make more DNA. During transcription, DNA is copied to RNA, and
during translation, RNA is read to create proteins.
What is the central dogma of molecular biology? List its chain of events.
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The process of making protein from DNA is known as the “central dogma”.
However, it is not a linear step, but instead requires two steps: Transcription and
Translation, with an intermediate molecule, RNA. DNA → RNA → Protein.
The central dogma of molecular biology is an explanation of the flow of genetic
information within a biological system. It is often stated as "DNA makes RNA,
and RNA makes protein".
The Central Dogma states that once "information" has passed into protein it
cannot get out again. In more detail, the transfer of information from nucleic
acid to nucleic acid, or from nucleic acid to protein may be possible, but transfer
from protein to protein, or from protein to nucleic acid is impossible. Information
here means the precise determination of sequence, either of bases in the nucleic
acid or of amino acid residues in the protein.
The Central Dogma is the biological process that transfers Genetic information
from DNA to RNA, and then into Proteins.
A Central Dogma is an explanation of the flow of Genetic information in a cell,
including the replication of the DNA, the transcription of the RNA, and the
translation of the RNA to create the Proteins.
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Steps of the Central Dogma
The central dogma takes place in two stages:
1. Transcription
The enzyme RNA Polymerase transfers information from one strand of DNA to
another strand of RNA during transcription. Three parts of the DNA strand are
involved in this process: the promoter, the structural gene, and the terminator.
DNA strands that synthesize RNA are called template strands, and DNA strands
that Code for RNA are called coding strands. RNA polymerases that are DNA-
dependent bind to the promoter and catalyze the 3' to 5' directions of
polymerization.
The newly synthesized RNA strand is released from the terminator sequence as
it approaches the terminator. RNA strands released after transcription undergo
further modifications post-transcriptionally.
2. Translation
Proteins are enCoded by RNA by a process called translation. Translation
involves energy and is an active process. The energy comes from the charged
tRNA Molecules.
The translation process is initiated by ribosomes. Ribosomes are made up of two
subunits, one larger and one smaller. As a result, the larger subunit consists of
two tRNA Molecules positioned together so that enough energy can be expended
to form a peptide bond.
The mRNA enters the smaller subunit and is then held by the tRNA Molecules
present in the larger subunit that are complementary to the codon. In this way,
two codons are held together by two tRNA Molecules placed close together and
a peptide bond is formed between them. This process results in long polypeptide
chains of amino acids.
Genetic Code
Proteins are manufactured from RNA and their Genetic Code contains
information about them. In general, three nucleotides and four nitrogenous bases
collectively Code for an amino acid, forming a triplet codon. As a result, there
are 64 amino acids possible, including 4 x 4 x 4 amino acids. There are 20 amino
acids found naturally.
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As a result, the Genetic Code deteriorates. Due to the characteristics of the
Genetic Code, some amino acids are enCoded by more than one codon at a time,
causing the amino acid to degenerate. There is only one codon for each amino
acid and the Code is universal regardless of the organism.
In total, there are 64 codons, of which three are stop codons that end transcription
and one is an initiator codon, i.e. AUG, which Codes for methionine.
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The Genetic Code
As soon as Watson and Crick proposed the double helix model of DNA
in 1953, scientists began to study the problem of how a linear or helical
DNA molecule could encode a linear protein molecule. Cracking the
genetic code became a hot topic and even attracted George Gamow (of
the Big Bang Theory), a physicist. The sequence of insulin was the only
protein sequence available and it was scrutinized very carefully. At that
time, it was not known that all amino acid sequences could be encoded
in genes. Gam ow, concentrating on the insulin sequence and the fact
that 20 amino acids are used in protein sequences, discovered a very
compelling code.
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