STUDY ON BIOCHIPS USING
MICROARRAY TECHNOLOGY
1.1 INTRODUCTION
Molecular biology is the branch of
biology that deals with the molecular basis of biological activity. This field
overlaps with other areas of biology and chemistry, particularly genetics and biochemistry.
Molecular biology chiefly concerns itself with understanding the interactions
between the various systems of a cell,
including the interactions between the different types of DNA, RNA and protein biosynthesis as well as learning how
these interactions are regulated.
In molecular
biology, biochips are
essentially miniaturized laboratories that can perform hundreds or thousands of
simultaneous biochemical reactions. Biochips enable researchers to quickly
screen large numbers of biological analytes for a variety of purposes, from
disease diagnosis to detection of bioterrorism
agents.
Day by
day usage of Biochips is increasing. The scope of Biochips in molecular biology
is vast and still lot of developments is going on. This study covers the
Biochips using microarray technology.
1.2 HYPOTHESES
Molecular
biology is a latest field of science the application in the modern world is
wide. The scope of biochips usage in molecular biology is still a question mark
and lot of research works are going on behind this.
Looking
the latest technologies and usage of biochips in molecular biology there is a
wide scope for conducting a good study. Extracting this opportunity a study is
formulated and data are collected.
Since
this is a developing field the change of a good study is possible in vast
level. Looking this field it is necessary to conduct a study which will help to
gain more details about this study.
1.3 METHODOLOGY
Collection of data for the purpose of studying functioning
of various departments and the organization as a whole is based on two types of
data .They are :-
1. Primary.
2. Secondary.
Primary Data
Primary Data is a
data collected by the investigator himself for the purpose of a specific
enquiry or study. Mainly data is obtained through Direct Observation and Direct
interview method.
Ø Observation:
- mainly done by observing the general environment and day to day operation of
the company.
Ø Interview: - Conducted face to face interview
with mangers and company employees.
Secondary Data
Secondary Data is obtained from sources like
Ø
Company Annual Report
Ø
Company Records
Ø
Previous reports
Ø
Websites
Ø
Magazines etc
1.4 SCOPE
-
Conduct a study about Biochips using microarray
technology
-
Understand its benefits in molecular biology
-
Study the advantage of Biochips
-
Get some idea about the usage of Biochips in
molecular biology
-
A comparison study of different Biochips
-
Study the scope of Biochips in the future
purposes
-
Understand the future of Biochips
1.5 SAMPLE
DESIGN
The microarray
— the dense, two-dimensional grid of biosensors — is the critical component of
a biochip platform. Typically, the sensors are deposited on a flat substrate,
which may either be passive (e.g. silicon or glass) or active, the
latter consisting of integrated electronics or micromechanical
devices that perform or assist signal transduction. Surface
chemistry is used to covalently bind the sensor molecules to the substrate
medium. The fabrication of microarrays is non-trivial and is a major economic
and technological hurdle that may ultimately decide the success of future
biochip platforms. The primary manufacturing challenge is the process of
placing each sensor at a specific position (typically on a Cartesian grid) on the substrate. Various
means exist to achieve the placement, but typically robotic micro-pipetting
(Schena, 1995) or micro-printing (MacBeath, 1999) systems are used to place
tiny spots of sensor material on the chip surface. Because each sensor is
unique, only a few spots can be placed at a time. The low-throughput nature of
this process results in high manufacturing costs.
Fodor and
colleagues developed a unique fabrication process (later used by Affymetrix)
in which a series of microlithography steps is used to combinatorially synthesize hundreds of
thousands of unique, single-stranded DNA sensors on a substrate one nucleotide
at a time (Fodor, 1991; Pease, 1994). One lithography step is needed per base
type; thus, a total of four steps is required per nucleotide level. Although
this technique is very powerful in that many sensors can be created
simultaneously, it is currently only feasible for creating short DNA strands
(15–25 nucleotides). Reliability and cost factors limit the number of
photolithography steps that can be done. Furthermore, light-directed
combinatorial synthesis techniques are not currently possible for proteins or
other sensing molecules.
As noted above,
most microarrays consist of a Cartesian grid of sensors. This approach is used
chiefly to map or "encode" the coordinate of each sensor to its
function. Sensors in these arrays typically use a universal signalling
technique (e.g. fluorescence), thus making coordinates their only
identifying feature. These arrays must be made using a serial process (i.e.
requiring multiple, sequential steps) to ensure that each sensor is placed at
the correct position.
"Random"
fabrication, in which the sensors are placed at arbitrary positions on the
chip, is an alternative to the serial method. The tedious and expensive
positioning process is not required, enabling the use of parallelized
self-assembly techniques. In this approach, large batches of identical sensors
can be produced; sensors from each batch are then combined and assembled into
an array. A non-coordinate based encoding scheme must be used to identify each
sensor. As the figure shows, such a design was first demonstrated (and later
commercialized by Illumina) using functionalized beads placed randomly in the
wells of an etched fiber optic cable (Steemers, 2000; Michael, 1998) Each
bead was uniquely encoded with a fluorescent signature. However, this encoding
scheme is limited in the number of unique dye combinations that can be used and
successfully differentiated.
1.6 SOURCE OF
INFORMATION
The main source of information for
this particular study is the research associates working in this field and some
molecular biology labs.
The articles and books pertaining
to this field are also referred for this study. Internet is used for collecting
some general data about this field.
Referred some of the earlier
researcher’s research finding for collecting some particular data.
History
The term biology
is derived from the Greek word βίος,
bios, "life"
and the suffix -λογία, -logia, "study of." The Latin
form of the term first appeared in 1736 when Linnaeus
(Carl von Linné) used biologi in his Bibliotheca botanica. It was
used again in 1766 in a work entitled Philosophiae naturalis sive physicae:
tomus III, continens geologian, biologian, phytologian generalis, by Michael Christoph Hanov, a disciple of Christian Wolff. The first German
use, Biologie, was used in a 1771 translation of Linnaeus' work. In
1797, Theodor Georg August Roose used the term in a book, Grundzüge der
Lehre van der Lebenskraft, in the preface. Karl Friedrich Burdach used the term in 1800
in a more restricted sense of the study of human beings from a morphological,
physiological and psychological perspective (Propädeutik zum Studien der
gesammten Heilkunst). The term came into its modern usage with the
six-volume treatise Biologie, oder Philosophie der lebenden Natur
(1802–22) by Gottfried Reinhold Treviranus, who
announced:
The objects of our research will be the different forms and
manifestations of life, the conditions and laws under which these phenomena
occur, and the causes through which they have been effected. The science that
concerns itself with these objects we will indicate by the name biology
[Biologie] or the doctrine of life [Lebenslehre].
Although modern
biology is a relatively recent development, sciences related to and included
within it have been studied since ancient times. Natural philosophy was studied as early as the
ancient civilizations of Mesopotamia, Egypt, the Indian subcontinent, and China. However, the
origins of modern biology and its approach to the study of nature are most
often traced back to ancient Greece. While the formal study of medicine dates
back to Hippocrates
(ca. 460 BC – ca. 370 BC), it was Aristotle
(384 BC – 322 BC) who contributed most extensively to the development of
biology. Especially important are his History of Animals and other works where he
showed naturalist leanings, and later more empirical works that focused on
biological causation and the diversity of life. Aristotle's successor at the Lyceum, Theophrastus,
wrote a series of books on botany that survived as the most important contribution of
antiquity to the plant sciences, even into the Middle Ages.
Scholars of the
medieval Islamic world who wrote on biology included al-Jahiz
(781–869), Al-Dinawari (828–896), who wrote on botany,[7]
and Rhazes (865–925) who wrote on anatomy and physiology.
Medicine was
especially well studied by Islamic scholars working in Greek philosopher
traditions, while natural history drew heavily on Aristotelian thought,
especially in upholding a fixed hierarchy of life.
Biology began
to quickly develop and grow with Antony van Leeuwenhoek's dramatic
improvement of the microscope. It was then that scholars discovered spermatozoa,
bacteria, infusoria and
the diversity of microscopic life. Investigations by Jan
Swammerdam led to new interest in entomology
and helped to develop the basic techniques of microscopic dissection
and staining.
Advances in microscopy
also had a profound impact on biological thinking. In the early 19th century, a
number of biologists pointed to the central importance of the cell.
Then, in 1838, Schleiden and Schwann
began promoting the now universal ideas that (1) the basic unit of organisms is
the cell and (2) that individual cells have all the characteristics of life, although they
opposed the idea that (3) all cells come from the division of other cells.
Thanks to the work of Robert Remak and Rudolf
Virchow, however, by the 1860s most biologists accepted all three tenets of
what came to be known as cell theory.
Meanwhile,
taxonomy and classification became the focus of natural historians. Carl
Linnaeus published a basic taxonomy for the natural world in 1735
(variations of which have been in use ever since), and in the 1750s introduced scientific names for all his species.[10]
Georges-Louis Leclerc, Comte de
Buffon, treated species as artificial categories and living forms as
malleable—even suggesting the possibility of common
descent. Though he was opposed to evolution, Buffon is a key figure in the history of evolutionary thought;
his work influenced the evolutionary theories of both Lamarck and Darwin.
Serious
evolutionary thinking originated with the works of Jean-Baptiste Lamarck, who was the first to
present a coherent theory of evolution.[12]
He posited that evolution was the result of environmental stress on properties
of animals, meaning that the more frequently and rigorously an organ was used,
the more complex and efficient it would become, thus adapting the animal to its
environment. Lamarck believed that these acquired traits could then be passed
on to the animal's offspring, who would further develop and perfect them.[13]
However, it was the British naturalist Charles
Darwin, combining the biogeographical approach of Humboldt, the uniformitarian geology of Lyell,
Malthus's
writings on population growth, and his own morphological expertise and
extensive natural observations, who forged a more successful evolutionary
theory based on natural selection; similar reasoning and evidence
led Alfred Russel Wallace to independently reach
the same conclusions. Although it was the subject of controversy (which continues to this
day), Darwin's theory quickly spread through the scientific community and soon
became a central axiom of the rapidly developing science of biology.
The discovery
of the physical representation of heredity came along with evolutionary
principles and population genetics. In the 1940s and early
1950s, experiments pointed to DNA as the component of chromosomes
that held the trait-carrying units that had become known as genes. A focus on new
kinds of model organisms such as viruses and bacteria, along with the discovery of the double helical
structure of DNA in 1953, marked the transition to the era of molecular genetics. From the 1950s to present
times, biology has been vastly extended in the molecular
domain. The genetic code was cracked by Har Gobind Khorana, Robert
W. Holley and Marshall Warren Nirenberg after DNA was
understood to contain codons. Finally, the Human Genome Project was launched in 1990 with
the goal of mapping the general human genome. This
project was essentially completed in 2003,[15]
with further analysis still being published. The Human Genome Project was the
first step in a globalized effort to incorporate accumulated knowledge of
biology into a functional, molecular definition of the human body and the
bodies of other organisms.
Foundations of modern
biology
Cell theory
Cell theory states that the cell
is the fundamental unit of life,
and that all living things are composed of one or more cells or the secreted
products of those cells (e.g. shells).
All cells arise from other cells through cell division.
In multicellular organisms, every cell in the organism's
body derives ultimately from a single cell in a fertilized egg.
The cell is also considered to be the basic unit in many pathological
processes. Additionally, the phenomenon of energy flow
occurs in cells in processes that are part of the function known as metabolism.
Finally, cells contain hereditary information (DNA) which is passed from cell to
cell during cell division.
Evolution
Natural selection of a population for dark coloration.
A central organizing concept in biology is that
life changes and develops through evolution, and that all life-forms known have
a common origin. The theory of evolution postulates that all organisms
on the Earth,
both living and extinct, have descended from a common ancestor or an ancestral gene pool.
This last universal common ancestor of all organisms is believed to have
appeared about 3.5 billion years ago. Biologists generally regard the
universality and ubiquity of the genetic code
as definitive evidence in favor of the theory of universal common descent for
all bacteria, archaea,
and eukaryotes
(see: origin of life).
Introduced into the scientific lexicon by Jean-Baptiste de Lamarck in 1809, evolution was
established by Charles Darwin fifty years later as a viable scientific model
when he articulated its driving force: natural selection.
(Alfred Russel Wallace is recognized as the
co-discoverer of this concept as he helped research and experiment with the
concept of evolution.) Evolution is now used to explain the great variations of
life found on Earth.
Darwin theorized that species and breeds developed
through the processes of natural selection
and artificial selection or selective breeding. Genetic drift
was embraced as an additional mechanism of evolutionary development in the modern synthesis
of the theory.
The evolutionary history of the species—which
describes the characteristics of the various species from which it
descended—together with its genealogical relationship to every other species is
known as its phylogeny. Widely varied approaches to biology generate
information about phylogeny. These include the comparisons of DNA sequences
conducted within molecular biology or genomics,
and comparisons of fossils
or other records of ancient organisms in paleontology.
Biologists organize and analyze evolutionary relationships through various
methods, including phylogenetics, phenetics,
and cladistics.
(For a summary of major events in the evolution of life as currently understood
by biologists, see evolutionary timeline.)
A Punnett square
depicting a cross between two pea plants heterozygous for purple (B) and white
(b) blossoms
Genetics
Genes
are the primary units of inheritance in all organisms. A gene is a unit of heredity
and corresponds to a region of DNA
that influences the form or function of an organism in specific ways. All
organisms, from bacteria to animals, share the same basic machinery that copies
and translates DNA into proteins. Cells transcribe a DNA gene into an RNA version of the gene, and a ribosome
then translates the RNA into a protein, a sequence of amino acids.
The translation code from RNA codon to amino acid is the same for most
organisms, but slightly different for some. For example, a sequence of DNA that
codes for insulin
in humans also codes for insulin when inserted into other organisms, such as
plants.
DNA usually occurs as linear chromosomes
in eukaryotes,
and circular chromosomes in prokaryotes.
A chromosome is an organized structure consisting of DNA and histones.
The set of chromosomes in a cell and any other hereditary information found in
the mitochondria, chloroplasts,
or other locations is collectively known as its genome. In eukaryotes, genomic DNA is
located in the cell nucleus, along with small amounts in mitochondria
and chloroplasts. In prokaryotes, the DNA is held within an
irregularly shaped body in the cytoplasm called the nucleoid.
The genetic information in a genome is held within genes, and the complete
assemblage of this information in an organism is called its genotype.
Homeostasis
The
hypothalamus
secretes CRH, which directs the pituitary gland
to secrete ACTH.
In turn, ACTH directs the adrenal cortex to secrete glucocorticoids,
such as cortisol.
The GCs then reduce the rate of secretion by the hypothalamus and the pituitary
gland once a sufficient amount of GCs has been released.
Homeostasis is the ability of an open system to regulate its internal environment to maintain
stable conditions by means of multiple dynamic equilibrium adjustments controlled by interrelated regulation
mechanisms. All living organisms, whether unicellular
or multicellular, exhibit homeostasis.
To maintain dynamic equilibrium and effectively
carry out certain functions, a system must detect and respond to perturbations.
After the detection of a perturbation, a biological system normally responds
through negative feedback. This means stabilizing conditions by either
reducing or increasing the activity of an organ or system. One example is the
release of glucagon when sugar levels are too low.
Basic
overview of energy and human life.
Energy
The survival of a living organism depends on the
continuous input of energy.
Chemical reactions that are responsible for its structure and function are
tuned to extract energy from substances that act as its food and transform
them to help form new cells and sustain them. In this process, molecules
of chemical substances that constitute food play two roles; first, they
contain energy that can be transformed for biological chemical reactions;
second, they develop new molecular structures made up of biomolecules.
The organisms responsible for the introduction of
energy into an ecosystem are known as producers or autotrophs.
Nearly all of these organisms originally draw energy from the sun. Plants and
other phototrophs use solar energy via a process known as photosynthesis
to convert raw materials into organic molecules, such as ATP, whose bonds can be broken to release energy. A
few ecosystems,
however, depend entirely on energy extracted by chemotrophs
from methane, sulfides,
or other non-luminal energy sources.
Some of the captured energy is used to produce biomass
to sustain life
and provide energy for growth and development. The majority of the rest of this
energy is lost as heat and waste molecules. The most important processes for
converting the energy trapped in chemical substances into energy useful to
sustain life are metabolism and cellular respiration.
Study and research
Structural
Schematic of
typical animal cell depicting the various organelles
and structures.
Molecular
biology is the study of biology at a molecular level.[36]
This field overlaps with other areas of biology, particularly with genetics and biochemistry.
Molecular biology chiefly concerns itself with understanding the interactions
between the various systems of a cell, including the interrelationship of DNA,
RNA, and protein synthesis and learning how these interactions are regulated.
Cell
biology studies the structural and physiological
properties of cells, including their behaviors,
interactions, and environment. This is done on both the microscopic
and molecular
levels, for single-celled organisms such as bacteria as
well as the specialized cells in multicellular organisms such as humans. Understanding
the structure and function of cells is fundamental to all of the biological
sciences. The similarities and differences between cell types are particularly
relevant to molecular biology.
Genetics is the
science of genes, heredity, and
the variation of organisms. Genes encode the information necessary for
synthesizing proteins, which in turn play a central role in influencing the
final phenotype
of the organism. In modern research, genetics provides important tools in the
investigation of the function of a particular gene, or the analysis of genetic interactions. Within organisms, genetic
information generally is carried in chromosomes,
where it is represented in the chemical
structure of particular DNA molecules.
Developmental biology studies the process by
which organisms grow and develop. Originating in embryology,
modern developmental biology studies the genetic control of cell growth,
differentiation, and "morphogenesis,"
which is the process that progressively gives rise to tissues,
organs,
and anatomy. Model
organisms for developmental biology include the round worm Caenorhabditis elegans, the
fruit fly Drosophila melanogaster, the
zebrafish Danio rerio,
the mouse Mus musculus,, and the weed Arabidopsis thaliana. (A model organism
is a species
that is extensively studied to understand particular biological phenomena,
with the expectation that discoveries made in that organism provide insight
into the workings of other organisms.)
Physiological
Physiology studies the mechanical, physical, and
biochemical processes of living organisms by attempting to understand how all
of the structures function as a whole. The theme of "structure to
function" is central to biology. Physiological studies have traditionally
been divided into plant physiology and animal physiology,
but some principles of physiology are universal, no matter what particular organism
is being studied. For example, what is learned about the physiology of yeast cells can also apply to human
cells. The field of animal physiology extends the tools and methods of human physiology
to non-human species. Plant physiology borrows techniques from both research
fields.
Physiology studies how for example nervous, immune, endocrine, respiratory, and circulatory systems, function and interact. The study of these
systems is shared with medically oriented disciplines such as neurology
and immunology.
Evolutionary
Evolutionary research
is concerned with the origin and descent of species,
as well as their change over time, and includes scientists from many
taxonomically oriented disciplines. For example, it generally involves
scientists who have special training in particular organisms
such as mammalogy, ornithology, botany, or herpetology,
but use those organisms as systems to answer general questions about evolution.
Evolutionary biology is partly based on paleontology,
which uses the fossil
record to answer questions about the mode and tempo of evolution, and partly on
the developments in areas such as population genetics and evolutionary theory. In the 1980s, developmental biology re-entered evolutionary biology
from its initial exclusion from the modern synthesis
through the study of evolutionary developmental biology.
Related fields often considered part of evolutionary biology are phylogenetics, systematics,
and taxonomy.
Systematic
A phylogenetic tree
of all living things, based on rRNA gene data, showing the separation of
the three domains bacteria, archaea,
and eukaryotes
as described initially by Carl Woese.
Trees constructed with other genes are generally similar, although they may
place some early-branching groups very differently, presumably owing to rapid
rRNA evolution. The exact relationships of the three domains are still being
debated.
The
hierarchy of biological classification's eight major taxonomic ranks.
Intermediate minor rankings are not shown. This diagram uses a 3 Domains /
6 Kingdoms format
Multiple speciation
events create a tree structured system of relationships between species. The
role of systematics is to study these relationships and thus the
differences and similarities between species and groups of species. However,
systematics was an active field of research long before evolutionary thinking
was common.
Traditionally, living things have been divided into
five kingdoms: Monera; Protista; Fungi; Plantae; Animalia.[52]
However, many scientists now consider this five-kingdom system outdated. Modern
alternative classification systems generally begin with the three-domain system: Archaea
(originally Archaebacteria); Bacteria
(originally Eubacteria) and Eukaryota
(including protists, fungi, plants, and animals) These domains reflect whether
the cells have nuclei or not, as well as differences in the chemical
composition of the cell exteriors.
Further, each kingdom is broken down recursively
until each species is separately classified. The order is: Domain; Kingdom; Phylum; Class; Order; Family; Genus; Species.
Outside of these categories, there is a series of
intracellular parasites that are "on the edge of life" in terms
of metabolic
activity, meaning that many scientists do not actually classify these
structures as alive, due to their lack of at least one or more of the
fundamental functions that define life. They are classified as viruses, viroids, prions, or satellites.
The scientific name of an organism is generated
from its genus and species. For example, humans are listed as Homo sapiens. Homo
is the genus, and sapiens the species. When writing the scientific name
of an organism, it is proper to capitalize the first letter in the genus and
put all of the species in lowercase. Additionally, the entire term may be
italicized or underlined.
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