Biochipss

CDGI’S
CHAMELI DEVI SCHOOL OF
ENGINEERING, INDORE
Bio Chips
by
Arvind Carpenter
(0832CS121020)
Mr. Ajay Jaiswal
(Assistant Professor)
DEPARTMENT OF COMPUTER SCIENCE
ENGINEERING
EVEN SEMESTER 2015 – 2016

i
CDGI’S
CHAMELI DEVI SCHOOL OF ENGINEERING,
INDORE
DEPARTMENT OF COMPUTER SCIENCE
ENGINEERING
CERTIFICATE
Certified that this is the bonafide record of the seminar report on
Bio Chips
Carried out by
Arvind Carpenter (0832CS121020)
Of VI semester (Department of Computer Science Engineering) during the Even
Semester 2015 – 16. He has satisfactorily completed the seminar report and
presentation as prescribed by the Rajiv Gandhi Technical University, Bhopal, in
partial fulfillment towards the award of B.E. Degree in Computer Science
Engineering.
Signature of Guide Signature of Seminar coordinator
(Name: Mr. Ajay Jaiswal) (Name:Mr. YashwantSingh Patel)
Date:30/04/2015 Date:30/04/2015
Signature of HOD
(Name: Mr. Surendra Shukla)

1
ABSTRACT
The human body is the next big target of chipmakers. It won’t be long before biochip implants will
come to the rescue of sick, those who are lost, gunned soldiers and wandering mental patients etc.
Medical researchers have been working to integrate chips and people for many years, often plucking
devices from well known electronic appliances.
Biochips are being used to genetic, toxicological, protein and biochemical researches. It can also be
used to rapidly detect chemical agents used in biological warfare so that defensive measures can be taken.
Currently implanted systems have got a range of about two to twelve inches.
The civil liberties debate over biochips has obscured more ethically benign and medically useful
applications. By using Agilent 2100 Bioanalyzer streamline processes of RNA isolation, gene expression
analysis, protein expression, protein purification and more.

2
CDGI’S
CHAMELI DEVI SCHOOL OF ENGINEERING, INDORE
DEPARTMENT OF COMPUTER SCIENCE ENGINEERING
ACKNOWLEDGEMENT
I have immense pleasure in expressing my sincerest and deepest sense of gratitude towards
my Guide Mr. Ajay Jaiswal (Assistant Professor) for the assistance in preparing and
presenting the seminar. I also take this opportunity to thank Seminar Coordinator and Head
of the department, for providing the required facilities in completing my seminar report.
I am greatly thankful to my Parents, Friends and Faculty members for their motivation,
guidance and help whenever needed.
Arvind Carpenter
(0832CS121020)

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Contents
Chapter No. Description Page numbers.
Certificate i
Synopsis 1
Acknowledgement 2
Contents 3
1 Introduction 4
2 Biochip definition 5
3 Structure and working of an already implanted system 6 - 8
4 Biochips currently under development 9 - 13
5 The Agilent 2100 Bio analyzer 14
6 Biochips in noninfectious diseases 15-16
7 DNA biochips 17
8 Conclusion 18
9 References 19
List of Figures
Title of Figure Page
numbers.
Components of Bio Chip 7
Bio Chip and Syringe 8
Reader and Scanner 9
The S4MS Chip Sensing Oxygen or Glucose 11
The Clarion Cochlear Implant 13
The Circuitry Of The Implanted Part Of The Cochlear Implant 13

4
INTRODUCTION
Most of us won’t like the idea of implanting a biochip in our body that identifies us uniquely and can
be used to track our location. That would be a major loss of privacy. But there is a flip side to this! Such
biochips could help agencies to locate lost children, downed soldiers and wandering Alzheimer’s patients.
The human body is the next big target of chipmakers. It won’t be long before biochip implants will
come to the rescue of sick, or those who are handicapped in someway. Large amount of money and research
has already gone into this area of technology.
Anyway, such implants have already experimented with. A few US companies are selling both chips
and their detectors. The chips are of size of an uncooked grain of rice, small enough to be injected under the
skin using a syringe needle. They respond to a signal from the detector, held just a few feet away, by
transmitting an identification number. This number is then compared with the database listings of register
pets.
Daniel Man, a plastic surgeon in private practice in Florida, holds the patent on a more powerful
device: a chip that would enable lost humans to be tracked by satellite.

5
BIOCHIP DEFINITION
A biochip is a collection of miniaturized test sites (micro arrays) arranged on a solid substrate that
permits many tests to be performed at the same time in order to get higher throughput and speed. Typically,
a biochip’s surface area is not longer than a fingernail. Like a computer chip that can perform millions of
mathematical operation in one second, a biochip can perform thousands of biological operations, such as
decoding genes, in a few seconds.
A genetic biochip is designed to “freeze” into place the structures of many short strands of DNA
(deoxyribonucleic acid), the basic chemical instruction that determines the characteristics of an organism.
Effectively, it is used as a kind of “test tube” for real chemical samples.
A specifically designed microscope can determine where the sample hybridized with DNA strands in
the biochip. Biochips helped to dramatically increase the speed of the identification of the estimated 80,000
genes in human DNA, in the world wide research collaboration known as the Human Genome Project. The
microchip is described as a sort of “word search” function that can quickly sequence DNA.
In addition to genetic applications, the biochip is being used in toxicological, protein, and
biochemical research. Biochips can also be used to rapidly detect chemical agents used in biological warfare
so that defensive measures can be taken.
Motorola, Hitachi, IBM, Texas Instruments have entered into the biochip business.

6
STRUCTURE AND WORKING OF AN ALREADY IMPLANTED
SYSTEM
The biochip implants system consists of two components: a transponder and a reader or scanner.
The transponder is the actual biochip implant. The biochip system is radio frequency identification (RFID)
system, using low-frequency radio signals to communicate between the biochip and reader. The reading
range or activation range, between reader and biochip is small, normally between 2 and 12 inches.
The transponder
The transponder is the actual biochip implant. It is a passive transponder, meaning it contains no
battery or energy of its own. In comparison, an active transponder would provide its own energy source,
normally a small battery. Because the passive contains no battery, or nothing to wear out, it has a very long
life up to 99 years, and no maintenance. Being passive, it is inactive until the reader activates it by sending it
a low-power electrical charge. The reader reads or scans the implanted biochip and receives back data (in
this case an identification number) from the biochips. The communication between biochip and reader is via
low-frequency radio waves. Since the communication is via very low frequency radio waves it is nit at all
harmful to the human body.
The biochip-transponder consists of four parts; computer microchip, antenna coil, capacitor and
the glass capsule.
COMPONENTS OF BIOCHIP

7
Computer microchips
The microchip stores a unique identification number from 10 to 15 digits long. The storage capacity
of the current microchips is limited, capable of storing only a single ID number. AVID (American
Veterinary Identification Devices), claims their chips, using a nnn-nnn-nnn format, has the capability of over
70 trillion unique numbers. The unique ID number is “etched” or encoded via a laser onto the surface of the
microchip before assembly. Once the number is encoded it is impossible to alter. The microchip also
contains the electronic circuitry necessary to transmit the ID number to the “reader”.
BIOCHIP & SYRINGE
Antenna Coil
This is normally a simple, coil of copper wire around a ferrite or iron core. This tiny, primitive, radio
antenna receives and sends signals from the reader or scanner.
Tuning Capacitor
The capacitor stores the small electrical charge (less than 1/1000 of a watt) sent by the reader or
scanner, which activates the transponder. This “activation” allows the transponder to send back the ID
number encoded in the computer chip. Because “radio waves” are utilized to communicate between the
transponder and reader, the capacitor is tuned to the same frequency as the reader.
Glass Capsule
The glass capsule “houses” the microchip, antenna coil and capacitor. It is a small capsule, the
smallest measuring 11 mm in length and 2 mm in diameter, about the size of an uncooked grain of rice. The
capsule is made of biocompatible material such as soda lime glass.
After assembly, the capsule is hermetically (air-tight) sealed, so no bodily fluids can touch the
electronics inside. Because the glass is very smooth and susceptible to movement, a material such as a
polypropylene polymer sheath is attached to one end of the capsule. This sheath provides a compatible
surface which the boldly tissue fibers bond or interconnect, resulting in a permanent placement of the
biochip.

8
The biochip is inserted into the subject with a hypodermic syringe. Injection is safe and simple,
comparable to common vaccines. Anesthesia is not required nor recommended. In dogs and cats, the biochip
is usually injected behind the neck between the shoulder blades.
READER AND SCANNER
The reader
The reader consists of an “exciter coil” which creates an electromagnetic field that, via radio signals,
provides the necessary energy (less than 1/1000 of a watt) to “excite” or “activate” the implanted biochip.
The reader also carries a receiving coil that receives the transmitted code or ID number sent back from the
“activated” implanted biochip. This all takes place very fast, in milliseconds. The reader also contains the
software and components to decode the received code and display the result in an LCD display. The reader
can include a RS-232 port to attach a computer.
How it works
The reader generates a low-power, electromagnetic field, in this case via radio signals, which
“activates” the implanted biochip. This “activation” enables the biochip to send the ID code back to the
reader via radio signals. The reader amplifies the received code, converts it to digital format, decodes and
displays the ID number on the reader’s LCD display. The reader must normally be between 2 and 12 inches
near the biochip to communicate. The reader and biochip can communicate through most materials, except
metal.

9
BIOCHIPS CURRENTLY UNDER DEVELOPMENT
1. Chips that follow footsteps
2. Glucose level detectors
3. Oxy sensors
4. Brain surgery with an on-off switch
5. Adding sound to life
6. Experiments with lost sight
Chips that follow footsteps
The civil liberties debate over biochips has obscured their more ethically benign and medically
useful applications. Medical researchers have been working to integrate chips and people for many years,
often plucking devices from well known electronic appliances. Jeffry Hausdorff of the Beth Israel
Deaconess Medical Center in Boston has used the type of pressure sensitive resistors found in the buttons of
a microwave oven as stride timers. He places one sensor in the heel of a shoe, and one in the toe, adds a
computer to the ankle to calculate the duration of each stride.
“Young, healthy subjects can regulate the duration of each step very accurately,” he says. But elderly
patients prone to frequent falls have extremely variable stride times, a flag that could indicate the need for
more strengthening exercises or a change in medication. Hausdorff is also using the system to determine the
success of a treatment for congestive heart failure. By monitoring the number of strides that a person takes,
can directly measure the patient’s activity level, bypassing the often-flowed estimate made by the patient.
Glucose level detectors
Diabetics currently use a skin prick and a handheld blood test, and then medicate themselves with the
required amount of insulin. The system is simple and works well, but the need to draw blood means that
most diabetics do not test themselves as often as they should. The new S4MS chip will simply sit under the
skin, sense the glucose level, and send the result back out by radio frequency communication.
A light emitting diode starts off the detection process. The light that it produces hits a fluorescent
chemical: one that absorbs the incoming light and re-emits it at a longer wavelength. The longer wavelength
of light is detected, and the result is send to a control panel outside the body. Glucose is detected because the
sugar reduces the amount of light that a fluorescent chemical re-emits. The more glucose is there the less
light that is detected.
S4MS is still developing the perfect fluorescent chemical, but the key design innovation of the S4MS
chip has been fully worked out. The idea is simple: the LED is sitting in a sea of fluorescent molecules. In
most detectors the light source is far away from the fluorescent molecules, and the inefficiencies that come
with that mean more power and larger devices. The prototype S4MS chip uses a 22 microwatt LED, almost
forty times less powerful than a tiny power-on buttons on a computer keyboard. The low power
requirements mean that energy can be supplied from outside, by a process called induction. The fluorescent
detection itself does not consume any chemicals or proteins, so the device is self sustaining.

10
THE S4MS CHIP SENSING OXYGEN OR GLOUCOSE
Oxy Sensors:
A working model of an oxy sensor uses the same layout. With its current circuitry, it is about the size
of a large shirt button but the final silicon wafer will be less than a millimeter square. The oxygen sensors
will be useful not only to monitor breathing inside intensive care units, but also to check that packages of
food, or containers of semiconductors stored under nitrogen gas remain airtight.
Another version of an oxygen sensing chip currently under development sends light pulses out into
the body. The light absorbed to varying extends, depending on how much oxygen is carried in the blood, and
this chip detects the light that is left. The rushes of blood pumped by the heart are also detected, so the same
chip is a pulse monitor. A number of companies already make large scale versions of such detectors.
The transition of certain semiconductors to their conducting state is inherently sensitive to
temperature, so designing the sensor was simple enough. With some miniature radio frequency transmitters,
and foam-rubber earplugs to hold the chip in place, the device is complete. Applications range from sick
children, to chemotherapy patients who can be plagued by sudden rises in body temperature in response to
their anti-cancer drugs.
Brain surgery with an on-off switch:
Sensing and measuring is one thing, but can we switch the body on and off? Heart pacemakers use
the crude approach: large jolts of electricity to synchronize the pumping of the heart. The electric pulses of
Activa implant, made by US-based Medtronics Inc., are directed not at the heart but at the brain. They turn
off brain signals that cause the uncontrolled movements, or tremors, associated with disease such as
Parkinson’s.
OPTICAL
FILTER
PHOTODIODE DETECTOR
FLUORESCENT
MOLECULES
LED

11
Drug therapy of Parkinson’s disease aims to replace the brain messenger dopamine, a product of
brain cells that are dying. But eventually the drug’s effects wear off, and the erratic movements come
charging back.
The Activa implant is a new alternative that uses high-frequency electric pulses to reversibly shut off
the thalamus. The implantation surgery is far less traumatic than thalamatomy, and if there are any post-
operative problems the stimulator can simply be turned off. The implant primarily interferes with aberrant
brain functioning.
Adding sound to life
The most ambitious bioengineers are today trying to add back brain functions, restoring sight and
sound where there was darkness and silence. The success story in this field is the cochlear implant. Most
hearing aids are glorified amplifiers, but the cochlear implant is for patients who have lost the hair cells that
detect sound waves. For these patients no amount of amplification is enough.

12
THE CLARION COCHLEAR IMPLANT
THE CIRCUITRY OF THE IMPLANTED PART OF THE COCHLEAR IMPLANT
The cochlear implant delivers electrical pulses directly to the nerve cells in the cochlea, the spiral-
shaped structure that translates sound in to nerve pulses. In normal hearing individuals, sound waves set up
vibrations in the walls of the cochlea, and hair cells detect these vibrations. High-frequency notes vibrate
nearer the base of cochlea, while low frequency notes nearer the top of the spiral. The implant mimics the
job of the hair cells. It splits the incoming noises into a number of channels (typically eight) and then
stimulates the appropriate part of the cochlea.
The two most successful cochlear implants are ‘Clarion’ and ‘Nucleus’.

13
Experiments with lost sight
With the ear at least partially conquered, the next logical target is the eye. Several groups are
working on the implantable chips that mimic the action of photoreceptors, the light-sensing cells at the back
of the eye. Photoreceptors are lost in retinitis pigmentosa, a genetic disease and in age related macular
degeneration, the most common reason for loss sight in the developed world. Joseph Rizzo of the
Massachusetts Eye and Ear Infirmary, and John Wyatt of Massachusetts Institute of Technology have made
a twenty electrode 1mm-square chip, and implanted it at the back of rabbit’s eyes.
The original chip, with the thickness of human hair, put too much stress on the eye, so the new
version is ten times thinner. The final setup will include a fancy camera mounted a pair of glasses. The
camera will detect and encode the scene, then send it into the eye as a laser pulse, with the laser also
providing the energy to drive the chip.
Rizzo has conformed that his tiny array of light receivers (photodiodes) can generate enough
electricity needed to run the chip. He has also found that the amount of electricity needed to fire a nerve cell
into action is 100-fold lower than in the ear, so the currents can be smaller, and the electrodes more closely
spaced.
For now the power supply comes from a wire inserted directly in the eye and, using this device,
signals reaches the brain.
Eugene de Jaun of Hopkins Wilmer Eye Institute is trying electrodes, electrodes inserted directly in
to the eyes, are large and somewhat crude. But his result has been startling. Completely blind patients have
seen well-defined flashes, which change in position and brightness as de Jaun changes the position of the
electrode or amount of current.
In his most recent experiments, patients have identified simple shapes outlined by multiple
electrodes.
In one US project chips are implanted on the surface of the retina, the structure at the back of the
eyes. The project is putting its implants at the back of the retina, where the photoreceptors are normally
found.

14
THE AGILENT 2100 BIOANALYZER
The Agilent 2100 bioanalyzer is the industry’s only platform with the ability to analyze DNA,
RNA, proteins and cells. Through lab-on-a-chip technology the 2100 bioanalyzer integrates sample
handling, separation, detection and data analysis onto one platform. It moves labs beyond messy, time
consuming gel preparation and the subjective results associated with electrophoresis. And now, with our
second generation 2100 bioanalyzer, we have integrated an easier way to acquire cell based parameters from
as few as 20,000 cells per sample.
The process is simple: load sample, run analysis, and view data. The 2100 bioanalyzer is designed to
streamline the processes of RNA isolation, gene expression analysis, protein expression, protein purification
and more. One platform for entire workflow!

15
BIOCHIPS IN NONINFECTIOUS DISEASES
Biochips and Proteomics
Biochip technology was largely established by the development of micro array biochips for
genomics research. The emergence of the biochip was perhaps an inevitable development, an expansion of
existing chemistries and concepts into the information rich world of genomics. The GeneChip, developed at
Affymax, remains the best known example of a biochip.
The essential property of a biochip is the use of solid phase support and interfacial chemistry to
capture molecules from a sample and present them for analysis. The use of a solid support provides the
separation and isolation of an analyst, and creates the opportunity for high density micro arrays of sampling
sites. Combined with scalable production techniques, often borrowed from semiconductor fabrication, it also
offers the potential of high sample throughput. There are no absolute restriction on the types of molecules
that can be analyzed using a biochip, only technical problems related to binding, retention and assay.
With the maturing of genomics, some limitations of genome-based research have become apparent.
Although extremely useful, characterization of a cell based upon its genes or gene transcripts is only an
indirect view. From an engineering perspective, the complete state of cell might be defined by its molecular
composition. While this includes DND, RNA, small molecules, and ions, this state is defined by proteins
and peptides. Consequently, proteomics, the systems level study of proteins, represents a direct view of the
state of a cell and its parent organism. With some abstraction, in clinical practice the protein profile obtained
from a biological sample may be seen as synonymous to the phenotype and overall health state of a patient.
SELDI Protein Biochips
A major challenge in molecular biology, and particularly biochip development, is the detection of
analytics present in mixtures at extremely low concentrations. Mixtures create limitations for the optical
detection methods typically used with biochips, while low concentrations present problems when traditional
separation techniques, such as 2-D electrophoresis, are applied.
Surface Enhanced Laser Desorption Ionization Time-of-Flight Mass Spectroscopy (SELDI-TOF
MS) was developed in the last decade as a powerful tool for overcoming these limitations, and is now being
commercialized by several companies.
With a SELDI protein biochip, proteins are captured at a target site using techniques that are similar
to traditional chromatographic techniques, the analysis of the biochips, however, is quite different. Instead of
optical detection, the bound proteins are combined with a charge and energy transfer molecule and assayed
using laser desorption ionization time-of-flight mass spectroscopy. With TOF MS, it becomes possible to
simultaneously identify hundreds or thousands of proteins and peptides bound to a single site. TOF MS is
also capable of detecting analytes present in nanomole to sub-femtomole quantities, corresponding to
millimolar to Pico molar concentrations in a typical biological sample. Because of these capabilities, SELDI
biochip surfaces can be prepared with diverse chemistries that have varying degrees of protein-binding
specificity, and their selectivity may be further enhanced through variations in protein capture and retention
protocols.

16
Bioinformatics with SELDI Biochips
In practice, the SELDI-TOF technique provides mass spectra of proteins unmatched in both its
sensitivity and its ability to identify hundreds of proteins simultaneously. A collection of protein mass
spectra can be obtained from diverse biochip surfaces, using varied protein binding protocols, creating a
protein map. The information in this protein map combines protein molecular weight with chemical
knowledge derived from the protein binding interactions at the biochip surface.
Protein maps are rich descriptions of the biological sample, which characterize the psychological
state of a patient. Their information destiny and complexity often defies simpler linear analysis. In order to
best utilize this data, LumiCyte has developed software that incorporates the latest techniques for data base
mining, pattern recognition, and artificial intelligence. Some of the challenges include managing large
volume data sets, searching for reproducible patters in data, which has variable alignment and instrument
artifacts, and dealing with the inherent variability present in biological samples. Classification and analysis
methods that have been successful include both trained artificial intelligence tools, such as support vector
machines and genetic algorithms, as well as unsupervised cluster analysis.
Applying these tools to the differential analysis of protein maps rapidly uncovers the extent and
nature of protein variations. This analysis can be applied to samples from multiple patients of differing
phenotypes, where it leads to early detection of disease, even in asymptomatic patients. It also provides a
powerful tool for discriminating between physiologically distinct diseases that present similar or even
identical symptoms. With samples from a single patient, analysis of protein maps reveals early onset of
disease, disease progression, and the patient’s response to therapy.
Challenges ofprotein biochips
A number of challenges remain that define the current boundaries of SELDI biochip technology. For
physical scientists, the optimization of surfaces that capture and present proteins is an ongoing activity, and
the development of TOF MS for detection over an even wider dynamic range is essential to find rare,
important proteins in the presence of ubiquitous, common proteins. For biological scientists, sequencing
proteins that are discovered with SELDI-TOF MS and interpreting the complex network of revealed proteins
are tasks that expand with every new sample set.
For applied mathematicians and software engineers, creating new pattern recognition tools is
important as we attempt to identify weaker and weaker signals in the protein map capture.

17
DNA BIOCHIPS
A new DNA biochip developed by Tuan Vo-Dinh and colleagues at the Department of Energy’s
(DOE) Oak Ridge National Laboratory (ORNL) could revolutionize the way the medical profession
performs tests on blood. Instead of patient having to wait several days for the results form a laboratory, they
are virtually immediate with the matchbox-sized biochip. And it requires less blood with no sacrifice on
accuracy.
In addition to time savings, the DNA biochip eliminates the needs for radioactive labels used for
detection. This greatly reduces cost and potential health effects to technicians and lab workers handling
samples and performing tests. It also reduces disposal costs because chemically labeled blood must be
handled according to strict regulations.
To be useful for detecting compounds in a real-life sample, a biosensor must be extremely sensitive
and able to distinguish between, for example, a bacteria, virus or chemical or biological species. ORNL’s
DNA biochip does that.
Unlike other biosensors based on enzyme and antibody probes, The DNA biochip is a gene probe-
based biosensor.

18
CONCLUSION
Within ten years you will have a biochip implanted in your head consisting of financial status,
employment and medical records.
Even in a grocery store, sensor will read the credit chip and will automatically debit the account for
purchase.
A biochip implanted in our body can serve as a combination of credit ca5rd, passport, driver’s
license and personal diary. And there is nothing to worry about losing them.
It is said that by 2008, all members of typical American family including there pets will have
microchips under their skin with ID and medical data .

19
REFERENCES
 www.eurobiochips.com
 www.whatis.com/definition
 www.drugandmarket.com
 www.biochips.org
 www.knowledgefoundation.com
 www.bioarraynews.com
 www.biochips.ifrance.com

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