21-04-2011, 12:48 PM
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BIOINFORMATICS
breaking the medical barriers
ABSTRACT :
Days aren’t far off when beauty saloons will perform fundamental body changes apart from customizing looks of the people . If you aren’t born perfect , free from any disease and deformity , you need not despair . If you lack mathematical aptitude it will be incorporated in your mind . If you aren’t tall enough stature will be changed accordingly . If you are weak and not sturdy enough , your physique could be improved . At the first sign of the defect and deformity , people will stop around for a better and stronger organically grown heart , brain kidney or the liver etc . Mankind will be able to prolong its life or for that matter even may live forever
If you think this is the script for a science fiction movie , you are mistaken .It’s the future reality . All this is possible with a technology called BIOINFORMATICS. The convergence of biology, computer science, electronics and mathematics into the bioinformatics domain will be the enabling factor behind such innovations.
Bioinformatics is the application of biology , computer science , electronics , IT and mathematical and statistical tools in the domain of life sciences .This paper comprises of the live examples of the advancement of bioinformatics and its areas of applications like Motorola and IBM etc.
By using Bioinformatics today, we have :
DNA Chip : DNA Chip is small flat surface on which strands of one half of the DNA double-helix (called probes) are placed.
Protein Chip : Protein Chip is similar to DNA chips , except that these sample individual proteins that makes up the DNA .
Biochip : Biochip is an IC whose electrical and logical functions are performed by protein molecules appropriately manipulated.
Gene Chip : Gene chip reclassify diseases on the basis of their underlying molecular signals rather than misleading surface symptoms.
The human gene study has unlocked the DNA code, resulting in unlocking secrets of 23 human chromosomes. This will enable life science engineers to realize new drugs to treat diseases. Electronics and life science engineers are taking advantages of the similarities between the bio/gene chips and electronic circuits to evolve novel manufacturing techniques.
If such is the pace of development of bioinformatics than in future we can expect humans to live much longer and even become immortal……
INRODUCTION :
Days aren’t far off when beauty saloons will perform fundamental body changes apart from customizing looks of the people . If you aren’t born perfect , free from any disease and deformity , you need not despair . If you lack mathematical aptitude it will be incorporated in your mind . If you aren’t tall enough stature will be changed accordingly . If you are weak and not sturdy enough , your physique could be improved . At the first sign of the defect and deformity , people will stop around for a better and stronger organically grown heart , brain kidney or the liver etc . Mankind will be able to prolong its life or for that matter even may live forever If you think this is the script for a science fiction movie , you are mistaken .It’s the future reality .The future is often stranger than fiction . The convergence of biology , computational science , electronics and mathematics into the bioinformatics domain will be the enabling factor behind such innovations .
Dr . John Satini , a former researcher at Massachusetts Institute of Technology (MIT) , now heads a start-up company named Microchips that develops silicon chips with tiny wells filled with drug compounds . The drug compounds can be released in the human body in a controlled manner via the preprogrammed microchip .
What bioinformatics is ?
Bioinformatics is the application of biology , computer science , electronics , IT and mathematical and statistical tools in the domain of life sciences . Vijay S . Shukla , Director of Bioinformatics Institute of India , Noida , emphasizes the importance of advanced computational approaches in enabling bioinformatics researchers to organize , search , access , retrieve and analyze biological data .
Bioinformatics finds application in medicines for recommending individually tailored drugs based on an individual’s profile .
MAIN BODY :
Bioinformatics has given birth to various chips working at DNA level . Bioinformatics helps in controlling DNA as under :
DNA Control via RF Signal :
Researchers at MIT have moved a step towards integrating electronics and biological functions . They have been able to control biomolecules using RF energy and nanocrystal antenna . They remotely controlled the behavior of DNA , the basic building block of humans and other forms of life , causing it to switch from one state to another at will .
How it was done ?
An electronic interface to the bio molecule was created . RF magnetic field was inductively coupled to a 1nm long nanocrystal antenna linked covalently to a DNA molecule . The inductive coupling , i.e. the transfer of energy to the nanocrystal energy , increased the local temperature of the bound DNA , allowing the change of state to take place , while leaving molecules surrounding the DNA relatively unaffected . The switching was fully reversible , as dissolved molecules dissipated the heat in less than 50 pikoseconds . Thus RF signal generated outside the body can control changes in DNA . The signal used in the experiment was 1 GHz.
Human Electronics :
The nucleus is the most obvious organelle in the human cell . With in the nucleus is the DNA (deoxyribonucleic acid) responsible for providing the cell with its unique characteristics . The DNA is similar in every cell of the body , but depending on the specific cell type , some genes may be turned on or off - that’s why a liver cell is different from a muscle cell .
In DNA the medium is a chain of two units (phosphate and ribose) , and the most easily recognizable message is provided by a sequence of letters (bases) attached to the chain . The DNA has two sequences of letters wrapped around each other in the form of a double helix . One is the compliment of the other , so that the sequence of one string (strand) can be inferred from the sequence of the other . The DNA sequence of bases encodes 20 amino acids . Under instructions received from DNA , amino acids join together in the same order as they are encoded in DNA to form proteins . Chains of amino acids , which folds in very complicated ways , play a very important role in determining how we interact with the environment .
Moving towards the chips :
“ Mapping the human genome is akin to transcribing the text of a very big book”, says Nicholas Naclerio ,VP and GM of the Biochip Systems Unit of Motorola . He adds , “We all have this text without understanding of what it means . Its like knowing the alphabets but not being able to read anything .There is to go a long way before it will make sense .” Sevaral electronics companies have joined the ranks of public biotech companies and started funding start-ups that develop Biochips . Agilent Laboratories ,a unit of Agilent Technologies , has been researching biochips . Its Chemical Analysis Group has introduced the first commercially available ‘lab-on-a-chip’. The device prepares biological samples , handles fluids and performs biochemical analysis……..all on one microchip .
The lab-on-a-chip functions like a microprocessor . It carries out complicated multistep processes . DNA chips use a chemical that causes the DNA to fluoresce when a match occurs . Electronics circuits can be incorporated on the chip to detect various stages of the DNA . DNA carries an electric charge . That charge can be read on the chip just like a memory array . Motorola manufactures lab-on-a-chip devices on a process development line akin to the one used for semiconductor and MEMS technology . The manufacturing process is a kind of MEMS technology . Semiconductor processes such as photolithography and etching are used to make chips . But since the feature size of these chips is much larger than of typical IC’s the related process equipments are similar to those used in the flat-panel industry or a high-density circuit board facility , rather than the chip fab .
DNA Chip :
DNA Chips are small flat surfaces on which strands of one half of the DNA double-helix (called probes) are placed. Because one-half of the DNA double-helix naturally bonds with its complementary other half (a process called hybridization) this chip can be used to identify the presence of particular genes in a biological sample . These chips , called micro arrays , can be manufactured using semiconductor technology on variety of surfaces (including glass and plastic) .
DNA Chip used to detect pathogens :
Detecting pathogens, whether from natural diseases or biological weapons, is about to get faster and more convenient, thanks to a new technique that can sense harmful DNA and immediately alert a doctor or scientist. The research, published in the April 9 issue of the Journal of the American Chemical Society, uses custom-designed loops of DNA that emit colored light in the presence of a specific creature's DNA. The loop-laden chip could be used to detect anything from a bacterium or virus, to the specific DNA of a plant or person.
The new chip is remarkable in that it eliminates many of the time-consuming steps normally taken in identifying an organism by its DNA. Traditionally, workers in a laboratory have to make thousands of copies of a piece of DNA they want to test. Then a complex series of steps must be performed to attach a special molecule to the DNA, which will act as a fluorescent beacon, making the DNA strand easy to detect. These beacon-outfitted pieces are then mixed with control DNA sequences to see if any match. Matching sequences would adhere to one another, betraying their presence via the beacon.
The Rochester team, Krauss and Benjamin Miller, associate professor of dermatology, and post doctoral fellow Hui Du, has created a new technique that is far simpler. A scientist might only have to place a drop of the solution in question onto a small chip or card and watch for a change of color to indicate whether specific DNA is present. The chips are sensitive enough that copying may be unnecessary, as are complex beacon attachments, and the chips could be easily manufactured so doctors could instantly detect dozens or hundreds of pathogens right in their office. Future soldiers would also be able to identify unknown biological substances quickly and surely on the battlefield.
A chip using the new method would be constructed like a field of wilted sunflowers-customized sequences of DNA are bent like hairpins, with one end "planted" into a layer of metal and the other end hanging down alongside it . This dangling end contains a molecule called a flourophore , which , like the brilliant head of a sunflower, shines brightly when properly lighted. With all of the sunflowers' heads bent down to the ground, the field as a whole looks green because the fluorophore is short-circuited when directly on the metal. When "watered" with the right DNA sequence, however, the flowers stand erect, turning the entire field-and thus the chip-from green to bright yellow.
The unfolding of the chip's detector DNA strands happens when new DNA with a precise sequence is dripped onto the chip. The chip's DNA is designed to prefer to be bonded with a specific DNA sequence, such as a sequence unique to anthrax, than to remain folded over on itself. The new DNA bonds along the length of many of the chip's DNA and the two form a sort of rigid stem that lifts the beacon. The all-important beacon is pre-attached to the detector strand of DNA, rather than needing to be attached to each and every strand of DNA being tested
Currently, the Rochester team has developed chips that can detect an antibiotic-resistant type of stalph bacteria, and they're working on chips that can detect the non-antibiotic-resistant strain as well. A laser is also needed at present to highlight the "sunflower head," but Miller and Krauss are working on ways to make the signal from the beacon more easily visible.
Protein Chips :
Protein Chips are similar to DNA chips , except that these sample individual proteins that makes up the DNA . The market for these devices is less immediate because medical science is far from identifying and mapping all the 100,00 proteins that makes up DNA .
“With experience and expertise in semiconductor technology , electronics , softwares , MEMS , high density interconnects and flat-panel manufacturing - Motorola has the capability to develop biochips in high volume ,” says Mr.Naclerio .He points out that electronics companies can take advantages of some parallels between electronics and biology .
Biochip and the chip electronics :
Biochip is an IC whose electrical and logical functions are performed by protein molecules appropriately manipulated. Advances in molecular biology and semiconductor micro fabrication have resulted in new formats for hybridization arrays. These arrays consists of several electrodes covered by a thin layer of agarose. Each micro electrode is capable of generating a controllable electric current that can be used to draw biological samples, reagents and probes to specific locations on the chip surface. The no. of genes covered by these arrays depends on the no. electrodes made with in the area of the array.
Cell microarrays are high-density arrays of microwells fabricated on an optical fibre plane with a packing density of 10 wells per sq.cm. Each individually addressed microwell can accommodate a single living cell . A charged-couple device detector is used to monitor and spatially receive flurescence signals from each cell. The technology provides a reliable method to validate new disease-infected cells for early evaluation of potential drugs. The micro total analysis system (micro TAS) or a lab-on-a-chip for integrated bio-chemical analysis periodically transforms biochemical information into an electronic or optic signal. The components on the lab-on-a-chip device can be divided into active and passive components. Biological fluids to be tested are activated using the electrokinetic principle. Electrokinetic flow is generated when electrodes, attached with computer-driven power supplies, are placed in reservoirs of each end of a channel and activated to generate electric current through the channel under these conditions. Fluid flow takes through electro-osmosis and electrophoresis
BIOINFORMATICS
breaking the medical barriers
ABSTRACT :
Days aren’t far off when beauty saloons will perform fundamental body changes apart from customizing looks of the people . If you aren’t born perfect , free from any disease and deformity , you need not despair . If you lack mathematical aptitude it will be incorporated in your mind . If you aren’t tall enough stature will be changed accordingly . If you are weak and not sturdy enough , your physique could be improved . At the first sign of the defect and deformity , people will stop around for a better and stronger organically grown heart , brain kidney or the liver etc . Mankind will be able to prolong its life or for that matter even may live forever
If you think this is the script for a science fiction movie , you are mistaken .It’s the future reality . All this is possible with a technology called BIOINFORMATICS. The convergence of biology, computer science, electronics and mathematics into the bioinformatics domain will be the enabling factor behind such innovations.
Bioinformatics is the application of biology , computer science , electronics , IT and mathematical and statistical tools in the domain of life sciences .This paper comprises of the live examples of the advancement of bioinformatics and its areas of applications like Motorola and IBM etc.
By using Bioinformatics today, we have :
DNA Chip : DNA Chip is small flat surface on which strands of one half of the DNA double-helix (called probes) are placed.
Protein Chip : Protein Chip is similar to DNA chips , except that these sample individual proteins that makes up the DNA .
Biochip : Biochip is an IC whose electrical and logical functions are performed by protein molecules appropriately manipulated.
Gene Chip : Gene chip reclassify diseases on the basis of their underlying molecular signals rather than misleading surface symptoms.
The human gene study has unlocked the DNA code, resulting in unlocking secrets of 23 human chromosomes. This will enable life science engineers to realize new drugs to treat diseases. Electronics and life science engineers are taking advantages of the similarities between the bio/gene chips and electronic circuits to evolve novel manufacturing techniques.
If such is the pace of development of bioinformatics than in future we can expect humans to live much longer and even become immortal……
INRODUCTION :
Days aren’t far off when beauty saloons will perform fundamental body changes apart from customizing looks of the people . If you aren’t born perfect , free from any disease and deformity , you need not despair . If you lack mathematical aptitude it will be incorporated in your mind . If you aren’t tall enough stature will be changed accordingly . If you are weak and not sturdy enough , your physique could be improved . At the first sign of the defect and deformity , people will stop around for a better and stronger organically grown heart , brain kidney or the liver etc . Mankind will be able to prolong its life or for that matter even may live forever If you think this is the script for a science fiction movie , you are mistaken .It’s the future reality .The future is often stranger than fiction . The convergence of biology , computational science , electronics and mathematics into the bioinformatics domain will be the enabling factor behind such innovations .
Dr . John Satini , a former researcher at Massachusetts Institute of Technology (MIT) , now heads a start-up company named Microchips that develops silicon chips with tiny wells filled with drug compounds . The drug compounds can be released in the human body in a controlled manner via the preprogrammed microchip .
What bioinformatics is ?
Bioinformatics is the application of biology , computer science , electronics , IT and mathematical and statistical tools in the domain of life sciences . Vijay S . Shukla , Director of Bioinformatics Institute of India , Noida , emphasizes the importance of advanced computational approaches in enabling bioinformatics researchers to organize , search , access , retrieve and analyze biological data .
Bioinformatics finds application in medicines for recommending individually tailored drugs based on an individual’s profile .
MAIN BODY :
Bioinformatics has given birth to various chips working at DNA level . Bioinformatics helps in controlling DNA as under :
DNA Control via RF Signal :
Researchers at MIT have moved a step towards integrating electronics and biological functions . They have been able to control biomolecules using RF energy and nanocrystal antenna . They remotely controlled the behavior of DNA , the basic building block of humans and other forms of life , causing it to switch from one state to another at will .
How it was done ?
An electronic interface to the bio molecule was created . RF magnetic field was inductively coupled to a 1nm long nanocrystal antenna linked covalently to a DNA molecule . The inductive coupling , i.e. the transfer of energy to the nanocrystal energy , increased the local temperature of the bound DNA , allowing the change of state to take place , while leaving molecules surrounding the DNA relatively unaffected . The switching was fully reversible , as dissolved molecules dissipated the heat in less than 50 pikoseconds . Thus RF signal generated outside the body can control changes in DNA . The signal used in the experiment was 1 GHz.
Human Electronics :
The nucleus is the most obvious organelle in the human cell . With in the nucleus is the DNA (deoxyribonucleic acid) responsible for providing the cell with its unique characteristics . The DNA is similar in every cell of the body , but depending on the specific cell type , some genes may be turned on or off - that’s why a liver cell is different from a muscle cell .
In DNA the medium is a chain of two units (phosphate and ribose) , and the most easily recognizable message is provided by a sequence of letters (bases) attached to the chain . The DNA has two sequences of letters wrapped around each other in the form of a double helix . One is the compliment of the other , so that the sequence of one string (strand) can be inferred from the sequence of the other . The DNA sequence of bases encodes 20 amino acids . Under instructions received from DNA , amino acids join together in the same order as they are encoded in DNA to form proteins . Chains of amino acids , which folds in very complicated ways , play a very important role in determining how we interact with the environment .
Moving towards the chips :
“ Mapping the human genome is akin to transcribing the text of a very big book”, says Nicholas Naclerio ,VP and GM of the Biochip Systems Unit of Motorola . He adds , “We all have this text without understanding of what it means . Its like knowing the alphabets but not being able to read anything .There is to go a long way before it will make sense .” Sevaral electronics companies have joined the ranks of public biotech companies and started funding start-ups that develop Biochips . Agilent Laboratories ,a unit of Agilent Technologies , has been researching biochips . Its Chemical Analysis Group has introduced the first commercially available ‘lab-on-a-chip’. The device prepares biological samples , handles fluids and performs biochemical analysis……..all on one microchip .
The lab-on-a-chip functions like a microprocessor . It carries out complicated multistep processes . DNA chips use a chemical that causes the DNA to fluoresce when a match occurs . Electronics circuits can be incorporated on the chip to detect various stages of the DNA . DNA carries an electric charge . That charge can be read on the chip just like a memory array . Motorola manufactures lab-on-a-chip devices on a process development line akin to the one used for semiconductor and MEMS technology . The manufacturing process is a kind of MEMS technology . Semiconductor processes such as photolithography and etching are used to make chips . But since the feature size of these chips is much larger than of typical IC’s the related process equipments are similar to those used in the flat-panel industry or a high-density circuit board facility , rather than the chip fab .
DNA Chip :
DNA Chips are small flat surfaces on which strands of one half of the DNA double-helix (called probes) are placed. Because one-half of the DNA double-helix naturally bonds with its complementary other half (a process called hybridization) this chip can be used to identify the presence of particular genes in a biological sample . These chips , called micro arrays , can be manufactured using semiconductor technology on variety of surfaces (including glass and plastic) .
DNA Chip used to detect pathogens :
Detecting pathogens, whether from natural diseases or biological weapons, is about to get faster and more convenient, thanks to a new technique that can sense harmful DNA and immediately alert a doctor or scientist. The research, published in the April 9 issue of the Journal of the American Chemical Society, uses custom-designed loops of DNA that emit colored light in the presence of a specific creature's DNA. The loop-laden chip could be used to detect anything from a bacterium or virus, to the specific DNA of a plant or person.
The new chip is remarkable in that it eliminates many of the time-consuming steps normally taken in identifying an organism by its DNA. Traditionally, workers in a laboratory have to make thousands of copies of a piece of DNA they want to test. Then a complex series of steps must be performed to attach a special molecule to the DNA, which will act as a fluorescent beacon, making the DNA strand easy to detect. These beacon-outfitted pieces are then mixed with control DNA sequences to see if any match. Matching sequences would adhere to one another, betraying their presence via the beacon.
The Rochester team, Krauss and Benjamin Miller, associate professor of dermatology, and post doctoral fellow Hui Du, has created a new technique that is far simpler. A scientist might only have to place a drop of the solution in question onto a small chip or card and watch for a change of color to indicate whether specific DNA is present. The chips are sensitive enough that copying may be unnecessary, as are complex beacon attachments, and the chips could be easily manufactured so doctors could instantly detect dozens or hundreds of pathogens right in their office. Future soldiers would also be able to identify unknown biological substances quickly and surely on the battlefield.
A chip using the new method would be constructed like a field of wilted sunflowers-customized sequences of DNA are bent like hairpins, with one end "planted" into a layer of metal and the other end hanging down alongside it . This dangling end contains a molecule called a flourophore , which , like the brilliant head of a sunflower, shines brightly when properly lighted. With all of the sunflowers' heads bent down to the ground, the field as a whole looks green because the fluorophore is short-circuited when directly on the metal. When "watered" with the right DNA sequence, however, the flowers stand erect, turning the entire field-and thus the chip-from green to bright yellow.
The unfolding of the chip's detector DNA strands happens when new DNA with a precise sequence is dripped onto the chip. The chip's DNA is designed to prefer to be bonded with a specific DNA sequence, such as a sequence unique to anthrax, than to remain folded over on itself. The new DNA bonds along the length of many of the chip's DNA and the two form a sort of rigid stem that lifts the beacon. The all-important beacon is pre-attached to the detector strand of DNA, rather than needing to be attached to each and every strand of DNA being tested
Currently, the Rochester team has developed chips that can detect an antibiotic-resistant type of stalph bacteria, and they're working on chips that can detect the non-antibiotic-resistant strain as well. A laser is also needed at present to highlight the "sunflower head," but Miller and Krauss are working on ways to make the signal from the beacon more easily visible.
Protein Chips :
Protein Chips are similar to DNA chips , except that these sample individual proteins that makes up the DNA . The market for these devices is less immediate because medical science is far from identifying and mapping all the 100,00 proteins that makes up DNA .
“With experience and expertise in semiconductor technology , electronics , softwares , MEMS , high density interconnects and flat-panel manufacturing - Motorola has the capability to develop biochips in high volume ,” says Mr.Naclerio .He points out that electronics companies can take advantages of some parallels between electronics and biology .
Biochip and the chip electronics :
Biochip is an IC whose electrical and logical functions are performed by protein molecules appropriately manipulated. Advances in molecular biology and semiconductor micro fabrication have resulted in new formats for hybridization arrays. These arrays consists of several electrodes covered by a thin layer of agarose. Each micro electrode is capable of generating a controllable electric current that can be used to draw biological samples, reagents and probes to specific locations on the chip surface. The no. of genes covered by these arrays depends on the no. electrodes made with in the area of the array.
Cell microarrays are high-density arrays of microwells fabricated on an optical fibre plane with a packing density of 10 wells per sq.cm. Each individually addressed microwell can accommodate a single living cell . A charged-couple device detector is used to monitor and spatially receive flurescence signals from each cell. The technology provides a reliable method to validate new disease-infected cells for early evaluation of potential drugs. The micro total analysis system (micro TAS) or a lab-on-a-chip for integrated bio-chemical analysis periodically transforms biochemical information into an electronic or optic signal. The components on the lab-on-a-chip device can be divided into active and passive components. Biological fluids to be tested are activated using the electrokinetic principle. Electrokinetic flow is generated when electrodes, attached with computer-driven power supplies, are placed in reservoirs of each end of a channel and activated to generate electric current through the channel under these conditions. Fluid flow takes through electro-osmosis and electrophoresis
