" I Just Found It "

U.N. To Establish Protocols For When We Make Contact With Aliens

2010-10-01T23:38:00.002+05:30

The United Nations Office of Outer Space Affairs (UNOOSA) has announced that it will consider drafting protocols for what to do when we finally make contact with extra-terrestrial civilizations in space. What's prompting the UN to consider this possibility is the fact that astronomers are expected to announce, perhaps later this year or next year, that our satellites (such as Kepler and Corot) have identified earth-like planets in space. So far, almost 500 large Jupiter-sized planets have been discovered.

Random Numbers Created Out Of Nothing

2010-10-01T10:16:00.001+05:30

It's something from nothing. A random number generator that harnesses the quantum fluctuations in empty space could soon sit inside your computer.
A device that creates truly random numbers is vital for a number of applications, including cryptography.
Algorithms can generate numbers that pass statistical tests for randomness, but they're useless for secure cryptography if the algorithm falls into the wrong hands. Other methods using entangled ions to generate random numbers are more reliable, but tend to be slower and more expensive.
Now Christian Gabriel's team at the Max Planck Institute for the Science of Light in Erlangen, Germany, has built a prototype that draws on a vacuum's random quantum fluctuations. These impart random noise to laser beams in the device, which converts it into numbers.

Undersea cauldrons replicated life's ingredients - life - 27 May 2010 - New Scientist

2010-05-28T12:37:00.000+05:30

The precursor of life may have learned how to copy itself thanks to simple convection at the bottom of the ocean.

Lab experiments reveal how DNA replication could have occurred in tiny pores around undersea vents.

The work shows that DNA can be both concentrated and replicated under a very simple set of conditions.

Novel Nanoparticle Vaccine Cures Type1 Diabetes In Mice

2010-04-11T12:42:00.006+05:30

An innovative nanotech "vaccine" has been proven to cure type 1 diabetes in mice, and paves the way to do the same for humans. A dose of therapeutic nanoparticles given to diabetic mice restored healthy sugar levels in the rodents.

The nanoparticles making up the vaccine, thousands of times smaller than the cells they act on, are coated with protein fragments that suppress the autoimmune response that's characteristic of diabetes. Most importantly, unlike existing treatments for autoimmune disorders, the particles do all this without compromising the rest of the immune system.

In autoimmune diseases like type 1 diabetes, the body basically wages war on itself. The nanovaccine helps to suppress the immune attacks by blocking the stimulus that causes the aggressive T-cells to attack.

The technology behind the nanovaccine, following further research, may prove widely applicable to treat other autoimmune diseases, like arthritis and multiple sclerosis, as well.

NANO : "giving a new life to BIO"

2009-12-05T11:52:00.002+05:30

A NANOMETER – suddenly it seems to have grown immensely. A radical revolution has been brought about by nanotechnology and a lot more expected to come.

What actually is Nanotechnology? - It is a technology for doing things on a very small scale.

What is that scale? - Definition includes anything smaller than 100 nanometers, where 1 nanometer (nm) is equal to one billionth of a meter.

Nanotechnology works by exploiting the unique properties of particles at the nano – scale and applying it at the desired place, using basically a bottom-up approach. This is really a vast domain. It can be either for physics, for chemistry, for biology, for materials, for medicine and so forth. The size dependent properties of nanomaterials make them unique and of great use in many areas of human activities. As a tool, nanotechnology has got an immense perceived potential for diverse fields of science. When we say science, let’s give our first consideration to, biology – ‘the study of life and living organisms’ because it is this ‘life’ that really distinguishes us from the dead, leaving philosophy apart. The most necessary requirement to prove one living is to possess an inherent ability to replicate. This property starts at the level of DNA. Hence, life starts with DNA coming into existence. What else, even the groundwork for nanotechnology was laid 50 years ago, when Nobel-prize winner physicist Richard Feynman talked about "the problem of manipulating and controlling things on a small scale". He said he was inspired by biology, which showed that nature had mastered the art of compressing massive amounts of information in tiny molecules called DNA.

It has now been very well known by X ray diffraction methods and other analysis by scientists that a DNA chain is approximately 2.2 to 2.6 nm wide and its one nucleotide unit is 0.33 nm long. Even most of the proteins are of the order of 5 nm. In simpler terms, this size comparison indicates the ‘confluence of nano and bio’ where nano provides the tools and bio offers the inspiring model and also nanoparticles can very easily used as probes in monitoring the processes of living organisms without much interference. Just considering the simplest example here, the fact that nanoparticles share the size domain with proteins, makes them possible to be used in bio-labeling. Even nanoparticles are replacing the organic dyes in application that require high photo-stability. Now the major trend in further development of nanomaterials to apply in biological systems is to make them multifunctional and controllable by external signals or by local environment thus turning them into nano-devices. In medicine nanoparticles applications are highly concentrated on drug delivery and now nanotech strategy may help in creating new artificial organs for human bodies. Many such applications based on the property of nanoparticles are leading to the commercialization of the newly but rapidly emerging field of Nanobiotechnology. The applications of nanotechnology to biology will prove to be very crucial with advancements in this particular area of research, which is reflecting clearly in recent science policies around the globe. In the recent years there has been witnessed an increase in interest towards nanoparticles and their biological effects and applications. Other than cancer therapy and tissue engineering these now include bottom-up and molecular self-assembly, biological effects of naked nanoparticles and nano-safety, drug encapsulation and nanotherapeutics, and novel nanoparticles for use in microscopy, imaging and diagnostics. Hence, for this beneficial and demanding convergence, it becomes quite necessary to bring together the biologists and the nanotechnologists for better comprehension of nature, sustainable development and improving human performance.
It holds a great promise !

- Kirti Bhatotia

The NANOBIO Conference - Zurich 2010

2009-08-25T20:47:00.001+05:30

The Third International NanoBio Conference will take place at ETH Zurich, August 24-27, 2010. For this 4-day conference, there will be at least 36 invited internationally renowned speakers for plenary and two parallel sessions, as well as poster sessions and an industrial exhibition. We expect around 500 participants, 250 - 300 posters and about 15-20 exhibitors.

This meeting gathers the leaders of this progressive field from all over the world helping scientists to get an update on the most recent achievements in the different topics of nanobiotechnology, to discuss, to network, to exchange stimulating new ideas, and to take responsibility in forming public opinion about nanobiotechnology.

Sessions topics include:

NanoBio Sensing
NanoBio Materials
NanoBio Interfaces
NanoBio Devices
Drug delivery & Nanomedicine
Nanomedical imaging
Nanotoxicology
Biomimetic and Bioinspired Nano-Structured Materials and Interfaces
Nano-scale Characterization Techniques and Single Molecule Analysis

Now Exploring New "Nano - Bio" Therapy That Fights Brain Cancer !!

2009-08-22T13:36:00.000+05:30

Scientists have now developed a method of targeting brain cancer cells by using titanium dioxide nanoparticles bound to a biological material.......a great job using convergence of technologies

This new nano-bio technology might eventually provide an alternative form of therapy that targets only cancer cells and does not affect normal living tissue.

It is a real example of how nanoand biological interfacing can be used for biomedical application.

Brain cancer treatment is really challenging......The significance of the work lies in the ability to effectively target nanoparticles to specific cell surface receptors expressed on brain cancer cells.

Now the scientist are in a position to develop this exciting technology in preclinical models of brain tumors, with the hope of one day employing this new technology in brain tumour patients......

Indian scientists create world's hardest nano-composite ....

2009-08-21T16:36:00.000+05:30

A team of five Bangalore-based researchers headed by Dr CNR Rao, scientific advisor to the Indian prime minister, has discovered the world's hardest plastic nano-composite material, which is also capable of being used in missiles and aircraft.

The team created the material by reinforcing ordinary plastic with nano-diamonds, a sheet of layered carbon honeycomb and tiny carbon nano-cylinders. Nano dimensions are smaller than the width of a single strand of human hair, with one nano-metre being one millionth of a millimetre.

The team reinforced a common polymer with nano-diamond, a new age material called graphene (one atom thick carbon honeycomb sheet) and carbon nano-tube producing the new material.The mechanical properties like hardness and stiffness (after moulding) improved by as much as 400 per cent compared to those obtained with single reinforcements.Although the use of nano-materials as reinforcing agents is nothing new, the Bangalore team has been innovative in using a combination two nano-materials to reinforce a polyvinyl alcohol polymer.

Despite being the world's hardest plastic nano-composite, the newly developed reinforcement material constitutes only one per cent of the weight of the composite.

Besides displaying excellent mechanical properties, the scientists said the reinforced polymer also reveals semi-conducting behaviour, which too can be exploited.

To assess the practical applications that the new material can be put to, scientists will have to analyse the material's toughness and ductility. This is the next step.

Good Luck......

IBM using DNA & NANOTECH to build next-generation chips...

2009-08-21T14:51:00.002+05:30

IBM Research provided an update on their efforts to use DNA& Nanotechnology to build more powerful computer chips.

Researchers at IBM are using a combination of DNA and nanotechnology in an effort to build more powerful and energy efficient computer chips that also are cheaper to make.

Powerful. Faster. Energy efficient. Easier to manufacture.IBM says that pretty heady combination is possible because DNA molecules can be used as scaffolding so carbon nanotubes can assemble themselves into precise patterns. This could help chip manufacturers move from 45 nanometer processor technolgy to 22-nm or lower, according to IBM.
And that could help processor designers keep pace with Moore's Law - the 40-plus-year-old prediction by Gordon Moore that the number of transistors on a chip will double every two years.
"The cost involved in shrinking features to improve performance is a limiting factor in keeping pace with Moore's Law and a concern across the semiconductor industry," said Spike Narayan, manager of science and Technology at the IBM Research group, in a statement. "The combination of this directed self-assembly with today's fabrication technology eventually could lead to substantial savings in the most expensive and challenging part of the chip-making process."
While companies, like Intel Corp. and Advanced Micro Devices, Inc., have long been cramming more and more transistors -- the building blocks of the processor -- onto a chip, some observers have long predicted that leakage and energy consumption would become significant roadblocks to the law at some point.
And researchers are hot on the trail of technologies that will allow them to continue shrinking chips, while also making them more powerful and less expensive to build.

Processor manufacturers today use optical lithography, which uses light to transfer the semiconductor pattern. That process can make it difficult for engineers to shrink the pattern, a key part of boosting chip performance.
IBM is looking for the DNA to act as scaffolds, or miniature circuit boards, for the highly precise assembly of chip components, like nanotubes, nanowires and nanoparticles. Using this technique, manufacturers should be able to build "significantly smaller" chips than has been possible with current semiconductor fabrication technology, according to IBM.

DNA SEQUENCING

2009-07-28T12:29:00.000+05:30

DNA sequencing is the process of determining the exact order of the bases A, T, C and G in a piece of DNA.

In essence, the DNA is used as a template to generate a set of fragments that differ in length from each other by a single base. The fragments are then separated by size, and the bases at the end are identified, recreating the original sequence of the DNA.

The most commonly used method of sequencing DNA - the dideoxy or chain termination method - was developed by Fred Sanger in 1977 (for which he won his second Nobel Prize). The key to the method is the use of modified bases called dideoxy bases; when a piece of DNA is being replicated and a dideoxy base is incorporated into the new chain, it stops the replication reaction.

Key principles

A DNA molecule carries information in the form of four chemical groups or bases, represented by the letters A, C, G and T. The order of bases on a DNA strand is the DNA sequence.
Most DNA sequencing is carried out using the chain termination method. This involves the synthesis of new DNA strands on a single stranded template and the random incorporation of chain-terminating nucleotide analogues.
The chain termination method produces a set of DNA molecules differing in length by one nucleotide. The last base in each molecule can be identified by way of a unique label. Separation of these DNA molecules according to size places them in the correct order to read off the sequence.

How does it work?

The DNA to be sequenced is provided in single-stranded form. This acts as a template upon which a new DNA strand is synthesised. DNA synthesis requires a supply of the four nucleotides (the building blocks of DNA), the enzyme DNA polymerase and a primer (a short sequence annealed to the template which initiates the new DNA strand). The nucleotides added to the growing DNA strand are complementary to those in the template strand.
Sequencing is achieved by including in each reaction a nucleotide analogue that cannot be extended and thus acts as a chain terminator. Four reactions are set up, each containing the same template and primer but a chain terminator specific for A, C, G or T. Because only a small amount of the chain terminator is included, incorporation into the new DNA strand is a random event. Each reaction therefore generates a collection of fragments, but every DNA strand will end at the same type of base (A, C, G or T).
The primers or nucleotides included in each of the four reactions contain different fluorescent labels allowing DNA strands terminating at each of the four bases to be identified. The reaction products are then mixed and separated by gel electrophoresis, which separates DNA molecules according to size even if they differ in length by only a single nucleotide. As the DNA strands pass a specific point, the fluorescent signal is detected and the base identified. The whole process can be extensively automated.

How is it used?

The most obvious application of DNA sequencing technology is the accurate sequencing of genes and genomes. Only about 500-800 bases can be sequenced in one experiment so larger DNA molecules, including whole genomes, must be broken into smaller fragments before sequencing and then reassembled by searching for overlaps. Accuracy is achieved by sequencing each template several times.
Lower-fidelity single-pass sequencing is useful for the rapid accumulation of sequence data at the expense of some accuracy. Another application of DNA sequencing technology is resequencing the same DNA molecule over and over. This is necessary, for example, in the typing of single nucleotide polymorphisms.

Maxam-Gilbert sequencing

In 1976-1977, Allan Maxam and Walter Gilbert developed a DNA sequencing method based on chemical modification of DNA and subsequent cleavage at specific bases . Although Maxam and Gilbert published their chemical sequencing method two years after the ground-breaking paper of Sanger and Coulson on plus-minus sequencing, Maxam-Gilbert sequencing rapidly became more popular, since purified DNA could be used directly, while the initial Sanger method required that each read start be cloned for production of single-stranded DNA. However, with the development and improvement of the chain-termination method , Maxam-Gilbert sequencing has fallen out of favour due to its technical complexity, extensive use of hazardous chemicals, and difficulties with scale-up. In addition, unlike the chain-termination method, chemicals used in the Maxam-Gilbert method cannot easily be customized for use in a standard molecular biology kit.
In brief, the method requires radioactive labelling at one end and purification of the DNA fragment to be sequenced. Chemical treatment generates breaks at a small proportion of one or two of the four nucleotide bases in each of four reactions (G, A+G, C, C+T). Thus a series of labelled fragments is generated, from the radiolabelled end to the first 'cut' site in each molecule. The fragments are then size-separated by gel electrophoresis, with the four reactions arranged side by side. To visualize the fragments generated in each reaction, the gel is exposed to X-ray film for autoradiography, yielding an image of a series of dark 'bands' corresponding to the radiolabelled DNA fragments, from which the sequence may be inferred.
Also sometimes known as 'chemical sequencing', this method originated in the study of DNA-protein interactions (footprinting), nucleic acid structure and epigenetic modifications to DNA, and within these it still has important applications.

Chain-termination methods

Part of a radioactively labelled sequencing gel
While the chemical sequencing method of Maxam and Gilbert, and the plus-minus method of Sanger and Coulson were orders of magnitude faster than previous methods, the chain-terminator method developed by Sanger was even more efficient, and rapidly became the method of choice. The Maxam-Gilbert technique requires the use of highly toxic chemicals, and large amounts of radiolabeled DNA, whereas the chain-terminator method uses fewer toxic chemicals and lower amounts of radioactivity. The key principle of the Sanger method was the use of dideoxynucleotides triphosphates (ddNTPs) as DNA chain terminators.
The classical chain-termination or Sanger method requires a single-stranded DNA template, a DNA primer, a DNA polymerase, radioactively or fluorescently labeled nucleotides, and modified nucleotides that terminate DNA strand elongation. The DNA sample is divided into four separate sequencing reactions, containing the four standard deoxynucleotides (dATP, dGTP, dCTP and dTTP) and the DNA polymerase. To each reaction is added only one of the four dideoxynucleotides (ddATP, ddGTP, ddCTP, or ddTTP). These dideoxynucleotides are the chain-terminating nucleotides, lacking a 3'-OH group required for the formation of a phosphodiester bond between two nucleotides during DNA strand elongation. Incorporation of a dideoxynucleotide into the nascent (elongating) DNA strand therefore terminates DNA strand extension, resulting in various DNA fragments of varying length. The dideoxynucleotides are added at lower concentration than the standard deoxynucleotides to allow strand elongation sufficient for sequence analysis.

The newly synthesized and labeled DNA fragments are heat denatured, and separated by size (with a resolution of just one nucleotide) by gel electrophoresis on a denaturing polyacrylamide-urea gel. Each of the four DNA synthesis reactions is run in one of four individual lanes (lanes A, T, G, C); the DNA bands are then visualized by autoradiography or UV light, and the DNA sequence can be directly read off the X-ray film or gel image. In the image on the right, X-ray film was exposed to the gel, and the dark bands correspond to DNA fragments of different lengths. A dark band in a lane indicates a DNA fragment that is the result of chain termination after incorporation of a dideoxynucleotide (ddATP, ddGTP, ddCTP, or ddTTP). The terminal nucleotide base can be identified according to which dideoxynucleotide was added in the reaction giving that band. The relative positions of the different bands among the four lanes are then used to read (from bottom to top) the DNA sequence as indicated.

DNA fragments can be labeled by using a radioactive or fluorescent tag on the primer , in the new DNA strand with a labeled dNTP, or with a labeled ddNTP.
There are some technical variations of chain-termination sequencing. In one method, the DNA fragments are tagged with nucleotides containing radioactive phosphorus for radiolabelling. Alternatively, a primer labeled at the 5’ end with a fluorescent dye is used for the tagging. Four separate reactions are still required, but DNA fragments with dye labels can be read using an optical system, facilitating faster and more economical analysis and automation. This approach is known as 'dye-primer sequencing'. The later development by L Hood and coworkers of fluorescently labeled ddNTPs and primers set the stage for automated, high-throughput DNA sequencing.

Sequence ladder by radioactive sequencing compared to fluorescent peaks
The different chain-termination methods have greatly simplified the amount of work and planning needed for DNA sequencing. For example, the chain-termination-based "Sequenase" kit from USB Biochemicals contains most of the reagents needed for sequencing, prealiquoted and ready to use. Some sequencing problems can occur with the Sanger Method, such as non-specific binding of the primer to the DNA, affecting accurate read out of the DNA sequence. In addition, secondary structures within the DNA template, or contaminating RNA randomly priming at the DNA template can also affect the fidelity of the obtained sequence. Other contaminants affecting the reaction may consist of extraneous DNA or inhibitors of the DNA polymerase.

Dye-terminator sequencing

An alternative to primer labelling is labelling of the chain terminators, a method commonly called 'dye-terminator sequencing'. The major advantage of this method is that the sequencing can be performed in a single reaction, rather than four reactions as in the labelled-primer method. In dye-terminator sequencing, each of the four dideoxynucleotide chain terminators is labelled with a different fluorescent dye, each fluorescing at a different wavelength. This method is attractive because of its greater expediency and speed and is now the mainstay in automated sequencing with computer-controlled sequence analyzers . Its potential limitations include dye effects due to differences in the incorporation of the dye-labelled chain terminators into the DNA fragment, resulting in unequal peak heights and shapes in the electronic DNA sequence trace chromatogram after capillary electrophoresis . This problem has largely been overcome with the introduction of new DNA polymerase enzyme systems and dyes that minimize incorporation variability, as well as methods for eliminating "dye blobs", caused by certain chemical characteristics of the dyes that can result in artifacts in DNA sequence traces. The dye-terminator sequencing method, along with automated high-throughput DNA sequence analyzers, is now being used for the vast majority of sequencing projects, as it is both easier to perform and lower in cost than most previous sequencing methods.

Automation and sample preparation

Modern automated DNA sequencing instruments (DNA sequencers) can sequence up to 384 fluorescently labelled samples in a single batch (run) and perform as many as 24 runs a day. However, automated DNA sequencers carry out only DNA size separation by capillary electrophoresis, detection and recording of dye fluorescence, and data output as fluorescent peak trace chromatograms. Sequencing reactions by thermocycling, cleanup and re-suspension in a buffer solution before loading onto the sequencer are performed separately. In the past, an operator had to trim the low quality ends every sequence manually in order to remove the sequencing errors. However, today, software like Fast Chromatogram Viewer can automatically trim the ends at batch.

Large-scale sequencing strategies

Current methods can directly sequence only relatively short (300-1000 nucleotides long) DNA fragments in a single reaction. . The main obstacle to sequencing DNA fragments above this size limit is insufficient power of separation for resolving large DNA fragments that differ in length by only one nucleotide. Limitations on ddNTP incorporation were largely solved by Tabor at Harvard Medical, Carl Fuller at USB biochemicals, and their coworkers.

Genomic DNA is fragmented into random pieces and cloned as a bacterial library. DNA from individual bacterial clones is sequenced and the sequence is assembled by using overlapping regions.
Large-scale sequencing aims at sequencing very long DNA fragments. Even relatively small bacterial genomes contain millions of nucleotides, and the human chromosome 1 alone contains about 246 million bases. Therefore, some approaches consist of cutting (with restriction enzymes) or shearing (with mechanical forces) large DNA fragments into shorter DNA fragments. The fragmented DNA is cloned into a DNA vector, usually a bacterial plasmid, and amplified in Escherichia coli. The amplified DNA can then be purified from the bacterial cells (a disadvantage of bacterial clones for sequencing is that some DNA sequences may be inherently un-clonable in some or all available bacterial strains, due to deleterious effect of the cloned sequence on the host bacterium or other effects). These short DNA fragments purified from individual bacterial colonies are then individually and completely sequenced and assembled electronically into one long, contiguous sequence by identifying 100%-identical overlapping sequences between them (shotgun sequencing). This method does not require any pre-existing information about the sequence of the DNA and is often referred to as de novo sequencing. Gaps in the assembled sequence may be filled by Primer walking, often with sub-cloning steps (or transposon-based sequencing depending on the size of the remaining region to be sequenced). These strategies all involve taking many small reads of the DNA by one of the above methods and subsequently assembling them into a contiguous sequence. The different strategies have different tradeoffs in speed and accuracy; the shotgun method is the most practical for sequencing large genomes, but its assembly process is complex and potentially error-prone - particularly in the presence of sequence repeats. Because of this, the assembly of the human genome is not literally complete — the repetitive sequences of the centromeres, telomeres, and some other parts of chromosomes result in gaps in the genome assembly. Despite having only 93% of the full genome assembled, the Human Genome Project was declared complete because their definition of human genome sequencing was limited to euchromatic sequence (99% complete at the time), excluding these intractable repetitive regions.

Resequencing steps.

Sample prep: Extraction of nucleic acid. Template prep: Amplification and preparation of a small region of the target region. Sequencing steps.
The human genome is about 3 billion (3,000,000,000) bp long; if the average fragment length is 500 bases, it would take a minimum of six million (3 billion/500) to sequence the human genome (not allowing for overlap = 1-fold coverage). Keeping track of such a high number of sequences presents significant challenges, only held down by developing and coordinating several procedural and computational algorithms, such as efficient database development and management.
Resequencing or targeted sequencing is utilized for determining a change in DNA sequence from a "reference" sequence. It is often performed using PCR to amplify the region of interest (pre-existing DNA sequence is required to design the PCR primers). Resequencing uses three steps, extraction of DNA or RNA from biological tissue; amplification of the RNA or DNA (often by PCR); followed by sequencing. The resultant sequence is compared to a reference or a normal sample to detect mutations.

New sequencing methods
High-throughput sequencing
The high demand for low cost sequencing has given rise to a number of high-throughput sequencing technologies. These efforts have been funded by public and private institutions as well as privately researched and commercialized by biotechnology companies. High-throughput sequencing technologies are intended to lower the cost of sequencing DNA libraries beyond what is possible with the current dye-terminator method based on DNA separation by capillary electrophoresis. Many of the new high-throughput methods use methods that parallelize the sequencing process, producing thousands or millions of sequences at once.

In vitro clonal amplification
As molecular detection methods are often not sensitive enough for single molecule sequencing, most approaches use an in vitro cloning step to generate many copies of each individual molecule. Emulsion PCR is one method, isolating individual DNA molecules along with primer-coated beads in aqueous bubbles within an oil phase. A polymerase chain reaction (PCR) then coats each bead with clonal copies of the isolated library molecule and these beads are subsequently immobilized for later sequencing. Emulsion PCR is used in the methods published by Marguilis et al. (commercialized by 454 Life Sciences, acquired by Roche), Shendure and Porreca et al. (also known as "polony sequencing") and SOLiD sequencing, (developed by Agencourt and acquired by Applied Biosystems). Another method for in vitro clonal amplification is "bridge PCR", where fragments are amplified upon primers attached to a solid surface, developed and used by Solexa (now owned by Illumina). These methods both produce many physically isolated locations which each contain many copies of a single fragment. The single-molecule method developed by Stephen Quake's laboratory (later commercialized by Helicos) skips this amplification step, directly fixing DNA molecules to a surface.

Parallelized sequencing
Once clonal DNA sequences are physically localized to separate positions on a surface, various sequencing approaches may be used to determine the DNA sequences of all locations, in parallel. "Sequencing by synthesis", like the popular dye-termination electrophoretic sequencing, uses the process of DNA synthesis by DNA polymerase to identify the bases present in the complementary DNA molecule. Reversible terminator methods (used by Illumina and Helicos) use reversible versions of dye-terminators, adding one nucleotide at a time, detecting fluorescence corresponding to that position, then removing the blocking group to allow the polymerization of another nucleotide. Pyrosequencing (used by 454) also uses DNA polymerization to add nucleotides, adding one type of nucleotide at a time, then detecting and quantifying the number of nucleotides added to a given location through the light emitted by the release of attached pyrophosphates.
"Sequencing by ligation" is another enzymatic method of sequencing, using a DNA ligase enzyme rather than polymerase to identify the target sequence. Used in the polony method and in the SOLiD technology offered by Applied Biosystems, this method uses a pool of all possible oligonucleotides of a fixed length, labeled according to the sequenced position. Oligonucleotides are annealed and ligated; the preferential ligation by DNA ligase for matching sequences results in a signal corresponding to the complementary sequence at that position.
Other sequencing technologies
Other methods of DNA sequencing may have advantages in terms of efficiency or accuracy. Like traditional dye-terminator sequencing, they are limited to sequencing single isolated DNA fragments. "Sequencing by hybridization" is a non-enzymatic method that uses a DNA microarray. In this method, a single pool of unknown DNA is fluorescently labeled and hybridized to an array of known sequences. If the unknown DNA hybridizes strongly to a given spot on the array, causing it to "light up", then that sequence is inferred to exist within the unknown DNA being sequenced. Mass spectrometry can also be used to sequence DNA molecules; conventional chain-termination reactions produce DNA molecules of different lengths and the length of these fragments is then determined by the mass differences between them (rather than using gel separation).
There are new proposals for DNA sequencing, which are in development, but remain to be proven. These include labeling the DNA polymerase, reading the sequence as a DNA strand transits through nanopores, and microscopy-based techniques, such as AFM or electron microscopy that are used to identify the positions of individual nucleotides within long DNA fragments by nucleotide labeling with heavier elements (e.g., halogens) for visual detection and recording. In October 2006 the NIH issued a news release describing novel sequencing techniques and announcing several grant awards.
In October 2006, the X Prize Foundation established the Archon X Prize, intending to award $10 million to "the first Team that can build a device and use it to sequence 100 human genomes within 10 days or less, with an accuracy of no more than one error in every 100,000 bases sequenced, with sequences accurately covering at least 98% of the genome, and at a recurring cost of no more than $10,000 (US) per genome."

COMPONENTS OF A RESEARCH ARTICLE

2009-07-27T10:50:00.000+05:30

COMPONENTS OF A RESEARCH ARTICLE

Title

Purpose: To attract readers interested in this field of study. The importance of the title cannot be overstated as it is a major determinant of whether the paper will be read. It is the only aspect of the article that appears in tables of contents and in many of the databases used for literature searches.

Content: The title should indicate the focus of the paper, and should contain enough relevant “keywords” (i.e., search terms) to enable readers to find this paper when searching a relevant database.

Style: There are two types of titles:

1. Descriptive titles, which states the focus of the study:

The effect of heat on ice.

2. Conclusion titles, which provide the authors’ main conclusion from their study.

Heat melts ice.

For research articles, we prefer a descriptive title. It “lets the data speak for themselves” (an important concept in research) and allows the author to provide the necessary restrictions on the conclusions, restrictions that usually cannot be accommodated in a title. (For example, that heat melts ice only as long as sufficient time is provided to allow the ice molecules to reach the melting point of water, which is 0°C for pure water at sea level.)

There is another reason for preferring descriptive titles: Should evidence later come to light that indicates the authors’ conclusion is incorrect, the authors’ curriculum vitae will not contain a permanent reminder of this mistake! In some cases, a journal’s Instructions to Authors will specify which style of title to use.

Often authors are asked to provide a second, briefer title. Referred to as the running title, this title will appear as a header on every other page of the printed article. Like the full title, the running title should be chosen with care.

Length: A title should be short yet provide enough keywords so that individuals will be able to find it when searching relevant databases. A general recommendation is 5-10 words.

Authors

Purpose: To specify the individuals responsible for the research presented in the paper.

Content: The definition of who should be an author (and in what order the list should be provided, see below) varies with the field, the culture, and even the research group. Because of this potential for ambiguity, the rules to be used for determining authorship, including the order of authors, should be clearly agreed upon at the outset of a research project.

Our belief is that authorship denotes an “intellectual contribution” to the work, and that an author should be able to explain and defend the work. This definition of authorship is probably the most common one among researchers and journal editors. Note that within this framework, “honorary authorship” ¾ listing someone as an author who has not made an intellectual contribution (e.g., the head of the department or that individual who provided the funds) ¾ would be considered unethical.

In many areas of science, students typically publish papers in which their advisor is an author. However, in some other fields, e.g., education and many areas of the humanities, students frequently are the sole author on their papers.

Independent of the method used to determine authorship, it is essential that all authors have given their consent to be designated as such and have approved the final version of the manuscript. One author is chosen as the “corresponding author.” The editor of the journal will direct all correspondence to this individual who then has responsibility for keeping the other authors up-to-date with regard to the status of the manuscript.

Style: Like authorship, the order in which the authors are listed varies with field and culture. Often the order of the authors denotes their contribution to the work. For example, in some fields the first author has made the largest contribution, the remaining authors are listed in descending order of effort. On the other hand, in many fields the senior author (the one responsible for overseeing the project) is listed last, and the person that did most of the day-to-day work on the project is listed first. A third possibility, no longer very common, is to list the authors alphabetically.

When possible, it is advisable for researchers to pick a format for their name that they will continue to use throughout their professional life. Thus, John A. Jones, John Jones, and J. A. Jones are each sufficiently different that it might be difficult for someone to know that each name refers to the same author. Changing ones name because of marriage provides a particular challenge in this regard. Some individuals choose not to change their professional name under these circumstances.

Addresses

Purpose: To indicate the institution(s) at which the research was performed, and to provide readers with a way of contacting the authors.

Content: There are three types of addresses listed on a paper:

1. The main addresses listed under the names of the authors indicate where the work was performed.

2. The corresponding address is usually listed as a footnote to the list of authors. This indicates to the publisher and, later, to the readers, where the “corresponding author” can be contacted regarding any questions related to the article. Recently, many authors have been including multiple forms of “addresses,” including regular mailing addresses, fax numbers, and email addresses.

3. Current addresses are often listed for any authors who have moved to a different institution between the time that the research was performed and the manuscript is published.

Note that if an author has moved since completing the research, it is inappropriate to list their current address as the main address. One of the criteria for evaluating an institution is the nature of the work that is done under their auspices, and thus an accurate indication of this credit should be provided.

Style: If the research was conducted at more than one department or institution, then superscripts should be used to indicate which author worked in which location.

Abstract

Purpose: To provide a brief summary of the paper. Along with the title, this is one of the most important components of a research article. After reading the title, researchers commonly scan the abstract to determine what the authors found, and based on this information they often decide if they will read the rest of the paper.

Content: The abstract is written as a mini-paper, i.e., it contains the following information in this order:

1. Introduction: a few sentences to provide background information on the problem investigated

2. Methods: techniques used

3. Results: the major results presented in the paper; provide quantitative information when possible.

4. Discussion: the authors’ interpretation of the results presented

5. Final summary: the major conclusions and “big picture” implications. Note that this is the most important part of the abstract, as researchers will often read this part of the abstract first, to see if the implications of the study are important enough to warrant the reading of the full paper.

In most cases, abbreviations are not permitted in an abstract.

Searchable databases and on-line journals now make it relatively easy to obtain titles and abstracts of scientific publications. One of the implications of this is that it can no longer be assumed that only specialists in ones discipline will read the abstract. Indeed, the readership can now be assumed to include policy makers, and both advocates and opponents of the research performed. Thus, authors are advised to take this into account when writing their abstract by (1) making it as intelligible as possible to a general readership, and (2) taking extra care to avoid stating things that might be misconstrued by readers who are uninformed and/or unsupportive of the type of research described.

Tense: The abstract should be written in the past tense for the authors’ work, present tense for general knowledge and other researchers’ work.

Length: The number of words permitted in the abstract is usually specified in a journal’s Instructions to Authors. Commonly it is 150-300 words.

Introduction

Purpose: To provide the reader with background on the research described in the paper.

Content: The introduction consists primarily of the following types of information, generally provided in this order:

1. Why the study was undertaken: What gap in the knowledge of the field were the authors trying to fill by undertaking this study? What problem were the authors trying to address?

2. The nature of the work performed: The variables that were investigated and the methods that were used.

3. The state of the problem at the end of the study: A brief statement of the major findings presented in the paper, and implications of the study ¾ for example, how the work contributes to “the big picture,” questions left unanswered, new questions that have emerged.

Note: whereas the information from #1 and #2 are essential components of an introduction, some individuals believe that the information from #3 is optional. We strongly recommend including this information as it helps the reader to evaluate more accurately what they are reading in the sections that follow. This point helps to highlight one of the major distinctions between scientific writing and many other types of prose writing ¾ in scientific writing everything is done to avoid mystery or suspense.

It is essential that the Introduction should provide a brief but scholarly review of the relevant literature with appropriate references (see “References,” below). Authors should neither unduly inflate their contributions nor obscure controversy by ignoring papers that have already been published.

Abbreviations should generally not be used in the title or abstract, and only sparingly in other parts of the manuscript. A rule of thumb is not to use an abbreviation unless the word is used at least 10 times or is best recognized in its abbreviated form. When an abbreviation is to be employed, it should be defined the first time it is used and then always used thereafter. For example,

The questionnaire was given to 100 employees of the Environmental Protection Agency (EPA), as well as 50 former EPA employees.

Most journals will provide a list of abbreviations that do not need to be defined because they are commonly used. Consult the Instructions for Authors.

Tense: What the authors did/found is in the past tense; everything else is in the present tense.

Length: Generally not more than 500 words.

Methods

Purpose: The methods section serves two functions: (1) to enable readers to evaluate the work performed (e.g., did the authors use the most appropriate and accurate techniques for their work?), and (2) to permit readers to replicate the study if they desire to do so.

Content: All aspects of the methodology used in the study must be described thoroughly enough so that scientists working in that field would be able to replicate the work. This includes both what was used as well as what was done. Thus, sometimes this section is referred to as “Methods and Materials.”

If the method has already been published in the scientific literature (whether or not it was written by the same authors), readers should be referred to the original description for the details of the method. However, it is important to include enough information so that readers are able to evaluate the work being presented without having to refer to another publication. This means specifying the critical variables for that type of work, for example, how long the samples were incubated, how many minutes subjects were allowed to work on a task, or what strain of laboratory rats were used. In addition, it is essential to indicate any deviations from the method cited.

Often the company (including city and state) that manufactures a particular reagent is specified to reduce any ambiguity about what was used; likewise, the model number for a piece of equipment is often indicated.

Tense: Past tense.

Style: If several different procedures are described, it is preferable to subdivide the methods section via the use of headings. This enables readers to refer quickly back to a specific method.

Results

Purpose: To provide the data collected.

Content: The contents of the Results section depend on type of article:

In full-length research articles, the more common type of article, only data - what was observed - is included in this section. Interpretations should be reserved for the discussion section. The idea behind this format is to “let the data speak for themselves.” However, some authors like to include some introductory or transition material to help the flow of this section.

In short research articles (sometimes called “short” or “brief” communications), results and discussion (interpretation) are sometimes mixed. Refer to the journals’ Instructions to Authors for guidance.

Tense: Authors’ results should be in past tense, and general statements in present tense.

Style: If the results of several different experiments are described, it is preferable to subdivide this section via the use of headings.

Length: This usually is the shortest section of a manuscript.

Discussion

Purpose: To provide the reader with a plausible interpretation of the data reported and to relate these findings to what other investigators have found.

Content: The section provides the following information, generally in this order:

1. Summary of conclusions: what the authors conclude from their data, for example, relationships between variables, trends, etc.

2. Relation to other results: the relation of these findings to previous work, e.g. “supports the findings of Alvarez et al., (1994)” or “is contrast to …”

3. Aberrant results: any abnormalities or exceptions inherent in the data or in relation to with respect to the scientific literature, and if possible, explanations for these aberrations. (Note: item #3 and #4 may be intermixed.)

4. Implications: theoretical or practical implications of the work, i.e., “the big picture”

5. Grand summary: a summary of the results and conclusions reported in the paper

Tense: Current knowledge is stated in present tense, the author’s work is stated in past tense.

Style: If headings were used in the results section, it is very convenient for the reader if the relevant portion of the discussion is presented under the same headings.

Length: generally, up to 1500 words.

Acknowledgments

Purpose: To recognize and thank those individuals and organizations whose contributions to the work presented should be acknowledged but are not extensive enough to merit authorship.

Content: When applicable, the following information is presented in this order:

1. Individuals other than authors who made a significant contribution to the research by donating important reagents or materials, collecting data, providing extensive advice on drafts of the manuscript, etc. Typically, the nature of the contribution is noted; for example

The authors thank Dr. Marcia Jones for providing the genetically modified mice used in these studies, and Mr. David Wendall for his assistance in analyzing the tissue samples.

2. If the work has been presented at a conference, then this is often noted. For example,

Portions of this work were presented at the 25^th Annual Society for Neuroscience Meeting, November 11-16, 1996, San Diego, CA.

3. Organizations that funded the research. The general format for this information is

This work was supported by U.S. Public Health Service Grant MH43947.

Note that it is essential to get permission from any individual whose help is acknowledged. Also, many scientific societies and journals are indicating that it is essential to disclose any financial support that has been provided for the work.

Length: Limit to significant contributors.

References

Purpose: To provide the full citation for article referenced in the text.

Content: A complete reference includes all of the authors’ names, the title of the article, the journal name, the volume number, page numbers, and the year of publication.

Style: A wide range of styles is used for citing references in the text and bibliography. Check the journal’s Instructions to Authors for information about the content and formatting of references.

Within the text, articles are cited by providing the author and year of the article (e.g., Fischer and Zigmond, 1996). When there are more than two authors, the first author is provided together with e. al. (e.g., Fischer et al..., 1996). If more than one reference is cited for a given point, they are usually listed in chronological order (e.g., Zigmond and Fischer, 1995; Fischer et al., 1996). If there is any ambiguity, a letter can be added to the year of publication (e.g., Fischer et al., 1995a; 1995b).

At the end of the paper a list of references, or bibliography, is provided. This list must be limited to the references cited within the text and most often is provided in alphabetical order.

In some cases citations appear in the text as numbers, usually a superscript, which then refer to a particular item in the reference list.

It is the obligation of the authors to provide a scholarly listing of the primary references of relevance to the paper. Authors are obliged to do a thorough review of the key areas of the scientific literature as part this process. In general, original research articles rather than review articles should be cited, and the research articles should be the earliest ones that made the particular finding.

It is essential that authors check each reference that they cite. Simply copying a reference from the bibliography of a published paper is inadequate since errors in referencing are very common. In checking a reference, authors must not only make sure that the citation is accurate but also that the text actually supports the point for which it being used as a reference.

References that are not readily available or are in a language not understood by the author present a particular challenge. In the former case, most libraries provide a service that enables authors to obtain papers from a wide range of other libraries. An alternative that is sometimes available is to contact directly the author of the article in question and request a copy.

Articles in foreign languages sometimes provide enough information in their tables and figures to permit an accurate comprehension of their results, even if the language itself is not understood. In this regard it is helpful that a number of scientific terms are the same in English as in many other languages. Alternatively, it usually is possible to have an article translated by a local service.

If a reference cannot be checked by the author, the only alternative to not citing it is to cite it as a secondary reference (e.g., Hooke, 1665, as cited in Fischer, 1995).

If citations are needed for more than one point in a sentence, it is helpful for the reader if the citations appear throughout the sentence, rather than as a collection at the end. For example,

Previous studies have shown that this compound can exist in a solid (Wang and Beauford, 1993), liquid (Jones et al., 1992), or gaseous (Diaz, 1995) state.

Length: Ideally, a paper will list all the references necessary to document each point that is made by the authors. In practical terms, however, most journals will impose a limit in order to conserve space. A rule of thumb is no more than 6 references for a particular point and no more than 100 references per paper.

Tables and Figures

Purpose: To report data that are too numerous or complicated to be described adequately in the text; to reveal trends or patterns in the data.

Content: Tables; possible figures include graphs (bar, line, scatter), diagrams, cartoons (i.e., chemical structures or mechanisms), and photographs.

Style: Figures are usually in black and white. Color is extremely expensive to publish, and should only be used when it provides unique information. (Note: For further details see “Construction of Tables and Figures,” which will be posted soon.)

Number: Limit the number of tables and figures to those that provide essential information that could not adequately be presented in text.

Table and Figure Legends

Purpose: To provide a knowledgeable reader with the information required for understanding the table or figure.

Content: The composition of a legend depends on the item it refers to. It should provide information regarding the conditions of the experiment, but not give a summary or interpretation of the results. In addition, statistical information is often provided. This may include

1. The number of times an experiment was performed or a condition was tested.

2. What the values in the table or figure represent, for example mean ± S.E.M. (standard error of the mean)

3. The statistical test used in analyzing the data

4. Whether the test was “one-tailed” or “two-tailed” (if relevant)

5. The p value that was used in determining significance

6. If an asterisk or other mark is used in the table or graph to denote statistically significant results, then this mark should be defined.

For example, the statistics portion of a figure legend might look like this,

n=5 for each condition. Values represent mean ± S.E.M. Data were analyzed using a one-tailed Student’s t-test. * denotes significance, p < 0.05.

Tense: Past tense.

Style: Each table and figure should be understandable on its own, without reference to the text.

Within a manuscript, the placement of the legend varies depending on whether it refers to a table or figure:

Table: The title, table, and legend should appear on the same page, in the order listed.

Figure: Each figure should appear on a separate page. The numbered legends are listed one after another (i.e., several to a page). The title for a figure comprises the first sentence in the figure legend.

Transgenic Mice

2009-07-20T10:04:00.000+05:30

The masses need to start watching videos like this and other such informative source so as to learn what science is ACTUALLY doing.......

How much is a scientist worth?

2009-07-20T09:45:00.000+05:30

'It is incomprehensible that you spend 10 years of your life educating yourself and then you are earning the same amount as a bus driver'

The demise of this valuable resource of postdocs represents a great loss of scientific potential, creativity and progress.......

Many aspects of this scenario must be changed........
A revolution surely needs to be started......now