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Villain of Molecular Biology: Why are we not reproducible in research?

Bhardwaj V - F1000Res (2015)

Bottom Line: In the USA alone $28 billion per year spent on preclinical research is not reproducible.Within this opinion article, I provide a brief historical account of the discovery of the Watson-Crick DNA model and introduce another neglected model of DNA.This negligence may be one of the fundamental reasons behind irreproducibility in molecular biology research.

View Article: PubMed Central - PubMed

Affiliation: Molecular Biology and Genetics Domain, Lovely Professional University, Punjab, India.

ABSTRACT
Worldwide, there is an issue of  irreproducibility in life science research. In the USA alone $28 billion per year spent on preclinical research is not reproducible. Within this opinion article, I provide a brief historical account of the discovery of the Watson-Crick DNA model and introduce another neglected model of DNA. This negligence may be one of the fundamental reasons behind irreproducibility in molecular biology research.

No MeSH data available.


Image by Paul Blow in article “Reproducibility: The risks of replication drive” by Mina Bissel,Nature, 2013. Used with permission from Macmillan Publishers Ltd.Nature ©201354.
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f1: Image by Paul Blow in article “Reproducibility: The risks of replication drive” by Mina Bissel,Nature, 2013. Used with permission from Macmillan Publishers Ltd.Nature ©201354.

Mentions: There are many publications which have reported huge errors of various molecular techniques (for more details see25–36). You may have experienced, non-specific amplification of DNA in a PCR reaction, non-specific hybridization in Southern and northern hybridization and then have tried harder to find out conditions which give you better results. You may have experienced, non-specific cloning reactions and then must have tried to screen out a specific clone out of non-specific ones. Even today we do not have answer as to why petunia flowers turn white on overexpression of a gene which should have made it more purple37. None of our gene knockout technology explains whether they have taken out one and only one gene and the remainder of the genes have not been affected. To the best of my knowledge, there is no whole genome sequence information available for knock out organisms. I wish to inform readers that the Human Genome Project is not yet complete even though its first draft was announced 15 years ago38. All over the world, billions of dollars are still invested in a hope to find solutions for various diseases. How can we find solutions if the molecular techniques used show errors and many times we are unable to reproduce the same findings in different labs. In 2012 the Biotechnology Company Amgen with a team of 100 scientists found that only 10% (6 out of 53) of research published by reputable labs in top journals is reproducible and 90% of money ($28 billion) is wasted. It looks like that even after development of high throughput techniques and instruments, research worldwide is losing accuracy and precision. It is a worse situation for biotechnology/pharmaceutical industries who are going to invest or have invested millions of dollars for their new drug development programme. It’s again a far worse situation for the public who are looking forward to scientists one day finding solutions to deadly diseases and producing cheaper drugs and the best treatments soon39,40. Recently Professor Eric Lander (one of the leaders of the Human Genome Project, and a member of US President Barack Obama’s scientific advisory panel) visited India and gave an exclusive interview stating that we will have a solution for most cancers in the next 25–30 years (http://www.ndtv.com/video/player/ndtv-special-ndtv-24x7/mapping-the-human-genome-the-eric-lander-interview/358410). I totally disagree with his statements as with the current ways of doing research, it may take many thousand years to find ultimate solutions for mankind’s problems. A recent report by John Arrowsmith revealed that the Phase II success rate for new development projects has decreased by 10% in the last few years. It will definitely increase the cost of new drugs in the future. It will also decrease the trust of the public Government and funding agencies in scientific activities41. But still a question arises, who is the ‘villain’ behind these problems? Yes, the B- form of DNA is a ‘hero’ of molecular biology but there is also a ‘villain’ of molecular biology. It’s a form of DNA which is actually much less studied, discussed and used in designing molecular techniques. It is “parallel stranded duplex DNA” which was first reported by Ramsing & Jovin and Sandeet al. in 1988. There are few reports in favour of parallel stranded DNA which summarize that there is no drastic difference in parallel and antiparallel DNA having mixed AT/GC composition42–47. Recently we have developed a PD-PCR technology based on parallel stranded DNA and we have concluded that two PCR products can be synthesized from a single stranded template DNA, one by conventional PCR and another by our approach48. In 2008, Lestienneet al. reported a novel property of TFO (Triplex forming oligonucleotides-known for transcription inhibition) that Triple helix primer (THP) bounded to the duplex DNA in a parallel orientation can initiate DNA synthesis by various DNA polymerases of phage, retrovirus, bacteria and humans49,50. There are reports which state that Southern hybridization reaction can be performed using parallel complementary probe and gene silencing can be applied using parallel complementary RNA51–53. It also makes me think whether earlier scientists have developed a 100% accurate genome sequence of Human which has only been developed on the basis of antiparallel complementarity in DNA. I strongly believe technical errors observed in various molecular techniques can be ruled out by considering both parallel and antiparallel complementarity of DNA. A probe for Southern blotting/northern blotting can be designed such that it binds to its target only in an antiparallel manner. Primers for PCR can be designed in a similar way. There is a need to develop siRNA and microarray chips keeping in mind parallel and antiparallel hybridization of DNA. Science without errors will increase reproducibility in research worldwide (Figure 1).


Villain of Molecular Biology: Why are we not reproducible in research?

Bhardwaj V - F1000Res (2015)

Image by Paul Blow in article “Reproducibility: The risks of replication drive” by Mina Bissel,Nature, 2013. Used with permission from Macmillan Publishers Ltd.Nature ©201354.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4544406&req=5

f1: Image by Paul Blow in article “Reproducibility: The risks of replication drive” by Mina Bissel,Nature, 2013. Used with permission from Macmillan Publishers Ltd.Nature ©201354.
Mentions: There are many publications which have reported huge errors of various molecular techniques (for more details see25–36). You may have experienced, non-specific amplification of DNA in a PCR reaction, non-specific hybridization in Southern and northern hybridization and then have tried harder to find out conditions which give you better results. You may have experienced, non-specific cloning reactions and then must have tried to screen out a specific clone out of non-specific ones. Even today we do not have answer as to why petunia flowers turn white on overexpression of a gene which should have made it more purple37. None of our gene knockout technology explains whether they have taken out one and only one gene and the remainder of the genes have not been affected. To the best of my knowledge, there is no whole genome sequence information available for knock out organisms. I wish to inform readers that the Human Genome Project is not yet complete even though its first draft was announced 15 years ago38. All over the world, billions of dollars are still invested in a hope to find solutions for various diseases. How can we find solutions if the molecular techniques used show errors and many times we are unable to reproduce the same findings in different labs. In 2012 the Biotechnology Company Amgen with a team of 100 scientists found that only 10% (6 out of 53) of research published by reputable labs in top journals is reproducible and 90% of money ($28 billion) is wasted. It looks like that even after development of high throughput techniques and instruments, research worldwide is losing accuracy and precision. It is a worse situation for biotechnology/pharmaceutical industries who are going to invest or have invested millions of dollars for their new drug development programme. It’s again a far worse situation for the public who are looking forward to scientists one day finding solutions to deadly diseases and producing cheaper drugs and the best treatments soon39,40. Recently Professor Eric Lander (one of the leaders of the Human Genome Project, and a member of US President Barack Obama’s scientific advisory panel) visited India and gave an exclusive interview stating that we will have a solution for most cancers in the next 25–30 years (http://www.ndtv.com/video/player/ndtv-special-ndtv-24x7/mapping-the-human-genome-the-eric-lander-interview/358410). I totally disagree with his statements as with the current ways of doing research, it may take many thousand years to find ultimate solutions for mankind’s problems. A recent report by John Arrowsmith revealed that the Phase II success rate for new development projects has decreased by 10% in the last few years. It will definitely increase the cost of new drugs in the future. It will also decrease the trust of the public Government and funding agencies in scientific activities41. But still a question arises, who is the ‘villain’ behind these problems? Yes, the B- form of DNA is a ‘hero’ of molecular biology but there is also a ‘villain’ of molecular biology. It’s a form of DNA which is actually much less studied, discussed and used in designing molecular techniques. It is “parallel stranded duplex DNA” which was first reported by Ramsing & Jovin and Sandeet al. in 1988. There are few reports in favour of parallel stranded DNA which summarize that there is no drastic difference in parallel and antiparallel DNA having mixed AT/GC composition42–47. Recently we have developed a PD-PCR technology based on parallel stranded DNA and we have concluded that two PCR products can be synthesized from a single stranded template DNA, one by conventional PCR and another by our approach48. In 2008, Lestienneet al. reported a novel property of TFO (Triplex forming oligonucleotides-known for transcription inhibition) that Triple helix primer (THP) bounded to the duplex DNA in a parallel orientation can initiate DNA synthesis by various DNA polymerases of phage, retrovirus, bacteria and humans49,50. There are reports which state that Southern hybridization reaction can be performed using parallel complementary probe and gene silencing can be applied using parallel complementary RNA51–53. It also makes me think whether earlier scientists have developed a 100% accurate genome sequence of Human which has only been developed on the basis of antiparallel complementarity in DNA. I strongly believe technical errors observed in various molecular techniques can be ruled out by considering both parallel and antiparallel complementarity of DNA. A probe for Southern blotting/northern blotting can be designed such that it binds to its target only in an antiparallel manner. Primers for PCR can be designed in a similar way. There is a need to develop siRNA and microarray chips keeping in mind parallel and antiparallel hybridization of DNA. Science without errors will increase reproducibility in research worldwide (Figure 1).

Bottom Line: In the USA alone $28 billion per year spent on preclinical research is not reproducible.Within this opinion article, I provide a brief historical account of the discovery of the Watson-Crick DNA model and introduce another neglected model of DNA.This negligence may be one of the fundamental reasons behind irreproducibility in molecular biology research.

View Article: PubMed Central - PubMed

Affiliation: Molecular Biology and Genetics Domain, Lovely Professional University, Punjab, India.

ABSTRACT
Worldwide, there is an issue of  irreproducibility in life science research. In the USA alone $28 billion per year spent on preclinical research is not reproducible. Within this opinion article, I provide a brief historical account of the discovery of the Watson-Crick DNA model and introduce another neglected model of DNA. This negligence may be one of the fundamental reasons behind irreproducibility in molecular biology research.

No MeSH data available.