The reason for FundScience
As a member of The American Association of Immunologists (AAI), I receive the monthly AAI newsletter that keeps me up-to-date on current happenings in the world of Immunology (and sometimes science in general). This month’s newsletter also included a letter to members from the Executive Director of AAI, where she was asking members to “continue their support to AAI by renewing their membership, which is so important specifically in this current economic climate, where a strong AAI voice in Washington is essential to Immunologists”. The letter continued to tell us, in actual numbers, what a hard hit science has taken in these last 8 years. According to this newsletter, the NIH has had a 14% loss in purchasing power since 2003. 14% in 5 years, think about it! Stepping out of my scientist-skin, I ask a serious, unbiased question: what type of a society takes money away from medical advancement? As a person who is witnessing this first-hand, I cannot tell you how many cases I have heard off in which brilliant scientists have lost their funding and have either had to leave research all together or move to another country like Singapore, which has realized that advancement in science and healthcare is the touchstone of any successful civilization. If history has taught us a few things it is that many ancient civilizations were wiped off the face of the earth due to their inability to deal with disease, famine and draught, all which can have solutions in science.
This is where non-profit organizations like FundScience come into play. The unique thing about FundScience is that the general public is put in direct access with the scientific method. This begins to disslove the misunderstandings about science, scientific techniques and the timeline from the advent of a thought/idea to the fruition of that idea.
11.26.08 by MarkGetting some press
We’ve recently been written up in The Scientist. Alla Katsnelson did a short piece on us for The Scientist’s community and we’re getting positive responses in other blogs and media. We have some much more interesting news mentions coming next week though.
11.14.08 by dgaddyGene Therapy for Rheumatoid Arthritis
Introduction.
Gene therapy offers great possibilities for the treatment rheumatoid arthritis (RA). RA was the first orthopedic condition to be targeted by gene therapy. Initially, RA, a non-lethal disease that is not regulated by a single gene, may not have been an obvious target for gene therapy. However, while traditional surgical and pharmaceutical methods of treating RA have met with limited therapeutic success and have failed to produce a cure, the past several years have seen extensive progress toward development of gene therapy for arthritis. Numerous vectors and therapeutic genes have been investigated in animal models of arthritis, and the potential of gene therapy to treat or manage RA has been demonstrated in several clinical studies. Gene therapy offers the possibility of overcoming many of the limitations of current biologic therapies by providing long-term, high-level localized expression of therapeutic genes, potentially in as little as a single dose.
Gene therapy emerged as a novel strategy to treat arthritis in the early 1990s. Fundamentally, arthritis gene therapy involves the transfer of complementary DNA (cDNA) encoding antiarthritis gene products, which may be difficult to administer by more conventional methods. Gene therapy offers the promise of long-term expression of antiarthritis gene products, as well as targeted delivery to and expression in affected tissues, limiting potential systemic side effects.
Background on the Disease.
Arthritis is the leading cause of disability among adults in the United States, affecting approximately 21% (more than 46 million) adults. Rheumatoid arthritis (RA) affects approximately 1.3 million adults in the United States, and more than 60 million people worldwide [1]. RA is characterized by inflammation of the synovial lining and destruction of extraarticular bone and cartilage [2]. It is believed that arthritogenic peptides, either from foreign or self proteins, are presented to T cells preferentially by RA-associated MHC molecules on antigen-presenting cells [3]. Activated T cells produce a variety of proinflammatory cytokines, including TNF?, IL-1 and IL-6. The inflammatory response induced by these cytokines is directly responsible for the overt RA symptoms, including joint pain, swelling, effusion and stiffness.
Existing Therapies.
Despite the prevalence and rising economic burden of RA, effective therapies for this disease remain limited, and there is no cure. Current therapies consist of early, aggressive and continuous treatment with non-steroidal anti-inflammatory drugs (NSAIDs) and disease-modifying antirheumatic drugs (DMARDs). Among the DMARDs, methotrexate has long been the drug of choice for RA, but newer biologic targeted therapies have emerged in recent years. These targeted therapies include Orencia®, a fusion protein composed of the extracellular domain of cytotoxic T lymphocyte antigen-4 fused to an immunoglobulin (CTLA4-Ig); Kineret®, an interleukin-1 receptor antagonist (IL-1Ra); Remicade®, a chimeric anti–TNF? antibody; Humira®, a fully human anti–TNF? antibody; and Enbrel®, a soluble TNF? receptor [4]. As a result of these therapies, the outlook for RA patients is better than at any time in our history. However, it is important to remember that these drugs provide treatment, not cures. In addition, the chronic nature of the disease necessitates lifelong treatment for most patients. Therefore, the long-term efficacy, safety and expense of these drugs remain concerns, particularly due to the high systemic doses and repeated intravenous or subcutaneous administrations necessary to achieve therapeutic results.
Overview of Preclinical Gene Therapy Studies.
Given the success of biologic targeted therapies, various strategies have been employed to utilize these immunomodulatory agents in RA gene therapy. Multiple preclinical RA gene therapy studies have demonstrated that gene therapy vectors, including retrovirus and adenovirus vectors, expressing IL-1Ra produce high levels of the transgene in target tissues and inhibit inflammation and cartilage loss in animal models. Similarly, numerous studies have demonstrated the effectiveness of blocking TNF? activity via gene therapy, including the suppression of inflammatory cell infiltration, pannus formation, cartilage and bone destruction, and expression of joint proinflammatory cytokines in animal models [4].
Furthermore, AAV expressing a TNFR:Fc fusion gene under the control of an inflammation-inducible NF-?B promoter delayed disease onset and decreased the incidence and severity of joint damage in mouse and rat arthritis models [4]. This type of gene therapy, utilizing a disease-inducible promoter, is of particular interest in autoimmune diseases like RA, which are characterized by flare-ups followed by periods of disease regression. By utilizing the inflammation-inducible NF-?B promoter, high levels of transgene expression are obtained only during disease flares, preventing unnecessary exposure of the patient to immunosuppressive agents during periods of disease regression.
In addition to proinflammatory cytokines, an important role for NF-?B signaling has been established in RA. NF-?B controls the expression of proinflammatory mediators of RA, including TNF?, thus may serve as a master regulator of the disease. In terms of gene therapy, both adenovirus and AAV have been utilized to deliver NF-?B inhibitors to synovium, successfully preventing expression of proinflammatory cytokines [5, 6].
A variety of growth factors have also been studied as therapeutics for RA. Bone morphogenetic proteins (BMPs), particularly BMP-2 and BMP-7, have been shown to induce chondrogenesis and osteogenesis when delivered by adenovirus or AAV vectors [4]. Additional growth factors that have been studied in relation to RA gene therapy include transforming growth factor (TGF)-?1 and insulin-like growth factor (IGF)-1. Adenovirus or AAV vectors expressing TGF-?1 have been used to transduce mesenchymal stem cells (MSCs) and drive ex vivo differentiation of MSCs into chondrocytes, facilitating cartilage repair in animal models [7]. Similarly, ex vivo chondrocytes transduced with an adenovirus expressing IGF-1 enhanced matrix synthesis and cartilage repair in horses [8]. These studies suggest important roles for growth factors in RA gene therapy, and indicate that a variety of growth factors may be able to join the list of effective RA therapies.
Overview of Clinical Gene Therapy Studies.
Early arthritis gene transfer trials used retrovirus vectors in ex vivo protocols to deliver IL-1Ra to the metacarpophalangeal joints of RA patients [9]. These safety and feasibility studies illustrated that gene transfer to RA joints could be safe and effective, but the low numbers of patients enrolled prevented any conclusions with regard to efficacy. A similar Phase I trial has been initiated by TissueGene, Inc utilizing retroviral vectors to transduce human chondrocytes, which are then mixed with normal human chondrocytes and injected into the knee of patients with degenerative joint disease. Currently, 16 patients have been treated in the United States and South Korea, with approximately 50% of the treated patients demonstrating symptomatic improvement [4, 10].
Another ongoing RA gene therapy trial is sponsored by Targeted Genetics, Inc and is evaluating the safety and efficacy of a single-stranded rAAV2 virus expressing the complete coding sequence of a TNFR:Fc fusion protein, which is identical to Enbrel®. This trial received much publicity in 2007 because of the death of an enrolled patient. Subsequent investigation determined that the death of the subject was not likely due to the virus vector [4]. Despite the death of this subject, the Targeted Genetics trial has shown promising results. The AAV vector appears safe, in that there is no evidence of circulating TNFR:Fc or extraarticular over-expression of TNFR-Fc, which would have indicated vector dissemination and amplification in extraarticular tissues. Clinical response was assessed using patient reported outcomes, revealing moderate improvement in target joint pain and swelling [11].
Conclusions.
Over the past several years, significant advancement has been made in the field of arthritis gene therapy. Numerous vectors and therapeutic genes have been tested and shown to have varying degrees of efficacy. However, while more than 1000 gene therapy clinical trials have been conducted or are ongoing, at least 32 of which have entered Phase III, only a limited number of these trials have been in the field of arthritis. Those trials that have attempted to combat arthritis have shown significant promise, while also serving as reminders that more work is needed. Future clinical trials are already being designed that will incorporate lessons learned from earlier trials, helping the field continue to move forward. With the recent Chinese approval of Gendicin [12], the world’s first commercially available gene therapy, for head and neck cancers, the field of gene therapy seems poised to finally realize its long-standing potential. The hope remains that gene therapy will soon join the arsenal against RA and other orthopedic diseases.
References.
1. Lundkvist J., Kastäng F., and Kobelt G. (2008). The burden of rheumatoid arthritis and access to treatment: health burden and costs. The European Journal of Health Economics. 8, S49-S60.
2. Smolen J., and Aletaha D. (2008). The burden of rheumatoid arthritis and access to treatment: a medical overview. The European Journal of Health Economics. 8, S39-S47.
3. Gregersen P.K., Silver J., and Winchester R.J. (1987). The shared epitope hypothesis. An approach to understanding the molecular genetics of susceptibility to rheumatoid arthritis. Arthritis Rheum. 30, 1205-1213.
4. Gaddy D.F., and Robbins P.D. (2008). Current status of gene therapy for rheumatoid arthritis. Current Rheumatology Reports. 10, 398-404.
5. Amos N., Lauder S., Evans A., Feldmann M., and Bondeson J. (2006). Adenoviral gene transfer into osteoarthritis synovial cells using the endogenous inhibitor IkappaBalpha reveals that most, but not all, inflammatory and destructive mediators are NFkappaB dependent. Rheumatology (Oxford, England). 45, 1201-1209.
6. Tas S.W., Adriaansen J., Hajji N., Bakker A.C., Firestein G.S., Vervoordeldonk M.J., and Tak P.P. (2006). Amelioration of arthritis by intraarticular dominant negative Ikk beta gene therapy using adeno-associated virus type 5. Human gene therapy. 17, 821-832.
7. Pagnotto M.R., Wang Z., Karpie J.C., Ferretti M., Xiao X., and Chu C.R. (2007). Adeno-associated viral gene transfer of transforming growth factor-beta1 to human mesenchymal stem cells improves cartilage repair. Gene therapy. 14, 804-813.
8. Goodrich L.R., Hidaka C., Robbins P.D., Evans C.H., and Nixon A.J. (2007). Genetic modification of chondrocytes with insulin-like growth factor-1 enhances cartilage healing in an equine model. 89:672-685. J Bone Joint Surg Br. 89, 672-685.
9. Evans C.H., Robbins P.D., Ghivizzani S.C., Herndon J.H., Kang R., Bahnson A.B., Barranger J.A., Elders E.M., Gay S., Tomaino M.M. et al. (1996). Clinical trial to assess the safety, feasibility, and efficacy of transferring a potentially anti-arthritic cytokine gene to human joints with rheumatoid arthritis. Human gene therapy. 7, 1261-1280.
10. Lee K.H. (2008). Preclincal and early clinical analysis of allogeneic chondrocytes transfected retrovirally with TGF-beta1 gene for degenerative arthritis patients. 5th International Meeting of Gene Therapy of Arthritis and Related Disorders.
11. Mease P., Wei N., Fudman E., Kivitz A., Schechtman J., Trapp R., Hobbs K., Anklesaria P., and Heald A. (2008). Safety, Local Tolerability and Clinical Response After Intra-articular Administration of a Recombinand Adeno-associated Vector Containing a TNF Antagonist in Inflammatory Arthritis. EULAR Congress 2008.
12. Wilson J.M. (2005). Gendicine: the first commercial gene therapy product. Human gene therapy. 16, 1014-1015.
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How some research is never published.
One issue that you will hear us gripe about here (and try to find a solution for) is the lack of mediums to discuss or publish “non-data”. What i mean by non-data is anything that can’t be published but might be useful. In that list I include hypotheses that were not correct, or data that is unpublishable or unreproducible.
You ask why non-data would ever be published eh ? Well while positive results are great and lead to new avenues, all the negative results help others not waste time doing useless time consuming experiments. Another reason why non-data is important is that your non-data may actually support somebody else’s research (some examples I will get to in another post). The problem is how to organize it, and how to constitute exactly what a piece of non-data entails.
Anyway. on to the meat of this “depressing” story. Let’s talk about Antidepressants 
This NYT article describes how some makers of antidepressants didn’t disclose about 1/3 of their drug related studies. This is nothing new for most of us in the scientific field. Many times when we receive funds from biotech firms or pharmaceutical firms to do research there are strings attached. That’s not to say the strings are all bad. The funding is necessary to bring some research into industry but one of the most prevalent string is that the corporation funding a research project usually has the final say on what data can be published, and when. They pay the research, they own the rights, and are accountable to shareholders.
Most of the time that is alright, but for drug trials that is another story. When patients are involved it is important to weigh the good aspects of a drug to the bad aspects. Well what if the FDA never sees the really bad data? Can they still make an informed decision on the safety of a drug? I’ll let the public think about that one. To be fair it’s not the FDA’s problem if information doesn’t come their way. There needs to be less ambiguous congressional guidelines set to monitor drug studies either earlier on in the process, or to require full disclosure.
David Vitrant
The Lowly Fruit Fly Takes a Giant Swat!
by Syam Anand
Who would imagine that scientists are mindlessly wasting taxpayer dollars on stupid fruit flies? That too, not the money that came through the NIH after peer review, but from ear marks- those wasteful “pork-barrel” projects that help politicians channel money for projects in their pet constituencies! Is it not a shame that this has been going on behind our backs until the most popular governor in USA decided to bring out this activity into the open in her first major policy speech?
During her first major policy speech, she made fun of the lowly fruit fly and the researchers who are after it. Amazingly, she even managed to garner a few laughs from the audience.
Watch the portion of the speech for yourself here.
http://www.youtube.com/watch?v=HCXqKEs68Xk
Poor fruit flies! Also, those poor souls of scientists who worked and continue to work on them!
Outrageously ignorant- that is how I would summarize the fruit fly remarks.
This is what happens if you don’t believe in science. This is exactly what happens if you don’t understand how science works. This is what happens if you don’t know that “WHAT IS TRUE FOR E. COLI IS ALSO TRUE FOR THE ELEPHANT”. This is what happens if you don’t understand evolution (whether you believe in it or not and to what scale). The list is long. But since it starts sounding personal, I will get back to the point.
The point is lowly organisms such as fruit flies have contributed more than what one can wish for when compared to studying “real patients”. Who could imagine that another low-life, in fact an even better description would be a “life-less thing” such as the T4 bacteriophage- a virus that infects E. coli- would lay the foundations of modern molecular biology and genetics? The answer is- those scientists who thought ahead of their time and understood the potential of systematically understanding how small “things” work in order to understand how big things also work. This is based on something called the universality of rules (with some exceptions for the sake of argument). Even laymen will get it, provided they keep their eyes and ears open. This is as simple as the laws of motion being the same in physics irrespective of what model you are using for your studies.
The fact is that studying fruit flies is exactly the way to accelerate research to understand how brain functions. I don’t know if fruit flies have a soul! But I sure know they have brains, even though they are tiny! In fruit flies, you can knock-out (functionally or physically remove) individual genes and proteins and ask questions about how it affects brain or any other bodily functions. And the fly would not complain, right? You can’t imagine doing that with so much convenience and economy in humans (even the dumbest person would agree). In fact, fruit fly research has identified components that affect not just brain function, but also developmental and genetics defects, thus helping scientists to extend these observations to other model systems and human beings.
FYI GOVERNOR: “About 75% of known human disease genes have a recognizable match in the genetic code of fruit flies (Reiter et al (2001) Genome Research: 11(6):1114-25), and 50% of fly protein sequences have mammalian analogues. An online database called Homophila is available to search for human disease gene homologues in flies and vice versa. Drosophila is being used as a genetic model for several human diseases including the neurodegenerative disorders Parkinson’s, Huntington’s, spinocerebellar ataxia and Alzheimer’s disease. The fly is also being used to study mechanisms underlying aging and oxidative stress, immunity,diabetes, and cancer, as well as drug abuse.”- CITED FROM WIKIPEDIA!
At this rate, the governor would argue to stop supporting research using mouse or guinea pig models, or the coveted Danio rerio (zebra fish), which is again another low-life not worthy of studying. Check out the following video, which is an example to understand how studying these low-lives help improve human health.
http://www.youtube.com/watch?v=ZItgyfuxsfM
There are similar countless examples in scientific literature.
If it is really true that a Senator or Congressman really used an earmark for funding fruit fly research, I congratulate that person for showing the courage to invest money for the future of public good. Flexibility is good, especially for funding science as there are too many ideas out there, which you cant clearly bet on, unless you give it a chance. That is what makes this country strong and a leader in fundamental and applied science. Hope better sense prevails in people. I hope laymen and CIPs (curious and interested people) educate themselves adequately from reliable sources before falling prey to misinformation campaigns about certain scientific investigations.
Long live T4 phages, fruit flies, zebra fishes, darwin’s finches and all low-lives!
Syam Anand
Pittsburgh, USA
Does Open Source Apply to Science?
Release early, release often- the mantra of open source softwares- can it be applied to Fundscience?
By Syam Anand
I want to first introduce the mantra of open source softwares to the small minority of those who may not be aware of it. “Release early and release often” summarizes the philosophy of people who work and support open source softwares. Open source softwares thrive on the committed efforts of groups of people who work from different parts of the world. They put their brains together for a common goal- constant improvement based on feedback. They are not part of any real organization. But they always evolve into an organization of sorts that is governed by operating principles that co-evolve with them keeping in tune with changing priorities. The good thing about evolution is, it tests and selects the fittest. Being more flexible thus makes them more adaptable as an organization.
From a strategic perspective open source softwares thrive on “real” feedback and “real” solutions. People who actually uses these softwares work on it and to improve it and keeps on improving it. First, they don’t wait to come up with packages such as version x or version y and then try to sell it in a form that cannot be tinkered with (similar to a biology kit whose information in “proprietary” and you don’t have access to it, even if you own the kit!). Second, they don’t set the intervals with which they come up with updates, beforehand. They do it on a regular basis. If a software has a bug, it is explained in the open for possible solutions. When a solution is found, it is notified to everyone. As a practicing scientist, it seems very similar to what we do everyday for every aspect of laboratory life, except for funding. We regularly do experiments, we regularly improvise and find better ways to ask questions and get answers. But when it comes to funding, we can do it three times a year for NIH and once a year for the foundations. Of course, we regularly work towards getting funded!
When you talk to any scientist (established or beginner) about funding avenues that are currently available, one constant complain you hear is that it takes a huge amount of time to get a proposal reviewed and funded. This is true for NIH (since I am a biologist, I would restrict myself to NIH) and foundations that fund research. By huge I mean, upto ONE WHOLE YEAR! Herculean efforts, planning and lots of luck seem to be a requirement to survive the transition periods. Consider the rate at which funding is granted nowadays- 10% of grants that require substantial amounts of preliminary evidence (which in turn takes money, time and manpower to generate!). This means if one has to rewrite and resubmit, which takes another year, a few lives and careers will be on the line and soon off the line. And it actually happens in real life. A glaring example is that of Dr. Prasher who did not win the nobel for GFP because he ran out of funds and had to give his GFP clone to two other scientists who went on to win this year’s nobel in chemistry. It seems he is driving a courtesy shuttle now! (read the blog by dgaddy in fundscience.org on GFP). This brings me to the point I wish to make- fund early and fund often is the way to go, if anyone wants to be different and make a difference in the way research is funded.
Fund early and fund often is easier said than done, as one has to consider the availability of funds, availability of reviewers and the time constraints this would place on the reviewers. Since the success of open source strategies depends on cooperation between individuals who are knowledgeable, building an interactive community and providing a forum for concurrent evaluation of proposals are the starting steps. The next step would be to remain flexible. Too many rigid rules for submission, evaluation and granting funds would make it look the same. Make it simple and flexible and let it evolve.
If there is a possibility of funding one project every month, I would rate that as more rewarding for supporting science ON TIME, rather than 12 grants at the end/beginning of every year. Fund early and fund often. If fundscience can adapt this mantra, it will address one low point of every funding agency that I know- TURNAROUND TIME. This is a niche that fundscience can evolve into and make its own habitat. How to achieve this objective is a matter of discussion, debate and planning. But this is one requirement that is yet to be a major focus for a scientific funding agency. One argument against this would be that competition is not going to be uniform in every month. My answer to that is that competition wont be uniform no matter how it is done, as scientists come up with fresh ideas regularly and there is no clear way to mark a genius from a dumbo other than wait and see how and what he/she does in a relatively long period of time. There is no point in holding a science Olympics to see who wins!
As a closing argument, I feel that if a scientific paper can be reviewed in two weeks time (accelerated papers take this long) and a suitability report for a journal (such as science/ nature) can be obtained overnight from their editorial boards, a short write-up (one-three pages) can be read and reviewed and put to vote within a month. Another fresh beginning would be to put the submitted proposals for a vote not just by the “experts” (for which there are other forums such as NIH and the innumerable foundations) but by everyone including Ph.D students, post-doctoral fellows, doctors, engineers and people who are curious and interested to participate. If you can vote for electing your president, you could vote on the science that you wish you fund directly too! The role of experts will be to moderate the discussion and voting in a fruitful and non-partisan manner.
As for which projects can be funded (since the public is directly involved, this is a concern for a lot of people), the institutional review board and research administration to which the scientist making the proposal is answerable will ensure that all rules and regulations are met with and research is conducted ethically and responsibly.
Syam Anand
Pittsburgh, USA.
FundScience Enters the Google Competition!
We recently stumbled upon Google’s project 10 to the 100th. This concept is very similar to how FundScience would like to approach the problem but with more feedback from the community. We think that ideas should be funded on the merit of the idea, and scientific logic. Many great ideas are never tested because there are no preliminary results and no funding to get those results.
As part of our application we did our first 30 Second Clip, with real live scientists from different walks of life. Unfortunately we where limited to 30 seconds but we will be coming out with a larger clip in the coming weeks.
[youtube]http://www.youtube.com/watch?v=09E6WwCeNxo[/youtube]
We are also beginning to film new science technique oriented videos for the public (and other scientists as well). If you would like to make your own, or have suggestions for videos or topic you want covered please comment below or send us an email.
Thanks,
David Vitrant
Bug’s Life
Bacteria are ubiquitous microorganisms (typically in the scale of a few micro meters; a micrometer is one ten thousandth of a centimeter) that are present in almost every habitable nook and corner of earth. Some of them have even specialized for surviving seemingly uninhabitable places such as hot water springs and extremely dry or acidic environments. In an era of high personal hygiene what would amaze most of us is that there is an abounding presence of these minute life-forms in our own bodies. It is estimated that in our own bodies they outnumber our cells nearly one to ten! Most of these harmless bacteria live on our skin and inside our digestive tract. Among the advantages of harboring these bacteria are nutritional and immune system-stimulatory functions. This suggests that they are useful to us in many ways than we previously thought plausible. However, under certain circumstances such as immune depletion, these harmless bacteria can become dangerous and even fatal to the host. One notorious example is Staphylococcus aureus, which lives on our skin. It is estimated by CDC (Centers for Disease Control and Prevention), USA that S. aureus causes more infections than AIDS! Worse, this bug seems to be able to develop resistance to any drug that is thrown at it from time to time. Thus we have Methicillin Resistant Staphylococcus aureus (MRSA) and Vancomycin Resistant Staphylococcus aureus (VRSA) among others that make a substantially long list.
Watch the following video to get a grasp on the “grapes of wrath”.
More information about MRSA and the challenges it pose, is available in the following video.
So the question is what does one do if a superbug keeps developing resistance to every known antibiotic? The answers are not simple. In fact, it requires concerted action at all levels of our community as it involves both personal and policy initiatives. There are some simple steps that the public can do such as washing hands and taking care not to share personal stuff through which these bacteria spread most of the time. As for doctors, a simple step such as washing their hands after attending individual patients would decrease the risks of spreading the infection from one patient to another. Hospital management could step in and try to keep high-risk patients in isolation as S. aureus has been reported to flourish and spread in hospital environments. As for scientists like me, we have to up our ante to discover more viable targets and increase the available arsenal against these bugs. We should also try to take our discoveries from the “bench-top to the bed-side” by actively collaborating with the drug industry. Those of us with business acumen could even don the entrepreneurial hat ourselves. The demands for an ever-growing arsenal is always high in order to succeed in this fight. This is also true for a lot of other bugs as well, such as multi drug-resistant tuberculosis and AIDS.
In the beginning, screening for antibiotics was a relatively simple but laborious process where people hunted for fungal samples from soil for anything that kills bacteria in culture. In nature, several fungi produce antibiotics as means of efficiently competing with their smaller cousins for survival space, in this case soil. In the period that followed, people have successfully modified naturally occurring compounds isolated from such screens-such as penicillins-to increase their efficacy as more and more drug-resistant bugs evolved. However, we seem to have run out of steam with these approaches.
Fortunately, scientific advance provided us with alternatives. By screening synthetic combinatorial chemical libraries (such collections often contain several thousand compounds) and structure-based design principles, we can design drugs that specifically target essential proteins present inside these bugs. However, it is not easy to predict targets and perform large screens in the absence of supporting basic research. Basic research into fundamental life processes in bugs is capable of providing additional valuable targets that can be exploited for therapeutic purposes. Unique metabolic pathways and essential proteins discovered by basic researchers should provide viable antimicrobial targets for future.
The recent discovery of a potent agent against MRSA is a glaring example of the triumph of basic research, interdisciplinary approach and the entrepreneurial attitude of one scientist who lead the effort. The research group led by current director of the Institute of Cell and Molecular Biosciences, New Castle University (UK), Prof. Jeff Errington, discovered the Achille’s heel of the superbug while they were studying it’s cell division machinery. During his studies, he noticed that the rounded shape of S. aureus made it highly susceptible to the inhibition of cell division unlike some of its bacterial cousins who had a more elongated shape. He then went on to exploit these findings by starting a spin-out company Prolysis Ltd. Recently scientists from Prolysis published their findings of a novel lead compound directed against the cell division machinery of S. aureus in Science (Science. 2008, 321, pages 1673-1675). Interestingly the compound has “potent and selective anti-staphylococcal activity”. A new company Nugenis Ltd is expected to take over the drug screening opportunities emerging from the Errington lab as Prolysis evolves into a drug development company. The case serves as one more classic example where the entrepreneurial spirit of a basic researcher is set to pay big dividends for public health by taking his discovery from the “bench-top to the bed-side”.
Syam Anand
Pittsburgh, USA.
Scientist Who Discovered GFP Gene Left Out of Nobel Prize
On October 8th, the Nobel Prize in Chemistry was awarded to 3 scientists for their work on green fluorescence protein (GFP), a protein that is now utilized by scientists around the world to label cells and proteins and to study a variety of conditions. Congratulations to these scientists, and their brilliant work that has contributed enormously to the work of so many other scientists, including myself. However, a story that has been under-reported is that of the scientist who originally discovered and cloned the gene that encodes GFP. The work of Osamu Shimomura, Martin Chalfie, and Roger Tsien, the 3 winners of the prize, would not have been possible with the previous work of Douglas Prasher. Prasher originally cloned GFP and had the vision to see what an important impact this protein could have.
Prasher’s GFP work was funded by the National Cancer Institute. In his grant he suggested that it should be possible to take the GFP gene out of the jellyfish cell and attach it to cancer cells so that they would be labeled with a fluorescent tag. Prasher managed to find the gene for GFP in Aequorea victoria and was able to express it in bacteria. In 1992 he published a paper in Gene; it reported the cloning of GFP and the sequence of the 238 amino acids in GFP, shown below. Sadly it was only a two year grant and the funding ran out before he could express the GFP clone he had produced in a manner that would result in a fluorescent GFP.
Unfortunately, the NCI did not agree with his vision and see the potential impact of this major discovery. His funding ran out and, despite searching for several years, he was unable to find additional funding from other sources. Because of this, the career of an exceptional scientist came to an end. Douglas Prasher, Ph.D now drives the courtesy shuttle for an auto dealership in Alabama. Before leaving science, Prasher gave his cloned genes to two of the three scientists who won the Nobel Prize this year.
This story illustrates the importance of funding in science. The National Institutes of Health are responsible for providing most of the funding to the biomedical science community. Unfortunately, the budget for the NIH has remained stagnant for several years, and shows no signs of increasing in the near future. Because of this, thousands of worthwhile projects go unfunded each and every year in this country. We could sit back, cross our fingers and hope the best projects get funded. But, as history shows, that is simply not the case. How many unfunded projects could have led to a major discovery, a Nobel Prize, or a cure for a major disease? We will never know. But the goal of FundScience is to play a role in insuring that does not continue to happen in the future.
Douglas Prasher was interviewed this morning on NPR. You can hear his story here.
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PCR without the PCR machine!
Sounds like fiction? Guess not. It is a distinct possibility now. This innovation is likely to revolutionize field applications of PCR and further expand its commercial potential.
For those of you, who are unfamiliar with PCR: PCR stands for Polymerase Chain Reaction. Since 1983, when the idea of PCR was first conceived by Kary Mullis, it has grown to be the method of choice for economically amplifying fragments of DNA or RNA over a billion times with the help of polymerases- enzymes that make more copies of nucleic acids such as DNA and RNA. Due to its ability to make more of the same from very less of the starting material, PCR is the backbone of both basic-science labs and application-oriented labs such as biotech and forensics. The expiration of the original PCR patent is bound to bring in more innovations and cheaper methods from competing players in the multi-million dollar PCR industry!
Watch the following movie, which explains the molecular basis of the reaction in layman’s terms. In essence the two strands of DNA act as molds for making more DNA molecules that contain the same coded sequence information.
http://www.youtube.com/watch?v=_YgXcJ4n-kQ
Until recently, the PCR machine was an indispensable part of PCR reaction as it drives the temperature cycles in the PCR. Recently, scientists have successfully attempted to replace the PCR machine with helicases to achieve amplification of DNA. Currently PCR uses three different temperatures that cycle multiple times to accomplish amplification. The first step of denaturation melts the DNA by increasing the temperature to 94°C. In nature however, molecular machines called helicases carry out DNA melting. Helicases melt double helical DNA by using chemical energy provided as ATP. They hydrolyze ATP and utilize the energy released for mechano-chemical cycles that help them to physically separate DNA strands in a stepwise manner. Inside living cells, helicase reactions support a variety of DNA and RNA transactions.
There were a couple of challenges that had to be overcome to ensure specific and successful amplification of DNA with the help of helicases. Initially the process used a mesophilic (optimal temperature if neither too hot or too cold; typically between 30-37°C) version of a DNA helicase called UvrD from Escherichia coli (EMBO Reports, 2004, 5: 795-800). High temperatures increase the specificity of the annealing step in PCR. Therefore, in the next step, specificity was increased by using a thermophilic (high-temperature loving; typically between 50-72°C) version of UvrD helicase from Thermoanaerobacter tengcongensis (Journal of Biological Chemistry, 2005, 280: 28952-58). However the challenge of amplifying long stretches of DNA remained. Technically termed processivity, which is nothing but how long an enzyme stays and does its work on a molecule of DNA before falling off, this was another hurdle to be overcome. The longer an enzyme stays on the DNA without falling off, the longer it is likely to keep doing its job on the molecule. In this case, a highly processive helicase could melt long stretches of DNA and therefore help in amplifying long templates of DNA. This would increase the practical value of the technique.
The processivity issue was recently addressed by fusing the helicase to a DNA polymerase (Gene, 2008, 420: 17-22). Whereas the helicase alone could amplify only short substrates, its fusion to DNA polymerase (DNA polymerase by itself is so processive that it can copy the entire genome of E. coli, which is more than 4 million base pairs without falling off) made it much more processive. The helicase-DNA polymerase fusion can efficiently amplify DNA fragments upto couple of thousand base pairs length, which brings it into the realm of practical use.
Further improvements in processivity and specificity should see the technique finding wider use in biology laboratories. The technique christened Helicase-dependent amplification of DNA (HDA) would find applications in diagnostics and environmental monitoring by driving down costs and increasing its accessibility for applications in the field. HDA should be a huge benefit for people who do not want to routinely do PCR, to those who are not experts and also for whom investing in a PCR machine is not worth it. Along with the ability to detect amplified DNA by non-electrophoretic methods, HDA should make the PCR process user-friendlier. It would also increase the application potential of PCR-based techniques where there is a shortage of skilled personnel, especially in poorer nations. In the words of HDA’s original proponents, “the development of simple portable DNA diagnostic devices to be used in the field and at the point-of-care” should be around the corner.
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