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Antimony, x-rays, childhood obesity
Science news links for March 12-15, including the latest on my SpectroscopyNOW.com column:
- Feverish New World X-ray – X-ray crystallography has allowed US researchers to discover exactly how one type of New World hemorrhagic fever virus latches on to and infects human cells. The work offers a much-needed lead for new treatments.
- Marking up childhood obesity – Metabolic fingerprinting has been shown to be a powerful tool for exploring Biomarkers in a range of disorders and the pathophysiological mechanisms of disease. A new study has now applied the technique to childhood obesity to intriguing effect.
- Myrtle medicine – German researchers have successfully devised and implemented a total synthesis of myrtucommulone A, tracking progress and structures using NMR spectroscopy. The compound is physiologically active in anticancer and antibacterial screens, and the synthesis opens up the potential for making simpler, but active analogues.
- Antimony analysed in food packaging – A simple, yet sensitive, method for detecting inorganic antimony in food packaging has been developed using cloud point extraction combined with electrothermal atomic absorption spectrometry (ETAAS).
- Unlocking the opium poppy’s biggest secret – Researchers at the University of Calgary have discovered the unique genes that allow the opium poppy to make codeine and morphine
- What is the difference between a heart attack and cardiac arrest? –
- Antibiotics against stomach cancer – Helicobacter pylori often causes stomach ulcers and, in extreme cases, gastric cancer. f1000 Medicine Reports, Seiji Shiota and Yoshio Yamaoka discuss the possible eradication of H. pylori infections using antibiotics.
- How cars are killing us – Cars are lethal, but nowhere more so than in the developing world.
- The Spicy Disciplinarian
- Cancer, pneumonia, regulations, theranostics
- Alchemy, Hydrogen Economics, Lead-free Crime
- Stinging Heavy Metal Resistance
- Resistance is not futile
Antimony, x-rays, childhood obesity is a post from: Sciencebase Science Blog
Total alchemist
A good, old-fashioned total synthesis of a natural product caught The Alchemist’s attention this week, as did the notion of spiking the hydrocarbon picene with potassium atoms to turn it into a superconductor.
In a related carbon field, Chinese chemists have broken the rules to crack bucky eggs and US scientists have looked to molecular midwifery to help explain the origins of life.
In environmental news, the tragic story of BPA is told from the chemical perspective and an award to a Swedish team could help studies of oxygen depletion in the Baltic Sea that might one day lead to a route to remediation.
More details and all the links can be found on ChemWeb. You could also get the latest chemistry news and more by subscribing to the email newsletter.
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Total alchemist is a post from: Sciencebase Science Blog
Whatever happened to the audiophile?
Back in the 1970s my parents had friends who had stacks of hi-fi separates with gold contact wiring and speaker stands on metal spikes. They were only playing Perry Como on vinyl, but that was their idea of fun, so good luck to them. When the CD emerged on to the market with its claims of superior quality and scratch resistance, the hi-fi enthusiasts split into two camps: those who clung to their “warmer” but crackly analogue vinyl and their hissy tapes and those who went digital and got optical wires to hook up their shiny new CD player to those spiky speakers.
Manufacturers propagated the upward spiral for both camps marketing ever more elaborate systems and even selling green pens to colour the edge of a CD to prevent laser leakage. Personally, I grew up with a “stereogram” and a personal radio-cassette and was quite happy with it, whiling away countless hours listening to prog rock, Jean Michel Jarre, Talking Heads, and the occasional Perry Como album.
But, was it all for nothing? Within another generation the notion of digital audio had been compressed using the audio equivalent of the lossy image format jpeg and music fans were listening on pocket devices or watching Youtube clips with embedded music on poor-quality computer speakers and really not caring either way, whether the sound was great or not.
Jerald Hughes of University of Texas Pan American in Edinburg writing in the International Journal Services and Standards has a nice table showing the technical specification of the human ear and comparing it to the various analogue formats:
| Audio system | Frequency range/Hz | Decibel range/dB |
| Human ear | 20-22,000 | 110+ |
| Vinyl LP | 30-15,000 | 50-60 |
| 8-track tape | 45-8000 | 45 |
| Cassette tape | 50-12,000 | 45-50 |
| Chrome cassette | 50-16,000 | 60 |
| Reel to reel | 30-20,000+ | 66+ |
So, the only system that ever came close to the full range of human hearing was reel-to-reel and I don’t recall seeing many of those around even among the most extravagant separates hi-fi aficionados of my parents’ acquaintance.
So, how does the CD fit into this picture?
| Audio system | Frequency range/Hz | Decibel range/dB |
| Human ear | 20-22,000 | 110+ |
| Compact disc | 20-22,000 | 90+ |
| DVD audio | 10-95,000 | 144 |
Not bad? It really was a golden era, then, apart from that lack of “warmth” and “colour” that the analogue stalwarts claimed. And, with DVD audio quality (and SACD, superaudio CD) far outstripping even CD. These latter formats are well-known to devoted adherents of jazz and classical where dynamic range and complex frequency content tends to be more common than in rock and pop, although there are serious mastering problems with many modern recordings in all genres.
Today, there are almost as many audio “formats” as there are audio files. One can choose a download or rip at almost any rate, a lossy or lossless compression algorithm, and countless other options and codecs to playback a music file on myriad devices. But, consumers in general, have gravitated towards a quality that is much lower than the human ear is capable of discerning and much lower than top-end equipment is capable of reproducing. It’s as if the hi-fi nuts never existed…
Perhaps that’s the point though, my generation was perfectly content to listen to vinyl albums duplicated on cassette tapes (remember: home taping is skill in music killing music, it never did) and today, the kids are quite happy to listen to downloaded 128kbps mp3 files through the cheap earbuds that come with portable music players.
Human senses and sensibilities have limits. It’s not that the human ear cannot receive the finest of musical details, it most certainly can, it’s just that most people perceive satisfaction in listening to a good-quality mp3 and are not worried about the top notes or the quiet moments that might be lost in the compression process that squeezes their collection of thousands of songs on to a sliver of silicon embedded in a case no bigger than a thumbnail.
Audio cassettes were popular because they were convenient – mix tapes, copying albumbs, recording off the radio all infinitely simpler with cassettes than with a reel-to-reel machine. In the post-digital era of music on chips rather than disks consumers are trading-off audio quality for convenience just the same as they ever did. Same as it ever was. Same as it ever was.
Jerald Hughes (2009). Emergent quality standards for digital entertainment experience goods: the case of consumer audio Int. J. Services and Standards, 5 (4), 333-353
I spoke to Hughes who confessed that he too is a prog-rock fan, and admitted that the first album he ever bought with his own money was the YesSongs triple live album. He also told me he is still listening to his Technics direct-drive turntable with hyperelliptical stylus through Bose 501 speakers and said, “it really IS ‘warmer’…”
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Whatever happened to the audiophile? is a post from: Sciencebase Science Blog
Forensic saliva test within spitting distance
The latest issue of SpectroscopyNOW is online. This week I cover everything from MRI for testicular cancer to egg-shaped carbon balls by way of energy molecules, copper proteins, secret writing, first up a forensic test for distinguishing saliva deposits from other substances at a crime scene:
Non-destructive spit test – Raman spectroscopy can identify samples of an unknown substance at a crime scene as human saliva during forensic analysis, according to a US study, the technique would preserve DNA evidence. I asked research team leader, Igor Lednev to tell me about his aspirations for the technique.
“The major motivation of this research project, funded by the National Institute of Justice, is to bring our novel method to the forensic lab and a crime scene as soon as possible,” he told me. “The method is at the developmental stage at the moment and several further developments need to be done before moving to the “real” world crime scene.” These include (i) automation of the technique and making it a user-friendly “black-box type” apparatus, (ii) expansion to potential mixtures of body fluids, (iii) protection from possible interference from substrate materials and possible contaminants, and (iv) expansion to possible evidence degradation under various environmental conditions.
To achieve those goals the team is collaborating with “real world” practitioners, CSIs including Barry Duceman, Director of Biological Science, at the NY State Police Forensic Investigation Center and John Hicks, Director of the Northeast Research Forensic Institute. Lednev revealed to me that a first prototype of the device should be in forensic laboratories within two to three years.
Also, in my SpectroscopyNOW column this week:
MRI on the ball – MRI proves to be a good diagnostic tool for testicular cancer and could spare some men unnecessary surgery.
Focus on energy molecule – Organisms use ATP as a universal energy storage molecule, now carbon nanotubes, modified with luciferase, have been used as near-infrared detectors for cellular ATP. The work has potential for studies of ischaemia, Parkinson’s disease, hypoglycaemia and more.
Copper, on the beat with NMR – The first NMR spectroscopy study of the copper site in an important blue metalloprotein, azurin, has been undertaken. Copper mediates many biochemical redox reactions and azurin plays an important role in catalysing electron transfer in cellular reactions.
Sunscreen spies – Sunscreen and boron can work together to make a compound that changes colour when touched under ultraviolet light. The compound changes from blue-green to yellow with the gentlest of rubs and then reverts quickly to blue-green when gently warmed, although the process is reversible at room temperature.
Bucky eggs cracked – Unusual egg-shaped fullerene molecules are rulebreakers because they do what no other fullerenes seem to do – fuse three pentagons of carbon atoms, according to chemists in China. The discovery of these molecules could lead to new insights into fullerene chemistry as well as offering new opportunities for synthesising novel materials.
Forensic saliva test montage by Albany’s Aliaksandra Sikirzhytskaya.
Virkler, K., & Lednev, I. (2010). Forensic body fluid identification: The Raman spectroscopic signature of saliva The Analyst, 135 (3) DOI: 10.1039/b919393f
- Colour MRI, Agent Prion, Testing Testosterone
- Alchemy, Hydrogen Economics, Lead-free Crime
- Pre-eclampsia, NIR, Nano-dots
- Light, Trials, Balls
- Leukemia Tweezers
Forensic saliva test within spitting distance is a post from: Sciencebase Science Blog
Hacking your online identity
Geo-location services are very useful, helping you find a post office, ATM, decent restaurant, or hooking up with friends. They are commonly used in conjunction with smart phones and other mobile devices that ping your location (based on network coordinates or the global positioning system, GPS) back to the owner of a given system.
Location-based services also represent a security threat, especially if you hook whereabouts up to the likes of FourSquare and other social networking sites that can be set to reveal publicly your status in a timely way and reveal your precise position to all and sundry. Now, a new security awareness site, going by the ironically informative name of PleaseRobMe.com, demonstrates the hazards inherent in location-based services. The site’s strapline proclaims that they are: “Listing all those empty homes out there” and in interviews this week the owners have been telling the media that they’re not helping burglars but warning users about revealing too much about themselves on the networks.
This latest debacle, if you can call it that, highlights once again the fact that individuals are not necessarily aware of the privacy and security issues associated with revealing personal information and their identity online. Some observers have suggested that digital identity online will be “the next big thing”. One can imagine that it certainly will be, especially as governments, businesses, healthcare organizations, and others will increasingly require us to prove our identity digitally when we access their services online. But, wherever there is a lock guarding something precious, there is someone who will go set out to pick that lock.
If you’re not worried about privacy just check out these sites to see what systems can find out about you without your even logging in – EFF Panopticlick experiment and web tracking, what the internet knows about you.
As such, identity management, known in the “industry” as IdM is a more and more important aspect of one’s online persona for joining, interacting, and leaving countless systems. There are numerous protocols available, such as OpenID and the OAuth systems that allow you to login to one service by verifying you with a prior login process on a third-party trusted site.
Researchers in the UK explain that IdM could be reaching crisis point. “There is overwhelming evidence that current IdM is failing us, says Mark Pawlewski of Loughborough University and colleagues. Pawlewski is a Principal Researcher working for BT Innovate and Design.
Countless websites require registration and logins and users are now faced with the task of remembering dozens of usernames and passwords or else suffering “password fatigue” whereby they employ insecure practices, such as using the same username and password combination on multiple sites. The researchers have an explanation for the IdM problem:
At the root of the problem is the fundamental flaw that the internet was not designed, but evolved without a uniform system of digital identity in place. There have been numerous attempts to solve this problem, such as Microsoft Passport, but many of these have failed leaving a scattering of inconsistent, ad hoc, partial solutions.
One of the challenges is to give users immediate access to a particular site where they have not already registered, but do meet the requirements for access, e.g., being over 18 years of age and possessing a valid credit card. The OpenID system (and others such as Card Space and Liberty Alliance) goes part way to addressing this issue, as do the linkage systems employed by Facebook apps and similar systems that allow one to comment on some blogs using Facebook or other credentials. However, it would be foolhardy to trust a Facebook app with the login for one’s bank account. An Identity Provider (IdP) that mediates between users and websites is clearly needed.
But, there are only a very limited number of IdPs around and they provide only very limited functionality, certainly none is at the trust level yet for the average user to connect with the e-commerce sites they use, such as amazon.com, their online banking, or even all of their social media and networking accounts from Facebook to Twitter via LinkedIn.
Unfortunately, preserving the status quo is the approach adopted by sites and internet service providers. After all, the creation of an IdM system and trusted IdPs will not be cheap and will also face the resistance of the millions of internet users happy to create yet another username-password. On the bottom line, it is a matter of preventing fraudsters from getting a key to unlock one’s virtual valuables.
If service providers maintain fraud at an “acceptable”, level then the status quo will persist. However, if there is a surge in identity fraud the costs of which outweigh the necessary investment in IdM, then we might just see the emergence of a system that is simple, secure, and safe. In the meantime, just keep up the good work with those complex passwords and don’t tell everyone on the internet when you’re heading out the door, you might as well not lock up if you do.
So, how do you hack your online identity? Well, there’s lots of advice out there, this post from Liverpool University says it well.
T. Martin, C. Durbin, M. Pawlewski, & D. Parish (2010). Future vision of identity Int. J. Liability and Scientific Enquiry, 3 (1/2), 86-98
- We’re Still Not Facebook: Lessons from Late Adopters (readwriteweb.com)
- Your Life Online Could Affect Your Job Search (regulargeek.com)
- Test the water before you throw the client in (flackrabbit.com)
- PleaseRobMe: Like Foursquare, but for crooks (inquisitr.com)
- Password Sitter
- Staying in with Friends on a Wireless Mesh
- ID Theft
- Gen-F Scientists Ignoring Social Networking
- No Spies Under My Bed
Hacking your online identity is a post from: Sciencebase Science Blog
Time-keeping alchemy
Time-keeping with quantum mechanics caught The Alchemist’s eye this week with a truly long-term view while secret writing that uses a mix of sunscreen and boron could lead to new scratch and read products.
Ionic liquids hold much promise in gas chromatography of biofuels, we learn, and a lethal combination of anticancer drug and protein inhibitors offers a new, effective approach to ovarian and breast cancers.
Chemists in China have boiled a bucky egg and broken the rules, and finally, a fourth NSF award for chemists at Kansas State University.
Write-ups and links to full articles now on ChemWeb.com
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Time-keeping alchemy is a post from: Sciencebase Science Blog
Four ways to connect with Sciencebase
Simply click one of the four icons above to get to the Sciencebase Facebook, Delicious, RSS, and Twitter pages for far too much science and tech than even I know what to do with…
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Royal stamps for Royal Society
Royal Mail Stamps has issued a commemorative set of stamps in the UK to celebrate the 350th anniversary of the Royal Society this year. The stamps feature ten of the most prominent fellows of the Royal Society:
- Robert Boyle – Chemistry
- Sir Isaac Newton – Optics
- Benjamin Franklin – Electricity
- Edward Jenner – Vaccination
- Charles Babbage – Computing
- Alfred Russel Wallace – Evolution
- Sir Joseph Lister – Antiseptic Surgery
- Ernest Rutherford – Atomic Structure
- Dorothy Hodgkin – Crystallography
- Sir Nicholas Shackleton – Earth Science
The stamps marry portraits of Fellows with imagery representing their science. Apparently, the list was selected by leading figures in the Society.
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Royal stamps for Royal Society is a post from: Sciencebase Science Blog
Shedding light on photosynthesis
The rules have changed regarding photosynthetic law, The Alchemist learns, while it turns out that plants use steroid hormones just like those found in mammals. Another type of plant could lead to a novel anticancer drug.
In polymer news, an approach to locking in plasticizers could eradicate problems associated with PVC in toys and medical devices. Dutch scientists have looked at the smallest chunk of graphite in the form of the coronene molecule and explained its phantom bands.
Finally, chemistry often gets a bad press, but when chemists attempt to lighten the mood they get criticized for dumbing down, the RSC offers a riposte to complaints from those who disapprove of its publicity stunts.
More in The Alchemist on ChemWeb.com
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Shedding light on photosynthesis is a post from: Sciencebase Science Blog
Interview with David J Newman (Pt. II)
This is Part II of the unabridged transcript of an interview with Dr David Newman, Chief at the Natural Products Branch of the NCI in Maryland. The interview was conducted for a new quarterly newsletter – Chemistry Matters. You can read Part I in which Dr Newman discussed how natural products can lead to novel leads for pharmaceuticals.
In Part II, he tells us about the highlights, the lows, and the future of natural product research in the pharmaceutical drug discovery process.
Q. What specific highlights have there been? Any recent breakthrough drugs?
A. To answer the second part of the question first. For obvious reasons, I cannot go into compounds that are still in the early development pipeline as I can only provide information that is in the “public domain” due to IP issues.
The story of Taxol® above is one. A more recent one is the work that we did with Eisai America on the evaluation of a compound that now is known as Eribulin that though made by Eisai chemists, is derived from a very potent marine sponge metabolite known as halichondrin B. We had to extract 1 metric tonne of the sponge to get 300 milligrams of hali B working in conjunction with New Zealand government scientists and academic chemists in NZ. Once we had the material, we were able to perform preclinical studies with both it (the NP) and the Eisai compound, then perform preclinical studies on eribulin (as it had a much better TI than the NP to my chagrin!) and ultimately “honcho” it through the DTP system in conjunction with Eisai scientists to Phase I clinical trials under CTEP auspices. It is now in Phase III.
Another is an inhibitor of the protein chaperone known as heat shock protein 90 HSP90). When NCI intramural scientists showed that HSP 90 was inhibited by an old but well-known antiparasitic agent known as geldanamycin, NPB had the problem of finding a producing microbial culture and then generating over 3 kilograms of pure geldanamycin in order to permit other chemistry groups within DTP to produce what is now known as 17-allylamino-geldanamycin, which was licenced, together with other compounds / information to the then Kosan Pharmaceuticals (now part of Bristol Myers Squibb) where it is currently in Phase III trials. This was the first “signal transduction agent” to go into clinical trials.
Q. What challenges do you face in general?
A. Two in particular. Access to countries in order to collect materials for investigation and the perception that NPs are “old hat” and that combinatorial chemical processes coupled to high throughput screening has made NP investigation obsolete / not “cutting edge”!
In the first case, this is due to the fact that the US, though it signed the Convention on Biodiversity (CBD) the treaty was never ratified by the US Senate, a constitutional requirement for all foreign treaties. NCI luckily had realized that formalized methods of recompense to countries that permitted us to collect was something that was lacking, and so in the late 1980s, devised the NCI’s Letter of Collection (LoC), which was first signed with the Malagasy Republic in 1990, three years before Rio. Although monetary royalties cannot be part of such an agreement due to US Law (such a statement would “encumber any future invention” as the act of collection is not a patentable process), methods such as training and aid in development of compounds is permitted. NCI has formal LoCs with over 20 countries and if a country permits us to collect, even if there is no formal LoC in place, the tenets (in particular the source country commitment, see below) are observed.
What has also occurred is what my old Chief (Gordon Cragg) and I have called the “Myth of Green Gold”, where totally unrealistic expectations have been foistered upon developing countries, often by developed country organizations, such that the idea that a “patent means a drug with millions of dollars of income” has become paramount. Nothing could be further from the truth, but it, and other ideas as to what is required to actually develop a drug from an extract, has caused immense problems as legal and political systems try to put in place laws that would permit collections to be investigated.
Without naming the countries involved, I will give a couple of examples. One country has in their law the statement that any agreement with an offshore organization means a “commercial agreement must be in place” even if it is with NCI for example. This country does not have the capability to develop a drug due to lack of infrastructure.
In another case, a state within a country currently does not permit materials to be worked on in other states in the same country, even though they have neither the population nor infrastructure to perform the necessary work to discover and develop a NP derived compound as a drug candidate….”it must be done in state X”…….
In the case of HTS plus combinatorial chemistry as a substitute for NP discovery, currently I know of only one approved drug in any disease that is a “de novo” combinatorial product and that is sorafenib, a kinase inhibitor. Combinatorial chemistry is absolutely magnificent for “lead optimization” but unless it uses focused libraries, a lot of which now closely resemble NPs in terms of their elemental composition, numbers of rings and presence of multiple chiral centers, they simply “occupy space on a test plate”.
Plus what has become quite evident is that assaying against isolated enzymes gives rise to a very large number of “hits” and very few “leads” and even less “leads” that have activity either in cellulo or in vivo, and if they do, the loss in potency is orders of magnitude from in vitro to in vivo. Even more troubling is the recent papers that show that a significant number of “hits” are in fact artifacts of the assays (usually due to physical interference, not genuine activity).
Q. How can traditional medicine (Chinese/Ayurvedic etc) help in the search for novel leads?
A Provided the data is rigorous and not anecdotal, such information can lead us to areas that we have not investigated in the past. What do I mean by rigorous? The plant(s) {and they are almost all plant-derived} must have been identified taxonomically, the part(s) of the plant(s) used must be identified and shown to only be that particular part or parts from the correct plant. Most importantly, the growth and / or cultivation of the plant must have been defined according to one of the recognized herbals (often what is known as the “Emperor’s Red Book” in Traditional Chinese Medicine {TCM}) and the plant(s) provided be harvested at the time / climatic conditions / storage as defined above.
If multiple preparations are being assessed from the nominally same plant but from perhaps different areas, climates, time of year etc., then there must be adequate evidence of chemical content (say an HPLC fingerprint) and biological activity to compare with the “active” fingerprint / activity. This is the equivalent of a certificate of analysis (CoA) that is required for regular medications and / or their contents.
Sadly, in a very large number of cases, parts, if not most, of the “requirements” above are lacking in a very large number of the preparations and reports; faith is not a substitute for evidence under those conditions.
Q. What future do you see for natural products research?
A. For obvious reasons, I am biased. However, what Mother Nature has is almost 4 Billion years of evolution to practice her “biological chemistry” and in designing molecules that interact with proteins. Due to the massive commonalities shown by comparative genomics between Homo sapiens and microbes, compounds from such organisms may and often do, interact with human proteins that are paralogs of those found in lower organisms. Why do I say microbes? Because in a large number of cases, the compounds that we find may well be the product(s) of interactions between microbes and their hosts such as marine invertebrates or plants and they were probably designed as defensive agents to stop predators.
This is almost certainly the case with marine-sourced materials where the nominal producing organism is an invertebrate as they have to filter-feed and to do that, they must have a “toe-hold” on a suitable surface. Since they do not have teeth or claws, their defences are chemical in nature. I often joke that WMDs are alive and well on an active coral reef and we are finding extremely potent agents that kill cells from such areas (halichondrin B above is one example, Yondelis from the tunicate E. turbinata is another).
Thus investigation of the chemical structures of NPs that are potent agents in “your disease of choice” will lead you to structures that are the products of aeons of experimentation and that can be utilized to design simpler molecules with less toxicity and perhaps better pharmaceutical properties. Certainly when one bears in mind that 70+% of all approved antitumor drugs World Wide since the 1930s are natural products, modified natural products, contain the natural product pharmacophore or are simply spatial mimics of NPS such as ATP (the kinase inhibitors), then the utility of NPs is proven as leads to drug candidates.
Are NPs themselves going to be drugs in their own right? Not necessarily, but with the advent of modern synthetic processes, modifications will be.
Newman, D. (2008). Natural Products as Leads to Potential Drugs: An Old Process or the New Hope for Drug Discovery? Journal of Medicinal Chemistry, 51 (9), 2589-2599 DOI: 10.1021/jm0704090
Check out the free associated newsletter Pharma Matters Reports with whom I’m working with Thomson Reuters.
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Interview with David J Newman (Pt. II) is a post from: Sciencebase Science Blog
A natural interview with David Newman
David Newman is Chief at the Natural Products Branch, Developmental Therapeutics Program, DCTD, at the National Cancer Institutes in Frederick, Maryland, USA. I interviewed him for Issue 1 of a new quarterly newsletter called Chemistry Matters in Pharma.
This is Part I of the unabridged transcript of that interview in which Dr Newman told me of the ins and outs of natural product chemistry and how it can lead to new pharmaceuticals for a wide range of diseases.
Q. What is your approach to natural products?
A. The remit of the natural products branch (NPB) is to find novel leads to agents that may be of utility as antitumor drugs. Note, not drugs per se at this stage, but structures be they old or new, that have the biological potential to lead to drug candidates. To do this, we have, over the years, run collections for plants, microbes and marine organisms, World-wide in the case of the plants and marine organisms, and predominately in the US for microbes, though before the Convention on Biodiversity, we did collect microbes in various places outside of the US and its territories. Currently we are collecting microbes and marine invertebrates.
All materials are brought to NCI-Frederick at the US Army’s Fort Detrick in Northern Maryland where we have the necessary equipment to “convert” the plants and marine invertebrates into water-based and organic-based extracts, and the ability to isolate, purify and then ferment, microbes before their fermentation broths are also extracted. We currently have over 140K plant, 30K marine and roughly 30K microbial extracts arrayed in test plates (dry) and with bottles containing more of the extracts (amounting to roughly 650K bottles/vials) all stored at minus 20o C.
Materials are tested by NCI in its 60 human cell line screening system and also made available under very strict guidelines to researchers both inside of the NIH and to academic, non-profit and small and large businesses world-wide with very strict guidelines that require that any organization discovering a lead that ultimately is commercialized, MUST work with the country of origin in its commercialization. In the event that NCI/NIH scientists find a lead of interest that is patented in the name of DHHS (the Department of Health and Human Services, NIH’s parent organization), then any organization that licences that patent MUST, within one year produce an agreement with the country of origin that covers their benefits from the licence. If not provided, the licence is pulled. We call this the “source country commitment” and in a less-refined form, it was in force three years before the Convention on Biodiversity.
Q. What day-to-day chemistry is your team engaged in to achieve those goals?
A. Both basic and at times rather esoteric bioactivity-driven isolation processes that rely extensively on HPLC-MS and UHPLC-MALDI-TOF instrumentation, coupled to extensive databases, both in-house and commercial. All forms of chromatographic isolations are used and in some cases, we will go back to older techniques because they “work”, particularly when we are dealing with charged molecules. Access to standard spectroscopic instruments is also part of the process, though we also have extensive instrumentation attached to the HPLC-MS trains in addition to the mass spec.
Q. How does this research mesh with NCI aims?
A. The Developmental Therapeutics Program which NPB is part of, has the express aims of discovering and developing up through preclinical trials, agents from both natural and synthetic sources that have the potential to enter clinical trials as potential antitumor agents. There is another Program, known by the acronym CTEP (Clinical Trials Evaluation Program), part of whose job is to take molecules that we “produce” and conduct clinical trials on them.
We will accept molecules from any source either from our own work or from outside and carry them through the system(s) at Uncle Sam’s expense, even up through Phase II clinical trials. For the molecules that come in at the early DTP level, they all go through the 60 human cell line panel and if justified into early in vivo assays with no IP being taken by NCI. We consider this to be routine assessments. So the NP compounds definitely mesh with NCI’s aims.
Q. How do you assess the natural products you find in terms of toxicity and synthesis issues? What’s your group’s remit on those aspects of the work?
A. Part of the initial process at the crude extract stage is an assessment of their “cytotoxicity” in the 60 cell line screen at 1 dose level. Those that have “cytotoxicity” above a certain nominal level then proceed to the regular 5 dose 60 cell line screen. An assessment is then made of the “patterns of activity” in the full screen and a decision is then made as to dropping it or continuing.
Because we currently have the capacity in our in vivo testing, we have actually gone back many years in concept and actually test the crude extract (after a quick toxicity test) in the hollow fibre (HF) assay in nude mice. If we find activity, then we will move to very specific xenograft (XG) studies using cell lines that either showed activity in the HF assay or sometimes, will go with a specific cell line in XGs due to its activity in the 60 cell line. If the XG is “active” in protecting against the effects of the tumor with respect to control mice, then we will “dereplicate” chemically and find out what the “active component(s) are.
Although this may look like going backwards in time to the early 1960s, what it has permitted us to find, are synergistic mixtures of known compounds that are active in the XG assay(s) at levels well below what the pure compounds show activity at, and in one particular case, one of the compounds has never shown activity, only very significant toxicity as the individual compound. The Therapeutic Index (TI) of that particular compound is almost equivalent to 1 as a single agent!
Q. How do you take this research into the drug pipeline and thence clinical trials and ultimately the pharma market?
A. DTP or CTEP will accept suitable molecules from any source either from our own work or from outside and carry them through the system(s) at Uncle Sam’s expense, even up through Phase II clinical trials. For the molecules that come in at the early DTP level, they all go through the 60 human cell line panel and if justified into early in vivo assays with no IP being taken by NCI. We consider this to be routine assessments. So the NP compounds definitely mesh with NCI’s aims. (from answer to Q3 above).
In addition to these trials, we will if it is our compound (meaning our patent), competitively licence the molecule for further development. This also occurs if it is not a patentable compound (such as Taxol®) where no company would perform clinical trials. This compound was discovered under one of our earlier collection programs where we utilized the skills of academic and non-profit chemists to isolate and identify natural products. The material was taken through Phase II clinical trials by NCI and collaborators and once it had shown activity in ovarian cancer in female patients, it was licenced to Bristol Myers Squibb under a competitive Cooperative Research and Development Agreement (CRADA) that included requirements for further clinical trials and methods of obtaining the compound from natural sources. This is a much too long a story to go into in a Q & A session but it has been described in a lot of articles and books.
Part II of my interview with David J Newman will appear on Sciencebase.com soon.
You can read more about Dr Newman’s perspective on natural products and how it is not so much old school as the new dope:
Newman, D. (2008). Natural Products as Leads to Potential Drugs: An Old Process or the New Hope for Drug Discovery? Journal of Medicinal Chemistry, 51 (9), 2589-2599 DOI: 10.1021/jm0704090
Check out the free associated newsletter Pharma Matters Reports with whom I’m working with Thomson Reuters.
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A natural interview with David Newman is a post from: Sciencebase Science Blog
Prostate problem probed
http://www.spectroscopynow.com/coi/cda/detail.cda?id=23050">Pinpointing prostate problems – The chemical cousin of magnetic resonance imaging, MR spectroscopy, could be used to pinpoint the exact location of prostate cancers and to determine the aggressiveness of a tumour without major surgical intervention, according to research published in the journal Science Translational Medicine.
“Magnetic resonance (MR) spectroscopy which can analyse the biochemistry rather than the physical structure of tissues could give oncologists a better way to home in on prostate cancers at the early stages of growth and so ultimately improve treatment success rates,” team leader Leo Cheng of Harvard U told me.
Twenty-year old HIV problem – Science journalists (and press officers alike) are often lambasted for using the word breakthrough, but when twenty years of research culminates in a development with the potential to change the way drug research for HIV/AIDS is undertaken, we can be forgiven, surely. An X-ray diffraction study of the enzyme integrase has led to a breakthrough in our understanding of how retroviruses replicate. The structural results lay bare a problem that scientists have been trying to solve for more than two decades.
Sniffing out the Tempranillo – It’s unclear how common fraud is in the wine industry, but certainly there is the opportunity for unscrupulous producers to blend wine of the same variety from different areas and claim it comes from the most well-renowned regions. Now, Australian scientists have developed a new approach to testing the origin of wines based on a sophisticated statistical analysis of the wine’s spectra.
Atomic biodiesel assessment – Metal contaminants in your car’s biofuel will cause the build up of sludge inside the engine and potentially cause it to fail, replacing a burned out engine is not the green option for those hoping to save the environment by burning crops instead of oil in their vehicles. Now, Brazilian scientists have turned to Flame atomic absorption spectrometry (FAAS) to quickly and cheaply determine the metal content of biodiesel with a view to improving quality control on this renewable fuel.
Wu, C., Jordan, K., Ratai, E., Sheng, J., Adkins, C., DeFeo, E., Jenkins, B., Ying, L., McDougal, W., & Cheng, L. (2010). Metabolomic Imaging for Human Prostate Cancer Detection Science Translational Medicine, 2 (16), 16-16 DOI: 10.1126/scitranslmed.3000513
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Prostate problem probed is a post from: Sciencebase Science Blog
Summer born lucky are born rich
If you want to feel lucky in life, make sure you are born to well-off parents and don’t worry about whether your birthday is in the summer or winter.
In 2005, well-known psychologist Richard Wiseman and his colleagues surveyed 30,000 people via the internet to see if there is a relationship between the season in which one is born and whether or not one considers oneself lucky. They found that for Brits of all ages groups, birth during the summer half-year was associated with significantly higher belief in being lucky, whereas those born in the winter half-year did not feel lucky.
Wiseman and colleagues, reported that the maximum positive influence was found for the month of May and November was the most negative month. The result applied to all age groups and both male and female alike across the UK. It was, they suggested, to do with seasonal variations in the levels of the brain chemical, monoamine neurotransmitter.
German economist Gerd Grözinger of the University of Flensburg was not convinced, how could one’s personal outlook be determined so simply by non-social factors such as the season of one’s birth. He suspected that money or a lack thereof may have more to do with the perception of luck and that rich parents tend to have their babies in the summer half of the year.
Wiseman, of course, is a renowned academic in his field and also an expert popularizer or psychology and science in general. He has been involved in many highly publicized experiments in the UK that have utilized the power of TV, radio, and other media, including online social media to reveal the light and shade of the human condition. Regardless, Grözinger was not persuaded by the arguments in the 2005 summer luck research paper and has attempted to reproduce the experiment, as is the wont of scientific endeavour.
He analysed the German Socio-Economic Panel (GSOEP) database. This is an ongoing survey begun in 1984, which contains information on age, gender, month of birth, subjective well-being and socioeconomic situation. In order to mirror the Wiseman study, he pulled data for people under 65 years of age, giving him a data set of 18,000 people.
Plotting the date of birth against “happiness” indicators, Grözinger got a zig-zag graph with peaks in March, June, September, and November and lows in April, August, October and December/January. This contrasts starkly with the Wiseman plot of luck perception by month with its sole peak in May and its low in November.
But, it was when Grözinger began to dig into the impact of socio-economic factors that he began to see a more interesting effect.
Other researchers have pointed out in happiness research, that socioeconomic factors influence answers people give on well-being: having a higher income and a better education exerts a positive influence, while simply being born to a well-to-do family background will help later in life. “It is only reasonable to assume that such influences are also to be found in the state of feeling lucky/happy,” Grözinger says.
This correlates well with a 1984 study that more non-manual (male) workers were born in the spring and more manual workers in the autumn. “If in the UK, a social class effect explains the seasonal values reported by Wiseman in the lucky study, then one would expect that, here, the ‘upper classes’ would show relatively more births earlier in the year than the ‘lower classes’, and this is exactly what the 1984 paper found.”
“Measurements of seasonal differences in well-being, happiness, or feeling lucky should be interpreted quite carefully. Possible effects seem to be quite minimal and volatile and any distribution found could simply be the influence of (again: seasonally distributed) social stratification,” Grözinger concludes.
CHOTAI, J., & WISEMAN, R. (2005). Born lucky? The relationship between feeling lucky and month of birth Personality and Individual Differences, 39 (8), 1451-1460 DOI: 10.1016/j.paid.2005.06.012
Gerd Grözinger (2010). Born lucky – or just lucky to be born rich? A note Int. J. Public Policy, 5 (4), 430-435
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Summer born lucky are born rich is a post from: Sciencebase Science Blog
Correct your chemical spelling mistakes
Chemist Adam Azman contacted me more than two years ago to ask if I knew of a free or open source chemistry spellchecker custom dictionary for Word or OpenOffice. Searches had revealed only paid-for dictionaries. We both agreed that a free chemical spellchecker would be very useful to all scientists working with chemicals, so Adam set about creating from scratch an open access chemistry dictionary.
The spellchecker files were originally hosted on Chemspy.com and is now available on Sciencebase.com. Adam did a lot of extra work with Tony Williams of Chemspider to develop the new, improved version 2.0: Chemistry Dictionary for Word/OpenOffice. 1.5Mb zip file.
You can read more about how Adam’s chemistry dictionary got to where it is on Adam’s chemistry blog.
Keywords: Open Access Chemistry Dictionary, Open Source Chemistry Dictionary, Microsoft Word Chemistry Dictionary, OpenOffice Chemical Dictionary.
Original post 2008-02-08 15:03 updated 2008-12-17 16:11 updated 2009-07-27 14:01 updated 2010-02-10 10:05
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Correct your chemical spelling mistakes is a post from: Sciencebase Science Blog
Nerdy passwords, secure and memorable
WARNING: Do not simply use the formula of a common chemical without obfuscating it in some way. It could be dictionary cracked very easily if you do.
Coming up with a secure password that cannot be bruteforce or dictionary attacked but that is easy to remember is quite troubling. So, here’s the nerdiest approach yet.
Think of a compound, any compound, but preferably one with which you are familiar. If you’re in science, then you could pick a compound associated with your research thesis or perhaps the medication you needed to get through the viva.
Now, work out, or look up, its chemical formula. BUT DO NOT STOP THERE…Next, think of a simple algorithm to obfuscate the formula (reverse it and chop off each end perhaps, or if it is a long formula extract all the numbers and put them at one end instead of after each element symbol, you get the idea). Of course, if you pick a compound that happens to share the first couple of letters with the name of the site to which you are logging in, then that should make it easier to remember too.
If you suffer from hayfever you might be using flixonase, when you login to flickr, for example. Formula: C25H31F3O5S, password could be CHFOS253135 or 5O3F13H52. No bruteforce hack attack is going to figure those out in a hurry. Specialists in secondary messenger chemistry with a MySpace account could choose myo-inositol (C6H12O6 –> CHO6126), while nutritional chemists could hide their Facebook behind Factor II (vitamin B12) C63H89CoN14O14P –> CHCONOP63891414.
Of course, you will have to think of your own examples, but with CAS and ChemSpider registering tens of millions of structures, that should not be too hard to do.
Of course, being a chemist you also know about InChi and Smiles string, which could provide you with an even more sophisticated password. The InChi string for aspirin, for instance, is <span class=”chem:inchi”>InChI=1/C9H8O4/c1-6(10)13-8-5-3-2-4-7(8)9(11)12/h2-5H,1H3,(H,11,12)/f/h11H</span>. You could make your obfuscating algorithm to remove all the zeros and reverse the string. The Smiles string is not quite so long O=C(Oc1ccccc1C(=O)O)C, but what about choosing that and adding the same string reversed to the end of the original?
It could all get very convoluted and seemingly random very quickly. But, isn’t that the aim of a good password? According to the password strength tester, the untouched Smiles string for aspirin is “best”, but apply an algo and it will be even better.
The neat part is that you pick a compound you will remember, you can look up its formula any time and you know the obfuscating algorithm. So you thus have a memorable password that is essentially a pseudo-random alphanumeric.
Originally posted Jun 18, 2007 @14:00
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Nerdy passwords, secure and memorable is a post from: Sciencebase Science Blog
How to get your fill of Sciencebase goodness
Do you lie at wake at night worrying that you might have missed the latest words of wisdom on Sciencebase? Are you concerned that a new post might have published that you desperately wanted to comment on and now it’s too late? Well…fear not. There are so many ways to connect with Sciencebase and sibling sites Sciencetext Tech Talk and the SciScoop Science Forum that you really can rest easy.
On Facebook – become a Sciencebase fan and you get to read the headlines from SB, ST, SC and more as they appear. You can also comment right there and then without having to hop back and forth between sites.
On Twitter – join the almost 6500 followers who keep up to date with the Sciencebase family live as posts appear and as other links, tidbits, and headlines are added.
On Delicious – If you’re wondering what tasty extras Sciencebase has found you should also join the delicious network. This page is also now playing host to incoming press releases tagged “forsciencebase”.
On Youtube – Sciencebase keeps several playlists, the Random Samples selection is growing slowly with some of the most interesting video clips.
Via RSS/Newsfeed – You can quickly and easily add the Sciencebase newsfeed to your RSS reader, aggregator, iGoogle page, or any of dozens of other systems using this link. Just click through and follow the instructions.
Via Newsletter – If you prefer not to jump into social media and would like a more traditional connection route to Sciencebase, click this link and follow the instructions to subscribe to the email newsletter for updates from the site.
If you’re a true traditionalist, you can even email Sciencebase’s David Bradley at david.bradley-at–sciencebase.com and he might even reply.
Check out the Sciencebase Tizmo page for a snapshot of the whole Sciencebase family of sites and the Gizapage for related social networks.
Oh, by the way, if you visit Sciencebase from one of the social networking, social media, social bookmarking (call them what you will), the RSS feed or another subscribed/bookmarked route, you shouldn’t see the block of ads at the top of each post. So, there’s another reason to get connected with Sciencebase.
Thanks to Brad Sams at Neowin for the inspiration for the opening par.
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How to get your fill of Sciencebase goodness is a post from: Sciencebase Science Blog
Making carbon dioxide useful
My SpectroscopyNOW column is now live. This week self-perception, trapping and using carbon dioxide, cosmic coronene, mopping up radioactive caesium, photosynthesis and magic spectral lines:
Red lenses – US scientists have used MRI to show that apparently the less you use your brain’s frontal lobes, the more you perceive your behaviour through rose-tinted spectacles. They publish details in the February issue of the journal NeuroImage.
Carbon dioxide trap and drop – The reduction of greenhouse gas carbon dioxide to a useful chemical industry feedstock material, carbon monoxide, can be catalysed by a ruthenium-substituted polyoxometalate according to a new study. The work holds the promise of our developing a carbon-neutral energy platform.
Cosmic coronene’s phantom spectral bands – Anomalies in the spectra of an aromatic molecule called coronene could have implications for our understanding of astrochemistry and for making nanotech devices from graphene.
A metal sponge for cleaning up nuclear waste – An inorganic material with an open framework can selectively trap caesium ions, including its 137 isotope, one of the most significant radioactive isotopes left behind after the Chernobyl nuclear reactor fire. Caesium-137 is one of the main residual sources of lethal radiation in the nuclear industry.
Narrow view of photosynthesis – Fluorescence line-narrowing and resonance Raman properties of various chlorophyll molecules have been measured in organic solvents. The work sheds new light on one of life’s most important biochemical processes – photosynthesis – and might one day allow scientists to take another step closer to emulating the reactions to trap solar energy
The long and the long of it – A novel NMR technique has measured the largest distance between two atomic nuclei using NMR, demonstrating that tritium magic angle spinning NMR could be a promising tool for structural applications in the biological and material sciences.
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Making carbon dioxide useful is a post from: Sciencebase Science Blog
Science based risk assessment
Ask people why the enter the lottery and they will usually tell you that “you’ve got to be in it to win it”. As far as it goes that’s true, but it still doesn’t get around the odds of you picking the right numbers being vanishingly (although not quite homeopathically) small at 14 million to 1 against for 6 numbers from a 1-49 selection.
Compare their feelings about their chances of winning the lottery to succumbing to the toxic effects of their favourite tipple or a disease triggered by dietary whim and they may well respond, that such problems are more likely to happen to “other people”.
It’s part of the human condition we perceive the positives chances as being much more likely to happen to us than the negatives, despite the fact that the odds are usually stacked against us.
The issue of probability and its kissing cousin risk assessment is not one to be taken lightly when we are talking about the effects of pollution, genetically modified crops, the incidence of disease, nanotechnology, the impact of vaccines, and the safety of everything from vehicles to chewable children’s toys. Indeed, there are advocates for taking the precautionary principle for each and every one of these issues and many others. They feel that no matter how long the odds, avoidance, abstinence and absolute bans are the only way forward until “science” can give us a yes or no answer regarding safety in all its manifestations.
So, we hear that nanotechnology should be banned until it has been proven to be safe, or that we should avoid vaccinating our children because there is a risk of some obscure connection between a suspected contaminant or additive and an illness that may or may not happen. This is always irrespective of the risks associated with not moving forward with advances such as nanotechnology and the commonly lethal effects of the disease against which one would hope to vaccinate.
Trouble is, in the Popperian philosophy of science, this most human endeavour cannot provide a yes or a no answer to any question involving experimental data. It can only ever offer long or short odds. Unfortunately, most people outside science, and quite a few of them within, are not keen on establishing public policy, health and safety rules, and other agendas on such a basis. This has led to politicians overriding the strong advice of their retained experts in a wide range of fields in recent years and the lambasting of those experts when the rare problem does arrive.
Terje Aven of the University of Stavanger in Norway, a Professor of Risk Analysis and Risk Management, is developing a new approach to quantitative risk assessment that would be applicable to a wide range of industries and circumstances and is based on a new scientific framework. The framework is underpinned by knowledge and probabilities based on hard data, expert judgments and modeling. An important feature of the framework is identification and descriptions of uncertainties that extend beyond the probability numbers.
Fundamentally, the framework will never provide the definitive, yes-no answers that some people crave when discussing risk. However, it does offer a foundation for sensible dialogue that could help society balance the risk-benefit equation for a whole range of issues.
Terje Aven (2009). A new scientific framework for quantitative risk assessments Int. J. Business Continuity and Risk Management, 1 (1), 67-77
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Science based risk assessment is a post from: Sciencebase Science Blog
Early Valentine’s Alchemist
The Alchemist this week learns of a golden opportunity to make a fundamental industrial feedstock, ethylene, from natural gas, rather than oil.
In microfluidics, a droplet of acid finds its way out of a maze, while an accidental mineral could become the material of choice for magnetic tunnel junctions. In the zone between chemistry and physics, German researchers have discovered a new way to produce free electrons, which might help explain biological radiation damage, and in health PFOA emerges as a risk factor for thyroid problems.
Finally, more than half a million small molecules have found a home in Cambridge, UK thanks to a grant from the Wellcome Trust.
Find out more in this week’s Alchemist on ChemWeb.com
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Early Valentine’s Alchemist is a post from: Sciencebase Science Blog
How to teach physics to your dog
There have been rough guides, books for dummies, even howtos for idiots, but Chad Orzel is probably the first to take explain an important corner of human endeavour solely to his dog in How to teach physics to your dog
Nevertheless, Orzel uses humour and clarity to explain the ins and outs of black holes and quantum entanglement to his dog and along the way teaches us some of the fundamentals the vexed the greats, among them Bohr and Einstein.
Meanwhile, Sean Carroll takes us on a journey from Eternity to Here
Inventors and Inventions
Also landing on the Sciencebase desk this month, one of those idiots books I mentioned earlier. This time it’s The complete idiot’s guide to phobias
Finally, here’s a title that will undoubtedly get the so-called intelligent design crowd What Darwin Got Wrong
Jerry Fodor and Massimo Piattelli-Palmarini suggest that the evidence does not point to evolution taking place through a single survival of the fittest mechanism, rather that there are countless biological causes that totally eradicate “intention” from biology and evolution. If the ID crowd were perturbed by Darwin, then they should be very scared of the new guys as they remove the last vestiges of metaphysical guidance from our creation. There are no gods, no mother nature, and no grand design.
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How to teach physics to your dog is a post from: Sciencebase Science Blog