Author: David Bradley

Censorship

Check out Indiana University’s Censearchip. It allows you to see how search engine censorship (on Google or Yahoo) in various countries affects the search engine results pages (SERPs) you see depending on where you search from (well if you’re in China, France, Germany, and the USA. It’s quite fascinating to see the tag clouds it generates to show the differences between searching in different countries.

The tool’s developers, Mark Meiss and Filippo Menczer at the Indiana University School of Informatics, caution that ‘In order to give as accurate a comparison as possible, we’ve disabled the ‘SafeSearch’ feature that search engines use to block images with explicit violent or sexual content from their search results. Some of the images returned may be quite graphic and inappropriate for children. Please exercise caution in your searches!’

You have been warned.

Chemical Reference Searching

An excellent new resource is now available through the ChemSpy chemical search site thanks to a collaboration with William Griffiths. Will runs ChemRefer.com a site dedicated to the Open Access chemical literature and allowing users to trawl for current and archival research papers from a wide range of publications. To search ChemRefer and the other direct access search engines at ChemSpy, simply enter your keywords and click the appropriate search engine. Available alongside ChemRefer are Chemindustry.com search, Chmoogle and Pubchem name searching, Google Scholar, ChemFinder, and the NIST WebBook

Metabolic Reaction

Portuguese researchers have developed a technique for classifying genomic-wide metabolic reactions, which they suggest will open up a new approach to diversity analysis of metabolic reactions and comparison of metabolic pathways as well as being generally compatible with the conventional “EC” classification of enzymes.

You can read my complete story on this at spectroscopnow.com

Worming Out Crystal Structures

The crystal structure of the anthelmintic drug praziquantel used to treat schistosomiasis (also known as bilharziasis or snail fever), has been determined by researchers in Singapore. Their study used the thermal properties of the drug, including melting point phase diagram and solubility, to determine the optimum conditions to allow them to separate its isomers chromatographically and to find the best approach to crystallisation. Such research could lead to improved drugs to treat parasitic infections.

Read on…

Unleaded Babies

Exposure to environmental poisons is suspected of disturbing the secondary sex ratio, i.e. the difference in numbers of girls and boys born as opposed to the ratio of girls and boys conceived. Indeed, several countries, including Canada, Denmark, England and Wales, Germany, The Netherlands, and the USA, have seen the secondary sex ratio shift during the last hundred years or so that the number of girls among live-births has risen significantly. One of the more significant declines is seen in Mexico, although some countries, Ireland, in particular, have seen the reverse, with more boys.

You can read the complete story in my news story on SpectroscopyNOW.com

Nothing to be Scared of

SciScoop contributor and University of Buffalo medic Bradford Frank sent us a copy of his latest book “Terror Unleashed” recently. Frank’s hypothesis is that the human race is soon to face a whole range of major crises from bird flu and oil shortages to financial collapse and devasting terrorist attacks. He begins by emphasising that the ideas he presents, are just that, ideas, and that there is no proof any of the events he describes will come to pass. However, what he does hope to achieve is to raise awareness of the potential threats to you, your family, your nation, and your planet.

You can read it, go into denial, and dismiss it as pure, unadulterated scaremongering. Or, you can absorb the warnings, make provision for their occurrence, and feel smug and fairly secure should they ever come to pass. For instance, it does seem like it is only a matter of time before we enter a period of financial depression, after all the boom-bust cycles of modern economics are well founded in history. Again, bird flu is the virus of the day, but it needn’t be H5N1 that leads to an influenza epidemic on a bigger scale than that of 1918-1919, there are dozens of emerging viruses just waiting to spring across the species gap from their current animal hosts. As to the impending oil shortage, global warming, nuclear terrorism, and electromagnetic pulses…we’ll certainly know about them if and when they hit.

Frank’s book is scaremongering. That’s for sure. And, if he weren’t a well-respected MD at a well-known US university, he might be the kind of man to walk the city streets with a placard proclaiming “The End of the World is Nigh”. The only trouble is, he might actually be right.

Frank’s website points to resources that could help in an emergency, but I also suggest you check out Stephen Jones’ Bird Flu Survival Guide.

Da Vinci Debate

It’s quite bizarre isn’t it that Dan Brown’s novel should cause such a stir? It’s not even named properly. “Da Vinci” is not how the great polymath was known, no one knows his surname or whether he was known as anything but “Leonardo” in his lifetime. The “Da Vinci” monicker was tacked on later, simply because he came from Vinci, Italy.

Anyway, Brown is currently embroiled in a legal debacle with the authors of another book (The Holy Blood and the Holy Grail) who claim that he plagiarised their purportedly non-fictional history of the alleged marriage to Mary Magdelene of Jesus Christ and the continuation of his blood line to modern times. Quite bizarre. It’s like someone trying to sue Michael Crichton for writing about dinosaurs (there must be thousands of non-fiction authors holding their breath right now), or nanotechnology, or global warming or emergency rooms…

As far as I recall, Brown cites the HB&HG in his book, so I’m not even sure how it could possibly be plagiarism, but then that’s English law for you.

The really odd (I don’t think) thing about this whole legal case is that both the dVC and the HB&HG are actually published by the same publisher. And, could it also be pure coincidence that it’s reached the courts in the same month as the film of dVC hits the big screens in the UK? I suspect not. Either way, the plot is pretentious and puerile and I really wish I hadn’t bothered reading the book. I can only recommend that if you haven’t yet, don’t bother. Jurassic Park is more likey, to be honest.

Critical Trials TGN1412

The BBC reports today that six men are on the critical list after becoming seriously ill while taking part in a clinical trial of a new drug for treating leukemia and arthritis: BBC Report.

The previously healthy young men were being paid (up to £150, $330 a day) to take part in the early stages of a trial of the novel drug TGN1412. However, within hours of their first injection, they reacted adversely (suffering multiple organ failure) and were put in intensive care. The two men receiving placebo in the trial are fine.

The compound in question is biopharmaceutical company TeGenero’s humanized CD28-SuperMAB (TGN1412) which is in trials for rheumatoid arthritis and B-CLL (B-cell chronic lymphocytic leukemia). Following standard toxicity studies it was entered into initial clinical trials. “The drug was developed in accordance with all regulatory and clinical guidelines and standards,” explained Dr Thomas Hanke, Chief Scientific Officer of TeGenero AG, in a statement, “In pre-clinical studies, TGN1412 has been shown to be safe and the reactions which occurred in these volunteers were completely unexpected.”

Adverse reactions to drugs in clinical trials are exceedingly rare, but then TGN1412 is not your everyday small molecule type drug. TeGenero developed this drug, a superagonistic monoclonal antibody, with the aim of balancing T cell (a type of white blood cell) activation by triggering receptors on another group of white blood cells known as T lymphocytes. Today’s events are likely to provide animal rights activists with new fodder to push for animal testing to be banned, they will undoubtedly cite this unforeseen problem as further evidence that animal tests cannot show how a drug might act in people.

Ganesh Suntharalingam of Northwick Park Hospital told the BBC that, “The drug, which is untested and therefore unused by doctors, has caused an inflammatory response which affects some organs of the body.” Why this should be so is unclear. The UK’s Medicines and Healthcare products Regulatory Agency (MHRA) has withdrawn authorisation for the trial (obviously) and doctors in other countries have been sent a warning not test it.

Sciencebase will keep you posted on events as we hear them, in particular we’ll try to bring you the results of the ongoing investigation as soon as we can. It may emerge that a clinical error is to blame rather than there being a biological problem with the drug itself, we will have to wait and see.

This very unfortunate incident comes just one day after widely acclaimed findings were revealed showing how the totally unrelated statins could reverse atherosclerosis. Such positive results that inspire public confidence in the pharmaceutical industry are almost as rare as the present negative result!

Richard Ley of the Association of the British Pharmaceutical Industry was reported as saying “This is an absolutely exceptional occurrence.” and “cannot remember anything comparable.”

Keeping Pace with Genetic Variation

A gene associated with disease might vary from a healthy gene in one individual DNA base pair – a so-called point mutation. Investigating point mutations and diagnosing genetic disease would benefit from a simple, cost-effective and rapid sequencing technique.

Now, Japanese researchers have developed a new approach for a miniaturized system that detects small differences in DNA sequences with high sensitivity. In contrast to other methods, this technique works without labeling the bases and exploits a field effect transistor (FET) to detect changes in the charge on DNA molecules.

According to Toshiya Sakata and Yuji Miyahara multiple FETs can feel electrical fields and react to changes by changing the current that flows through their conducting channels. The researchers loaded the surface of an FET with short, single-stranded pieces of DNA. These probes are the exact counterparts to the sequence at the beginning of the DNA segment being investigated. If a sample containing the target DNA comes into contact with the surface, the target DNA binds to the probes. The polymerase chain reaction (PCR) is then used to reconstruct the complete target DNA strand. Cleverly, the team do not use all four DNA building blocks at once but dip the FET into four different solutions, each containing only one of the building blocks, one after the other. After each dip, the electrical characteristics of the FET are measured. If and only if a component has been added to the end of the chain, a change is registered. This occurs because each building block brings with it a negative charge, which changes the electrical field on the surface of the FET. In this way, DNA chains of a length up to about ten components can be precisely sequenced. Missing, extra, or changed nucleotides can be rapidly and unambiguously identified.

You can read more details in Angew Chem Int Edn, 2006, 45, 2225

Predicting Chemo Success

French researchers have identified almost 700 genes in the tumours of colorectal cancer patients
whose expression was different between patients who subsequently responded well to combined chemotherapy and patients who were resistant to the therapy. The findings could ultimately help cancer specialists decide which course of treatment for patients with colorectal cancer is most likely to work best.

Sandrine Imbeaud from the CNRS and Pierre and Marie Curie University, Villejuif, France, used microarrays to analyse the gene-expression patterns of samples from colon tumours and liver metastases collected from 13 patients with colorectal cancer. The microarray analyses were carried out before the patients were treated with combined chemotherapy of folinic acid,
5-fluorouracil and irinotecan. The team identified 679 genes that were produced differently in patients who later responded well to chemotherapy.

Details of the research were published today in the journal Genome Biology.