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Images reconstructed from human brain using fMRI

Very interesting news today, as Japanese scientists published a paper in Neuron discussing the reconstruction of images directly from the human brain using fMRI.  It does seem like neurology is making true progress, despite the popular notion that “we can never understand the human brain.” The future consequences of research like this may be controversial, but it’s the inevitable price of progress. Pink Tentacle covered this story along with a more technical overview by Brain Windows.

Visual Image Reconstruction from Human Brain Activity using a Combination of Multiscale Local Image Decoders.
Yoichi Miyawaki, Hajime Uchida, Okito Yamashita, Masa-aki Sato, Yusuke Morito, Hiroki C. Tanabe, Norihiro Sadato, Yukiyasu Kamitani.
Neuron – 10 December 2008 (Vol. 60, Issue 5, pp. 915-929)

The issue of gene patents [update]

Hospitals in Australia are stuck in a bad position when it comes to genetic testing. The Sidney Morning Herald has a piece discussing the patented gene SCN1A, which is used to diagnose a particular type of epilepsy in infants. The company that has the test patented, Genetic Technologies, won’t let hospitals do in house testing. Instead, they must resort to sending samples to Scotland to be tested…a process that takes a lot of time and costs much more than necessary. This results in worse care for the infants.

Babies with a severe form of epilepsy risk having their diagnosis delayed and their treatment compromised because of a company’s patent on a key gene.

It is the first evidence that private intellectual property rights over human DNA are adversely affecting medical care.

This is only the beginning of genetic testing. What role are patents going to play in this, especially considering that they seem to do more harm than good from the patent’s perspective. I wonder if there is some legal loophole that hospitals can use to get around this, at least in the United States. Perhaps it may work if the hospital conducted the test for internal research purposes only and then used the results after it had them, though I don’t know if this argument would hold up in court.

What do Think Gene readers think about this? Let’s hear your thoughts!

Novelty DTC genetic testing company torpedoes their way into NY Times

Today’s New York Times had a story about a new DTC novelty genetic testing company. It’s a rather obvious example of a torpedo. This article was seeded by a PR company — it’s only news because ATLAS Sports Genetics has investors that know their best shot at success is buying their way into the New York Times.

ATLAS Sports Genetics is offering a test for ACTN3, otherwise known as the speed gene. They charge $149. For $249, you get the “ATLAS Plus” kit. It tells you how high your kid jumps. The $1000 package comes with a timer. I kid you not; they charge an extra 750 dollars for a timer. I have a better idea for finding out if your kid is good at sports: sign him or her up for the soccer team. Or baseball, or football, or gymnastics, or whatever he or she wants to do.

The ACTN3 test is the preeminent example of a novelty genetic test. It tells you nothing useful. It’s for fun — entertainment purposes only. I mean, if they had a genetic test that indicated something useful about athletic ability, that would be one thing. The ACTN3 test gives something of an indication about whether your muscles are more suited for sprinting or endurance. No matter what version of ACTN3 you or your child have, you can still play sports! 23andMe tests for the ACTN3 mutation in their $399 product and ATLAS will not be able to compete with 23andMe. If you’re looking to be entertained by a genetic test, get a 23andMe, not an ATLAS.

Biomarker-driven mental health 2.0 also posted their reaction to this story.

World-first network linking experts in proteomics and metabolomics

Josh: We’re going to see an increase in sites like this where researchers from various disciplines can help each other out. This site has contact information for experts in various fields, allowing labs to more easily collaborate to do interdisciplinary research. I foresee sites like this becoming more “social”, where there are forums or means for researchers in one discipline to ask questions to experts in another discipline. It’s actually surprising that this doesn’t already exist, but I suppose most Web 2.0 technologies haven’t really been applied to other areas yet.

A world-first network linking experts in two leading biotechnologies, proteomics and metabolomics, has been launched by The Hon Gavin Jennings at The University of Melbourne.

The portal website of Proteomics and Metabolomics Victoria (PMV) was activated during the opening of Metabolomics Australia’s node at the University, and is now publicly accessible at

“Nowhere else is there a cross-sector network of this nature, involving collaboration between academia, trade and industry,” said Professor Mike Hubbard of the University of Melbourne’s Department of Paediatrics, who spearheaded the initiative.

PMV aims to provide education about proteomics and metabolomics, to help scientists access these technologies, and to facilitate practitioners’ interactions with the numerous companies supplying this field.

“Education and workforce development is a central concern shared by academic and commercial members, and together we aim to establish training schemes tailored to our collective needs.”

The State Government of Victoria supported establishment of PMV through funding of a proposal made jointly by Prof Hubbard and Monash University’s Professor Ian Smith.

Simply put, ‘proteome’ means all the proteins in an individual and ‘proteomics’ is the study of as many of those proteins as practicable.

Proteomics provides scientists with a variety of key benefits including deeper understanding of biological processes, increased diagnostic power, and access to information not available from gene-based approaches.

Similarly ‘metabolomics’ is the study of numerous metabolites, which are small molecules such as breakdown products of food, hormones and drugs.

Metabolomics provides scientists with several benefits that are both powerful in themselves and complementary to those of proteomics.

Through its link with the varied and dynamic nature of metabolism, metabolomics offers a very sensitive fingerprint for the status of a biological system (e.g. whether it is healthy or diseased or laden with performance-enhancing drugs).

Proteomics and metabolomics are used in many different research scenarios from academic laboratories in search of hot discoveries through to commercial applications in biotechnology, agriculture and medicine.

In the laboratory, these technologies are typically used to unravel basic biological mechanisms, details of which could lead to new understanding and ideas. Such “nuts and bolts” advances might in turn be harnessed by applications scientists to guide development of new drugs or diagnostics, for example.

“We hope to improve scientists’ access to proteomics and metabolomics, and facilitate interactions between the supply companies and practitioners of these technologies.”

“We also hope to give students and the public a clear understanding about our field, and illustrate its successful practice in Victoria.”

“The website showcases the depth of information and services available in Victoria.”

Source: University of Melbourne

HIV’s disguises no match for ‘bionic assassins’

Josh: This is a really neat idea. I’m guessing they would take CD8 cells from the patient, modify them, perhaps grow them in culture, and re-introduce them? I don’t think this is really going to be that practical in reality, and would probably be more expensive that taking anti-retrovirals.

HIV is a master of disguise, able to rapidly change its identity and hide undetected in infected cells. But now, in a long-standing collaborative research effort partially-funded by the Wellcome Trust, scientists from Oxford-based Adaptimmune Limited, in partnership with the Universities of Cardiff and Pennsylvania have engineered immune cells to act as “bionic assassins” that see through HIV’s many disguises.

The findings of the study, published online today in the journal Nature Medicine, may have important implications for developing new treatments for HIV and slowing – or even preventing – the onset of AIDS. Over 33 million people were estimated to be living with HIV worldwide in 2007. Although anti-retroviral drugs have been successful in delaying the onset of AIDS for several years, the drugs are expensive, have serious side effects and must be taken for life. No vaccine or cure yet exists and drug resistance is increasingly becoming a problem.

When viruses enter our bodies, they hijack the machinery of host cells in order to replicate and spread infection. When our body’s cells are infected with a virus they expose small parts of the virus on their surface, offering a “molecular fingerprint” called an epitope for killer T-cells from the immune system to identify. This triggers an immune response, eliminating the virus and any cells involved in its production.

As with other viruses, HIV enters the body and replicates itself rapidly. However, it also has the ability to mutate quickly, swiftly disguising its fingerprints to allow it to hide from killer T-cells.

“When the body mounts a new killer T-cell response to HIV, the virus can alter the molecular fingerprint that these cells are searching for in just a few days,” explains Professor Andy Sewell from Cardiff University, co-lead author of the study and long-term collaborator with Adaptimmune. “It’s impossible to track and destroy something that can disguise itself so readily. As soon as we saw over a decade ago how quickly the virus can evade the immune system we knew there would never be a conventional vaccine for HIV.”

Now, Professor Sewell and colleagues from Adaptimmune Ltd and the University of Pennsylvania School of Medicine have engineered and tested a killer T-cell receptor that is able to recognise all of the different disguises that HIV is known to have used to evade detection. The researchers attached this receptor to the killer T-cells to create genetically engineered “bionic assassins” able to destroy HIV-infected cells in culture.

“The T-cell receptor is nature’s way of scanning and removing infected cells – it is uniquely designed for the job but probably fails in HIV because of the tremendous capability of the virus to mutate,” says Dr Bent Jakobsen, co-lead author and Chief Scientific Officer at Adaptimmune Ltd, the company which owns the technology. “Now we have managed to engineer a receptor that is able to detect HIV’s key fingerprints and is able to clear HIV infection in the laboratory. If we can translate those results in the clinic, we could at last have a very powerful therapy on our hands.”

The researchers believe that HIV’s chameleon-like ability may still prevent the virus from being completely flushed out of the body. It could mutate and change its fingerprint further, hiding behind these new disguises and evading detection. However, each time the virus is forced to mutate to avoid detection by killer T-cells, it appears to become less powerful.

“In the face of our engineered assassin cells, the virus will either die or be forced to change its disguises again, weakening itself along the way,” says Professor Sewell. “We’d prefer the first option but I suspect we’ll see the latter. Even if we do only cripple the virus, this will still be a good outcome as it is likely to become a much slower target and be easier to pick off. Forcing the virus to a weaker state would likely reduce its capacity to transmit within the population and may help slow or even prevent the onset of AIDS in individuals.”

Pending regulatory approval, Professor Carl June and Dr James Riley from the University of Pennsylvania in Philadelphia will shortly begin clinical trials using the engineered killer T-cells.

“We hope to begin testing the treatment on patients with advanced HIV infection next year,” says Professor June. “If the therapy in that group proves successful, we will treat patients with early stage well-controlled HIV infection. The goal of these studies is to establish whether the engineered killer T cells are safe, and to identify a range of doses of the cells that can be safely administered.”

“The AIDS virus evades human immunity in all it infects,” says Professor Rodney Phillips, from the University of Oxford, where the collaborative research effort first began in 2003. “Until now no-one has been able to clear the virus naturally. Immune cells modified in the laboratory in this way provide a test as to whether we can enhance the natural response in a useful and safe way to clear infected cells. If successful the technology could be applied to other infectious agents.”

The researchers are now exploring using engineered receptors on killer T-cells as a way of improving immune responses to cancer.

Source: Wellcome Trust

Control of HIV-1 immune escape by CD8 T cells expressing enhanced T-cell receptor. Angel Varela-Rohena, Peter E Molloy, Steven M Dunn, Yi Li, Megan M Suhoski, Richard G Carroll, Anita Milicic, Tara Mahon, Deborah H Sutton, Bruno Laugel, Ruth Moysey, Brian J Cameron, Annelise Vuidepot, Marco A Purbhoo, David K Cole, Rodney E Phillips, Carl H June, Bent K Jakobsen, Andrew K Sewell & James L Riley. Nature Medicine. 09 November 2008; | doi:10.1038/nm.1779

New journal shows half-broken gene is enough to cause cancer

Josh: So while this research is very interesting, I would first like to call attention to biologists’ odd sense of humor. Apparently, SMAD4 stands for “Mothers against decapentaplegic homolog 4”. This is obviously some type of a joke made from MADD, but the bizarre sense of humor doesn’t stop here. Who can forget the signaling molecule Sonic Hedgehog (SHH), bride of sevenless (BOSS), frizzled, dishevelled, amongst many others that are escaping me at the moment.

Tumour suppressor genes do not necessarily require both alleles to be knocked out before disease phenotypes are expressed. Research published in BioMed Central’s new open access journal PathoGenetics reveals that only one allele of SMAD4 has to be damaged to put a person at risk of pancreatic and colorectal cancer.

Riccardo Fodde led a team of researchers from Erasmus MC, Rotterdam, who investigated SMAD4, a tumor suppressor gene implicated in pancreatic and colorectal cancer. They found that having one mutated SMAD4 allele was associated with the development of gastrointestinal polyps. This research is the first to address the molecular and cellular consequences of SMAD4 damage on a genome-wide scale.

This high quality research is typical of that which will be published in PathoGenetics, an open access journal created to meet the need for a resource focused solely on the pathogenesis of genetic diseases. The journal’s co-Editors in Chief are Professor Stylianos Antonarakis and Professor Andrea Ballabio. Ballabio said, “PathoGenetics will give scientists a unique opportunity to publish exciting research on the molecular mechanisms underlying the manifestations of disease phenotype”.

PathoGenetics will focus on both in vitro and in vivo studies on the cascade of events leading from gene mutations or genomic rearrangement to disease. The discovery of novel molecular and metabolic pathways relevant to disease pathogenesis will be given specific emphasis. The first issue includes a review by James Lupski and colleagues that deals with mechanisms for human genomic rearrangements and a groundbreaking piece on the methodology of knock-in vector construction by Nicholas Hastie and colleagues. According to Antonarakis, “Given its unique characteristics, PathoGenetics is likely to become the ideal journal for scientists from different backgrounds to publish and read exciting research on disease pathogenesis”.

Source: BioMed Central

Smad4 haploinsufficiency: a matter of dosage. Paola Alberici, Claudia Gaspar, Patrick Franken, Marcin M Gorski, Ingrid de Vries, Rodney J Scott, Ari Ristimäki, Lauri A Aaltonen, Riccardo Fodde. PathoGenetics 2008, 1:2 (3 November 2008)

Top 10 Genomics News from – Week of 19 Oct 08

Top 10 genomic news as voted by the genomics community.
Week of 19 Oct 08

  1. PLoS Medicine – Why Most Published Research Findings Are False
  2. YouTube – Current Issues in Computational Biology and Bioinformatics
  3. After whole genome sequencing comes PCR
  4. The Secondary Genomic Market and Medical Interpretation at HelixGene
  5. Sacred Intentions: Inside the Johns Hopkins Psilocybin Studies
  6. Why genetics takes time and why insurance sucks
  7. The Mouse Trap: The Maudsely debates: anti-depressants and placebo
  8. Breast cancer gene tests — not worth the price? – Breaking Bioethics-
  9. PGP sequence data disappointing
  10. The Howard Stern of Genomics……