Ethanol for a clean and bright future

Ethanol is a very usefull and versatile product, consumed in reasonable amounts it can turn boring parties into very interesting experiences. Aswell ethanol is a great substance to clean your laboratorytable with when you spilled some bugs on a clumsy monday morning.

Burning ethanol recycles atmospheric carbon instead of releasing fossilized carbon into the atmosphere thus reducing the accumulation of greenhouse gases. Japan recently authorized the substitution of up to 3% of gasoline with ethanol, which will help the country to meet its Kyoto Treaty commitments . To obtain ethanol Japan made a deal with Brazil. Export of ethanol to Japan will start in 2008 with 20 million litres.
Brazil, the second biggest producer of ethanol (after the US) is able to produce high volume and low cost sugar cane which gives the country a competitive edge in the production of ethanol for export. Biotechnology plays an important part in the ability of Brazil to keep up production with the increasing demand. 90% of the sugar cane genome was sequenced in 2003 and research groups in Brazil have been producing transgenic sugar cane varieties with better productivity, resistance to droughts and bad soils eversince.

"Brazil and Japan give fuel to ethanol market" , Nature Biotechnology 24, March 2006

Btw, if you after reading this article became inspired to actually consume ethanol, the best way to take it is in a diluted flavoured and very tasty form: Zubrowka. Drink it WITH applejuice (but don't MIX it with applejuice).

Dirk Jan, alien attack

The future of super-antibody drugs

What went wrong in the recent clinical trial disaster where six men ended on intensive care after getting ill during aclinical drugs trial in London? news article

In the "Can super-antibody drugs be tamed?" Michael Hopkin looks at what went wrong, and whether there is any future for 'superagonist' antibody therapies.

First inhalable insuline

Abit old news, but nevertheless very good news for all diabetes patients who hate needles.
Exubera, the inhalable insulin developed by Nektar Therapeutics based in San Franciso, has been approved in the US and Europe in late January this year. Exubera, the first inhalale version of insulin, offers diabetics an alternative to traditional needle-based delivery.

The technique in which the drug is delivered aerosolized might be promising for the delivery of other drugs aswell, as stated by John Patton, Nektar's cofounder and chief scientific officer:

"Patton believes that Nektar's inhalation technology is widely applicable to delivering other peptides, noting that although big pharma has shown keen interest in the specificity and efficacy of peptides, most have struggled with formulations. "What we've really done with Exubera is shown that you can get peptides into the lung, without a needle," he says. "I think we're opening up the chance for medicines that have had a really tough haul."

"First inhalable insulin approved", Nature Biotechnology 24 (2006)

No transgenic milk today

It seems the would be first market available drug produced in a transgenice farm animal, is not going to market in Europe (yet).

"The European Medicines Agency's (EMEA) decision back in February on recombinant human antithrombin-, an anticoagulant developed by GTC Biotherapeutics, was eagerly awaited because the product, known as Atryn, if approved, would be the first drug produced in a transgenic farm animal to reach the market. In the event, the EMEA did not approve the product, but not because of any direct concerns about its animal origins. Atryn was rejected because GTC simply did not present enough appropriate data to allay EMEA's concerns about its immunogenicity."

Read "Transgenic milk prospects turn sour", in Nature Biotechnology 24, 368 (2006)

Dirk Jan, date

Aging and the Cell nucleus

A very universal researchquestion is the question: how do humans age? Sure, research involving yeasts, worms and mice learned us that there is some kind of molecular basis that contribute to aging, but much remains to be known about human aging...

The cell nucleus of higher organisms is recognized as a complex and highly organized containing an individual's genetic information. One of the most important structural elements of the nucleus are the nuclear lamina, which have been studied extensively. The lamina is made up of tho different types of lamin proteins.

The fundamental connection between the nuclear architecture of the cell and aging was first observed in yeast (eukaryote, just like us humans). A mutation in the nuclear protein Sir 4 (localizes the nucelolus, subcompartment of the nucleus) lead to an extension of the lifespan. Later, the defenitive proof for a fundamental connection between nuclear architecture and human aging came. In 2003 researchers identified mutations in the lamin A gene (LMNA) as the genetic cause of the segmental premature aging disease Hutchinson-Gilford progeria syndrome (HGPS)

In 2005, Zhang and colleagues discovered that cells in HGPS patients have increased genomic instability and DNA and an ineffective DNA repair machinerey compared to healthy individuals. The link between genomic instability and accelerated aging is also appearant in Werner syndrome. This autosomal recessive disorder is caused by a non working WRN RecQ helicase, an enzym involved in DNA replication, recombination and repair.

One of the eventual goals of aging research would be to find "the fountain of youth", althought this won't be happen in near future, therapeutic treatment of people suffering from disorders such as HGPS has become very realistic indeed.

Read the article "The Cell Nucleus and Aging: Tantalizing Clues and Hopeful Promises" by Scaffidi et. al published in PLoS Biology, november 2005.

A new bug on the block!

Finding a new bug is not an easy task, most often the differences between the in vivo conditions of the natural habitat and in vitro conditions of the laboratory pose problems in succesfull growth and isolation of the microorganism.

However, researchers of the National Institute of Allergy and Infectious Diseases (NIAID) in Bethesda, Maryland, USA, have recently isolated a new pathogenic bacterium. The gram negative rod which is named Granulobacter bethesdensis (after the disease and the Bethesda location in which it was found) is thought to cause chronic infections in patients with a rare immune disorder called chronic granulomatous disease (CGD). The bacterium possibly plays a role in more common conditions, such as irritable bowel syndrome aswell, but this needs further investigation.

read the Nature news article or access the full text article (PLoS open access journal)

What is Science?

Everyday we get into our lab thinking we're busy with science, But What is Science actually? "What is Science? Some viewpoints from the perspective of the theory of science" by Sune Nordwall is a nice philosophical piece that takes us back to the concept of science.

Dirk Jan, painting

To compensate for all the very serious posts, here is Dirk Jan again!
I've selected a multilingual comic for all our English readers who are too lazy and stuborn to learn the beautiful Dutch language, the language that gives access to such fine literature!
enjoy!

Time spent in bed can make you a better gamer!

For everbody who loves sleep and gaming, good news!
Studies of the brain using the video game Duke Nukem have shown how sleep affects long-term memory. link

Cancer gene-therapy

Unfortunately cancer is omnipresent in our world. Almost everybody has seen people in their direct environment suffer because of this terrible disease. The object of current cancer therapies is to eliminate both primary tumours and metastases. For some reasons reasons, the later need to be treated by systemic agents (chemotherapy) which leads to significant systemic toxicity. This toxicity could be overcome by using more targeted approaches, such as gene therapy. In a recently published review-article Palmer et al. give an overview of gene therapy for cancer with a particular focus on the strategies that have entered clinical trials (Palmer et al. Cancer gene-therapy: clinical trials. Trends Biotechnol 24, 76-82, 2006).

There are several strategies possible in gene therapy for cancer. In Immunogene therapy researchers try to stimulate anti-cancer immune response, since the human body normally doesn’t develop a good immune response against tumours. Several gene therapy approaches using pro-inflammatory cytokines and co-stimulatory molecules have entered clinical trials. Other methods focus on overexpressing the tumour supressor gene p53, frequently mutated in human cancers. Antisense and RNA interference (RNAi) therapies target the inhibitation of the expression of mutant oncogenes, mutant genes crucial to the development of human malignancies. Pro-drug activation therapy focusses to express an activating enzyme within the tumour, locally activating a systemically delivered inactive pro-drug.
Most interesting is the use of genetically modified oncolytic virusses. An example is the use of a oncolytic adenovirus which replicates inside and lyses cancer cells but not normal cells. Gene therapy to manipulate apoptotic pathways focusses to induce cell-death in drug-resistant tumour cells. Several other approaches of cancer therapy are mentioned in the article, such as anti-angiogenic therapy (cutting the tumour of its blood supply), myeloprotective gene therapy (reducing the toxicity of chemotherapy) and transductional and transcriptional targeting of vectors.

The clinical trials of several gene strategies confirm that such treatments are safe and well tolerated. However with a few exceptions there is no impending evidence of significant clinical activity. A major obstacle is the ability to target tumour cells through systemic delivery. Transcriptional targeting might be chieved using tumour-specific promoters (micro-array technology and proteomics would identify novel tumour-specific targets) but this remains to be demonstrated by clinical trials. The article ends with a final remark that cancer-gene-therapy is likely to have the greatest impact as adjuvants and in combination with conventional therapies, presenting a major challenge for future clinical trial design requiring considerable investment in patient and financial resources.

Several ways to create ebooks for your Palm

There are several ways to store and view documents such as Ebooks for your Palm OS based PDA. If you want to view a document on your Palm which looks exactly the same as on your Windows or Macintosh desktop the program Repligo for Palm OS is something you want. Repligo converts any document that can be printed on your desktop PC to a repligo document. Unlike some other programs I've tried so far this program makes an exact copy of your PC document without noticable loss in the quality of pictures, graphs etc. Take a look at the example screenshots . Repligo desktop will nest itself on your PC like a virtual printer just like for example Adobe Distiller, used to create PDF files. When you print a document and select the virtual printer a repligo file will be created which is transfered to your PDA at the next synchronisation. You can then view the file on your PDA by using the Repligo viewer.

To create ebooks for youPalm build-in Ereader you can use the program Dropbook . This program is ideally suited to convert simple textfiles and turn them into ebooks which you read with Ereader. Dropbook is very easy to use and is available for both Windows and Palm. Reading ebooks with Ereader has several advantages, you can use all its nice features such as the autoscroll which automatically scrolls the text at a certain speed, ideal for lazy readers like me.

If you're looking for free Ebooks, just get yourself to the Gutenberg project which has 18000 ebooks available for download.


UPDATE: manybooks.net is a great site where you can download free ebooks. You can download in many format such as Ereader, Plucker, Isolo, I-pod notes etc.

A music database where nothing stays hidden

Discogs is a userbuild database of music information. I've been using this database for quite some time now and I never came across an artist I couldn't find. Discogs is the ideal place to find out more about those unknown artists occupying your playlists, bearing bizzare names like "The Attack People" (Well,some artists seem to be too obscure to be in Discogs even).

Artificial intelligence for bioreactors

For me bioprocess engineering is a somewhat boring topic. I remember the hours I spend on endless list of formulas, huge tables and dull calculations. However the whole field of bioprocess engineering and the optimalisation of bioreactors becomes alot more interesting when there is Artificial intelligence involved.

Microbial cells find a widespread use in industrial scale bioreactors to yield a product of interest. In most cases we wish to adjust the extracellular conditions of our used cells in such a way that the microbial population responds as we required, for example produce the most of a certain metabolite. This so called "tailoring" of the conditions requires judicious modeling and control, for this most conventional mathematical tools are less usable since they more suit ideal laboratory scale experiments.

The article Synthesizing cellular intelligence and artifical intelligence for bioprocesses by P.R. Patnaik (Biotechnol Adv 24, 129-33, 2006) reviews the current use of Artificial Intelligence (AI) to describe and control the overall behavior of a population of living cells in a bioreactor. The use of AI seems promising in a large number of different applications of bioreactors, offering new strategies for analyzing, improving and optimizing microbial processes on an industrial scale.

It’s fascinating to see the application of AI in some of the classical examples of modern Biotechnology, like the use of a neuro-fuzzy estimator and internal model control to optimize a penicillin fermentation pilot plant, an example mentioned briefly in the article.

A forum for the medicine world

Since I consider myself being part of the medical field ofcourse I need to attend to as much online medical field fora as possible. One interesting forum is Forum Lekar. This forum is dedicated to people in the medical field, no matter what speciality or at what level. The forum tries to be a place where healthcare professionals can share ideas, point of view and solve problems.

Especially interesting (for all the poor students) is the download section where you can downloadable textbooks covering basically all medical and related sciences.

Dirk Jan, special

On special request from Kazachstan some extra Dirk Jan comics will be posted this week!

How far would you go to feed your kids?

I know that most mothers will go tremendously far to keep their children alive (well, mostly). But some time ago I was amazed after reading a newsarticle about a women who was trapped in a collapsed building together with her baby. Stuck without food or water she kept her young child alive by cutting herself with a knife and feeding her baby small amounts of her own blood.

While reading Nature magazine, I came across a comparable example. It seems a certain type of Amphibian 'worms' feed young their own flesh. The little baby worms scrape the fatty skin from their mum's back when they are hungry!. Read the article here

What would drive the human being further?

This night I had a long conversation with a friend of mine who happens to be a communist about capitalism versus communism. Normally I don't like to discuss politics, perhaps because I don't know enough about politics and history to participate in any solid discussion. However I'm always fascinated by people who believe that a near perfect world with no poverty is possible. To quote my friend:

"what would drive the human being further?
the willingness to achieve more...Together right now we work/live/die only to satisfy our needs, what if we worked to satisfy the needs of the
society?"

I believe the human being is selfish, just like all other organisms are selfish. That is not something evil, it's just how we are (genetically) programmed. We care more about our own and our offsprings health then we do about our neighbors, not something we should be ashamed of, should we? Our programmed selfishness has helped us to prosper and grow, or atleast, prevent our extinction :)
Abuse... The wealthy abusing the poor, Rich men getting richer, Poor men strugling. Everybody can see examples of this when willing to open the eyes, but isn't this something which is happening as long as humans have been living together? Unlike my communist friend who thinks that this "abuse" is caused by an incapable capitalist system, I think abuse of others human beings is inherent to the selfish nature of humans.

Deepsea pica's

A long time ago I worked as a laboratory technician trainee with Galice Hoarau at the department of Marine Biology of the University of Groningen. I already knew he was a skilled diver then, but he turned out to be a good photographer aswell. Browsing his underwater photo's with the right music on the background is deeply relaxing

Dirk Jan, smurfborg

Every week I will try to post a Dirk Jan comic here. Dirk Jan is a Dutch "nerd" who finds himself in the most weird and funny situations together with his beer drinking friend Bert or dog Bello. Enjoy!

The only good german is a living german

Unfortunately, It seems we still have to wait a long time before we can see the nazi's (this time as zombies) invading Holland again. Althought the preproduction of the horror movie Worst Case Scencario already started somewhere in 2003, the actual production seems to have alot of delays...
Especially with the upcoming World Championship this year hosted in in Germany this movie will be very interesting indeed!

Watch the two classy trailers at gorehound website

Liftoff

And we got a liftoff!

after half the world starting their own weblogs I couldn't resist the temptation any longer, I just had to start something for myself aswell!

altogether I'm 100% Dutch this blog will be mainly written in English, not only is this a good way to practice my English writing skills, more people will actually be able to understand what I'm writing (so I hope).