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James Watson lectures cancelled

As the BBC reports (and the Register, and Nature News, and New Scientist, etc etc), many of James Watson's lectures over the next few days have been cancelled due to remarks he made in an interview with the Sunday Times, where he described the intelligence of Africans as lower than Europeans. This means, naturally, that the lecture of his that I was planning to attend on Sunday is also cancelled. It is still shocking, and a shame, when we discover the failings of "great" men.

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Telomeres are transcribed into RNA


Telomeric Repeat–Containing RNA and RNA Surveillance Factors at Mammalian Chromosome Ends


Claus M. Azzalin ,Patrick Reichenback ,Lela Khoriauli , Elena Giulotto , Joachim Lingner 

Just came across this today in my trawl through science news. First found in a New Scientist post, and then I read the originating Science article. Turns out the authors have discovered that telomeres, long thought to be transcriptionally silent, do actually have "TElomeric Repeat–containing RNA (TERRA) ranging in size from ~100 bases up to at least 9 kilobases". Further, "TERRA molecules are transcribed from different telomeres and are composed of subtelomeric-derived RNA and UUAGGG repeats". Further, the authors have found evidence that these TERRA molecules interact with the telomeres. Their conclusions include "It is possible that TERRA promotes telomeric
heterochromatin assembly by mechanisms similar to the X chromosome inactivation in females, which is mediated by
the long noncoding Xist RNA (25), or to the RNAi-mediated heterochromatinization of the telomeric dh-homologous
region in fission yeast […] SMG proteins regulate TERRA at chromosome ends and UPF1 and EST1A physically interact with DNA polymerase δ and telomerase, respectively […] We speculate that the telomeric defects induced by
SMG-depletion could derive from loss of coordination between TERRA and key enzymatic activities that assure
telomere replication and length homeostasis."

I'm interested in anything having to do with cell longevity and immortality, not just for its relevance to cancerous cells, but also because the Centre I work for specializes in ageing research, and telomeres can be thought of as cell clocks, as the telomeres are shortened with every cell division (in healthy cells). It short paper worth reading, even if it is quite jargon-heavy.

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News: Bio::Blogs, Gutsy, James Watson, Alzheimer’s Blood Test…

There's been some interesting news around recently, and I thought it would be nice to highlight some of it.

Tooting One's Own Horn

Firstly, the folks over at Bio::Blogs mentioned this site in their latest edition, #15, in the context of my posts on the Integrative Bioinformatics Conference in Belgium this past September. Thanks, guys! It's nice when you can post your notes as the talks happen, and I hope some people found something of interest in them. As Pedro Beltrao said, if you're interested, "Read all about it in chronological order from parts 1 to 10 (1,2,3,4,5,6,7,8,9,10)." Pedro's theme for this edition of Bio::Blogs is the both the increasing number of bioinformatics bloggers and the increasing prevalence for people to blog about their research as it's being done. I like to see this idea of openness pushing the boundaries of bioinformatics and into biology.

Ubuntu Gutsy Gibbon

Just like the geek I am slowly discovering that I am (and I say that with pride), I installed the pre-release version of the latest Ubuntu, Gutsy Gibbon (7.10), over the past week. I'm not as early as some in the department, who installed it weeks ago, but It was fun to install it before it was officially released: perhaps a little bit of a thrill, wondering if it will break my computers? So, one desktop and one laptop upgrade, plus a further desktop clean install later, and everything's working fine! The final release comes out tomorrow, so get ready to upgrade. I do 95% of all of my research using Ubuntu: the *only* thing I find I still have to switch to Windows for with regularity is the manipulation of word documents. Open Office still can't handle comments and tracked changes exactly the way I'd like, so when I'm collaboratively writing paper submissions I find I have to reboot into Windows. I'm trying to phase out the word document aspect of my writing, and phase in more Latex work, so hopefully even that aspect will be gone soon. Then, I'll just use Windows for lazy browsing at the weekend, and the odd windows-only app that I sometimes want to use.

James Watson

I was at swim practice last night, and people were saying what they were planning for the weekend. When I said I was going to see James Watson speak at the Centre for Life in Newcastle, only one person knew who he was. Sigh. But anyway, I'm really looking forward to it, even if it means an hour's train ride each way on a sunday, which in the UK is a big risk! Hopefully I'll be able to take some notes and post them here on Monday.

Alzheimer's Blood Test in the Works

I was interested to read an article on the BBC this week about the development of a blood test that, with 90% accuracy and from up to 6 years before symptoms become apparent, can determine if a person has Alzheimer's. The full article is available from Nature Medicine. It's great news, and an interesting paper.

FuGE paper in Nature Biotechnology

A paper has just appeared at Nature Biotechnology on "The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics". I had seen the paper earlier when it was under community consultation, but it is nice to see that it's now officially published. Standardized experimental metadata is the way to go!

First Asian Genome Sequenced

Catch up with this announcement over at naturenews.

IgNobel Prizes and News

Finally, though I am now sadly behind the times in mentioning that the 2007 IgNobels are out, I would still like to point out a few things. Firstly, I would like to say look out for the video of this year's ceremony – it should be posted shortly! Also, the IgNobel website isnt just useful to discover who won. Check out these news items from the past few days: "Military: Letter from Leffler" and "The medicinal value of alcohol".

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In The News Papers Semantics and Ontologies

I Spy an Ontology Helper

Here is what they have to say about their product, OntologyWidget, in the abstract (hosted on BioMed Central) from BMC Bioinformatics:

"We have developed OntologyWidget, an easy-to-use ontology search and
display tool that can be used on any web page by creating a simple html
description. OntologyWidget provides a rapid auto-complete search
function paired with an interactive tree display. We have developed the
web service layer that communicates between the web page interface and
a database of ontology terms. We are currently storing and maintaining
40 of the ontologies on the http://obo.sourceforge.net/ site as well as
a few others."

It piqued my interest, and so I had a play with their "sandbox" website. I was interested, as I'm part of the development team for SyMBA, a multi-omics high-throughput data archive. However, we plan to make OBI available to our users, which is in OWL format, and so OntologyWidget wouldn't be useful "out of the box". However, I like that someone's done what I'd have to do in a web front end anyway, which would save me some hassle if it can be made to work with OWL files. It's released with the MIT Open Source License, which I'm not all that familiar with myself, but which (one assumes) means that others can work on it. The other worry I have is that the paper has only just been published, yet their website states that: "Current version is 1.00. Last updated November 6 2006 – see included documentation for details
". So, perhaps they are updating the ontologies weekly (as they state in the paper), but they don't seem to have updated the code in 10 months or so. Perhaps it's an error on the web page.

I have to say that anything that makes adding ontology terms more easily usable is a fantastic idea, and I'm really glad to see it. We need to have more and easier usage of ontologies. I'll have a little look into this, and see if I like it.

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Root-locked Linux for the masses | The Register

Came across this in my regular news trawling, and thought it sounded interesting. I've often imagined how nice it would be to not have to deal with windows (I have a dual boot laptop with both XP and ubuntu fiesty on it), but also have known in my heart that so many people are (justifiably) not interested in learning curve of ubuntu or the like. I know it may not be realistic, but just the idea of all the bio labs using *nix makes me happy 🙂

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News Roundup: New Drug, New Find, New Toy, New Size, New Wonders

Recently there has been a lot of interesting things reported in the news. Below are a few items that I have found particularly interesting:

  • New Candidate Drug for Bipolar Disorder: All about a potential replacement for more traditional drugs such as lithium.
  • Extremely well-preserved 0,000-year-old Infant Mammoth found in Siberia. By a reindeer herder, no less. The picture provided is truly astonishing.
  • A USB typing-speed indicator light has been developed by a Japanese company and is on sale now. You can have a typing race with your friends! The Reg says that it's not for sale in Europe or the US yet, though. Shame.
  • The earth is believed to be 2.5 millimeters smaller in diameter than previously thought. Fantastic!
  • The "new" seven wonders of the world have been announced. I have to say that I'm quite disappointed, as the "new" only truly applies to the list, and not the wonders. 3 of the 7 wonders were built during the time the Ancient Greeks were (conceivably) around, and only one of those (the great wall of China) might have been unknown to them. Also, some of the countries that have these wonders were unhappy about their inclusion in the new list. It's all explained in the National Geographic article linked above.

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Of Prions and Panic

A couple of interesting, orthogonal news items appeared over the past few weeks, which I didn't get the chance to write up separately when they were first published, as I have been working to a deadline. Thankfully, that particular deadline has passed and I have some free time to talk a little about prions and (widespread) panic.

Prions

Perhaps it is already well-known to researchers working in the field, but it was a surprise to me when I came across a paper by Parkin et al. in PNAS describing the connection between "normal" prion proteins and the formation of beta amyloid plaques in the brain (electronic publishing date 15 June, print date 26 June 2007). This research was also picked up by the BBC.
(Edit 9 July: this has also now been picked up in New Scientist).

Basically, while misshapen versions of these prions are known to be causative agents of transmissible spongiform encephalopathies such as Creutzfeldt–Jakob disease, their function while in their normal shape is unknown. Parkin et al. hypothesize that the normal prions have a regulatory – specifically, inhibitory – role in the creation of beta amyloid plaques. Overexpression of the normal prions inhibited the cleavage of APP (amyloid precursor protein), the first step in the creation of beta amyloid. Conversely, the complete removal of the normal prion via either siRNA or the use of knockout mice resulted in significant increases in the level of beta amyloid.

This research implies that increasing the expression of the normal prion in the brain could help prevent the beta amyloid plaques forming in the first place. It is very encouraging to see so much interesting Alzheimer's research going on at the moment. While CISBAN researches other areas of ageing, including how telomere length affects the ageing process in the cell, I am always interested in research into other areas of ageing, including age-related illness.

Panic

OK, I stretched this analogy slightly in order to achieve pleasing alliteration. Go from "panic" to "Widespread Panic", a band who made one of my favorite songs, "Big Woolly Mammoth". This song leads me to another bit of science that's been in the news again recently: is it possible to re-create a woolly mammoth via 40,000-odd year old samples? The question was raised in Scientific American last week via a profile they were doing on Svante Pääbo from the Max Planck Institute for Evolutionary Anthropology in Leipzig.

This is not a new question, and Pääbo has published research in September 2006 in PNAS that described the most common errors introduced into ancient wolf mitochondrial DNA sequences via amplification and sequencing procedures. SA states that he has been doing similar work more recently on Neandertal and mammoth DNA. By determining more exactly which bits of the sequence are artefacts of either the degradation of the sequence over long stretches of time or the sequencing process, we are one step closer to being able to achieve the correct DNA sequences for very old tissue samples.

Of course, this doesn't mean that we are now able to successfully bring back extinct species. More than just the DNA itself is needed: the packaging of the DNA (notably the histones) and other assorted proteins are also necessary. One of SA's interviewees states that what is really needed is an intact cell, not just the DNA.

But this next step in the creation of a "clean" sequence does bring interesting ethical questions to the fore once again. Should we recreate an extinct species, if we could? Undoubtedly, once the techniques are available, some rich investor will try to get it done privately, even if the public research centers do not want to do it. One could argue that there is no place in today's world for Neandertals or mammoths. But what about those species that were killed in "the modern era" via ignorance or deliberate intent of Homo sapiens? The dodo was killed by humans and their associated animals such as rats and cats.Attempts had been made in the late 1800s to give the passenger pigeon, which once numbered in the billions in North America, protected status. However, it was rejected as people simply didn't believe the pigeon could be in decline. The last confirmed passenger pigeon died in captivitiy in 1914.

So, where do you draw the line? And what if we had not just DNA, but also intact cells? What if the bald eagle, recently taken off the endangered species list due to an impressive comeback over the decades, were to die off from a disease? Should all animals made extinct through methods attributable to humans be re-created? I can forsee that if a favorite pet species such as cats or dogs were made extinct through disease, there would be people clamoring for researchers to try it. Personally, I think there are good scientific reasons to seriously consider such methods in certain instances: I'm just not yet sure what those instances would be. Perhaps its just my love of sci-fi, or the sadness I feel at today's human excesses (me included, even with all our attempts to "be green") that makes me feel this way.

But I think it will happen, and within the lifetimes of people living today. The question is, how far will it go? From the passenger pigeon to Jurassic Park, anyone? 😉 Would we be doing it for the right reasons, if we did bring back the dodo or the passenger pigeon or the Quagga? Or, would it just be to make us feel better about ourselves? Perhaps "making ourselves feel better" would be a good-enough reason to bring back a species, perhaps not. How would it change endangered species legislation? Would it cause people to not worry about hunting a species to extinction, as it could just be "revived" in the same year? Indeed, would it become a goal for a certain type of hunter to make a species extinct? OK, maybe a little too much wandering into the land of sci-fi…

In any case, an exciting and fabulous time to live in, and what a fantastic area to work in.

Note from 5 July 2007: And, in an interesting addendum, National Geographic just published an article about the recent discovery of high-quality dodo bones that probably contain well-preserved DNA.

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Anesthetics may cause amyloid beta peptide clumping

As reported in Scientific American a few days ago, in vitro research performed by scientists at the University of Pittsburgh has shown that, if the anesthetic molecule is small enough, it will bind with a pocket in amyloid beta peptides. This binding results in a conformational change to the molecule, making it possible for them to clump together with other similarly misshapen peptides. Amyloid plaques, which are clumps of these proteins, are involved in Alzheimer's disease, though it is unknown at this time whether they are a cause or an effect of the disease. Some anesthetics are too big to fit into the peptide's "pocket", and therefore do not cause plaque formation. The examples provided in the article are as follows: "Halothane had the greatest clumping effect, yet it is rarely used in
North America and Europe. Two other anesthetics–isoflurane and
propofol–also cause clumping, but their effect is not as severe.
Another one, called thiopental, does not cause clumping at all because
its molecule is too big to fit inside the peptide's pocket."

The next step is to try to reproduce these results in a mouse model of Alzheimer's, to see if the in vivo effects are the same as the in vitro. Certainly an interesting area of research to keep an eye on.

The full article was published by Biochemistry (DOI: 10.1021/bi062184l, Abstract)

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Don’t ignore the “junk”: it’s always more valuable than you think…

Scientific American: What is junk DNA, and what is it worth?
A nice summary of why junk DNA is not junk was published a couple of days ago on the Scientific American website. In the past few weeks I've discussed on-and-off with a few people what junk DNA used to mean (and, more importantly, what it means now), and it would have been nice to be able to follow that up with an understandable resource for people to read. Here it is, and I hope others find it interesting. Don't forget: the interesting bits of the genomes (and epigenomes) are, well, all the bits!

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Polish scientists fight creationism

As Nature reported on the 26th of October this year in the article of the same title as this entry, Polish scientists have released a letter of protest against their deputy education minister Mirosl strokeaw Orzechowski, who has stated that “the theory of evolution is a lie”. Orzechowski is a creationist and a member of the ultra-right-wing LPR party. Fellow party member Maciej Giertych is, according to Nature, “lobbying for obligatory inclusion of creationism in Polish biology curricula”. Fortunately, neither the general scientific population nor Poland’s minister of science agrees with this minister’s views, and the scientists who wrote the letter hope that their quick action will prevent lasting damage to the educational system.

It is not about what they believe — it is about them attempting to force that belief onto the science curriculum. Hopefully, the scientists and their open letter will win the day.