Last week the New England Journal of Medicine (NEJM) published a paper on selective outcome reporting in clinical trials (Vedula et al. 2009). The primary and secondary outcome(s) of a clinical trial could for example be survival in cancer patients or rate of heart attacks and other cardiovascular events in patients taking cholesterol-lowering drugs. These outcomes are defined in the study protocol before the first patient is treated, and whether or not the primary outcome is reached (using statistical testing) defines whether a trial was positive or negative. The study protocol is approved by an institutional review board (IRB) and can only be changed later (and that includes changes in the protocol-defined outcomes) if again approved by the IRB.

The study in the NEJM examined the outcomes of 20 clinical trials for the drug gabapentin using internal documents of the drug companies Pfizer and Parke-Davis, and compared them to the outcomes reported for those trials that were published as peer-reviewed papers. The internal company documents were obtained as the result of litigation in which the company admitted guilt for off-label marketing (i.e. marketing for uses that were not approved by the Food and Drug Administration) of gabapentin.

12 of the 20 trials were published as peer-reviewed papers. In 8 of these 12 papers the primary outcome differed from the primary outcome defined in the protocol. New primary outcomes were introduced in 6 papers, and protocol-defined primary outcomes were not reported in 5 papers. Trials with primary outcomes that were not significant were either not reported as full paper or were reported with a changed primary outcome.

Selective outcome reporting has also been reported by other authors and is not limited to trials funded by drug companies.¹ Selective outcome reporting is a major problem because it a) distorts our scientific knowledge and b) is unethical as it involves research on human subjects. This could for example lead to repeated studies of a clearly ineffective or harmful drug or intervention. The distortion of our scientific knowledge by selective outcome reporting in scientific journals is also a concern for research in other areas. Confirmation of important research findings by independent groups is important, but a lot of research is probably repeated simply because negative results were not published. Some of these reporting biases could be avoided by making more unpublished research data available, either by Open Notebook Science or by publishing “unexciting negative” findings in peer-review journals or preprint archives such as Nature Precedings.

Clinical medicine tries to solve the problem of publication bias by making public registration of clinical trials mandatory before patient enrollment. This registration is required by most major medical journals since 2004². U.S. legislation also requires clinical trial registration and since 2008 (FDAAA: Push to open data in clinical medicine) this includes outcome reporting within 12 months after data for the last subject were received in the publicly available Clinicaltrials.gov database.³ These efforts should ensure ethical standards of clinical research, and help to avoid the kinds of biases reported in the paper by Vedula et al.

Clinical trial registries obviously also serve other purposes, as they help interested patients and their relatives and treating physicians to find clinical trials they want to participate in, and they help researchers and clinicians to do a systematic overview of the ongoing research in a particular field. Just as there are centralized databases (e.g. PubMed Central and the Current Controlled Trials metaRegister of controlled trials) and institutional repositories for fulltext papers, there are also both central (e.g. Clinicaltrials.gov] and institutional clinical trial registries. But in contrast to institutional repositories, there are no standard software tools available that an institution can use. I am involved in building a clinical trial registry for our institution, and the effort is both technically demanding, and socially challenging. The information in a clinical trial registry is constantly changing and we need to keep the efforts required by the individual reseachers at a mininum. We also have to walk a fine line of what information can be made publicly available, and here we follow the standards provided by both Clinicaltrials.gov and the WHO.

Vedula, S., Bero, L., Scherer, R., & Dickersin, K. (2009). Outcome Reporting in Industry-Sponsored Trials of Gabapentin for Off-Label Use New England Journal of Medicine, 361 (20), 1963-1971 DOI: 10.1056/NEJMsa0906126

¹ Chan AW et al. CMAJ 2004 doi:10.1503/cmaj.1041086

² De Angelis C et al. NEJM 2004 doi:10.1056/NEJMe048225

³ EudraCT, the mandatory European clinical trials registry is regretably not available to the public.

⁴ Both PubMed Central and Clinicaltrials.gov are efforts by the U.S. National Institutes of Health.

In September PLoS started to show usage data (downloads, citations, but also use of social bookmarking services and blog posts) for all their published papers (article-level metrics at PLoS – addition of usage data). PLoS is not the first publisher to do that, but certainly the largest to date. Two Nature Network bloggers wrote about these changes back in June (The Scientist: On article-level metrics and other animals) and August (Gobbledygook: PLoS One: Interview with Peter Binfield), and a number of blogs commented on this new feature, including:

• A Blog around the Clock: Article-Level Metrics at PLoS – Download Data
• The Scholarly Kitchen: PLoS Releases Article-level Metrics
• BMJ Group Blogs: Richard Smith: The beginning of the end for impact factors and journals
• Blue Lab Coats: Article Level Metrics Debut at PLOS

There are a number of reasons why article-level metrics are a good idea, and I hope that many other journal publishers will follow. But in this blog post I want to talk about some of the shortcomings of the current implementation of article-level metrics.

Article-level metrics should be combined from different places
Fulltext articles live in more than one place. Obviously at the journal publisher’s website, but in many cases also in one or more institutional repositories and at PubMed Central (or similar places for papers not published in the life sciences). Which of these places produces the most reliable article-level metrics or should the HTML views, PDF downloads, etc. from all these places be combined? The decentralized nature of institutional repositories makes it especially difficult to combine usage statistics from them, but there are projects that try to tackle this problem. A unique identifier is required to combine the usage data from these different sources, and we have the DOI for that. PubMed Central and similar large repositories could not only start to provide their own usage data, but also combine them with the usage data from those journal publishers that already provide them.

Article-level metrics need author identifiers
Evaluating the “impact” of a researcher is one obvious use for article-level metrics. In order to be able to do that for more than a handful of researchers, we need unique author identifiers. This year we have had many dicussions about author identifiers (including this blog and at the Science Online London Conference), and I hope that in 2010 we will finally see an evolving standard that is picked up by journal publishers. It would be in the interest of PLoS to combine their article-level metrics with an author identifier as soon as possible, most likely the proposed CrossRef ContributorID, rather than the Elsevier Scopus Author Identifier or the Thomson Reuters Researcher ID.

Article-level metrics should enhance literature searches
We all know how Google became the most popular search engine (Pagerank). And article usage data would be a tremendous boost for scientific literature databases such as PubMed. A literature search should sort the results by usage data (e.g. a combination of number of citations, HTML views and PDF downloads) rand not the rather boring publication date, author or journal name. Normally I would think that Google Scholar would be the first place to implement such a functionality, but I haven’t seen much innovation from Google Scholar lately.

Article-level metrics should not only be numbers
As we don’t want to reduce a paper to simple numbers, it is important to provide more than HTML views and PDF download counts. Citations counts are useful numbers, but linking to the citing papers is even more interesting. Similarly we want to see links to Faculty of 1000 recommendations and blog posts aggregated at ResearchBlogging.org. If we extend this further, we should probably start to think about a better name for article-level metrics. And I hope we never start to call this ALM.

PubMed Central was launched in February 2000 by the U.S. National Institutes of Health (NIH) as a free digital archive of journal articles. Just as PubMed, PubMed Central covers research in the life sciences, but not other areas of research, e.g. engineering, physical sciences or astronomy.

Some journal articles are available as full text as soon as they are published, and most journals provide free access to full text articles within a year of publication. Some journals only provide the full text of some articles, including research funded by the NIH under the NIH Public Access Policy. The majority of fulltext articles in PubMed Central are not Open Access, but are protected by copyright. These articles are often made available under a license that allows redistribution and reuse.

All articles are deposited using the NLM-DTD XML format, which is a standard text format suitable for text mining and long-term archiving. Most articles are deposited directly by the journals, so that authors do not have to get involved in the technical aspects of article deposition.

PubMed Central is a centralized archive of full text papers and not simply an interface to search these articles at the websites of the participating journals. Neither is PubMed Central an interface to search the various institutional repositories at universities and institutions. The NIH thinks that this centralized approach makes it easier to develop additional functionality, including the integration with other databases (e.g. the protein or nucleotide databases) hosted at the NIH.

UK PubMed Central was launched in 2007 as the first PubMed Central outside the United States (PubMed Central Canada, the second international PubMed Central, launched this week). In January 2010 UK PubMed Central will launch a number of new services, and I used the opportunity to ask UK PubMed Central Programme Manager Philip Vaughan a few questions.

This week (October 19-23) is Open Access Week – a good opportunity to think and write about this topic. On Monday I wrote in a blog post:

Open Access can be looked at from many different angles, including the researcher, the science library, the institution, the funding organization, the journal, the science journalist, and the general public. Most arguments for or against Open Access depend on that angle. As a researcher, I am most interested in whether Open Access will make my work easier. Again, a researcher can look at Open Access from different roles: reader, author, reviewer, editor.

In that blog post I then wrote about the role of the researcher as a reader. Now I want to look at the perspective of the researcher as an author.

Choice of journal
The decision of where to publish a manuscript for most researchers probably works something like “find the best journal where I can publish my work with the least amount of trouble”. Best journal usually is a subjective decision, but probably correlates with the Impact Factor of a journal. As the average quality of manuscripts is higher in a better journal, this will help to value your research in the eyes of granting agencies and job search committees. Better journal often means higher rejection rates and/or higher numbers of readers. Both factors – and journals that publish a relatively small number of papers – favor a subscription business model¹.

Publication cost
Most Open Access journals use an author-pays model to pay for publication costs. Funding agencies or institutions may pick up these costs, but authors may be left with costs of $2500 or more.

Institutional Repositories
Self-archiving in institutional repositories (green access) is a great way to make your publication freely available if the paper is published in a journal that is not Open Access. Unfortunately this often requires extra efforts by the researcher, and the publication will be more difficult to find in the repository than in the journal. This creates little incentive for a researcher to get involved in self-archiving.

Citation advantage
The effect of free access to the scientific literature on article downloads and citations is difficult to measure. Some², but not all studies³ show higher citation rates for articles that are freely available and this citation advantage might be modest⁴. Citations are generated by other researchers who have access to your paper, and therefore I’m not surprised if there is not much of a difference between papers in Open Access journals and popular journals that are subscribed my many institutions.

Better Access
Researchers in poorer countries will have easier access to papers published in Open Access journals, although many subscription journals wave access fees through initiatives such as Hinari. Open Access makes it easier for journalists, high school students, patient advocacy groups and many more people to read your papers. This is obviously of great value to these groups, but I haven’t seen many examples where the paper author directly benefitted from this.

Social responsibility
The argument that publicly funded research should be available to everybody at time of publication can be a motivation for many scientists, but I would be careful to turn this into an obligation. Different countries have different traditions, but in my home country Germany the independence of research and researchers (including the decision where to publish) has become a constitutional right after the atrocities committed in the name of “science” in Nazi Germany. All major German research organizations support Open Access, but in contrast to other countries there is no Open Access mandate.

Summary
Publishing in an Open Access journal has surprisingly little benefits for the author of a paper, and often means additional costs. Unless we want to mandate Open Access publishing from authors because it benefits the other stakeholders (which at least in Germany would be difficult), we should make publishing in an Open Access journal more attractive to authors. It looks like PLoS ONE is doing exactly that, as 400 manuscripts published per month testify.

¹ Heber J. Science in the open. Nature Materials 2009 doi:10.1038/nmat2497

² Eyenbach G. Citation Advantage of Open Access Articles. PLoS Biology 2005 doi:10.1371/journal.pbio.0040157

³ Davis PM et al. Open access publishing, article downloads, and citations: randomised controlled trial. BMJ 2008 10.1136/bmj.a568

⁴ Evans JA and Reimer J. Open Access and Global Participation in Science. Science 2009 10.1126/science.1154562

This week (October 19-23) is Open Access Week:

Open Access Week is an opportunity to broaden awareness and understanding of Open Access to research, including access policies from all types of research funders, within the international higher education community and the general public.

The following video from SPARC (the Scholarly Publishing & Academic Resources Coalition) is a good introduction:

Open Access can be looked at from many different angles, including the researcher, the science library, the institution, the funding organization, the journal, the science journalist, and the general public. Most arguments for or against Open Access depend on that angle. As a researcher, I am most interested in whether Open Access will make my work easier. Again, a researcher can look at Open Access from different roles:

• Reader
• Author
• Reviewer
• Editor

The role as a reviewer or editor for an open access paper should be essentially the same as for a paper with subscription-based access. The journal Nature Communications that launches in April 2010 with a hybrid publishing model of open access and subscription-based access will for example have reviewers and editors blinded to the author’s choice.

In this blog post I will look at Open Access from the perspective of the researcher as a reader.

Access
As a researcher in a German university I am privileged to have institutional access to most journal articles that I need for my work. I use the program Papers as my main reference manager. Papers allows me to order my currently 1715 references (and PDFs of fulltext paper to most of them) by journal. Among the 20 journals with the most papers in my library, my institution doesn’t have access to three of them:

• Cell (don’t ask)
• Lancet Oncology
• Nature Reviews Clinical Oncology

Obviously three important journals for someone doing clinical cancer research. I could ask my institution to start subscribing to these journals, start a personal subscription (I had a personal subscription to Nature Clinical Practice Oncology for two years before it was renamed to Nature Reviews Clinical Oncology) which would set me back 150-200 € per journal, or I could pay for an individual article (either through my library or directly from the journal). All this requires extra time and money, worth only if I think a paper/journal is really important.

PLoS Medicine is the only open access journal among the 20 most popular journals in my Papers library (The BMJ has free access to its research articles and is the 24th most popular). Unfortunately there are only a few Open Access journals publishing papers that are relevant to my work.

As many others I do work from home in the evening or on the weekend, or while travelling. I am lucky that I can access my university network through VPN and therefore can get fulltext access to journal articles (one of the most important VPN uses for me). But some researchers might not be so lucky, or spend precious extra time setting up and using VPN.

Researchers that work in a poorer country, or for a smaller university or small biotech startup will have much larger problems. Medical doctors in community hospitals or private practice may not have easy access to any of the relevant journals, and they might depend on reprints given to them by colleagues or representatives from drug companies.

Sharing
If several people work on a research project, they also want to share the relevant literature in the field. Most subscription-based journals retain the copyright to the paper and don’t allow storing in a retrieval system or transmitting of papers without permission. This could mean that you can’t email the PDF of a paper to a colleague even if you are the author or his institution also has a subscription. And this could also mean that you can’t use a reference manager such as Refworks or Mendeley to not only share references with your lab colleagues, but also the fulltext PDF files. Strictly following the copyright can make something as common as a journal club a complicated affair.

Permissions
As most subscription-based journals retain the copyright to the paper, you have to ask for permissions when reusing tables or figures. Most often this is the case when giving a lecture on a topic. For longer lectures this could mean a large number of required permissions, and the permissions might be granted just for a single occasion. Journals might not care much about using a single figure in a departmental seminar, but it definitely becomes an issue when the lecture is distributed electronically, e.g. as free OpenCourseWare publication of teaching material. Some journals provide Powerpoint slides for the tables and figures and explicitly permit the educational noncommercial use. In my experience most researchers aren’t aware that they are using copyrighted material in their slides, and I rarely see the required copyright attributions.

Added services
This category has great potential, but is currently not yet that relevant in my daily work. Open Access to fulltext articles allows things that aren’t possible or much more complicated with subscription-based access. This includes fulltext searches (to find information not in the title, abstract or keywords), semantically enhanced articles, and article-level metrics (recently introduced by PLoS).

Summary
Researchers at large research institutions often have institutional access to most relevant papers. They are often not aware of the restrictions imposed upon them by the copyright of papers retained by most subscription-based journals. Open Access papers not only are freely accessible, but allow the uncomplicated redistribution and reuse for research and teaching, as well as innovative ways to find interesting research.

The perspective of the researcher as a paper author is stuff for another blog post…

It was Anna Kushnir who started it all. Frustrated with the limitations of PubMed when finishing her PhD thesis, she wrote a blog post in March 2008 (I Am Not Yelling. Not Out Loud.) about her experience. The blog post created quite a stir in the blogosphere, especially among science librarians. At the heart of the controversy was Anna’s complaint that PubMed is too complicated to use, and that some science librarians felt PubMed simply is complicated and that users such as Anna should take better advantage of the resources available to better use PubMed. David Lipman, director of the NCBI and responsible for PubMed, said:

Although the current engine works well for some users and some queries, I understand Anna’s frustration and we are in the midst of a number of changes that will make PubMed work better for her and many other users.

In May 2009 a PubMed redesign was shown at the 2009 Annual Meeting of the Medical Library Association (MLA) in Honolulu, and the presentation explains a lot of the ideas behind the redesign. On September 30 the redesigned PubMed was unveiled to the public, and as early as next week it will become the default PubMed web interface.

Several science bloggers have already written about the PubMed redesign, including a very detailed blog post by Jacqueline Limpens.

What is PubMed?
MEDLINE is a database of more than 19 million citations for biomedical articles, hosted by the U.S. National Library of Medicine. PubMed is the freely available Web interface to that database. Not only is the content of PubMed available from other databases (e.g. Scopus or Web of Science), but PubMed can be searched not only via the Web interface, but also from within other applications, e.g. a reference manager such as Endnote or Papers. And PubMed doesn’t cover all scientific journals, many disciplines (e.g. physics, social sciences) aren’t included at all. In other words, the Pubmed web interface is not the only way to find biomedical articles, and in fact will not find literature not related to the life sciences. But the PubMed web interface is probably by far the most popular way to search for biomedical literature.

What is the target audience?
The PubMed website is intended for at least 5 different audiences:

• science librarian
• researcher in the life sciences
• clinician
• patient or patient relative
• teacher, high school student, journalist and anybody else interested in life sciences research

Before PubMed was announced in June 1997 by the U.S. vice president Al Gore as free web-based access to the MEDLINE database, most users were librarians, plus of a small group of academics with paid access (remember Grateful Med ?). Now we have a number of target audiences with different experience in literature search strategies and different intentions:

• librarian vs. academic vs. the general public
• basic life sciences research vs. clinical research

As PubMed is the most popular but not the only interface to the MEDLINE database, the primary target audience will not be a librarian, but someone with less experience in searching the biomedical literature (and less time). I would lump academics together with the general public here, and think that the typical PubMed search should be as simple as the typical Google search. Everything much more complicated than a simple input box should be moved to an advanced search options page, or should be done via a different interface to the MEDLINE database.

Searching for clinical literature is very different from searching for basic science research. Here a search is often done to help in the decision making for a particular patient, and evidence-based medicine is used to find the most relevant scientific literature (with meta-analyses and randomized controlled trials providing the best evidence).

Searching for basic science literature has very different goals. It is either finding the needle in the haystack, e.g. you want to find all the published literature on the C3PO gene, or you want to find a review article as an overview over a particular field. But basic science review articles don’t have the rigourous tools available to evaluate clinical research mentioned above, and here review articles only differ in the personal perspective of the reviewers and completeness and actuality of the primary literature that was covered. Searching for basic science literature should also be tightly integrated with the other databases at the NCBI. This is done via the Entrez Search Page, so that a search for C3PO also links to the organisms it was described in, e.g. this one:

I don’t think that a search interface to MEDLINE can be good at both the clinical and basic science literature. The current PubMed is much closer to the latter, so I think that the primary target audience for PubMed is the academic or general public interest in basic life sciences research. A good search interface for the clinical literature would be something very different and has to include both databases of evidence-based evaluations (particularly from the Cochrane Collaboration) and from ongoing and completed clinical trials (particularly Clinicaltrials.gov, just like PubMed also hosted at the NIH).

Where is Web 2.0?
A PubMed redesign in 2009 can’t be complete without looking at what Web 2.0 has to offer. This means that users should be offered a personal PubMed account that links to their libraries for fulltext articles, stores common searches, creates RSS outputs, allows sharing of search results with other users, publishes a link to an interesting article on Twitter, and possibly other enhancements (e.g. a public profile page of all your PubMed articles, but that wouldn’t work without author identifiers). This also means a clean design, use of Javascript/AJAX for the user interface, a version for mobile users (particularly iPhone), and frequent small updates instead of a big desgin change every 2-3 years.

And how is the redesigned PubMed?
After this rather long introduction, what do I like about the PubMed Redesign?

Like

• Clean, uncluttered design
• Saving a search as RSS is faster and more obvious. I hope that this will make many more people use RSS than email alerts for their regular searches (why I like RSS)
• Auto suggest: some of the most popular PubMed searches will be displayed based on the terms entered
• Some use of Javascript/AJAX

Dislike

• The DOI (the best unique identifier for a paper and the easiest way to link to the fulltext article) is still not displayed in the standard abstract view (you find the DOI in the Medline and XML views)
• Small design flaw: no easy way to go back from advanced search to basic search
• Layout is now different from MyNCBI and the other NCBI databases (maybe this is work in progress)
• (As far as I know) no version for mobile users
• No send to CiteULike/Connotea/Twitter/FriendFeed, etc. buttons (popular with many journals)

The redesign will make it easier for inexperienced users to do quick searches (as mentioned above, probably the target audience). Experienced librarians might like the redesign less, as advanced searches have not become easier. But overall the changes are minor. My biggest complaint is the lack of DOI integration. A wasted opportunity. And – as mentioned above – I think we need a different MEDLINE interface for searching the clinical medicine literature.

How do you like the redesign? Jacqueline Limpens is doing a poll on her blog.

Blogging is a great way to report from a scientific conference. This could be done either with regular blog posts written in the evening or after the conference, and/or live-blogging using tools such as Friendfeed or Twitter. One or more blogging scientists can not only add a unique perspective to the reports about a conference, but for smaller conferences blogging might be the only way to learn more about a conference you were unable to attend in person.

Conference blogging (particularly live-blogging) basically requires four things:

• a wireless network,
• a computer or mobile phone with a full battery,
• a hashtag (and other tools to find the conference blog posts), and
• a blogging policy by the conference organizers.

Wireless networks are now commonplace, but enough battery power (or power outlets that conference participants can use) can be difficult. A hashtag such as #solo09 for Science Online London is essential for live-blogging using Twitter.

The big problem is the blogging policy, or rather that there usually is a policy only for traditional media, but not for blogging. The blogging from the Cold Spring Harbor Biology of Genomes meeting in May by Daniel MacArthur started a very helpful discussion about blogging policies. It is impossible to write anything specific about a conference – and that’s the stuff that is most interesting – without a permission from the conference organizer and speaker. This is best done before the conference has started. A July Nature editorial argues that an opt-out policy, where everything can be blogged about unless the speaker or poster presenter specifically says so, is a reasonable alternative.

The organizers of the Annual Meeting of the German Genetics Society that took place two weeks ago in Cologne did this right. Not only did they invite Alex Knoll to become the official conference blogger, but they also put up a prominent link to his blog posts on the conference homepage, and they asked every speaker before the conference whether Alex would be allowed to blog about their talks. Because his blog on scienceblogs.de (Alles was lebt) is in German, he decided to put up his blog posts here. I’ve asked him a few questions about this experience.

1. Did you have fun being the official blogger for the German Genetics Society Meeting?
This conference blogging job was a first for me in many ways. I usually blog in German, so I wasn’t sure if I would be able to bring more than my dry, scientific English. I also knew beforehand that there would be no theme, that the meeting was a general one. I would have at least to give the impression of having understood the basics of the talks. There would be no flitting about from talk to talk, I wanted to get whole sessions without interruption.

But on the other hand, I also got to know lots of people, many more than I would have as a lowly PhD student. I attended a conference I almost certainly would not have without the invitation to come and blog.

And, as any other (science)blogger will tell you, blogging is a labour of love (don’t stab me in the back now!). So yes, I had a great time!

2. Blogging about the conference must have been a lot of work!
About as much as I expected. I was frantically typing away at my little netbook keyboard during the talks to take notes, and used any spare time to put together the posts. So I did not have as easy a time as regular conference attendees. No problem, I came to do a job!

3. Did you meet any other science bloggers at the conference?
As far as I’m aware, I was the only blogger attending, and also the only one tweeting from the sessions (no worries, no unpublished data got out that route).

4. What was the feedback from the speakers? What was your experience getting permissions from speakers to blog about their sessions?
I got the whole range. From the really open “Go ahead! Write what you want, put it online. I’ll talk about some unpublished stuff as well, but I don’t mind” to some who are not interested in getting their work out into a blog at all. Great news for the conference blogging crowd: the balance was tipped more to the pro side! Most of the speakers came out somewhere in between those two sides, probably being a bit cautious about that whole strange blogging stuff. But I got mostly positive feedback from them, and I believe the next blogger will have an easier time when blogging about their talks!

5. What tips would you give a conference organizer who wants to promote blogging?
They should make clear from the start if blogging about the talks is generally OK. That doesn’t mean all of the speakers have to allow blogging about their talk, but an official position will help everyone involved. You also don’t need to have an official blogger, but especially at smaller meetings asking someone to blog beforehand is probably the only chance to get a blogger there at all.

I also have advice for speakers: Start your talk by telling your audience if blogging about it is OK! If a part of your talk is unpublished, tell them that as well. Or put an icon on your slides to indicate which is good to blog about, for example as Daniel MacArthur from the Genetic Future blog has proposed. If bloggers know beforehand if and what part of the talk is good to go, they will be more willing to take notes in earnest!

Now that my guest posting here at Martin’s blog comes to an end, I would like to leave you with one of the last impressions, a rather lucky shot of Cologne Cathedral I took while leaving. Many thanks to Martin for hosting this conference blog!

The final guest post by Alex Knoll reporting from the German Genetics Society Meeting in Cologne.

Session V
Friday ended with two talks in session V, the first by Tony Hyman from the Max Planck Institute for Cell Biology and Genetics in Dresden. He looked at the ways that cells structure and organize their cytoplasm by comparison with non-biological systems.
Next up was a talk on the innate immune response against the influenza virus by University of Freiburg’s Otto Haller. When viruses infect mammalian hosts, a battle between interferons and virulence factors starts to rage. The interferon-induced GTPase Mx1 is an important resistance factor against influenza A viruses in mice. Most lab mouse strains are natural knockouts for Mx1, so they needed to create congenic, wild-type Mx1-expressing mice to research its function. Interestingly, Mx1 expression protects mice against the usually lethal 1918 Spanish flu influenza A, even at high doses. Mx proteins are highly conserved in mammalian species and belong to the dynamin superfamily of large GTPases. Otto Haller presented new and unpublished data (obtained in collaboration with Oliver Daumke´s group at the Berlin Max Delbrück Center for Molecular Medicine) on the role of the structure of the human MxA GTPase in repressing the virus.

Session VII
The final session of the meeting started with a talk by Andrew McMahon from the Harvard Stem Cell Institute in Cambridge, US, that I sadly missed. But one missed talk during the whole meeting is not that bad now, don’t you think?
Ueli Grossniklaus then talked about epigenetics in the struggle between the two parental genomes of an Arabidopsis embryo. At the University of Zürich in Switzerland, his group is looking at the timing of expression of paternal alleles and their phenotypic consequences, all controlled by the maternal genome.

The last talk was given by Bruce Beutler from the Scripps Research Institute in La Jolla, US. He is looking into the ways in which the mammalian immune system is able to recognize microbes as foreign, and then mount an adequate response. A first answer was found when the receptor for LPS, a component of all Gram-negative microbes, was identified by positional cloning as Tlr4, a Toll-like receptor. You perhaps know Toll as a developmental gene in the Drosophila embryo, but in adult flies, it is required for the immune response to fungal and bacterial infections. So perhaps other Toll-like receptors also recognize other microbial ligands? Yes, and Bruce Beutler’s group has been looking into the signalling pathways that lead from recognition by a Toll-like receptor to the induction of cellular responses. He and his group have used a forward genetic screen of randomly mutagenized mice. To date, they have generated over 100,000 mutant lines, and identified 32 mutations affecting Toll-like receptor signalling. This allowed them to deduce biochemical pathways that mediate much of the innate immune response. A similar feat was done with the genes involved in the resistance against mouse cytomegalovirus, with susceptibility mutations found in sensing and signalling pathways, but also in homeostasis and in development.

Another guest post by Alex Knoll reporting from the German Genetics Society Meeting in Cologne.

Saturday had two more sessions before the end of the meeting. Irina Stancheva from the Wellcome Trust Centre for Cell Biology at the University of Edinburgh started us into the day with a talk on epigenetics in mouse development.

One form of epigenetic silencing is methylation of cytosine bases in DNA. This is done by DNA methyltransferases like Dnmt1 for maintenance methylation, or Dnmt3a and Dnmt3b for de novo methylation, at CpG sequences enriched at promoters. During mouse embryonic development, DNA methylation is essential, for a loss of either of the DNA methyltransferases is embryonically lethal. Methylation and demethylation during development is surprisingly dynamic, with loss and new gain, and differences between the embryo and the trophectoderm. Besides the Dnmts, there are further proteins involved in the regulation of methylation levels. One interesting protein here is Lsh, a chromatin remodelling ATPase belonging to the SNF2 family. It seems to have a low ATPase activity in vitro, but it cooperates with several known factors like the DNA methyltransferases and Histone deacetylases. With mouse promoter microarrays, Irina Stancheva’s group compared wildtype and Lsh knockout cells, and found a reduction in promoter methylation when Lsh is missing. The patterns of DNA methylation observed in Lsh null cells suggest that this protein has a role in developmentally-programmed methylation events in the early mouse embryo.

Dominique Soldati-Favre from the University of Geneva in Switzerland gave an interesting talk about her work on apicomplexan parasites. This phylum includes important human and animal pathogens such as Toxoplasma gondii and Plasmodium falciparum causing toxoplasmosis and malaria respectively. They belong to the clade of Chromalveolates, whose ancestor acquired a plastid organelle by the secondary endosymbiosis of an alga. While some members of this clade are free living organisms or predators the Apicomplexa have evolved as obligate intracellular parasites. These parasites have developed an elaborated strategy to actively penetrate the host cells by a mechanism distinct from phagocytosis and involving gliding motility. This active mode of entry is favorable to the parasites, because this way they can evade the host cell defense mechanisms. To identify and study the molecular components of the vital process leading to host invasion, the Soldati’s group has developed genetic tools beginning from reliable DNA transfection up to the establishment of an inducible expression system for the malaria parasites based on transcription machinery elements similar to those found in plants. Studies performed on T. gondii have established that the mechanism of host cell entry is the result of a concerted action of adhesins involved in the attachment of the parasite to the host cell, the actin cytoskeleton and myosin motors that relocalize these adhesins from anterior to posterior pole of the parasite, and proteases that finally release these adhesins from the parasite surface.

Another guest post by Alex Knoll reporting from the German Genetics Society Meeting in Cologne.

As promised, I attended the second Plant Genetics session of the meeting, thus missing the Epigenetics session.

I learned an important lesson at the first talk by Juliette de Meaux from the Max Planck Institute for Plant Breeding Research: Bring sweets for the audience, and you have everyone on your side! Her research is on the molecular basis of variation in the life cycle of the model plant species Arabidopsis thaliana. Natural Arabidopsis strains grow in very different climates, and therefore have to adapt their annual life cycle to the environmental conditions: germinating their seeds early or late, flowering quickly after germinating or growing vegetatively for months. The ability not to germinate although there are good conditions is called seed dormancy. This can be a very important trait, for example if the Arabidopsis strain grows at a location where a short favorable period is followed by a recurring period detrimental to the growth of the plant. Then the plants which did not germinate even during the short favorable period have an advantage. But such changes in seed germination time need the whole life cycle to be fine-tuned: For the seeds of the following season to be ready before winter, the growth rate has to faster, or the flowering time shorter.
Because of the varying locations where Arabidopsis grows, there should be variation in life history strategies to be found for selection to act upon. For the model system of germination rate, Juliette de Meaux’ lab found a high variations in 180 natural genotypes they looked at. Some strains germinated at the day of harvest, while others didn’t germinate at all even 250 days after harvest, and most somewhere in between. If seeds were exposed to a cold treatment 250 days after harvest (to simulate winter), the strains that didn’t germinate after the 250 days suddenly started to germinate, while others decreased in their germination rate at longer times of cold exposure. Such and other measurements allowed for the analysis of a very complex dataset to derive the different strategies of life history in Arabidopsis. For example, there is a correlation of growth rate and flowering time to be found, but only in strains growing to the north (of Europe), not in the southern strains. They also looked at the molecular basis of this life history variation, and the consequences of it, which were interesting parts of the talk in and of themselves.

The second talk was by Rüdiger Simon from the Institute of Genetics at the University of Düsseldorf. Plants also possess stem cells, and they are located in niches (in plants called meristems) at the tips of the shoot and the root. For the shoot apical meristem (SAM), it is already known that it is composed of the stem cells and an organizing center underneath. The stem cell proliferation is regulated by a negative feedback loop: Cells in the organizing center express Wuschel, which promotes stem cell fate, but stem cells express Clavata3, that represses Wuschel via the receptors Clavata1 and Clavata2. Apart from that, there is a second negative feedback mechanism of regulating Wuschel activity known. But according to computer simulations by Rüdiger Simon and his colleagues, there are further factors needed to explain the observed distributions of cells and gene expression. They looked for such factors, and found the coryne mutant, which resembles known clavata mutants; it must be in the same pathway.
Rüdiger Simon’s lab also looked at the root tip stem cell niche, if it is perhaps also regulated by a Clavata-like pathway. Interestingly, they were able to find a Clavata3-related peptide in Cle40, that regulates the
Wuschel homolog WOX5. While this is similar to the situation in the SAM, there are also differences: WOX5 is produced in the QC, which resembles the organizing centre that expresses Wuschel , but Cle40 is not produced by the stem cells, but by already differentiated cells derived from those stem cells.

Next, Bhupendra Chaudary from Gautam Buddha University in Greater Noida, India, gave a short presentation on the fate of duplicated genes in polyploid cotton. After a genome duplication event, the evolutionary constraints on duplicated genes are relaxed, and one way change is possible is by generating differences in expression, allowing for subfunctionalization or neofunctionalization. They looked at expression differences in homoeologous genes (pairs of genes duplicated by a polyploidization event) in species of the cotton Gossypium, where parental diploid genomes as well as allopolyploids can be found. Interestingly, none of the parental genomes showed a dominant expression in the hybrids globally, but some tissue-specific transcriptional subfunctionalization.

The last talk of the session was given by Frank Kempken from the University of Kiel on mitochondrial mRNA editing in plants. Mitochondria possess their own rudimentary transcription and translation machinery, and in between they change the mRNAs in a way the nucleus doesn’t: they edit the mRNA sequence, usually by exchanging a C for an U to create novel stop codons, or to modify the amino acid sequence. How this is done is largely unknown.
Frank Kempken’s lab developed a system to work with isolated mitochondria, because genetic engineering of them in plants is not possible, and in vitro approaches have serious drawbacks. In their ‘in organello’ system, they can electroporate the isolated mitochondria in buffer, and observe the editing done to the expressed mRNAs. This allowed them to observe correct recognition of editing sites of Arabidopsis mRNAs in the mitochondria of maize, for example, or that mRNAs from chloroplasts are not edited in mitochondria. This would at least partially be expected, but somehow the plastid transcripts are not recognized by the editing machinery in the mitochondria.
Using a novel binding assay (which requires 10 liters of Arabidopsis cell culture per experiment, whew!) they were able to find proteins that bind to mRNAs at editing sites. A knockout mutant of one of them leads to growth retardation and smaller plants, exactly what one would expect when mitochondria don’t function properly anymore.