Open Notebook Science

The end of the road

noreply@blogger.com (AJCann) — Mon, 19 Jul 2010 09:15:00 +0000

When we announced our ONS chytrid project, someone joked Every time someone starts an ONS project, an angel gets their wings. We recently decided we had to pull the wings off the angel.

The good news is that the reasons have nothing to do with the ONS philosophy behind this project. Indeed, I was constantly surprised at how receptive people seemed to be to this approach. This should be some encouragement in the dark days that lie ahead, although I expect it won't be.

There are a number of reasons we have called a halt. I always had reservations about the amount of time I would have been able to devote to the project, and I was aware that to be successful, it would need more time than I would have been able to give. In the end, it was my institutional situation which sealed its fate, with both myself and my collaborator being warned off proceeding. Looking at the current UK funding situation, this simply isn't the time to invest my career in laboratory research anyway.

It is possible that the project might resume at a lower level than we originally envisioned at some future time, but I doubt it, and even if it did, significant involvement on my part is unlikely.

A sad day.

Research Collaboration

noreply@blogger.com (AJCann) — Tue, 11 May 2010 15:32:00 +0000

In the 30 years I've been doing scientific research, I've been involved in quite a few research collaborations. Some were good, others, not so good. Along the way, I figured a few things out. A good research collaboration occurs when the parties have different skills but both have something to gain.

Yesterday, Ben and I had a longish Skype chat with Matt Fisher (perched in his Pyrenean eyrie like a Bond villain :-) We discussed our mutual interests in chytrid and Ben and I explained some of the experiments we would like to perform with Bd. I think this conversation could form the basis of a valuable collaboration, and we hope in subsequent discussions to be able to develop our ideas into a concrete resource that will advance Bd research.

In subsequent emails the conversation turned to ONS. Encouragingly, Matt was supportive of this idea, having previously had good experiences in taking transparent approach to development of the EU RACE project (Risk Assessment of Chytridiomycosis to European amphibian biodiversity), as well as the collaborative approach to the Bd-Maps project.

I'm very hopeful that a fruitful collaboration with Matt Fisher will be the first tangible benefit to come out of the ONS approach we are taking to the development of this project.

Does chytridiomycosis cause downregulation of antimicrobial peptide expression?

noreply@blogger.com (AJCann) — Thu, 29 Apr 2010 09:16:00 +0000

Yesterday I popped downstairs to Paul Kelly's seminar on antimicrobial peptides (AMPs). I was well aware that he would be discussing mammalian AMPs and that the differences between mammalian and amphibian AMPs are substantial, but by immersing myself in the topic, I hoped it might generate some ideas, which it did.

Paul spends half his time working in London and the other half working, under shocking conditions, in Lusaka, Zambia. One of the observations arising from comparing these two (human) patient cohorts is that although the incidence of diarrhoeal disease is slightly higher in the Zambian patients, AMP expression in the gut is lower. Paul was careful to stress that this observation only holds true for the gut and not for human skin or other organs, and that the difference is not due to HIV infection. This raises the issue of whether pathogens may, in some circumstances, downregulate AMP expression.

The relationship between chytridiomycosis and amphibians AMPs is complex, but clearly a critical one. I can find nothing in the literature about the possibility that Bd might downregulate AMP expression - does this information exist?

Bd-Maps

noreply@blogger.com (AJCann) — Tue, 13 Apr 2010 09:34:00 +0000

Bd-Maps is a project at Spatialepidemiology.net which shows global surveillance data for Batrachochytrium dendrobatidis viewable as an interactive web-based map using the Google Maps and Google Earth interfaces. All isolate positions within the database are highlighted and allow drilling down via the map to obtain further epidemiological data, including amphibian distribution, genotype (if known) and associated epidemiological parameters.

All about Chytrid

noreply@blogger.com (AJCann) — Thu, 25 Mar 2010 09:00:00 +0000

The chytrid fungus Batrachochytrium dendrobatidis (Bd) is an emerging pathogen of amphibians worldwide. The aquatic zoospores of this primitive fungus infect larval or adult amphibians, and, depending on the host species and other factors as yet unknown, may cause anything from 0-100% mortality. Coupled with climate change, pollution and habitat loss, chytridiomycosis (or "chytrid", pronounced "kit-rid") is a serious threat to many amphibian species. Bd research has moved from obscurity to prominence very rapidly over the past few years, and two complete genome sequences are available (JAM81, JEL423):

http://dan.corlan.net/medline-trend.html

So where do we fit in?

We are trying to leverage our existing skills in molecular biology, antibody production, protein chemistry and microbiology to study this organism. In part, this is because of an interest in the environmental impact of this emerging pathogen, but we are also interested in studying Bd as a model organism to examine aspects of fungal biology and pathogenesis. We are currently interested in developing work in the following areas:

In vitro assays for Bd infection.
Development of reagents and assays for field studies.
The attachment phase of Bd infection.
The role of antimicrobial peptides in the amphibian response to Bd infection.
MicroRNAs in Bd infection.
Use of RNAi to manipulate Bd.

We will describe here our progress with these projects as the work evolves.

References:

A.J.Cann

Department of Biology

University of Leicester.

Who are these people?

noreply@blogger.com (AJCann) — Wed, 24 Mar 2010 16:03:00 +0000

I am Alan Cann, Senior Lecturer in the Department of Biology at the University of Leicester: PubMed, CiteULike. I did a BSc in Microbiology at The University of Sheffield in 1980, and a PhD in Virology at the University of Leicester in 1984, working on the molecular basis for neurovirulence in poliovirus. After that I worked on HTLV and HIV at UCLA for four years. In 1989-90 I worked on HIV at the MRC Laboratory of Molecular Biology in Cambridge, and at the end of 1990, moved back to the University of Leicester.

Ben Maddison is the joint P.I. on this project.

Other staff involved in this project include: Claire Baker, Jonathon Owen, Shila Patel and Helen Rees, all Research Scientists in the Department of Biology at the University of Leicester.

Doing the science thing

noreply@blogger.com (AJCann) — Tue, 23 Mar 2010 09:00:00 +0000

After publicly launching this new project yesterday, I spent a lot of the rest of the day sitting at a desk filling in forms. Risk assessments, biohazards, but fortunately COSHH is mostly taken care of so far. Ah yes, this is why we chose science as a career!

I did find some time over lunch to scan my RSS subscriptions, which among other things, came up with this paper:

Victoria Stodden: Open science: policy implications for the evolving phenomenon of user-led scientific innovation. JCOM. 9 (01) (March 2010)
From contributions of astronomy data and DNA sequences to disease treatment research, scientific activity by non-scientists is a real and emergent phenomenon, and raising policy questions. This involvement in science can be understood as an issue of access to publications, code, and data that facilitates public engagement in the research process, thus appropriate policy to support the associated welfare enhancing benefits is essential. Current legal barriers to citizen participation can be alleviated by scientists’ use of the “Reproducible Research Standard,” thus making the literature, data, and code associated with scientific results accessible. The enterprise of science is undergoing deep and fundamental changes, particularly in how scientists obtain results and share their work: the promise of open research dissemination held by the Internet is gradually being fulfilled by scientists. Contributions to science from beyond the ivory tower are forcing a rethinking of traditional models of knowledge generation, evaluation, and communication. The notion of a scientific “peer” is blurred with the advent of lay contributions to science raising questions regarding the concepts of peer-review and recognition. New collaborative models are emerging around both open scientific software and the generation of scientific discoveries that bear a similarity to open innovation models in other settings. Public engagement in science can be understood as an issue of access to knowledge for public involvement in the research process, facilitated by appropriate policy to support the welfare enhancing benefits deriving from citizen-science.

I sum up Victoria's excellent survey as follows. We are entering the third age of science:

Pre-17th century: Who you know - private correspondence and libraries.
17th-20th centuries: What you know - publication in scholarly journals.
21st century: How you know - open science online.

A.J.Cann

Department of Biology

University of Leicester.

Hello World

noreply@blogger.com (AJCann) — Mon, 22 Mar 2010 09:50:00 +0000

Most of my work over the last few years has been involved with science education, and much of the online effort has gone into surfacing aspects of the scientific literature by making it accessible to a student audience, and indeed the general public, should they be interested. Mostly, this has meant developing the MicrobiologyBytes website, along with its Twitter and Facebook satellites. In my "education hat on" guise, I write frequently online about my work on Science of the Invisible, Twitter and Friendfeed. So why would I need another public outlet?

Open notebook science (ONS) is the practice of making the primary record of a research project publicly available online as it is generated. This involves placing the personal, or laboratory, notebook of the researcher(s) online along with all raw and processed data, and any associated material. The approach can be summed up by the slogan "no insider information". This is far from the norm of scientific practice, but over the last year of talking to some of the leading practitioners of ONS, notably Jean-Claude Bradley and Cameron Neylon, I have become convinced that I would like to try it. This blog is one part of our feasibility test of ONS, a space where out part-formed thoughts, ideas, planning, and general commentary on ONS stuff will appear. The other part is our open notebook on Wikispaces, where all the data will be posted. Anyone familiar with ONS will immediately recognize that this is a clone of the Jean-Claude Bradley approach. I have discussed this with Jean-Claude and it seems sensible to carry out our first faltering steps in a tested format. If you want to follow our progress, subscribe to the RSS feed for this blog, or go to this page and subscribe with the feed reader of your choice. If you prefer, you can receive updates via your email account.

Open or closed? It's not that simple. There are many flavours of ONS, and it's not clear yet which one(s) we want or are able to pursue. Indeed, our style of "open" is one of the first things we need to work out about this project. For a variety of reasons, not all of the research done in our laboratory will switch to ONS. Initially, we intend to try it out with a new project we are developing (which I'll describe in a subsequent post here). Thus our approach to ONS is itself an experiment. Only time will tell if we are able or willing to continue in this format. Apart from funding, it depends whether this idea wins hearts and minds - not only in our lab, but beyond it. In part, that depends how much interaction we receive. the project we are beginning is a new field for us, so we don't expect the world to be queuing up to help us, but to be successful, the downside risk of ONS needs to be balanced by the upside of helpful positive interactions from interested observers.

A.J.Cann

Department of Biology

University of Leicester.