Monthly Archives: April 2009

Methods section remake

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Many of our readers have no doubt noticed a pronounced change in the Methods section of Nature Methods papers published online over the past several weeks. Brief Communications now have a Methods section for the first time ever and in manuscript types that already had a Methods section, the section has been expanded and moved to the end of the paper.

These changes are described in detail in an Editorial accompanying the May issue of the journal. The new design is similar to what Nature implemented in 2007 and we hope our authors and readers appreciate the greatly expanded space this provides for methodological details. We are relieved that we will no longer have to relegate important methodological details to Supplementary Information and we expect our authors will appreciate being able to include more citations in their papers.

A potential downside of this change is that the print and online versions of papers have quite different levels of methodological detail. What do you think? Those of you who are online readers may not have very strong opinions on this, but what about our print readers? If anyone who regularly receives a print copy of the journal is reading this, we would like your feedback as well.

April ’09 Conferences

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Better late than never I always say. Anyway, now that we are over two weeks into April I am finally posting the conference schedule for Nature Methods editors. Nathan (our technology feature editor) is already at AACR in Denver and Natalie (one of our Associate Editors) is on her way to the Keystone meeting in British Columbia.

American Association for Cancer Research (Denver, CO) April 18-April 22

AACR is celebrating their centennial and Nathan Blow, who edits the Technology Features, is already there. We have only published a few papers targeted directly to cancer researchers but these investigators are heavy users of general techniques and technology. There will undoubtedly be many company reps there for Nathan to talk to about their new and upcoming products.

Keystone Symposia – Stem Cell Niche Interactions (Whistler, British Columbia) April 21-26

This is the second year Natalie de Souza is attending this conference. It turned out to be productive last time and hopefully this year will be as good or better. Competition for high quality papers in the stem cell arena is tough but our recent publication of a very nice iPS cell paper by Allan Bradley was a very good development.

Keystone Symposia – The Biology of RNA Silencing (Victoria, British Columbia) April 25-30

The trips to Canada continue with Nicole Rusk going to see what is new in the area of RNA silencing. We have always had a strong interest in this area as evidenced by our Focus on RNA interference published back in 2006. Now much of the community seems to be focussing their attention on naturally occurring small RNAs.

Information on the Nature Methods editors can be found here.

Trace some neurons, get a big check

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The idea of tracing the structure of stained neurons to obtain functional insights into in situ neural networks isn’t new and dates back over 100 years to Ramón y Cajal. Just recently I discovered that copies of his books have been digitized by Google and the illustrations are incredible. See for example Studien über die Hirnrinde des Menschen.

Even though software now exists to automate this process, it seems that the performance still isn’t good enough to replace manual tracing of image stacks of labeled neurons. Neuroanatomists often spend days to months manually tracing the structures rather than rely on the software that currently exists for automating the process.

Two big players in the neuroscience field have decided to do something about this. On April 9th the Allen Institute for Brain Science and the Janelia Farm Research Campus of the Howard Hughes Medical Institute announced the DIADEM Challenge. The acronym is derived from Digital Reconstruction of Axonal and Dendritic Morphology. I wonder how long it took to come up with that one.

Over the next year groups and individuals are invited to download image stacks of real data and use their algorithms to create digital reconstructions of the neurons and submit them for evaluation. Five finalists will be invited to compete in a final round at the Janelia Farm Research Campus. The organizers will award a $75,000 cash prize to the winner whose algorithm performs the best. The results will be submitted for publication in a special issue of the journal Neuroinformatics.

The hope is that the competition will encourage the advances in automated neuronal tracing that will be required for researchers to construct a functional atlas of the brain — one of the principle goals of the research at Janelia Farm.

It is encouraging to see a competition devoted to a small community like this. Nature Methods previously argued that such competitions would be valuable for improving algorithms in such specialized applications. I’m excited to see that it is happening and wish the organizers and competitors are successful.

Top downloads for March ’09

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It’s a new month and time to see how papers published in Nature Methods have been received by our readers. I alway find it fascinating to see how the numbers of downloads compare to our opinion of each paper. I’ve listed the original research papers we published that received the most unique views (HTML) and downloads (PDF) in March in order of popularity and broken them down between papers published in the March issue and papers published in prior months.

Of course downloads for the March issue are based on nothing more than the title of the paper and maybe the editor’s extraordinarily brief summary. It isn’t until later that the number of downloads is more indicative of the quality and impact of a paper. For this reason the downloads of papers published prior to the March issue can be more interesting since they are more likely to be influenced by community discussion of which papers should be read and cited.

Top 4 research papers published in the March issue

1. High-efficiency labeling of sialylated glycoproteins on living cells

2. Quantitative interaction proteomics using mass spectrometry

3. Automated light-based mapping of motor cortex by photoactivation of channelrhodopsin-2 transgenic mice

4. Analysis of receptor oligomerization by FRAP microscopy

It is interesting to note that the two photoactivatable fluorescent protein papers from February made it into the March “Top 10” list below with the 3D STORM paper from last year. Super-resolution imaging related papers continue to be of high interest. It is clear though that next-generation sequencing papers continue to be the hottest papers in the journal and have barely budged from their standings last month.

Top 10 research papers published prior to the March issue

1. Mapping and quantifying mammalian transcriptomes by RNA-Seq

2. Photoactivatable mCherry for high-resolution two-color fluorescence microscopy

3. Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data

4. Stem cell transcriptome profiling via massive-scale mRNA sequencing

5. Stable knockdown of microRNA in vivo by lentiviral vectors

6. miRNA in situ hybridization in formaldehyde and EDC-fixed tissues

7. Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing

8. Whole-cell 3D STORM reveals interactions between cellular structures with nanometer-scale resolution

9. A bright and photostable photoconvertible fluorescent protein

10. Microfluidic control of cell pairing and fusion

Highlights of recent methods papers

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Each month, the editorial team gets together to select papers describing exciting new methods to cover in short news pieces in the Research Highlights section of the journal. We comb the recent literature in top general journals like Nature, Science and Cell, as well as top specialized journals in various subject areas, and we even take suggestions from authors! Unfortunately, we cannot cover all of the interesting methods papers we find, so each month I will highlight these papers, which didn’t quite make the cut, in Methagora.

Here are a few such papers describing intriguing methods, which were published within the last month or so. Enjoy!

Imaging intracellular viscosity of a single cell during photoinduced cell death

Nature Chemistry 1, 69 – 73 (2009)

Highly efficient neural conversion of human ES and iPS cells by dual inhibition of SMAD signaling

Nature Biotechnology 27, 275 – 280 (2009)

The Dynamic Control of Kiss-And-Run and Vesicular Reuse Probed with Single Nanoparticles

Science 323, 1448 – 1453 (2009)

Identifying the proteins to which small-molecule probes and drugs bind in cells

PNAS 106, 4617 – 4622 (2009)

Femtosecond characterization of vibrational optical activity of chiral molecules

Nature 458, 310 – 313 (2009)

A membrane interferometer

PNAS, published online March 23, 2009

Biodegradable luminescent porous silicon nanoparticles for in vivo applications

Nature Materials 8, 331 – 336 (2009)

Identification and quantitation of newly synthesized proteins in E. coli by enrichment of azido homoalanine-labeled peptides with diagonal chromatography

Mol. Cell. Proteomics, published online March 25, 2009

STED microscopy reveals crystal colour centres with nanometric resolution

Nature Photonics 3, 144 – 147 (2009)

Calling all photomicrographers

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Every year Nikon treats people to some of the most spectacular images the microscopic world has to offer when they unveal the winners of their annual Small World Photomicrography Competition. Last year Nature Methods highlighted the winning image on the cover of our November issue.

Now is the chance for all you scientist-photographers to comb through your favorite images or take spectacular new ones because yesterday Nikon announced that they are accepting submissions for this year’s contest from now until April 30th. Go to https://www.nikonsmallworld.com for more information and to see previous year’s winners.