In July of 2007, we highlighted several popular nonfiction science books on our “summer reading” lists in our Editorial. Given the abundance of nonfiction books on scientific topics, many of which are written for the general public, it was not too hard to identify a short list of stellar examples of science writing. For this month’s Editorial, we sought to highlight fiction books with realistic scientists (even more specifically, biologists) as main characters in laboratory settings.

This did not turn out to be a very easy task, because few books fall under the label of “science in fiction” or “lab lit”, and stories about biologists doing believable biology research are even rarer. The list of books of this sort featured in the Editorial is not comprehensive, but it is perhaps nearly so. If you are interested in finding more books in the science-in-fiction genre, LabLit.com is an excellent resource. This online magazine is edited by Jennifer Rohn, the author of Experimental Heart (one of the books profiled in the Editorial) and a practicing cell biologist at University College London. Rohn was inspired to try to raise the profile of books in this genre after reading Cantor’s Dilemma by Carl Djerassi, when she was in graduate school. LabLit.com has become quite a popular site, and now more than 80 books are profiled on the “lab lit list”. Many of these books have been best-sellers or won awards, indicating that there is interest from the general public in stories about scientists.

Despite the more in-your-face forms of entertainment – television, movies, the internet – an old-fashioned novel is still a source of pleasure for many of us. It’s also a fantastic medium for overturning stereotypes about scientists, and for getting more people interested in science and for educating them about what scientists do. It also allows authors to draw attention to the important issues of ethics and the societal and personal impacts of scientific research. The books highlighted in the July Editorial are great examples of realistic representations of biologists in page-turning stories.

Happy summer reading!

Posted by Allison Doerr at 09:26 AM | Permalink

Some readers may recall that we ran a cover on our January 2008 issue with an error that keen readers picked up immediately. After that experience we were pretty certain that some readers would question our use of what appears to be a common house fly on our current cover, instead of Drosophila melanogaster, the topic of several papers in the issue. Our keen-eyed readers have indeed noticed the discrepancy and notified us by email or posted about it on their blog here and here.

We acknowledge that it may seem as though an impostor sits on the 'throne' where the rightful heir should reside but as with all our cover art, we make cover decisions based primarily on artistic and visual impact rather than scientific accuracy. Our cover artist does a wonderful job creating or finding candidate images and we fell in love with this image as soon as we saw it and nothing she could do with the Drosophila melanogaster images we had on hand could match the weight and presence of the image. We felt anything else would fail to do justice to the weight of the content on the other side of the cover.

One reader kindly provided a photograph of Drosophila melanogaster that he took on a white background as an example of what could be done in a short amount of time and in five minutes of fun I mocked up a cover with it so our readers unfamiliar with Drosophila melanogaster can see what all the fuss is about.

No doubt there will continue to be occasions in the future when a scientific inaccuracy on the cover gives rise to comments from our readers and we welcome their comments even if we are unable to devote more resources to trying to ensure that covers are as scientifically accurate as they are aesthetically pleasing.

Posted by Daniel Evanko at 10:54 PM | Permalink | TrackBacks (0)

Below I've posted the rankings of the six most popular papers published in our May issue based on downloads and page-views during May. The most popular paper by a rather large margin was a paper describing mRNA-Seq analysis of single cells. Regular readers of this blog won't be surprised by this given the high level of interest that next-generation sequencing papers generally receive.

A surprising omission from the list is the paper by Allan Bradley and colleagues describing the use of transposons carrying reprogramming factors to generate iPS cells followed by removal of the transposons from the genome. After analyzing the download stats it looks like the explanation for this is the fact that we express-published the paper online ahead of the other papers from the May issue so it would appear soon after a similar paper in Nature. So although initial downloads were very high, they were trailing off during May. In contrast, downloads of newer papers from the May issue were still at their peak during May.

Discerning readers will note that the last paper in the list is actually a Correspondence. Because Correspondences sometimes contain original data we will now be including these in the rankings with original research papers when appropriate.

Top 6 research papers published in the May issue
1. mRNA-Seq whole-transcriptome analysis of a single cell
2. Universal sample preparation method for proteome analysis
3. Super-resolution video microscopy of live cells by structured illumination
4. Isolation of human iPS cells using EOS lentiviral vectors to select for pluripotency
5. Single molecule–sensitive probes for imaging RNA in live cells
6. Massively parallel exon capture and library-free resequencing across 16 genomes

As in past months, there has been very little movement in the list of most popular papers published in months prior to the issue month being analyzed. The main changes this month are the appearances of two papers from the April issue and an old paper from 2007 describing new far-red fluorescent proteins Katushka and mKate. The only explanation I come come up with for this is the appearance of an article in Science from Roger Tsien that compared the performance of a new fluorescent protein they developed to mKate instead of the more recent improved variant mKate2 published in this paper in The Biochemical Journal.

Top 10 research papers published prior to the May issue
1. Mapping and quantifying mammalian transcriptomes by RNA-Seq
2. Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data
3. Stem cell transcriptome profiling via massive-scale mRNA sequencing
4. Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes
5. Photoactivatable mCherry for high-resolution two-color fluorescence microscopy
6. Stable knockdown of microRNA in vivo by lentiviral vectors
7. Bright far-red fluorescent protein for whole-body imaging
8. Global mapping of protein-DNA interactions by digital genomic footprinting
9. Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing
10. Lifeact: a versatile marker to visualize F-actin

Posted by Daniel Evanko at 02:39 PM | Permalink

Our June issue, which went live online yesterday, includes an Analysis paper describing the results of a large-scale study to try to get to the root causes of irreproducibility in mass spectrometry-based proteomics. Despite the novel and valuable biological applications made possible by proteomics and the continuing impressive technological advances in mass spectrometry, the technology has been unable to completely shed its reputation of being poorly reproducible.

To attempt to pinpoint the sources of irreproducibility, John Bergeron and colleagues, as part of a Human Proteome Organization (HUPO) effort, sent a test sample consisting of 20 purified proteins at equal concentrations to 27 different proteomics labs. The study designers asked these labs to identify the 20 proteins by whatever mass spectrometry instrumentation and workflows they were used to using. Initially, only 7 labs correctly reported all 20 proteins! However, when the study designers re-analyzed the data from the labs that failed in the task, they found that almost all actually did have mass spectra for all 20 proteins in hand. Most of the problems therefore stemmed from the database searching approaches used to go from the raw spectra to a protein identification. Many of the labs also reported ‘false positives’ – proteins that were not actually in the test samples. However, it turned out that many of these false positives were real; they were contaminants introduced during the sample handling process.

This study reaches several interesting conclusions. First of all, and reassuringly, the authors found that the mass spectrometry technology itself is reproducible. However, because of the number of complicated steps required to go from an unknown sample to a protein identification, the success of each of the groups varied widely, demonstrating the need for careful sample handling and proper training. The authors also state that improvements in database search engines and the proteomic databases themselves are direly needed.

This work also shows the value of examining the reproducibility of new technologies and methods on a large scale, especially between labs, using carefully prepared test samples. These studies can be expensive and time-consuming, but they are highly beneficial. Broad guidelines for Analysis papers are provided in our April 2008 editorial, and authors interested in submitting such studies are encouraged to contact the editors beforehand.

This Analysis will be freely available for one month. Be sure to also check out the News and Views article by Ruedi Aebersold which accompanies the paper.

Posted by Allison Doerr at 04:42 PM | Permalink

The June issue of Nature Methods goes live today, with several papers, coincidentally, reporting on methods for the study of fruit flies.

As discussed in our editorial, Michael Dickinson, Pietro Perona and colleagues use machine vision to track individual flies as they interact within a group (Branson et al); this may prove useful to study social behaviour and how it is influenced by specific genes or neural circuits. In a News and Views Michael Reiser proposes that, with approaches such as these, phenotyping methods may be catching up with the well-established molecular genetics toolkit available for the fly. But of course, improvements in genetic resources are still needed. Also in the June issue, two groups (those of Hugo Bellen and Pavel Tomancak) present libraries that cover the entire genomes of Drosophila melanogaster and Drosophila pseudoobscura: Venken et al present high-coverage BAC libraries in the P[acman] system for D. melanogaster and Ejsmont et al present fosmid libaries for D. melanogaster and D. pseudoobscura. These resources allow modification of genes by recombineering (for instance, to make mutants or to add tags for visualization) as well as integration into precise sites in the genome, and should facilitate a wide variety of studies – including behavioural analyses – that require transgenesis in the fly.

Posted by Natalie De Souza at 07:50 AM | Permalink