So you want to work in Nature or other NPG journal...

As some of you may know, I have a deep interest in science publishing and a few days ago, I posted this question over at the "Ask the Nature Editor" forum.

I was wondering which of these two hypothetical scientists would have a better chance of entering the editorial team either at Nature or some of the other NPG journals.

a) Scientist with a recently awarded PhD degree. Published 2-4 papers during his/her formation. Works as an editor in a journal of a competing publisher for 1-2 years after obtaining his/her degree (the journal is one of his/her area of expertise). Applies for a job at NPG.

b) Scientist with a recently awarded PhD degree. Published 2-4 papers during his/her formation. Works as a postdoc for 1-2 years, publishing 1-2 more papers.
Applies for a job at NPG.

Both scientists are non-native English speakers.

What do you think? Who would have a better chance? Please post your thoughts!

You can then check Maxine Clarke's response here.

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Rules for presenting at Experimental Biology

Stop whatever you are doing! Yes, stop!... and go over to Professor in Training and read her hilarious post: Rules for presenting at Experimental Biology.

I especially liked the first one, because it's something that I generally have to remind my colleagues about:

1. Do not use comic sans on your slides. It sucks. And it makes you look stupid.

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(Image credit)

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Seminar bingo: Systems and Synthetic Biology edition

Remember PhD Comics' Seminar bingo? Every time you hear something at a lecture that is listed on your bingo sheet, you should cross it out and the first one to complete a straight line must yell out BINGO to win! (Not really ;-) Nobody will appreciate the interruption and you will be forever regarded as a mental patient)

OK, here's the Systems and Synthetic Biology edition, by Patrick Boyle:

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[H/T: Christina Agapakis at Oscillator]

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It's our time - American Association for Cancer Research

Here's an intriguing and "fact-filled video about the accomplishments and possibilities of cancer research, conceptualized by AACR President Tyler Jacks, Ph.D., and AACR Annual Meeting Program Chair Frank McCormick, Ph.D."

This comes from the AACR (American Association for Cancer Research) Youtube Channel.

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After a long day...

After a long day, which included Neurospora crassa RNA extraction and cDNA generation (from several samples), picking transformants into slants (way too many...), Neurospora transformation (again, several samples), reading papers, mentoring undergrad and a lot more (I had lunch about 3 hrs later than usual), there is nothing better than relaxing in a nearby bar with friends...

I think I'll start things off with a nice piscola

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(Top image credit)

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Thank you PLoS!

After a long wait, it finally arrived!! Here's a pic of me wearing my birthday present in the lab, courtesy of the Public Library of Science, taken last Friday.

I want to thank Liz Allen and Jessica Ashdown at PLoS for this kind gift. I will wear it proudly :-)

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Lab retreats: yay or nay?

Lately, I've been hearing a lot about lab retreats, mostly from labs abroad and I've been wondering why we don't have them here in Chile (or at least, it's not an activity that most labs here integrate into their yearly plans).

Is it because some PIs think it's a waste of "bench" time, or maybe because they think that lab meetings are enough to discuss the research of the different lab members, or maybe something else?

So, the following question is directed to fellow scientists working in labs that do have lab retreats. Why does your lab have lab retreats? In your opinion, what do lab retreats contribute to the advancement of the lab that weekly lab meetings can't? Do you like having them? Do you feel that every lab should have them? On the other hand, have you ever felt like the time spent in the retreat could be better spent in the lab? What about having them every other year, rather than every year, would this be better?

And to those who work in labs that don't have them, would you like to have them, or are you better off like this?

Please note that I'm all for lab retreats and I actually want to make them part of my lab's activities: I feel it's a good time to discuss new strategies, new directions and new techniques.
Anyway, I felt it was important to get input from people that have actually experienced lab retreats on a yearly basis.

Feel free to comment!

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(Image credit: both images are from lab retreats at Eric D. Brown's lab, which has a great website, by the way)

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Talking about a great work space....

Now THIS is the proper size for a desk in the lab (and the proper lighting as well)...

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(Image credit: the Nedivi Lab)

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Good luck, Roberto!

My dear friend and colleague, Roberto Munita (standing, blue t-shirt) left yesterday for a 3-month stay at John Mattick's Lab in the Institute for Molecular Bioscience, University of Queensland, Australia. The research at John's Lab is centered around the regulatory role of RNA.

We wish you success in this fascinating adventure! Keep us posted!

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About the picture: This was taken at a field trip during the Gene Expression and RNA Processing meeting, in Bariloche, Argentina, 2007. On the left, Francisco Barriga. The girls belong to different Argentinean labs.

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Rant!

Next, me ranting:

If the email address the corresponding author provides for a publication is no longer valid after ONLY two years, then he/she should be arrested and beat senseless. Even more so, when he/she doesn't even have a personal website.

Thank you.

-AMM

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(Image credit)

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Matryoshka dolls in biology, the connection between flowers, stem cells and fat and more, in my Picks of the Week from RB

Another week has gone by and some very interesting molbio blog posts have been aggregated to Researchblogging.org. Every week [see my opening post on the matter], I'll select some blog posts I consider particularly interesting in the field of molecular biology [see here to get a sense of the criteria that will be used], briefly describe them and list them here for you to check out.

Note that I'm only taking into consideration the molbio-related blog posts aggregated under "Biology". This issue includes articles from the last two weeks, as last week no Picks were posted.

Congratulations to everyone who got their post selected.

A recent paper from The Wellcome Trust Case Control Consortium, aiming to evaluate the role of copy number variants in genetic susceptibility to common diseases, concluded that common CNVs are “unlikely to contribute greatly to the genetic basis of common human diseases”.

Daniel MacArthur at Genetic Future finds this far from surprising and instead asks:

(…) why don't common CNVs play a major role in complex disease susceptibility?

Animals are generally home to a huge number of microorganisms and some of them establish beneficial symbiotic relationships with their hosts. Lucas Brouwers at Thoughtomics brings us a fascinating Matryoshka-like story of organisms and endosymbionts, discussing first a protist that inhabits the gut of some termites and later an endosymbiont called Blochmannia, which resides in the carpenter ant.

Organisms and their endosymbionts (Image credit)

All cells (including free-living organisms), can modulate their gene expression profiles in response to changes in their surroundings. In bacteria, extracellular signals are transduced into the cell predominantly by two-component systems, but “bacteria also contain multi-component systems, for both inter- and intra-cellular signaling” (See Bacterial signaling and studying diseases through exome sequencing, in my picks of the week from RB). Interestingly, “although Two-Component Systems (TCS) are found in all three superkingdoms of life (Archaea, Bacteria and Eukaryotes), they are suspiciously absent from the animal kingdom”.

LabRat tries to answer “why don't animals use TCSs?”


Ian York at Mystery Rays from Outer Space, comments on a recent paper reporting something that can easily be used in a House M.D. episode in the near future.

Mitochondria are derived from bacteria and “so might bear bacterial molecular motifs”. This Nature article shows, in Ian’s words, that “mitochondrial components, released from cells after damage, trigger innate immune responses through pathways that are more traditionally associated with pathogen-specific patterns” (my emphasis).
So, after cell disruption by trauma, these components can signal through innate immune pathways and create a sepsis-like state, but without infection!


“Flowers make fat and stars make bone”. This seemingly senseless phrase can be derived from a fascinating paper discussed by Rob Mitchum at Science Life, in which the authors set out to investigate if (and how) geometric shape cues can play a role in promoting the differentiation of mesenchymal stem cells to distinct lineages.

Geometric cues appear to have an important role in differentiation (Image credit)

Finally, in the last issue of Picks of the Week, I introduced a new category for my selections entitled “Honorable mention” (See "Dominant transposases, becoming famous for your lab mistakes and more, in my Picks of the Week from RB" for more details).

This week’s honorable mention goes to Merry Youle’s post on Small Things Considered, describing “holins”, small, phage-encoded integral membrane proteins that control the length of the infection cycle of some phages, by inducing the formation of holes in the bacterium's inner membrane after a determined period of time.

That's it for this week. Stay tuned for more MolBio Research Highlights!

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Some of the articles discussed in this week's selected posts:

Craddock, N., Hurles, M., Cardin, N., Pearson, R., Plagnol, V., Robson, S., Vukcevic, D., Barnes, C., Conrad, D., Giannoulatou, E., Holmes, C., Marchini, J., Stirrups, K., Tobin, M., Wain, L., Yau, C., Aerts, J., Ahmad, T., Daniel Andrews, T., Arbury, H., Attwood, A., Auton, A., Ball, S., Balmforth, A., Barrett, J., Barroso, I., Barton, A., Bennett, A., Bhaskar, S., Blaszczyk, K., Bowes, J., Brand, O., Braund, P., Bredin, F., Breen, G., Brown, M., Bruce, I., Bull, J., Burren, O., Burton, J., Byrnes, J., Caesar, S., Clee, C., Coffey, A., Connell, J., Cooper, J., Dominiczak, A., Downes, K., Drummond, H., Dudakia, D., Dunham, A., Ebbs, B., Eccles, D., Edkins, S., Edwards, C., Elliot, A., Emery, P., Evans, D., Evans, G., Eyre, S., Farmer, A., Nicol Ferrier, I., Feuk, L., Fitzgerald, T., Flynn, E., Forbes, A., Forty, L., Franklyn, J., Freathy, R., Gibbs, P., Gilbert, P., Gokumen, O., Gordon-Smith, K., Gray, E., Green, E., Groves, C., Grozeva, D., Gwilliam, R., Hall, A., Hammond, N., Hardy, M., Harrison, P., Hassanali, N., Hebaishi, H., Hines, S., Hinks, A., Hitman, G., Hocking, L., Howard, E., Howard, P., Howson, J., Hughes, D., Hunt, S., Isaacs, J., Jain, M., Jewell, D., Johnson, T., Jolley, J., Jones, I., Jones, L., Kirov, G., Langford, C., Lango-Allen, H., Mark Lathrop, G., Lee, J., Lee, K., Lees, C., Lewis, K., Lindgren, C., Maisuria-Armer, M., Maller, J., Mansfield, J., Martin, P., Massey, D., McArdle, W., McGuffin, P., McLay, K., Mentzer, A., Mimmack, M., Morgan, A., Morris, A., Mowat, C., Myers, S., Newman, W., Nimmo, E., O’Donovan, M., Onipinla, A., Onyiah, I., Ovington, N., Owen, M., Palin, K., Parnell, K., Pernet, D., Perry, J., Phillips, A., Pinto, D., Prescott, N., Prokopenko, I., Quail, M., Rafelt, S., Rayner, N., Redon, R., Reid, D., Renwick, A., Ring, S., Robertson, N., Russell, E., St Clair, D., Sambrook, J., Sanderson, J., Schuilenburg, H., Scott, C., Scott, R., Seal, S., Shaw-Hawkins, S., Shields, B., Simmonds, M., Smyth, D., Somaskantharajah, E., Spanova, K., Steer, S., Stephens, J., Stevens, H., Stone, M., Su, Z., Symmons, D., Thompson, J., Thomson, W., Travers, M., Turnbull, C., Valsesia, A., Walker, M., Walker, N., Wallace, C., Warren-Perry, M., Watkins, N., Webster, J., Weedon, M., Wilson, A., Woodburn, M., Wordsworth, B., Young, A., Zeggini, E., Carter, N., Frayling, T., Lee, C., McVean, G., Munroe, P., Palotie, A., Sawcer, S., Scherer, S., Strachan, D., Tyler-Smith, C., Brown, M., Burton, P., Caulfield, M., Compston, A., Farrall, M., Gough, S., Hall, A., Hattersley, A., Hill, A., Mathew, C., Pembrey, M., Satsangi, J., Stratton, M., Worthington, J., Deloukas, P., Duncanson, A., Kwiatkowski, D., McCarthy, M., Ouwehand, W., Parkes, M., Rahman, N., Todd, J., Samani, N., & Donnelly, P. (2010). Genome-wide association study of CNVs in 16,000 cases of eight common diseases and 3,000 shared controls Nature, 464 (7289), 713-720 DOI: 10.1038/nature08979

Cleveland, L., & Grimstone, A. (1964). The Fine Structure of the Flagellate Mixotricha paradoxa and Its Associated Micro-Organisms Proceedings of the Royal Society of London. Series B, Biological Sciences (1934-1990), 159 (977), 668-686 DOI: 10.1098/rspb.1964.0025

Koretke KK, Lupas AN, Warren PV, Rosenberg M, & Brown JR (2000). Evolution of two-component signal transduction. Molecular biology and evolution, 17 (12), 1956-70 PMID: 11110912

Zhang, Q., Raoof, M., Chen, Y., Sumi, Y., Sursal, T., Junger, W., Brohi, K., Itagaki, K., & Hauser, C. (2010). Circulating mitochondrial DAMPs cause inflammatory responses to injury Nature, 464 (7285), 104-107 DOI: 10.1038/nature08780

Kilian, K., Bugarija, B., Lahn, B., & Mrksich, M. (2010). Geometric cues for directing the differentiation of mesenchymal stem cells Proceedings of the National Academy of Sciences, 107 (11), 4872-4877 DOI: 10.1073/pnas.0903269107

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Two interesting papers on ChIP-Seq

Quick post just to direct your attention to two recent interesting papers using ChIP-Seq [See also [Techniques] Analyzing the genome-wide chromatin landscape: ChIP-Seq].

Comparing genome-wide chromatin profiles using ChIP-chip or ChIP-seq. Bioinformatics. 2010 Mar 5. [Epub ahead of print]

Annotation of gene promoters by integrative data-mining of ChIP-seq Pol-II enrichment data. BMC Bioinformatics. 2010 Jan 18;11 Suppl 1:S65.

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That struggling life in the lab...

I found this at the You'd Prefer An Argonaute blog and wanted to share it with you.

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Reposted from You'd Prefer An Argonaute:

Laboratory biological science hasn’t changed much in the last 40 years:

"What, the reader may ask, did we do in the 6 years between starting C. elegans genetics and publishing the first article on it? Since the animal has a short life cycle of 3.5 days, it should not have taken all that much time just to complement and map the mutations. Many visitors who came to the MRC Lab in Cambridge thought that we spent far too much time eating, drinking, and talking. Observing us only during normal working hours, you could see their point. If one arrived at the lab at the reasonable hour of 10 am, there was just time to open one’s mail before adjourning to the canteen for morning coffee, usually prolonged by a very interesting discussion on some aspect of science. This did not leave much time before lunch, which naturally was also accompanied by discussion that was terminated only by rushing off to attend an afternoon seminar on the Bohr effect in hemoglobin or the like. That brought one to afternoon tea and after that there was hardly enough time to start anything in the lab before adjourning to the pub for liquid and intellectual refreshment. It was only after dinner that the real work started and the lab then filled up with the owls. Even these bouts of work had to be interrupted, of course, for midnight coffee and more discussions".

Sydney Brenner, from In the Beginning Was the Worm . . .

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The Simpsons: PhDs and Grad Students

Here are the Simpsons mocking grad students and postdocs...




BTW, I make more that US 600 a year and I got rid of my pony tail BEFORE grad school, OK? :)

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