Archive for: December, 2013

Solar powered sea slugs: Is it all in the plastid?

Dec 19 2013 Published by under [Biology&Environment]

ResearchBlogging.org

Anyone who has followed this blog over the years knows that I have a bit of a thing for photosynthetic sea slugs. It's a complex story that has been worked on by several labs over a few years, and it is still not clear exactly what is going on. In short, there is a group of sea slugs that have the ability to feed on algae, and rather than digest their plastids (chloroplasts), the slugs store them in a reticulated intestine. Once full, the slugs stop feeding and apparently use the photosynthate produced by the plastids for several months. The catch, and why this is so interesting, is that plastids require proteins that are incoded in the nucleus of the alga. The sea slug digests the nucleus. So how does it work?

In 2008 evidence was published suggesting the slug had acquired nuclear genes from the alga. In 2010 I blogged about a study that countered this claim. In 2011 the story took a twist and it looked like the gene transfer story was an artefact. In 2012 the pendulum swung back and more data came out suggesting that ~60 algal genes reside in the sea slug nucleus.

What to make of all this? de Vries et al. have a different take and the secret may have been in the plastid all along.

The biggest hurdle that orphaned plastids have to deal with is degradation of the D1 protein of photosystem II. Most plastids we are familiar with require proteins that are encoded in the nucleus to be shuttled to the plastid in order to maintain the D1 protein. The plastids sequestered by sea slugs are divorced from their nucleus and the proteins it encodes. Therefore, they either have to be self-reliant to repair their photosystems or must rely on the host sea slug.

de Vries et al. suggest that the robust gene complement of plastids taken up by the sea slugs is directly responsible for their retention. Specifically, they site ftsH as instrumental in repairing the D1 protein of PSII. In many photosynthetic organisms, this protein is nuclear-encoded, but it remains in the plastids of the sea slugs' preference. In the absence of a nuclear contribution from the sea slug, the plastid may be able to repair itself for the lifespan of captivity in the slug.

Certainly this story is not over. This most recent paper even cites an "in press" manuscript that appears to demonstrate that the plastids are maintained in the slug for months in the dark, raising additional questions about how the slugs are utilizing the plastids. There have also been complications in the story based on different labs using different species of slugs (and their preferred algal food source) to ask the same questions. However, as this story continues to evolve the complex association between the slugs and the plastids they steal is slowly coming into focus.

References

Rumpho ME, Worful JM, Lee J, Kannan K, Tyler MS, Bhattacharya D, Moustafa A, & Manhart JR (2008). Horizontal gene transfer of the algal nuclear gene psbO to the photosynthetic sea slug Elysia chlorotica. Proceedings of the National Academy of Sciences of the United States of America, 105 (46), 17867-71 PMID: 19004808

Wagele, H., Deusch, O., Handeler, K., Martin, R., Schmitt, V., Christa, G., Pinzger, B., Gould, S., Dagan, T., Klussmann-Kolb, A., & Martin, W. (2010). Transcriptomic evidence that longevity of acquired plastids in the photosynthetic slugs Elysia timida and Plakobrachus ocellatus does not entail lateral transfer of algal nuclear genes Molecular Biology and Evolution DOI: 10.1093/molbev/msq239

Pelletreau KN, Bhattacharya D, Price DC, Worful JM, Moustafa A, & Rumpho ME (2011). Sea slug kleptoplasty and plastid maintenance in a metazoan. Plant physiology, 155 (4), 1561-5 PMID: 21346171

Rumpho ME, Pelletreau KN, Moustafa A, & Bhattacharya D (2011). The making of a photosynthetic animal. The Journal of experimental biology, 214 (Pt 2), 303-11 PMID: 21177950

Pierce, S., Fang, X., Schwartz, J., Jiang, X., Zhao, W., Curtis, N., Kocot, K., Yang, B., & Wang, J. (2012). Transcriptomic evidence for the expression of horizontally transferred algal nuclear genes in the photosynthetic sea slug, Elysia chlorotica. Molecular Biology and Evolution DOI: 10.1093/molbev/msr316

de Vries J, Habicht J, Woehle C, Changjie H, Christa G, Wägele H, Nickelsen J, Martin WF, & Gould SB (2013). Is ftsH the key to plastid longevity in sacoglossan slugs? Genome biology and evolution PMID: 24336424

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Fascinating PhD experiment starts at JHU

Dec 11 2013 Published by under [Education&Careers]

On of the favorite hobby horses of Drugmonkey's is the Too Many Mouths at The Trough hypothesis. The tl/dr version goes something like this: Federal science budgets are flat-lined or dropping. The effect of this budget regression is compounded by the fact that a somewhat recent Time of Plenty injected a LOT of PhD scientists in the research track. Combined, the reality is that funding lines are in the single digits and are unlikely to recover any time soon. What's the solution? Reduce the number of PhDs entering the system.

But how?

NIH is unwilling to make changes to training mechanisms and seems rather unwilling to even acknowledge there is a problem at all. Okay, then how do we reduce the number of PhDs granted? It'll have to come from the institutions, right? It would appear that Johns Hopkins is starting the ball rolling to do just that.

The new strategic plan recently announced publicly aims to reduce PhD admissions by 25%, pay existing and incoming graduate students better, focus on hiring younger faculty, increasing faculty teaching and hire additional per course people.

Now, I can see the objection to the increase in adjuncts/per course personnel. Most universities poorly compensate these people and provide them no job stability at all*. However, the rest of the plan** seems pretty reasonable if you are facing the realities of running a college dependent on federal funding of research.

If anyone should see this as a good thing, it would probably be grad students. Better pay and the potential of better prospects after graduation. If you read the article linked above, however, you'll note that they are the ones that appear most outraged. In fact, it was pretty interesting to interact with a few on twitter. While there seems to be some recognition that overall PhD numbers should decline, there are issues with the plan at JHU:

And, of course, the faculty are pissed too:

I mean, dude, that's a LOT of free labor that is not going to be there in a few years. Indeed, I'm sure faculty see this as a raw deal. PhD programs should be cutting back at other schools!

And here's the rub: Who is everyone? Who's interest need to be taken into account here? In the short term I get the objection by the faculty. I don't really get the grad student objection, but imma gonna chalk that up to echo chamber and lack of realistic long-view. Maybe someone can clue me in as to how this is a problem for the grad students. But the real kicker is that the crux of this strategy is in the propagation. Will other schools follow the lead? If the answer is yes, then this is the first domino to fall in making science funding sustainable in this country. If the answer is no, then we have a real Tragedy of the Commons here.

Any way it plays out, I think it's going to be fascinating theater that may well have massive effects on science funding for the next generation.

*The Affordable Care Act is, however, mandating health insurance for per course instructors, so it'll be interesting to see what that does to hiring strategies. It may actually start to become more cost effective for university to hire full time lecturers, thus changing the landscape.

**As reported, I have no special knowledge of the machinations here.

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Tuesday Tunes

Dec 10 2013 Published by under [Et Al]

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Repost: Dealing with proposal rejection

Dec 06 2013 Published by under [Education&Careers]

I posted this back in 2011, but it seems apt right now. A lot of people are hearing back about their proposals and I'm already hearing "Those stupid reviewers!" echoing down the halls. Always remember that the onus is on YOU to make sure your proposal is crystal clear.

NSF BIO panels are meeting right now, or have met in the last couple of weeks, depending on your panel of choice. That means funding decisions are working their way through the system and notifications will be forthcoming in the next few weeks. Unfortunately, ~90% of are going to be disappointed in the results. Also unfortunately, I have a LOT of experience being in that 90%.

While I have no problem providing advice for proposal writers based on my experience from both being on an NSF panel and through making (and theoretically, learning from) many mistakes along my path of grant writing, one of the biggest things I have learned is how to deal with proposal reviews for an unsuccessful proposal.

The first thing I do with my reviews is print them out and read them over fully. I've talked before about the NSF rankings and what they mean. I get the whole "these reviewers don't know their ass from their elbow" thing out of my system and put the reviews away for a couple of days. Then I'll go back to them and read them again, while making a list of things I need to address and things I got right. What did the panel focus on? What were common flaws perceived by more than one reviewers? How can I fix those? Will it require data or a change in the focus of the question being asked? What proposal flaws did they not come out and say, but are between the lines? What are the strengths to build on? What did reviewers not understand?

Once I have a good list, I use that instead of the reviews as a guide. For one, it separates any emotional reaction to the reviews from the revision process, but it also gives me a handy check list and reminder of what I need to address and clarify. After that, I'll set up a phone appointment with the PO. This is critical for getting a better feel for how the panel conversation went and why certain points became focal issues. It is also essential for advocating for the changes you plan to make and getting a read on whether the PO thinks those will adequately deal with the concerns. Take notes.

I can't stress enough how important it is to bounce ideas off the PO. More than once I thought I had a new strategy figured out only to have the PO say "but that's not going to address XXX". Whereas I was initially frustrated by some discussions I had with POs because it felt very one-sided, I was ignoring the subtly of the language they have to use. Talk about your revision ideas but even though you'll be doing most of the talking, you have to listen carefully to the reaction. Remember that they know exactly what people did and did not like about your proposal and that information may not appear in your panel summary, depending on how it was written.

Funding rates are not good right now, so it's important to make every application count. Remember that if there were parts of your proposal that the reviewers didn't "get" then you need to clarify the language there and make sure it is obvious what you want the reviewers to take away. It is YOUR JOB to make sure even the most distracted reviewer walks away from your proposal convinced it can work, because you have everything to lose if they don't. Your PO can help you figure out the direction to take your research questions, but you need to package it up all purty like.

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