Archive for: June, 2012

What's the point of grad committee meetings?

Jun 29 2012 Published by under [Education&Careers]

I don't even know how many committee meetings I have been to, either as a student or supervisor. Every place does them slightly differently and there is usually substantial freedom in the format and tone. Some include a formal presentation, written report before hand, or both. Others are a casual conversation.

As fas as I know, however, the point of having a committee meeting is mainly to get some constructive "outside" guidance on the work you are doing and have planned. Lot's of other things can come out of committee meetings, but making sure you don't have your head stuck up your advisor's ass is a key component. In most cases, a committee comes on board once you have a research plan in place and meets once or twice a year.

Based on this, I was surprised to read Algae Girl's post about her first committee meeting happening at the end of her third year. In a follow-up post she mentions she may be defending in December, indicating that her first committee meeting is happening at the 11th hour of her degree. Any input from the committee at this stage would, by necessity, be window dressing.

I have to say that I'm a little surprised a degree program would be set up that way, although it could just be how things fell for her. In my department, the committee needs to be established and a research proposal needs to be submitted to the grad school, no later than the end of year one. The committee has to sign off on the proposal and often has a meeting to discuss, including a presentation by the student. A considerable amount of feedback is given to the student at that time, which hopefully improves the overall research plan.

What do you see as the point of committee meetings, at least as they are intended (I've been to some useless ones)? How early and often are the done at your institution?

22 responses so far

Notes from the AE desk (2): How I choose reviewers

Jun 27 2012 Published by under [Education&Careers]

I've now been an associate editor for roughly 6 months and am starting to settle in. Things are good and I feel confident that the journal is making solid and progressive changes. I've learned a lot (including why I am handling 3x more manuscripts that I was told I would) and enjoyed parts of the experience.

One thing that can suck, however, is finding reviewers. People are busy, I get it. I'm familiar with the concept. Most people are over committed and the thought of adding one more straw to their camel's back is not very exciting. The journal I work with has about a 50% return rate for reviews, which isn't bad. My own personal rate is a bit better, but I do have manuscripts that I have needed to ask 6-8 reviewers just to get 2 to say yes.

Identifying reviewers is not all that different from filling a seminar series in that you need to invite enough people to fill all the slots without having to wait for everyone to respond before checking with the next person. I don't want to waste time picking reviewers because the journal is stressing turn-around. So, I often will invite 4 or 5 people right away, hoping to get three. I have never had all 5 say yes, but have gotten 4.

Usually the authors provide a few suggestions for reviewers and I will typically pick one to invite. Checking the history of these suggestions is key, however. You may or not be surprised by how many authors suggest reviewers who would fall under the COI definition of NSF. After picking a suggested reviewer, I search the journal database for key words. That means, for those of you new people wanting more reviews, get your keywords into your account at the journals you are active with. I find that those who have a history with the journal are more apt to review for it. Barring enough suitable candidates, I start searching Web of Science (more inclusive than PubMed for us non-metazoan peeps).

Of course, it's not as straight-forward as a couple of searches and emails. At some point it comes down to making judgment calls based your knowledge of the people in your field. There are people I would never send a review request to, no matter the circumstances. I am also more likely to send a request to someone I recognize as doing good work than someone I don't know. My goal is not just to get decent reviews back, but also to make my job easier when sorting through them.

Finally, there is a Naughty List kept by journals / publishers that notes all those times you were 87 days late on a review or never responded to a request. You people get flagged in the system to be avoided (which is one way to reduce your requests).

Once all that information is sorted, the emails go out and I wait to see if I need to break out the reserve list or go with the starters.

8 responses so far

Repost: Survivor gifts

Jun 27 2012 Published by under [Education&Careers]

This is a repost from a few years back, which I bring up again because I never seem to feel like I have a good answer.

In my experience, there is a sort of tradition in science that a supervisor gives a gift to a trainee leaving the lab. I think it's a nice gesture and I know I appreciated it when I left the various stops in my academic life. Of course, now being on the supervisor side of things, I've got to be the one coming up with the gift ideas.

I bring this up because I have a student graduating by the end of the summer and since my summer is a vortex of deadlines and travel it occurred to me that I should consider what I would get as a gift now rather than picking something up at the local convenience store 10 minutes before the defense. I mean, everyone likes fudgesicles, but they may not make the best going away gift.

The fall back for almost every supervisor is books. We all like books and there is an essentially endless number from which to choose, but unless you know what the person leaving is moving on to, picking the books that will be useful to them in the future is not all that easy. Plus, at the rate people move in most academic fields, you might as well be giving someone lead bricks.

Surely there are more innovative ideas out there.

29 responses so far

Grant LoRs: important or e-tree killing?

Jun 25 2012 Published by under [Education&Careers]

One thing I have noticed as a grant reviewer is the variability in letters of support included for different proposals. Personally, I rarely look at them unless a critical piece of the proposal relies on the availability of that individual. In most cases, anyone who is critical to the proposal is involved with it, but there may be aim-specific methodology that leans on the expertise of another lab.

But one often sees many other letters as well. I haven't observed a direct connection to career stage and number of letters gathered, nor between prominence of the PI and letter number. When I posed the question of letter gathering on Twitter, the response was as vague. Some claim it is best to cover all bases, whereas others weren't sure how useful the letters were.

From my perspective, I can see letters being important in 3 situations: 1) When proposing to use some new methodology, 2) Proposing to use someone else's software/database/etc. that needs to be maintained, and 3) Ass covering for aspects of the proposal you do not have data for.

Do people really get letters from those they do not plan to work directly with to let reviewers know they are some sort of player in the filed? This is where things get murky for me. I rarely, if ever, see this in NSF applications. In fact, NSF recently forced all LoRs to be a single sentence basically affirming that the letter writer was down with whatever had been said they would do in the proposal. No more. I get the impression that letters are seen very differently in the NIH world.

5 responses so far

A little pop for your day

Jun 14 2012 Published by under [Et Al]

This trends a little closer to pop than I normally go, but I like this under-produced version, compared to the studio version. Even if it means losing a little of the distinctive guitar riff. Sometimes less is more.

5 responses so far

Sea slugs stealing more than plastids

Jun 14 2012 Published by under [Biology&Environment]
I've been fascinated by the story of the Elysia sea slugs for some time and have blogged about it before. In 2010 I covered the first paper with decent molecular evidence of a gene transfer from an alga to a sea slug and a follow up study. Earlier this year a number of papers came out with some new twists and recently I saw another chapter in story by Pierce et al (2012) has made it to print.

Elysia chlorotica (source)

If this story is unfamiliar you can read all the background in the two previous posts linked above, but this system appears to be very unusual. Essentially the sea slug hijacks the plastds (chloroplasts) from an alga and keeps them functioning for nearly a year. The plastids are the only parts of the alga maintained by the slug and once they are established, the slug no longer feeds. Not a big deal except for the fact that plastids need thousands of proteins that are encoded in the algal nucleus and targeted to function in the plastid. Where do those proteins come from when the algal nucleus is gone?

For years people have believed that the answer lies in the sea slug nucleus. If genes of algal origin were currently encoded in the sea slug nuclei, then the animal might be able to keep the plastids going. One complication is the need for a protein targeting system to get the slug-manufactured proteins to the plastids that need them. In their native alga, four membranes separate the plastid lumen from the cytoplasm. It is not clear how many membranes remain around the plastids once the sea slugs have ingested them, but a 5' "targeting signal" on the unfolded peptide and a number of chaperonins are typically required for it to arrive at the intended destination. Thus, it is not as easy as just acquiring a couple of novel genes.

A simplified diagram of gene transfer and targeting back to the plastid. (source)

In order to identify algal genes in the sea slug, Pierce et al. (2012) took a circuitous route. First they sequenced the genome and transcriptome of the alga the sea slug feeds on, Vaucheria litorea. This was done to produce an as-complete-as-possible algal protein set. Next, they sequenced the transcriptome of adult sea slugs with plastids, starved for 2 months. The idea here is to ensure that no algal contamination should be present, just the hijacked plastids and whatever the sea slug is using to keep them active. At this point, it was a simple comparison: are there any algal genes in the sea slug transcriptome?

The first thing they discovered is that the plastids are transcriptionally active. Transcripts from genes encoded in the plastid were identified, indicating that the plastid is making proteins. Why is this important? Because the plastid can't make proteins without some help from the nucleus. Plastids do not encode a complete set of genes for the machinery to carry out protein synthesis.

Next, they scanned the slug for transcripts that could not be traced back to the plastid genome and found 52 hits for algal genes among the slug transcriptome. Many of these (27) represented genes with functions related to photosynthesis and carbon fixation, with the remaining having unknown function. Interestingly, all of the putatively algal transcripts found in the sea slug transcriptome were in very low copy number and most did not overlap. This is in strong contrast to typical plastid-targeted transcripts, which can be some of the most abundant in actively photosynthesizing cells.

Additionally, many of the transcripts had a small number of nucleotide changes (1-6bp), when compared to the algal copy. Is this an indication that they are indeed encoded in the sea slug genome and their sequence is drifting from that of the alga? Perhaps.

After a several paragraph bashing of papers I previously covered here the authors conclude that the sea slug Elyssia chlorotica nucleus contains at least 60 genes that have been stolen from its algal prey. It uses these genes to supply proteins to the hijacked plastid for their continued function, albeit in low transcript abundance. The sea slug genome is underway and nearly finished, so the story may reveal yet further surprises.

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

10 responses so far

There is an I in science

Jun 11 2012 Published by under [Education&Careers], Uncategorized

Science is a collaborative effort. Very rarely does a project ever get done by one person without the valuable input of others. Increasingly, funding agencies are looking to put money toward interdisciplinary research, on both large and small scales. Even universities are increasingly moving to shared space for research labs.

As a PI these waters can be a little tricky to navigate, but as a trainee they can become downright treacherous. Set aside the issues of 4 equal first authors for a second and think about the way we talk about science. At least in my field, it is extremely common for lab members to use "we" when discussing lab research. In many cases that is entirely valid - the full story is often a compilation effort. But there are exceptions.

One of the most critical time for a early-career scientist to say "I" is for job interviews. Interviewing for a postdoc, faculty or industry job? It's time to break out the I. Concerned about seeming selfish? Don't be. What is critical to get across during an interview is all the great things YOU did. Having the context of the lab's work is important, but do not leave what you did vs. what lab technician or the other postdoc did, remain ambiguous. Sell yourself for what you have contributed, while openly acknowledging the efforts of others.

This is what your interviewers want to see from you. Don't make them try and read between the lines.

3 responses so far

Repost for World Oceans Day: Solar Sea Slugs

Jun 08 2012 Published by under [Biology&Environment]

Today is World Oceans Day, so I thought I would repost the closest thing I have to a post on ocean life. This story is one that continues to get more interesting. I updated it (link below) to include some recent work last year and have been trying to find the time to write about another paper on the topic, published in 2011. Each new paper on these organisms has made the story both more interesting and more confounding, which is the kind of thing that always keeps my attention.

Original image here.

(Update here)

Sea slugs are far more interesting than their name might imply. Aside from being beautiful, they have some unusual ways of making a living. In the case of a few unrelated species, they steal for a living.

A handful of sea slugs have found away to make the most of the algae they eat. As they take in the cellular contents of the algae, they are able to separate the components and isolate the light harvesting organelles, the plastids. Whereas the majority of the chewed algal is digested, the plastids are spread throughout the specialized digestive track of the slugs so that they form a layer all over the upper part of the slug, giving it a green color. Depending on the species of slug, the animal can then rely entirely on the plastids for weeks to months as the sole source of energy, making them the solar powered slugs.

Elysia chlorotica feed on algae and then steal the plastids to harness solar energy.

But here is where the story gets interesting. It is well documented that plastids have high protein turn-over, especially in their light harvesting complexes. The constant barrage of photons breaks the antenna proteins down and they need to be constantly replaced. Those proteins, however, are not produced by genes encoded on the genome of the plastid. Instead, they are nucleus-encoded and targeted to the plastid by the cell cytosol, thanks to a signature extension on the 5' end of the transcript. Therefore, the algal nucleus is essential for the continued maintenance of functional plastids. But the slugs sequester ONLY the plastids, no nuclei. How do the slugs keep the plastids going for months in the absence of the algal nuclei and the essential plastid proteins they produce?

In 2008, it appeared that there might be an answer. Rumpho et al (2008) looked at the genome of E. chlorotica and identified genes that appeared to be derived from the algal nucleus. Gene transfer from the nucleus of an algal to that of an animal for the purpose of allowing the slug to maintain its own plastids! Needless to say, this story got a lot of press. The only issue was, there were very few genes found, and none of the major antenna proteins one would expect must be there. But it was a PCR-based survey, not a genome sequence, so people reasoned that the genes were there, just not PCR friendly for whatever reason.

Not so fast, claim Wägele et al. in an article released yesterday in Molecular Biology and Evolution. Wägele et al. sequenced cDNA from two slug species made from RNA transcripts (genes being expressed by the animal) extracted from plastid-containing slugs that were kept without a food source, and were thus entirely dependent on the plastids for carbon. Based on the findings of Rumpho et al. (2008), the expectation would be that genes encoded in the slug nucleus that had been transfered there from the alga for the purpose of plastid maintenance would be highly expressed under these conditions. Afterall, the plastids are actively photosynthesizing for the slug and have to deal with the wear and tear of the job.

But contrary to expectation, Wägele et al. found NO evidence of the antenna proteins, the Calvin cycle enzymes or the small subunit of RuBisCO (which is absent from the plastid of the algae the collected slugs were feeding on). This means that the plastids have no back-up proteins - once a protein that can not be made by the plastid breaks down, that's it. Based on what we know about plastids, this should happen within a matter of days - without a constant stream of new proteins from the nucleus, the photosynthetic apparatus should cease to work.

But that is NOT what we observe in the sea slugs. They maintain functional plastids for MONTHS. One explanation is that transcript levels of these critical proteins were too low for detection, but this is an entirely unsatisfying conclusion because 1) Next generation sequencing was used to produce very deep coverage of the transcripts, and 2) the small subunit of RuBisCO alone, accounts for roughly 15% of all transcripts in young plant leaves. The probability of missing all of the transcript necessary for the plastids to survive is virtually nil.

So what is going on? The answer, I'm afraid, is elusive. What we see in nature can not be explained by what we know about the components of the system. The proteins are not being made by the slug and the plastids can not survive as long as they do without replacement proteins, or so our current knowledge would suggest. Something has to give to explain our observations and I'm am eager to see what it is. With the E. chlorotica genome soon to be completed, answers may be on the horizon... or not.

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

One response so far

Musing on government regulation

Jun 06 2012 Published by under [Et Al]

Not to step on DrugMonkey's toes here, but I am continually struck by the obsession that many USians have with "freedoms". Perhaps it's our heritage and history stemming from the revolution. Maybe it is the perpetuated belief that the class system is more fluid in the US than other places. I honestly don't know. But the mere hint of government regulation of things that are demonstrably bad for people sets of a firestorm of protest.

The current "NOT R FREEDOMZ!!!" cry is coming from NYC, where the mayor wants to limit the sale of sugary soft drinks to 16oz. Mind you, this is just a measure to limit the serving size, but not the number of 16oz servings you buy. Although I wonder a little about the added waste of more cups vs. bigger cups, I can't really see this as a major issue. There is no "ban" as the media is fond of calling it, you can still drink as much soda as you want for the same price (i.e. no extra taxation).

It seems I am in the minority.

From the reaction to this move you would think Bloomberg was trying to ban fully automatic "hunting" rifles or armor-piercing bullets.

The noise from this NYC thing reminds me of the freak out over the smoking ban in restaurants and bars. I lived through this twice in two different places and the process was shockingly similar:

Step 1: Smokers and restaurant/bar owners lose their collective shit and claim that business will end, people won't go out, dogs and cats living together...

Step 2: Petitions, more freak out as the drop dead date approaches.

Step 3: Ridiculous anti-climax where nothing really changes except that the non-smokers don't wake up the next morning feeling like they slept in an ashtray.

Step 4: Business is actually better because a lot of people were staying away to avoid the smoke and everyone who wasn't still wants to eat and drink.

Step 5: One finds it very odd and backwards to visit a place that still allows bar smoking / waking-up-ashtray.

At the end of the day, the result was good for public health (unless you think those formerly avoiding the bars and restaurants are now less healthy) and did nothing to hurt business, nor personal freedom. So how is limiting the size of one's soda cup such an affront to everything we hold dear? Someone explain to me how government intervention for the betterment of public health is such a horrible thing, without going all unreasonably Orwellian on me.

41 responses so far

Semicolons should be like Kakapos

Jun 04 2012 Published by under [Education&Careers]

I have been reviewing a lot of other people's writing recently. More than is likely healthy. But if you ask me to read and comment on your stuff, I have one simple rule: lay off the fucking semicolons.

At the very most, semicolons should be like rare birds - exciting to see once in a while because of their rarity. They are not the type of punctuation to be used with reckless abandon, rather they often represent a poor compromise. Do you want your reader to stop, pause or what? Why have you left an incomplete sentence dangling there? Make a call, but don't abstain from voting here.

I can let one semicolon in a manuscript slide, so use it wisely. Any more than that and we're going to chat.

24 responses so far