Of Of Mice and Men: High school English class lives on in scientific paper titles

“The reviewers hated the title” (C.E. Brock illustration for Pride and Prejudice, 1895, via Pemberly.com)

Writing titles for scientific papers is hard. The title is the one element of the paper everyone reads if they so much as skim a journal’s table of contents e-mail. These days, you also want something that’ll fit in a tweet with room for the DOI link. So you want something informative, but also memorable — and ideally something that prompts people to click the link. That certain je ne sais quoi.

But also you don’t want to look unprofessional. You can’t go around calling your study organism cute even if this is quantifiably the case; you can’t reference risqué cocktail names or clichés about penises or especially trashy fantasy movies. What can you use to be more fun than just reporting your results, but, like, in the safest possible way?

One popular answer, based on a highly unsystematic survey of PubMed, is to use the title of a book that you probably read in high school English class. There are lots of excuses (no, really, as many as 1,061) to title a paper with Of Mice and Men in biomedical research. (And, um, in blogging about said research.) Following up on this Twitter exchange, I went to PubMed with some familiar old titles to see if any other members of the junior-year canon are more popular than John Steinbeck’s sad little tale.

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Friday action item: Figure out how to support a grad student without DACA

(Flickr: Ana Paula Hirma)

On Fridays while the current administration is in office we’re posting small, concrete things you can do to help make things better. Got a suggestion for an Action Item? E-mail us!

We haven’t done an Action Item in a while, but this week’s seen a decision from the Trump Administration that hits quite close to home, here in southern California: the announced end to DACA, the Obama administration policy that provides limited legal status for people who came to the U.S. as children without immigration documentation. Wednesday morning, my California State University colleague Terry McGlynn posed a question on Twitter that seemed, to me, pretty simple:

It turns out that this is not an easy question to answer. As CSU chancellor Timothy White explained in an interview with NPR the same day, California and the CSU system provide tuition support that doesn’t require legal status, and which will remain in place if DACA goes away six months from now, as it will if Congress doesn’t act. But going to graduate school isn’t, of course, only a question of tuition. In biology, we expect to be able to provide stipend support for grad students, usually through teaching and research assistantships as well as external fellowships. That makes graduate students employees, in a limited sense — and that may severely limit what biology departments and principal investigators can do to support students who lack documentation, even with the resources California provides.

Here at CSU Northridge, admission to the graduate program does not involve any inquiry into immigration status. But every employee provides evidence of eligibility to work in the U.S., whether as a citizen or as a documented immigrant with a work permit. According to a guide (PDF) available from the CSUN Dream Initiative website, it’s potentially possible to pay student researchers (including, I think, graduate RAs) with funding from some specific sources; but not with money from university funds, or from a governmental source like NSF. As the guide says under “Research”:

Sometimes undocumented AB 540 students [who have limited resident status in California without immigration documentation] are paid for this type of work in the form of a “stipend.” A stipend is a sum of money allotted on a regular basis, such as a salary for services rendered or an allowance. Undocumented AB 540 students may be eligible for stipends if the source of funding is tax-exempt. If the stipend comes directly from a public college or university’s funds, undocumented AB 540 students are not eligible. Remember, government funds are not available to undocumented AB 540 students.

CSUN’s FAQ on the DACA repeal explicitly calls out this issue — DACA recipients have had work permits that may or may not continue to be valid after the end of the program.

If you have current graduate students with DACA status, you’re probably already thinking about exactly these issues. If you don’t, now is as good a time as any to figure out what you’d do if you found out that a promising applicant to your lab might not have a work permit by the start of the next school year. Check to find out whether your campus has an equivalent to the Dream Initiative, or publications or resources provided in the wake of Tuesday’s announcement. If you can’t find those resources, maybe it’s time to get together with some colleagues to tell your administration that this is a priority. As for me, with CSUN’s and California’s resources in place — I’ll be thinking about who I can hire with any given funding source as I prioritize grant proposals for this semester.

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In the aftermath of fire, bluebird species boundaries may blur

Mountain bluebirds and western bluebirds, illustrated in Birds of the Pacific Coast (Flickr: Biodiversity Heritage Library)

One of the most clear-cut reasons that species evolve to fill different ecological niches is competition. Two otherwise similar species that use the same resources experience strong selection favoring the use of less-similar resources, if they have the option. The classic example is Darwin’s finches, which evolved different beaks to better use different seeds, and have radiated (or are radiating) into an array of different species as a result.

However, nothing is simple in evolutionary biology. Competition also brings closely related species into contact, as they jostle for access to the resources over which they’re competing. A new paper in the American Naturalist shows that, for two North American songbird species, this kind of interaction may provide an opportunity for interbreeding where none would otherwise exist — competition creating, in this case, a reduction in the genetic isolation between those two birds.

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Missing symbionts: do some animals lack resident gut microbiomes?

It seems like the field of “gut microbiomics” is having major breakthroughs almost every month these days. It’s very exciting to follow what is being discovered and gut microbes have now been linked with an array of important host traits, such as health, disease resistance, digestion, behavior, and longevity. The more one reads about gut bacteria and other microbes, the more convinced one gets of their importance for animals as hosts.

However, evidence are starting to emerge as to question whether all animals truly harbor gut microbiomes. Tobin Hammer and colleagues recently published a paper in PNAS where they laid out the case for the missing gut microbiomes of caterpillars. Hammer et al. (2017) sequenced guts and feces from 124 leaf-eating caterpillar species of 15 families and found unusually low densities of bacteria and fungal microbes present in their guts. Most bacteria present were highly similar to the ones present on their food (plant leaves), and therefore only transient and not residing in the caterpillar gut.

Figure 1 from Hammer et al. Comparisons of bacterial density, relative abundance of plant DNA, and intraspecific variability between caterpillars and other animals expected to host functional microbiomes. Please see the paper for detailed description. 

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RNA data ruins a tempting just-so story of mutualism between algae and salamanders

Most relationships between animals and microbes interface in one of two locations: on the outside of animal cells (mostly to the benefit of both parties, think gut microbiota) or on the inside of animal cells (mostly to the benefit of the microbe, think malaria). Currently, the only exception to the latter among vertebrates is the unique relationship between spotted salamanders (Ambystoma maculatum) and the green algae that can be found in the tissues of developing salamander embryos, Oophila amblystomatis.

I’ve written previously on how easy it may be to make tidy conclusions about this vertebrate-algae relationship, and how new work was beginning to build a more detailed case for symbiotic co-evolution between these taxa. I missed an important update in this line of research this May that shows this putative mutualism is not so, uhh, mutual.

John Burns and colleagues built on the discovery of O. amblystomatis entering and persisting in salamander cells by investigating the potential for gene expression changes that may happen during this invasion. Previous work established that when O. amblystomatis grows outside of salamander cells, but within membranes that protect the developing salamanders, the algae appear to benefit from the availability of embryo-generated waste while, in turn, the embryo absorbs the extra oxygen produced by the algae. How similar were circumstances inside the invaded salamander cells for both parties? To get at this question, the authors collected RNAseq data to compare gene expression between 1) algae that was inside or outside of salamander cells and 2) salamander cells that were with or without algae.

Modified final panels from Figure 1 (Burns et al. 2017). Deferentially expressed algal transcripts on left and differentially expressed salamander transcripts on right. “Intracapsular” in this case refers to outside of salamander cell, but still within the developing egg mass.

When it comes to changes in gene expression, the story of salamander-algae mutualism seems awfully one-sided. Less that 1% of salamander genes displayed any differential expression when their cells were with or without algae. In contrast, the algae showed six times the number of changes in expression when they were found inside salamander cells, and these changes don’t sound like “kumbaya” to me. Many of these changes were typically stress-associated, including the over-expression of heat shock proteins, shifts from oxidative to fermentative metabolism, and increases in autophagy proteins. The stress response shown by O. amblystomatis is hypothesized to be a general symptom from reduced efficiency of photosynthesis. Salamander cells, in contrast, take a much more relaxed stance on algal intrusion, showing a lukewarm immune responses and even suggestions of metabolic changes that could indicate the use of energy created by the captured algae.

In the conclusions, the authors put this new discovery into the context of other microbe-host interactions that have been canonized only to get upended by new data. Just because the story makes sense doesn’t mean that it isn’t worth going a level deeper – good advice for all of us.

 

Cited

Burns, J. A., Zhang, H., Hill, E., Kim, E., & Kerney, R. (2017). Transcriptome analysis illuminates the nature of the intracellular interaction in a vertebrate-algal symbiosiseLife6.

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The genomic architecture of ecological speciation

Figure from USDA Circular No. 101 (Quaintance 1908), depicting the apple maggot fly, Rhagoletis pomonella (Flickr: Internet Archive Book Images)

Speciation reshapes the ways genetic diversity is distributed in the genome — it’s been said that the establishment of reproductive isolation is essentially the evolution of genome-wide linkage disequilibrium. The “genomic islands of speciation” model of ecological isolation imagines genome-wide differentiation spreading outward from individual genes that experience selection for different variants in different environmental conditions. But the ways in which genes under differential selection are arranged in the genome, and how variation at those genes is assorted, also alters the opportunity for isolation to evolve.

A recent Molecular Ecology paper digs into this latter scenario, using linkage mapping and association genetics in a classic case of ecological isolation, the apple maggot fly Rhagoletis pomonella. Rhagoletis pomonella lays its eggs, and its larvae feed, inside the fruits of hawthorn. When European colonists arrived in North America and started planting domestic apple trees, some hawthorn flies discovered that apples were tasty, too, and they occasionally laid eggs on those. These apple-eating flies multiplied, and by about the middle of the nineteenth century they were numerous enough to attract attention as a pest in the orchards of the Hudson River valley in New York, and they’ve been spreading westward ever since.

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