Old School vs. New School
I’m going to try something different for this post. I usually write about one SRMP lab at a time, but sometimes you can’t ignore the way that individual research projects “speak” to one another. So this is a story about poop and dirt and the people that study them.
Let’s jump right into the poop, or more properly feces or scat. Your choice. It can tell you so much about the source animal including sex, identity, stress levels, pathogen loads, and of course diet. Joshua and Catherine - joined by SRMP alumna, Olivia - are working alongside Neil Duncan and I on a study to describe the diet of NYC coyotes. Olivia and others describe in detail how, but suffice to say, the key is identifying hard, undigested remains of prey (e.g. hair, bone, and teeth) that make it through the gut into the scat.
But there is the assumption that all prey are equally likely to be detected in scat. This is clearly violated, no? Take an easy example. Do urban coyotes eat human foods like Big Macs? Most research says, not often. The problem is that unless the coyote ate the foil wrapper there are no parts in a Big Mac to make it through the gut undigested. So, it is possible to underestimate the contribution of certain prey groups using traditional scat analysis.
Enter Claudia Wultsch, Tatyana and Alejandro. They are taking advantage of innovative next-generation sequencing (NGS for short) technologies to amplify and sequence prey DNA found in scat using a metabarcoding approach. At least some prey will make it through the gut even if hard parts aren’t ingested or there are no hard parts to the prey. In other words, if a NYC coyote ate a hamburger and the resulting scat found its way to Claudia’s lab, DNA of cow (assuming Big Macs are beef) would be amplified.
I saw the amount of data Claudia’s team was generating and it was astounding. They are focused mostly on jaguar diet (disclaimer, I’m a big fan of the jaguars, a study animal of my youth). For a test run of 24 scats, they generated over 28 million strands of DNA which they are now identifying to taxa. One jaguar sample even amplified mouse DNA, species that rarely--if ever--are listed as jaguar prey.
Do jaguars catch mice, a prey item overlooked by earlier studies? Or, as Claudia posited, did a mouse run over the scat? RUN OVER THE SCAT. This genetic technique is so sensitive that the poop might have been contaminated (can poop be contaminated?) by exogenic mouse DNA. So, while Neil and his team are worried that they are missing prey items, Claudia and her team are worried about counting animals as prey that maybe aren't!
It came from outer space
Personally speaking - the viewpoint on a non-astrophysicist - the themes of this blog post sound like the origin story for a 1960’s superhero: cosmic rays, neutrinos, gamma rays, and of course, IceCube Neutrino Observatory, a crazy array of sensors in Antarctica located under a kilometer of ice. Isn’t that where Superman’s Fortress of Solitude is hidden?
I can’t possibly cover (understand) the full scope of Marcos Santander’s work, but his team - Robyn, Emma, and Steven - are doing some very cool stuff. What you need to know is what scientists don’t know: Namely, what is the source of cosmic rays (nuclei or other high energy sub-atomic particles traveling near the speed of light through space)? So, the team’s project is pretty straightforward. Find the source of cosmic rays and thereby solve a long-standing mystery in astrophysics.
Will Marcos and his team of young, mad scientists discover the source of cosmic rays? Will they solve one of the biggest mysteries in astrophysics before SRMP graduation? Tune in tomorrow (June) to find out.
Of Lighting and Steenbok
Rock. Paper. Scissor. Shoot.
Four words that span generations and the globe.
A game played both out of - and in defeat of - boredom.
Contrary to the 80’s-inspired melodrama, rock, paper, scissor (RPS) find themselves squaring off, and in doing so, reveal much about the strange humans playing them. First, the game has very little to do with luck. There is strategy involved. If I lost throwing rock, do I try it again!? If I won throwing rock, do I use it again!? Ah, so many choices (okay, only 3). It is these agonizing choices - and fear of our opponent’s decisions - that prevent us humans from playing a random hand - which would be the best choice if only we could. RPS has actually been used by researchers as a model to explore human decision making through an evolutionary lens.
RPS may have the global monopoly on hand gesture games, but “War” or "N!ai" has all the style. Believed only to be played by Ju|’hoan or San peoples of Namibia and Botswana,War is a fast-paced, hand-gesture game, played to music, that pits two teams (Lightning vs Steenbok) of at most 5 players against one another. At any one time, only two people are playing, one per team. Unlike RPS, there are only 2 options: play your left or right hand. One team wins if the same hand is played (R-R or L-L). The other team wins if opposite hands are played (R-L, L-R). The round ends once one team loses 5 times. War is not played to a specified number of rounds, but rather ends whenever the players choose to stop or when time becomes limited, as they often play for tourists visiting the area.
Alex de Voogt and his SRMP team of Mohamed and Rebecca have hours of War video footage. The game is pretty fast and challenging to keep up with (and looks like a lot of fun). Moe and Rebecca are completing the first ever detailed study of this game and its mechanics.
I call thee “Maelstrom ”
After hours of wet lab work - transferring clear liquid into clear liquid - do you know what geneticists can’t wait to do? Name their genes and accompanying proteins. And apparently molecular biologists have a bit of fun doing it. Take the hedgehog gene. The name comes from a hairy phenotype expressed by those flies carrying the gene. And guess what that name is of a close gene variant? Sonic the Hedgehog. Perhaps this spices up scholarly articles.
Rick Baker - along with Fem and Prithi - are studying rates of evolution in an equally impressively named gene: Maelstrom (aka MAEL; Etymology, unknown), a gene that has spawned several other duplicate copies which can be found across the genome of Rick’s study animal, the stalk-eyed fly. And while the original copy is expressed in cells all throughout the body, the duplicates are only expressed in male gametes (e.g. testis). Finally, the team suspects an arms-race among the gene copies
What makes MAEL so appealing is its association with meiotic drive - a phenomenon of allelic competition that is manifested in killer sperm of stalk-eyed flies having the ability to control sex gene expression. While it is still extremely hard to find evidence of meiotic drive through lab work, it is widely theorized that meiotic drive is the reason why MAEL and similar genes may be undergoing positive selection.
So what is up with the gene copies? Rick suspects they are evolving faster (e.g.
showing higher mutation rates) than the original copy, but his team needs to test that. And why are the copies only expressed in the testis? Do the copies still function to suppress transposons? The team is set on answering these questions through bioinformatics (locating the protein, trimming the sequence, and aligning the copies to create a phylogenetic tree) and genetic lab work (PCR) with the hopes of finding evidence for positive selection.