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!
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.
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.
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.
.The famed AMNH scientist Ernst Mayr proposed the most widely known species definition or concept as ““groups of actually or potentially interbreeding natural populations, which are reproductively isolated from other such groups” By this logic, new species arise when populations are separated across space and time AND some isolating mechanisms evolve such that these separate groups - once members of the same species - can no longer successfully interbreed
Thankfully there is a buffet of species concepts (26 by one author’s count!) for young upstart evolutionary biologists like Sophia and Nancy to chose from ( and to critique)
Sophia and Nancy are wading through the morass of species concepts under the mentorship of herpetologist, David Kizirian, as part of a study to revise the taxonomy of the genus Dinodon, a snake with several species found across Asia. In David’s words, Dinodon’s taxonomy “is a mess.” Within the genus, there are some species that should be 2 and 2 species that should be one. Take for example a 2013 paper co-written by AMNH curator, Dr. Frank Burbink. He discovered that Dinodon was a paraphyletic group. In other words, the Dinodon genus represented a group of species whose members were descended from a common ancestor (good taxonomy) but left out some species who were classified under different genera (bad taxonomy). So Sophia and Nancy will be using morphological traits to see if the taxonomy of Dinodon can be improved. On this quest, the need to define what species concept they are using especially if they stumble across any new, hidden species.
A frequent theme of my SRMP blogs is how little we know. Usually I find that very uplifting (there will always be a quest for knowledge!), but not in the case of the Burmese Star Tortoise.
Very little is know about the ecology of this endangered tortoise because there are so few to be studied. As of the early 2000s, Burmese Star Tortoises (found only in Myanmar) were believed to be extinct in the wild. Over-harvesting, driven in part by the international pet trade, is largely responsible. Therefore, in 2007, remaining tortoises were captured and brought to special “head-start” facilities to be bred with the hope of one day reestablishing a viable, wild population.
A captive population that started with fewer than 20 tortoises is currently over 8,000 in 4 assurance colonies in Myanmar. And now, conservationists are starting to release these captive-bred tortoises back into the wild; however, before they do, all tortoises need to pass a health check. But how can you tell a turtle is healthy?
Dr. Suzanne Macey and her students Ariana and Michelle are working with a colleague, Dr. Bonnie Raphael, from the Wildlife Conservation Society (aka, the Bronx Zoo), to review the results from pathogen and hematological data that has been collected on these tortoises since 2013. Hematological screening can be used to flag problems like anemia, dehydration, or signs of prolonged infection. Those individual tortoises with immediate poor diagnoses, obviously receive medical treatment. Those that are cleared are considered for release.
Ariana and Michelle are taking a step back and are investigating the health of the captive head-start population as a whole. By analyzing the existing data, they are using statistical models to uncover patterns that can lead to creating better health standards for this poorly understood tortoise. E.g., what is a normal white blood cell count for a healthy tortoise? Do critical thresholds vary with sex or at the different head-start facilities? Vets don’t have this information, but the creation of “wellness” health standards for these tortoises is crucial for their future releases. This is why they need the results of Suzanne, Michelle, and Ariana’s study.
Prior to my visit to Rondi’s lab, I thought Jade was Jade. Ah, there is no boundary to my ignorance.
“Jade” is a common name shared by two unrelated mineral forms. There’s nephrite Jade (think most traditional Chinese carvings) which can be found all throughout Russia and China. Then there’s Jadeite which is exceedingly rare and found in Guatemala and Burma.
For years, Dr. George Harlow, Curator in Earth and Planetary Sciences at AMNH has been studying jadeite from the Guatemala Suture Zone, the boundary between the North American and Caribbean tectonic plates. This former subduction zone marks places on the earth where two plates meet and collide. Oceanic plates (most of the Caribbean plate) are made of denser rock than that of the continental crust and sink beneath the other. Water carried down with oceanic crust is heated and hydrates certain rocks to form serpentine minerals. Jadeite is formed by the passing of this fluid through and over parent rocks. (NOTE: Add Youtube video of George https://www.youtube.com/watch?v=TWofncaF2Ds)
Jadeite most commonly takes a hue of green; however, may include a variety of colors including pink, lavender and blue (Note: Add a picture of an Olmec head made of jadeite). Jadeite is fairly well studied, but something known as black jade that is found in close proximity to jadeite. Scientists don’t know from what parent rock it was derived or what that transformation process looked like. Knowing how a mineral forms can unlock clues to the evolution of the earth’s crust. Therefore black jade is like finding a blank page in the Earth’s history book. Khakima, Carlos, Rosa and Rondi are attempting to fill in the blanks studying black jade of the Guatemala Suture Zone
The process of understanding how black jade formed requires careful observation with a high powered petrographic microscope. The team are scanning thin slices of these rocks to find evidence of the original rock prior to it being altered by and recrystallized from fluids: they are looking for sections in the rocks without small fluid droplets trapped inside minerals, and for chemical zoning (areas with evidence of the mineral growth) to map the changes that black jade experienced from its parent rock to final form.
Peel back your skin & muscles and peer past your skull and you’d find three very important little semi-circular canals that make up your inner ear. These canals control your balance and aide in motion – and are the key to Brian Shearer, Elise, and Diana’s investigation of extant and extinct primate locomotion.
A micro-CT scanner allows you to penetrate a skull (and other things) without the very invasive and destructive process of physically opening up a skull. X-ray light is bombarded at the specimen. Bones reflect these x-rays differently according to their density, a phenomenon that allows for the creation of a three dimensional computer model. With this model or 3-D scan, bones are differentiated based on their density.
In their search for the semi-circular canal, Elise and Diana slowly e-dissolve their 3-D skull models leaving behind only the densest bones: ghostly teeth and the petrous, one of the densest bones in the human body and the bone that supports the semicircular canals.
Once located, Elise and Diana, start the process of rendering or digitizing the canals. Going layer-by-layer in this 3-D model they trace the canals’ outline and contours. When completed, the team will measure the size, volume, and the orientation of each canal, metrics that correlate with modes of primate location. For example, more perpendicular angle of orientation is associated with faster swinging in primates know for their brachiation (aka arm swinging locomotion).
The team hopes to explore the form of these semi-circular canals in both juveniles and adults across several extant (living) primates. In the end, better understanding the relationship between the form of the semicircular canals and locomotion in extant species may help paleontologist understand how extinct primates got around – simply by looking to its inner ear.
It’s a very humbling experience to hold a chondrite (aka a meteorite containing chondrules). Never mind that you are holding something from outer space. You are also holding one of the oldest objects in the solar system (~4.5 billion year old). And its study can unlock many mysteries into how our solar system formed.
Meteorites are rocks originating from space (e.g., an asteroid, the moon, etc.). Possibly less familiar is the chondrule. Chondrules are tiny, circular grains of minerals formed in the protosolar nebula (a molecular cloud swirling around our proto-sun) by the rapid melting of accreting dust. The chondrite is composed of inclusions (i.e. chondrules) embedded in matrix, a fine-grained mixture of minerals. In many cases, chondrules are surrounded by a “rim” of fine-grained material that resembles the matrix but has different textural and compositional properties.
The question is when and where did the rims form? In the solar nebula or later in our solar system’s history? The answer is important to understanding the origins of the earliest solids and how our solar system evolved. Kim Fendrich, along with Vivian, Nathanael and Annie used an electron microprobe to map the meteorite’s elemental composition and are using Adobe Illustrator to process these maps and characterize the various features within them.
Specifically, they will categorize the inclusions and quantify their abundance, measure the size and distribution of rims, and observe chemical relationships between the various components. They are doing so in search of meaningful correlations that may help clarify the accretionary processes that took place during the early stages of solar system formation.
SRMP mentor Luciana Gusmao studies deep sea anemones: their diversity,
evolutionary biology, and ecology. Apparently the deep North Atlantic is pretty well studied at least relative to the southern Hemisphere where in the case of the waters off Brazil only one - ONE - deep sea anemone has ever been documented. Until now.
Luciana and her SRMP team, Elena and Sebastian, have in their possession
a treasure-trove of unidentified (and possibly undescribed) sea anemones from off the coast of Brazil. Whatever Elena and Sebastian find from these previously unexplored depths will be a valuable contribution science. The team is very likely to add new localities for species previously known from elsewhere. But it’s possible that they will uncover an anemone never seen before.
So just how do you identify an anemone? DNA always comes to mind, but is probably out of the question at the moment. The anemones were preserved in formalin which makes DNA amplification tricky at best. Next stop: old-school comparative anatomy. In this case, it’s the arrangement of muscle fibers, mesenteries and the study of small capsules found in different body tissues known as nematocyst that help us differentiate deep sea anemones. To examine these features, Elena and Sebastian need to create slides, a lot of them.