Science Roundup

Its been a while since I've written something for this blog, but with my first year of my PhD done I can now devote a little more time to it. Anyways here's a quick roundup of some cool topics I found interesting these past months. 

HACE - Targeted mutations 

Geneticists are often interested in the way that mutations in DNA affect the function of a protein (remember: DNA --> RNA --> Proteins). This can kind of be done on DNA in a laboratory setting through a variety of ways like exposing cells to UV radiation or through knockdown experiments but creating targeted mutations has proved difficult and complex. In a recent pre-print by Dawn Chen et al., the researchers have developed a new technology called HACE that is able to make small nicks in a single DNA strand using a guided version of Crisper-Cas9. The Cas9 bit has a section of RNA loaded on it that recruits an enzyme and makes random mutations as it moves along where the break in the DNA was made. This way, scientists can now make much more specific evaluations on how a mutation in a location of DNA may affect its function. 

Scale Eater Fish

I recently learned of the Scale Eater Fish (Perissodus microlepis), a species of freshwater fish in Zambia. These fish sneak up on other fish and, like their name suggests, bite off their scales and eat them. What makes scientists interested in them is that they are an unusual case study in natural selection. Scale eaters have mouths that are a bit crooked and bend either to the left or to the right.

Whether a population of scale eaters has more left or right bent individuals in a given year depends entirely on how sick of their BS the other fish in the lake are. Fish start to become protective of whichever side is currently more likely to have their scales bitten off. So, when there are more right mouthed scale eaters, the other fish learn to begin to watch their right sides. This leads to a disadvantage for right mouthed fish but an advantage for left mouthed ones. Just as the fish think they've adapted to getting bit on one side, scale eaters that bite the other side suddenly become more common in the lake, with this cycle seeming to occur every five years or so. How genetic and non-genetic cues jointly influence the direction and the degree of mouth bent-ness is still being investigated and of major curiosity to population-geneticists. 

How we Lost our Tails

Humans lost our external tails about 25 million years ago, leaving only the coccyx in its place. A new paper by Xia et al., shows that this loss may have occurred due to a transposable element that inserted itself into an ancestor's gene. Transposable elements are bits of DNA that jump around either by being converted to RNA and then reconverted back to into DNA and placed in a new position, or by producing an enzyme that moves its place in the genome. The most abundant type of transposable element is called an Alu Element, which make up about 10% of our DNA. Most of the time, because most of your DNA is non-functional, their movement doesn't do much. But it seems that one Alu element's movement into the middle of our TBXT gene led to our ancestors losing their tails!

Bichir and the Immune System

This is a project I've been working on at my new lab here at NC State. Bichir, scientifically known as by their family name "Polypteriformes," are the oldest lineage of bony fish. Bichir have been around for about 300 million years and has changed very little, giving them their nickname as "living fossils." 

The Bony Fish Lineage - AKA Acintopterygii. The oldest lineage are at the top, the bichirs and reedfish. The lineage in the middle, the Teleostei, represent the majority of fish species. 

Because bichir are so old, they are some of the only bony fish lineages that did not go through the "Teleost gene duplication event." This event, in which a common ancestor of all Teleostei had its whole genome fully duplicated, lead to a massive explosion in the diversity of fish species. This makes the Polypteriformes interesting for looking into the evolution of all sorts of processes. Specifically, I've been working on looking into characterizing several genes associated with the immune system to see how they might have looked pre-duplication event. 

Stonefish Venom Genes

One really cool aspect of our immune system is the membrane-attack complex. This is a structure that our body forms that pokes holes in disease-causing invaders, causing water to rush into their membranes and kill them. 

Stonefish are notorious for being some of the most venomous animals on earth, with many incidents reported yearly of divers accidentally stepping on their sharp protruding spines, leading to immense pain. They are also really ugly (apologies to any stonefish reading this). I was surprised to learn that the venom causing protein from stonefish actually works the exact same way as our immune system due to it being an ancient branch of our own membrane-attack complex family. Just like how we use our proteins to form pores in invaders, the stonefish venom, SNTX, pokes a hole in the cells of whatever tissue is unfortunate to come into contact with them, leading to cell death.