AP Biology class blog for discussing current research in Biology

Author: actevetransport

Cas9: Dormant Killers?

Woah. Pretty aggressive title, but it did grab your attention, didn’t it?

What the Heck Even Is Cas9?

Well, Cas9 is an integral part of the CRISPR-Cas9 system. The Cas9 is able to latch on to a piece of DNA (it grabs on based on a piece of guide RNA, or gRNA in the complex) and cuts it. When this happens, the cell is like, “Oh no! Broken DNA! We must fix!”.  Now I know what you’re thinking… why fix something that ain’t broke? Well, what happens is that (in science being done today) the piece of DNA already has something wrong with it that the cell isn’t aware of such as a point mutation. Breaking the DNA just brings the problem to the cell’s attention so that it can fix the DNA. This was a defense mechanism in bacteria to work against viruses and the like by ‘cataloging’ the viruses they’ve encountered and using the system to cut up the viral DNA, but scientists thought it was pretty cool so they decided to figure out a way to make it work in animals.

Alright… Why Are They Killers?

Well… what these scientists have done is that they have developed a way to basically use the CRISPR-Cas9 system as a defense mechanism for diseases prevalent in humans and plants such as cancer or the West Nile virus. Basically, how this would work is that at the end of the Cas9 researches added a little protein tail that could only be cut by a specific protein. When this protein is cut, then the Cas9 would be ‘activated’ and would do its defensive duties. Scientists could change this protein to target different things, such as adding a protein that cancer cells make enzymes for. It was also used in plants to target certain viruses. So in short, this Cas9 DNA destruction mechanism is dormant until presented with the foe it has been essentially trained to fight.


So Is The World Cancer-Free?

Unfortunately not, my friend. Even though this is revolutionary stuff happening, the research done is mostly for plants in order to resist infectious diseases and viruses. It has, however, offered us insight into how we can manipulate this system to serve us in a beneficial way. They also, during this whole protein-tail process, figured out that they can get the protein to still work in different configurations that make it easier to add certain protein tails. They determined that by cutting Cas9’s amino acid chain and rearranging it in certain ways, it can have easier protease recognition sites as well as attachment sites for the protein.

Do you think this system will revolutionize medicine?

Will this eventually replace vaccines?

Will the continued research into gene editing come back to haunt us in the end?

Why Don´t We Grow Ears on Our Arms?

The Miracle of DNA Regulation

Now, the question posed is why we don’t grow ears on our arms. May I introduce to you: gene regulation. That’s right. Even though every single cell in your body has the same DNA, the body is able to ‘turn off’ different genes so that only ones that are necessary are read. This is why you do not grow ears on your arms, because those ear-making genes are ‘turned off’.

But… How?

This question has been plaguing scientists for quite a while, as we have discovered genes in the human genome that are ‘turned off’ but could potentially be quite useful such as the regeneration of limbs (same as a starfish or a crab). Now there has been a new breakthrough in how we understand gene regulation thanks to some researchers in Cambridge, Massachusetts. The binding domain’s function in gene regulation has been known for quite some time already. The mystery lied within the activation domain. It has now been discovered that the activation domain sort of acts as a net, capturing the molecules for gene regulation and anchoring the transcription ‘machinery’ by the gene that is to be transcribed.

But… How? What Does This Mean?

Well, the activation domain creates little droplets by mingling with transcription proteins that attract the transcription machinery stuff. It’s kind of like creating oil droplets in vinegar. This process is now called phase separation. This has grand implications for even more research on gene regulation and can even give more insight into diseases such as cancer. When do you think the next breakthrough will come? Do you think this is the key to unlocking how to turn genes on and off for good or is there much more work to be done?


Valuable Poop

Yep, that’s right. Poop can be valuable.

Wait? Isn’t that an oxymoron? Valuable poop?

Yes, as much of an oxymoron as it sounds, poop can be valuable. In a more recent treatment, fecal transplants have proved to be successful in helping with C. difficile infections. Antibiotics stop working, and all hope seems lost. However, there is a solution. Healthy people donate their stool (in the vernacular: poop) to those afflicted by a C. difficile infection in order to restore the health of their gut microbiome. The healthy microbial environment in the healthy stool restores the balance.

Look at that C. difficile, bad stuff!

How does this work? Do the microbiomes go to war?

Truth is, researchers are still trying to figure out exactly how the healthy gut microbiome is restored. We know that C. difficile can take over after treatment with antibiotics because it is faster growing and more resistant to antibiotics. They dominate the other microbes. The insertion of healthy stool with a balanced microbiome into a microbiome that is dominated by C. difficile will restore the microbiome’s diversity and balance. Basically, the healthy gut microbiome will kill or just outnumber the C. difficile, and then the problem is resolved. Scientists still aren´t really sure how this happens but are looking into it.

So what? I’ve never heard of a C. Difficile infection?

Good for you. C. Difficile has actually been afflicting many people in different ways, and some doctors even call it an ‘epidemic’. Even so, this new development has lead researches to believe that this could lead to something bigger. Some have tested if this same technique will help inflammatory bowel disease, to which they had promising results (however, still heterogeneous and statistically inconclusive). This is a creative way of using the microbial environment to help diseases, and an even more creative way to study microbial interactions.


Would you get a fecal transplant if it were recommended?

How do you think the C. Difficile is banished by the other microbes?

What do you think regarding the future of antibiotics?

Manta Ray “Eat”fficiency

Bonjour, tout le monde.

Manta Rays are Cool

So, as we know, manta rays are really cool. I mean, what kind of organism has wing-like features, can soar through water at nine miles per hour (two times faster than the speedy Michael Phelps), and is pretty cute? The answer: manta rays. The fact that they can swim really fast is no coincidence; nature built them this way. Researches just found another way that these rays are built to be the Lightning-McQueen of the sea (Lightning McSea). It has been discovered that manta rays have some sort of special filtration system used to separate their meal (plankton) from all other unnecessary stuff (fluid).

Well, yes, they are Filter Feeders, so what’s the Big Deal?

Most people used to think that all filter feeders were able to filter the same way: like pasta in a strainer. However, this analogy is not applicable to the awe-striking manta rays. They use a series of lobes and gaps to separate their meal from all the other stuff that comes into their mouths. The lobes act as walls, kind of, so that when the water passes through this space, the plankton ricochet off of the lobes, kind of like pinball, until it reaches the esophagus and goes down the hatch. The water in the vortex is able to eventually maneuver out of the manta ray’s mouth and back into the ocean (backwash much?). More specifically, the water gets pulled into vortexes that release it back into the ocean. The plankton are able to avoid these vortexes by bouncing off of the lobes which will eventually lead them to the esophagus. This contributes to their efficiency because with this system, they can just continuously have their mouth open. They don’t need to close their mouth to ‘clean their filter’.

Did Researches Watch Manta Rays Eat Until they Noticed Something?

The way this was discovered was by running a set of simulations to test what would get clogged in the ‘filter’. The researches noticed that when testing particles smaller than the pore size (which would be expected to go through if it were a pasta-draining mechanism) did not go through. With further analysis including dying particles to track their journey, they concluded that the manta ray had some sort of pinball mechanism helping them out. This new finding could help other studies in trying to capture small particles. This is really ground-breaking because until now, filter feeders’ mechanisms were all thought to be pretty much the same. This completely opens the door for more research to be done on other animals that are presumed to have the same mechanisms. It’s great to ask questions like ones that lead to this discovery, and even better to find their respective answers.


Do you think this discovery will lead to more research on filter feeders?

What other applications of this finding can you think of?

If other particles do manage to get through, do manta rays have cells that are able to break down things that aren’t what they normally eat?

Would they rather be in areas with low concentrations of small stuff, so it’s less of a chance something might get caught or in high concentrations, so there is more food per square foot? Would you hypothesize a taxis or kinesis reaction?


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