SCItations

Last month I wrote about the wonders and perils of the artificial intelligence program that predicts 3D protein structures, AlphaFold2. As an ion channel enthusiast , I naturally wanted to know how AlphaFold2 performs at predicting the structures of proteins embedded in cell membranes. When I search PubMed for articles that mention both "AlphaFold" and "ion channel" I only get 34 hits. This surprised me, given the hype and the general paranoia around AI replacing humanity. If we use these search results as a proxy for the state of the ion channel protein structure prediction field, I'd say the juice is still in the coconut. I wanted to know how well AF2 would do at predicting an ion channel protein structure, so I asked it to generate the structure of Kv2.1, a voltage-gated potassium ion channel that I studied during graduate school. Kv2.1 is a pretty important protein. It regulates neuron firing throughout the brain and body where it helps us learn new stuff, ...

I haven't spent too much time thinking about AlphaFold2 (AF2) since it entered the structural biology zeitgeist, but I was watching Veritasium's recent video on the topic and thought I would learn a bit more about it. For those who haven't heard of AlphaFold2, I highly recommend watching the video linked above, which explains AF2 better than I ever could. But the tl;dr version is this: AlphaFold2 is an artificial intelligence that takes any amino acid sequence (the building blocks of all proteins) as its input, and outputs the 3D protein structure it thinks that sequence is most likely to take. For some sequences, AlphaFold2 can do quite well at this notoriously complex task. On its debut in 2021, it was able to predict the 3D position of atoms in some protein backbones to within a few hundred nanometers! There are a plethora of articles out there speculating about how AF2 is going to change biology and the world at large. But someone recently asked me my opinion: "...

If you know me, you know that I am passionate about antibacterial soap. Passionate about how much a hate it, that is. I know it has it's place, like in hospitals, or in the homes of immunocompromised people, probably. But you won't find it in my house because I happen to think of antimicrobial resistance (AMR) as a real life boogey man, and as a healthy enough individual I want to do my best to not contribute to that particular monster. Development of, and access to novel antibiotics is a recognized unmet global public health need . That's one reason I found this study published last month so exciting. Ok, it was also because it overlaps with my interests in sensory neuroscience, but I won't be talking about that here. The Indiana University authors of the linked paper are searching for a therapy that, when used prior to or in combination with aminoglycoside antibiotics, will prevent drug-induced hearing loss. You see, aminoglycosides (AGs for short) are a class of ant...

A non-zero amount of what we call ‘medicine’ could be described as just controlled cell murder.  This was my revelation after researching a new treatment for certain cardiac arrhythmias called Pulsed Electric Field Ablation, which I became interested in when my father-in-law asked me how it worked during our Christmas visit. “How can it kill the heart cells and leave the nerves and blood vessels intact?” I had no idea. I know next-to-nothing about medical treatments for cardiac patients, much less how this Pulsed Field Ablation technique could have fewer side effects than the standard-of-care ablation techniques. A quick Google search piqued my curiosity when I learned that PFA is also sometimes called “high frequency irreversible electroporation”. While less catchy, that name revealed a bit more about the mechanism of action behind PFA - electroporation - which happens to be something I actually do know something about. Electroporation refers to the formation of holes (pores) in c...

As many of my readers know, I am a graduate student pursuing a PhD in molecular neuroscience. For those that think I'm crazy, maybe I am, but I hope you will feel a little crazy too after hearing a bit more about why I've chosen this path... Unless you are a student of neurophysiology or unlucky enough to have epilepsy you probably have never heard of ion channels. Ion channels are the proteins that control the “electricity” of your nervous system. Just like the components in an electrical circuit (resistors, transistors, capacitors, etc.),   ion channels are tiny elements in the circuitry of your brain. Ion channels switch on and off in precise ways to control when and where bioelectricity flows in your brain (and body).   I didn’t know ion channels existed until 2012 when I took a class in the Hendrix College Psychology department titled “Sensation and Perception.” It was here that I learned how my interaction with the world around me - my sense of taste, smell,...

I heard a great talk yesterday by Dr. Patrik Rorsman from the University of Oxford, who has a new way of thinking about type 2 diabetes. He believes some individuals who develop the disease may have a deficit in insulin exocytosis, but not by the mechanism that anyone would have predicted. It is abundantly clear that type-2 diabetes is not caused by a lack of available insulin in the pancreas. Therefore, Dr. Rorsman hypothesized that the mechanism of exocytic release of insulin may be perturbed in diabetic patients. However, when he made classical measurements to detect exocytic release in primary tissues, such as amperometry of cargo release and monitoring membrane capacitance, he saw no differences between healthy and diseased cells. It wasn’t until he engineered an elegant ATP-sensitive, feedback biosensor into his recording set-up that he detected a difference in exocytosis. What he found suggests that the equilibrium between kiss-and-run and full-fusion exoc...