I wrote a research article, but what does it mean?!?!?

I am in a room full of keys made of poison (don’t ask why). I grab one poisonous key to open a very specific door, causing me to let go of the slightly different non-poisonous key that has the job of adding an extra lock to the same specific door. This door leads to the tools needed to get rid of the other poisonous keys in the room by producing two tools. One can capture the poisonous key from my hand (or anywhere in the room) and hand it off to tool two, which throw it away out of the room. This continues until all of the poisonous keys are gone or at a low enough amount that I won’t succumb to the poison. The first tool also makes a tiny modification to the poisonous key in order to put said key through the slot of the second tool that gets rid of it. Keeping the door open for no reason is a bad thing (like the fridge door), hence having the non-poisonous key is good to have around which is what I had to let go to grab the poisonous key to open the door. Hence, too much of that non-poisonous key would prevent me from responding well or grab to the poisonous key…But what does it all mean?!?!?

It occurred to me that I wrote a scientific article and didn’t exactly say what I think it means to the field or to people that aren’t in the field. I’d like to take this time to correct that. In October of last year, I published my first senior author research article at the University of Arizona. It was entitled “Copper Chaperone CupA and Zinc Control CopY Regulation of the Pneumococcal cop Operon” in a journal called mSphere, and open access journal through the American Society of Microbiology. Now, before you run away screaming, let me try to explain what all that is. If you only partially understood the first paragraph, then you are in good shape.

Ok let me start by the obligatory, copper is toxic to a variety of bacteria, including Streptococcus pneumoniae or pneumococcus (yes, the one there is a vaccine for) and other potentially antibiotic resistant bacteria. We think understanding how copper kills bacteria is important to know so we can figure out how to make copper work better. We also want to know how the bacteria tries to fight back against the copper stress. We know somethings, like they have specialized systems for kicking out copper and these systems could be drug targets.

cupA paper model

The players:

S. pneumoniae has a copper export system, or the cop operon, to export copper (the poisonous key) that consist of an export protein (this exports the copper or the second tool listed above), a chaperone (this guides copper to the exporter for export and is CupA listed in the title, the first tool), and a repressor (this protein makes sure that the bacteria doesn’t make a bunch of proteins it doesn’t need, it, CopY, stops the cop operon from being on until it, see copper, then it releases the DNA so all three proteins can eventually be made aka, me in the story above). Zinc is the non-poisonous key listed. DNA is the door.

The article (which hopefully matches with the story above):

1. I mentioned that copper makes the CopY repression release the DNA, but zinc actually makes the protein clamp down on the DNA. These metals are right by each other on the periodic table so that is quite the effect. We didn’t know that happened with a metal export system before. Adding zinc with copper prevented the repressor from “opening the door” to the operon thus have the effect of killing the bacteria faster than just with copper alone. Copper and zinc make brass so this is known as my super hero name, the Brass Dagger.

2. If you look at the picture, copper II AKA Cu2+ AKA blue lighting (ok the last one is made up) comes into the bacteria, and copper I AKA Cu1+ AKA…well it’s brown like your pipes so…I got nothing…anyway. To get kicked out the cell, it has to be the 1+ version. That 2+ to 1+ is the gain of an electron, a negative charge hence the number going down. We believe that electron has to come from inside the bacteria somehow, but from what and from where? Well, we found that the chaperone (CupA) could give the copper an electron to make it go from Cu2+ to Cu1+. But where is that protein getting electrons from, stay tuned! Or better yet, why does it matter. Loosing electrons has to come at a cost to bacteria and we think trying to keep up with the copper reduction (that’s what adding an electron is called because you are reducing the charge from 2+ to 1+, like adding a negative number). This reduction ends up really harming the bacteria. This chaperone can also take the copper away from the repressor so that it can go back to “shutting the door.”

Hopefully the story above makes a bit more sense now in context.

Cool, can we exploit that? We think so, we hope so, but we need to keep digging. Anyway, that’s the paper. I hope you enjoyed this little review of my laboratory’s recent work. Happy to answer any questions.




Jumping into the Deep End of Science

I have this memory of when I was two or three years old. I have a floaty on me, but I have to jump into the water. I’m sure I was only two feet above the water and I was jumping towards an adult in the pool, but for me, it seemed to be 20 feet into swirling pool of sharks with laser beams on their heads.

laserbeam-sharkI was terrified. I was crying. But I jumped.

I don’t remember much about swimming until much later and by that time, I was already jumping into the deep end with a clear knowledge of knowing how to swim. Touching the bottom of the pool for fun and things of that nature. Swan dives and failed flips turned back and belly flops. I was comfortable in the pool. It took a while I’m sure, but I had to get over that initial fear by making that initial jump.

Recently, I jumped into a pool of a different sort. The pool of senior author research articles and major grant writing. This time, it is not a fear of drowning, but a fear of failure (although drowning under the shear amount of emails might be a real thing). But by becoming a PI, I knew this day would come. Not that I was just dipping my foot in the pool before, but these are bigger waters, bigger fish, and bigger stakes.

I just got back my first corresponding author research article paper review back and…um…it…um…well…at least the first reviewer and editor were kind, supportive, and helpful, but yeah, it didn’t go so well. I’ll refrain from talking about reviewer #2. Also asked someone to review my grant. Again, great, helpful, but soul crushing comments.

I am just fortunate that for this jump, I had a floaty. I had mentorship. I had someone I could ask for help. I had someones I could ask (and I’m sure they would point out the flaws in that last sentence). Do you have a floaty? If you don’t please try to find one. Try nrmnet.net, look for #BLACKandSTEM on twitter, go to your grad office, your boss, or just find a senior person and ask them (sometimes, it really is that simple). Engage the community you are in so you don’t have to recreate the mountain every time. Stand on shoulders, don’t succumb to the weight.

Even when it is the very nature of your position to jump, it is good to get the first one out of the way. It was exhilarating despite the outcome. It was terrifying, but maybe not as scarring as when I was younger (and clearly without the sharks with laser beams). Hopefully, because of the willingness to jump, and by finding floaties, I’ll be doing belly flops with a few low scored swan dives in no time.


State of the Scientific Union

Ladies and Gentlemen of the nation, it is with great disappointment I say that we, the scientific community, have failed you. We have hidden on our false intellectual pedestal. We throw around phrases like “you wouldn’t understand” and when we do try to explain, we start so far down the rabbit hole, it might have been better if we did not speak at all. For that, we cannot blame you for your ignorance. We cannot blame you when you become complacent about the importance of science or the lack of support (read funding). We cannot continue to complain to our colleagues, preaching to the choir, because in this case, the choir is not above reproach.

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We as scientists need to begin to cultivate relationships with our surroundings, not look down on them. We need to stop combating faith, but instead find common ground and work together (we are not enemies). We need to work with politicians, instead of always calling them out for their attack on science (again, we are not enemies). We must educate the public. The job of a scientist has changed. Each one of us is a scientific ambassador, whether or not we want to answer that call.

Above all, we need to stop saying “we need to” and simply just go “do.” If your involvement is minimal with the public, it is likely that your impact will be as well. Please allow me a moment of clarification though, we all have gifts and we naturally like to work within them, but changing the status quo will require us to step out of our comfort zone. Some scientist are better in the lab than in the public eye, but if that is you, find a constructive way to express, or have someone else express, the value of your contribution. Some people are much better in the lab, and some can hopefully do as I am right now, which is sounding the alarm, leading the charge from the trenches, and not standing on the hill. Reach out and reach often.

Moving forward, and moving now, I have a task for you. Find your “why.” Dig deep and truly reflect on why you do science. When you have it, write it down so you can draw inspiration from the reason. Next, express that to others. Notice I did not ask you to tell them what you do yet, or how you do it, I simply said just tell the why. If the public doesn’t know why we do something, then they will never care what it is that we do. If you find and communicate your why, I will guess that they will want to know “the what” of your science. But again stand firm, and state first the why. Why is it important to them, why is it relevant to them? Frame your problem in such a way that the listener wants to know what can be done. Then and only then, should you tell them the “what” and “how.”



Happy New Year Challenge!!

Happy New Year Everyone!!!


Ok scientists, I have a question, if I have to categorize you using an -ist, what would you call yourself (based on what you do, not your degree). Then a dash and what you do, then dash and what your degree is in. For instance I think I would be a microbiologist – biochemical host/pathogen interactions – biochemistry/biophysics. I’m curious to see how many categories we can get!! Use #ScienceClassify to keep track.


What I Learned in Journal Club #1

So this was cool. We discussed this paper in our most recent infectious diseases journal club.

Imagine this, you have spiderman, and he makes this web to catch bad guys. Some bad guys get picked up by the police and go to jail, but some bad guys actually use that very same web, cutting it in various ways, and turn it into a trap for the police. A trap that ultimately prevents those policeman from doing their job. How does this happen? How will you catch those bad guys now? Can you prevent the bad guys from cutting the webbing to hurt the policeman? Won’t someone please think of the children?

spiderman-webbing-wallpaper-free-download_Spiderman_wallpapers_78 2

Believe it or not, this process happens inside of you all the time. Here is a quick immune system primer before I get to how it is done.

Your immune system is really cool. It has various lines of defense. Most commonly, it is described as the primary response and the secondary response. The primary response (innate immune response) sees foreign things and tries to get rid of them with extreme force (usually it eats the pathogen to kill it). It isn’t very specific, it tries to get any foreign thing out fast. The secondary response (adaptive immune response) is the more specific response. Think of it as a group of soldiers that were literally born and bred to attack one thing and one thing only. They lay there waiting to strike until they see it then they take it down. And you can form millions of different groups to respond to different situations.

In the primary immune response, you have many types of cells. Here I will just tell you about two, neutrophils (cells that don’t live very long) and macrophages (cells that live longer). Both try to eat debris or invading pathogens. They also do a host of other things and each have a specialized function. Here is a really interesting video of a neutrophil chasing, tracking down, and killing a bacterium.

Now back to the spiderman story. The neutrophils actually spit out their DNA to form a web AKA a NET (Neutrophil Extracellular Trap) that bacteria can get caught in. This webbing has other things in it as well to help kill invading pathogens. Then the macrophages can come and scoop the bad stuff up and clear it from the body.

Here is where it gets interesting. A bacteria Staphylococcus aureus (Staph) has a way of getting out of the netting. Not only that, Staph can cut the DNA in such a way that is acts as a poison for the macrophages. Here is a write up about it. The actual article is subscription based. But if you are at a library or at a place with access, here is that article too.

So how do we get rid of the bad bacteria, we still have those secondary response soldiers. And we have research too, lots and lots of research.


Also, today is my 9 year anniversary. Yay us 🙂

And since you are still reading, make sure to subscribe.

It started with a Facebook post

My name is Dr. Michael D. L. Johnson. I have a B.A. from Duke University in music (yes music but that story will come later), and a Ph.D. in Biochemistry and Biophysics from University of North Carolina at Chapel Hill (yes the rival and that story will also come later). This is my science blog. Details of who I am will come later, but for now I will leave you with how this started.

I just want people to feel connected to the science that is being done. Feel proud, not afraid. So I posted something on Facebook and got some good dialog. Here it is, for better or for worse (hopefully for better).

“Yesterday I saw a talk from a prominent virologist. There was a bit of doomsday gloom with “what could happen” and it made me think of the way people think about scientific funding. People look at cancer, infectious diseases, and other illness’s and they get scared of what could be. So they say, we need to fund this project because I’m scared of the consequences if we don’t. That philosophy is clearly not working as many funding pipelines are drying up and it seems like fewer care as more begin to distrust. I acknowledge that there is fear of what scientist can do, or are capable of but please, reach out to us and have an open mind when we reach out to you. As we would believe you in how you do your job, have faith in how we do ours. Support us. Not out of fear, or even out of necessity. Support science out of pride, support science to be part of a solution, support science so that the latter will be greater. Yes, I know what it is that I am referencing there, how are we supposed to be put to work and take care of things that we don’t understand or worse yet, chose not to understand. Support us by trying to understand what it is we really do in laboratories because we like so many others are often not portrayed well on the TV screen. Support science to help mankind. Please understand that our discoveries are your discoveries, our cures are your cures, our triumphs are your triumphs.”

One great comment was “The increasing reports of misconduct and sloppy, irreproducible results is not helping science’s case unfortunately” to which I replied

What do we do then? No system is perfect; there will always be bad apples. Is there behavior excusable? Certainly not. Should we hide the results? Not at all. But by virtue of those who call out the research, colleagues calling out colleagues, or better stated, those who are qualified to call out each other, we are trying to balance ourselves. In truth, those reports should make individuals untrustworthy while making the community stronger; highlighting the strengths of the scientific method and peer review systems. We as a community are actively checking ourselves. The system isn’t perfect, misconduct will always happen and it makes a much better story that a kinase that you have never heard about (no offence to the kinase people, I’m sure it is a very important protein), but this is precisely the reason we need the support because there are so many obstacles to overcome. There is so much good to be done, call it naive but it does not make the statement untrue. That is the call to arms, that is what people need to take pride in, that is the battle.”

Then one of my dearest friends suggested I start a blog to get to my audience. Well…game on!!!