Author Archives: jeremysieker

Nostalgia and Brain Damage

I suppose it doesn’t make much sense to have some nostalgia before the year even finishes, but at the same time, it is crazy! I’m so glad I got to have this year with all of you guys. It seems like it’s been so long since we were sitting in BSB D310 enriching our third soil sample, trying to figure out why in the world we couldn’t find any phages. But here we are!

On a more scientific note, I came across this article today that talks about how exactly alcohol/other drug stressors can distress a fetus. With a mouse model, they were actually able to isolate the specific gene that fetuses seem to use to protect themselves from these toxins. However, what seemed interesting to me is that the article held a focus to the offspring’s future intolerance of the toxic substance, like alcohol, which is something that I never knew about.

This one’s for the guys.

Yup. Someone wrote a scientific article about whether or not beards are attractive.

The article also talks about negative frequency dependent selection. It’s the principle that the rarest phenotypes can often be advantaged by their uniqueness. That sounds like the most Hipster biological principle ever.

Pretty Cool

Okay, I’m reading this for my chemistry honors paper and I’m getting pretty excited cause it’s talking all about the genomics of Ebola and at least in the first few paragraphs, it’s all stuff that we have worked with in Arthrobacter! Not exactly the same things but it is so cool to be able to understand it!


Isn’t it crazy that given all our technology, all our accomplishments and research, but a little virus can still defeat us? It seems incredible that just because of a difference in genetic code and binding potential, an ebola virus is deadly, while a bacteriophage is just a bacteria lyser.

Finally Moving

Can I just say how nice it feels to be working on genomic annotation? I’ve been relatively un-surprised at the number of genes with unknown functions, but also at the number of genes with oddly-specific fuctions: or portions of a gene that code for things like immunoglobins that have no business being in a phage genome. I’m excited to see where this takes everybody in terms of the independent projects

Leishmania RNA virus

Outside of our little world, there are these things call NTD’s (neglected tropical diseases). One of the most common ones is called leishmaniasis, which is contracted by a sandfly bite, which transfers parasites into one’s body. We don’t really have these sandflies on this continent, so we are pretty safe from this, but check it out…in addition to the disease itself, turns out there is an additional infection spread by a virus that has come to latch itself onto the parasites. The Leishmania RNA virus seems to be an amplifier of all the contracted symptoms from Leishmaniasis. I want so badly for there to be a way to make it so this is no longer an issue. The central American strain of protazoans seem to be becoming resistant to the most common treatment, Antimony. Maybe there is a way to engineer a phage that can kill those little protazoa: it could make a huge difference.


Ok, I don’t know what it is, but something about neurology is just absolutely captivating to me. The idea of a nerve working with a charge and being SO precise about it is just dumbfounding to me. I mean, how can nerves be that precise and consistent when they are working with a charge as tiny as -50 milliVolts? I mean in my high school robotics competition, we had voltage gradation for different parts of the robots that made it so they would only work within a 3 or 4 volt range. If the stuff that us humans make can only work within a precision of 3000-4000 mV and that seems stringent, how much more amazing is it that God can make something (and trillions of that something) that works very precisely at changes as small as this. I don’t know, but it’s amazing to me. Take a second to think about how wonderful this all is. I mean, how ridiculous it all is! Just saying, we’ve got amazing stuff we get to learn about and we are some of the only few in the world that will ever get the chance to look into stuff like this as their JOB. Don’t waste any opportunities, guys.

Starting fresh

I’m pumped, I feel like this is where the actual ‘research’ begins, where we get into the real genetics and the true uncovering of something new. I was looking around to find some cool new thing about viruses and I actually found some stuff that really freaks me out

Who knew that the effects of a virus could be related to the onset of type 1 diabetes!? That’s crazy to me; between that and the possible effects that this phage stuff could have on treatment for tuberculosis, I’m really hoping we can find something new or actually discover something really important this semester. We’re going to do some cool stuff, guys!

I also found a pretty cool one about bacteriophages!

Unfortunately, this one is a bit defaming to phages, as it tells of how a specific phage targets and kills, “preys upon,” a bacteria that is neceessary for fixing atmospheric nitrogen into the soil.

Good semester guys

Even though none of this went quite like I expected, I’ve got to say this has been one of the funnest things. It’s been a fantastic semester, everybody. I’m pumped to dive in deeper this spring.

Last day of lab

This was it! It is a crazy, good, and bad feeling knowing that the lab portion of Phages has come to an end. Just think, guys, next semester we will have a whole new set of #phageworldproblems ! Today, this last day of lab, I came to find out that I accidentally left my restriction enzymes in the incubator for three days (36 times the optimal amount of time) so my restriction digests were VERY digested (except one, which didn’t digest at all…who knows?). But that gel was really cool! I had no idea what it was supposed to be showing but when Hao starting explaining it, it all started making a weird sort of sense.

The conclusions I have reached regarding many things in this class.

Science is crazy.

Mind = Blown.

Logic is No.

Still trying to figure out what happened

This has been rather confusing. my last two experiments have been a bit interesting, trying to figure out why my phage won’t show up (at all, even at a 10^0 concentration), and whatever my mistake was, it has left me phageless. I went in to do my Electron Microscopy and I broke Dr. Rushing’s perfect record, as she was unable to find any phages, and she had to give up after about 15 minutes of looking.

At this point, my options are very limited. Based on the current trends, my current lysates are all either faulty, contaminated, or simply containing a phage that refuses to grow (even my lysates that are from my purification rounds) and I have actually been forced to start a plaque assay from my original lysate: the one we all made together at the end of september.

It doesn’t matter very much, since we already have the phage we need, but it is just kinda discouraging to have failed like this. Oh well, I’m definitely looking forward to next semester’s lab more, now.

Hope everybody has a great break.