Hey Y’all!

I am so excited that Amigo is finished! I feel like it came and went so quickly! We just got Amigo and now his annotations are almost complete. Our group, Olaf’s Fan Club, divided our section of the annotations into two groups, and Sierra and I annotated the last 18 genes of Amigo’s sequence. Most of the genes we had were fairly easy to annotate. Glimmer and GeneMark called the longest ORF, all the coding potential was covered, but there were no BLAST matches. This, though somewhat disappointing that we do not know what any of those genes do, made annotating a pretty quick process. The bulk of our time was spent on the large gaps in between genes. Between a lot of genes, there were 60-100 bp gaps, which is larger than expected for a bacteriophage but too small to have a gene in between. Sierra and I decided that Amigo had a less dense genome, so it will be interesting to see if other schools had the same type of problem with their genomes. Some of the gaps were over 200 bp and had little blips of coding potential, and in those we added genes. We are not entirely sure if some of the added genes are actually valid, but we used the guidelines and tried to do what looked the best. I cannot wait to see what the other groups came up with and if we are consistent in our annotations throughout the class!

I hope everyone has a wonderful and safe spring break!

Good luck on the test tomorrow!

Hey guys!

I haven’t blogged in a couple of weeks, but with the last class’ discussion on the seemingly indisputable conflict between science and religion, I thought it might be a good topic to blog about. I am a Christian, and I believe that the conflict between science and religion stems from confusion and misconception. Science aims to investigate the “how” of life, by explaining principles that govern the natural world and can be observed. Religion, on the other hand, seeks to find the “why” of life by providing a belief system based on God and the supernatural. These two things are fundamentally different, but people often compare them like they concern the same things. Take the Ham-Nye debate that happened a few weeks ago. I think that debates between creationists and evolutionary scientists are unnecessary and unproductive. Creationists argue the “why,” and scientists argue the “how.” The arguments used in these debates presupposes the false dilemma, an either-or argument, but the two parties are comparing apples and oranges. Each side asserts that because this is an apple, that cannot be an orange, and vise-versa. I think such arguments just leave the majority of people offended or confused, and each side leaves without anything being resolved. I found an article that I thought was interesting about the subject. The link is below:

http://www.abpnews.com/ministry/congregations/item/8417-can-christianity-and-evolution-co-exist#.UwQeefldWSo

Hope you enjoy!

Hey guys!

I know we have spent a lot of time in class discussing the mechanisms and techniques of biotechnology, but I wanted to show you this video that really shows the practical medical implications of this technology. “Cracking Your Genetic Code” is a NOVA special from PBS that talks about how different bioinformatics and genomic research is being used in medicine today to help diagnose and treat genetic disorders. There is also a lot of the bioethics conversation incorporated into the video, so you get to see how this new technology may alter society and other aspects of life. It also goes through the history of some of the technology. All in all, this special is really great and well made. I watched it in AP Biology last year, and it is what really got me interested in genomics. It’s available online for free, and it’s only about an hour long. If you want to supplement what we are learning in class, I would recommend this video. Here is the link:

http://video.pbs.org/video/2215641935/

Enjoy! I hope you guys like it as much as I do!

Hey y’all!

I hope everyone had a great Christmas break! It’s good to be blogging again! I did not have the chance to share the virus I researched in class, but I thought I would share it now. It is hands-down the coolest virus I have ever read about. It’s called the mimivirus and it infects amoeba. What is really interesting about this virus is the sheer size. It has a diameter of about 400 nm, which is the third largest capsid size ever discovered. It has an icosahedral shaped capsid, which contains lots of enzymes and the virus’ double stranded DNA genome.  The genome is large, at over a million base pairs! Its genes do not only code for the typical virus things, but also code for aminoacyl tRNA synthase, and other proteins involved in protein synthesis and metabolism.

What makes this virus even more incredible is how it replicates. After it is engulfed by the amoeba by receptor-mediated endocytosis, it uses its own enzymes to replicate its DNA and transcribe it to mRNA. Most dsDNA viruses send their DNA to the nucleus to be replicated and transcribed using the host’s mechanism, but the mimivirus uses its own. It has a viral core, which does not degrade in the host’s cytoplasm, that acts as the new nucleus of the cell. It has both RNA and DNA polymerases, which it uses in replication and transcription. After transcription, the virus uses the host’s ribosomes to make the necessary proteins for the capsid and enzymes inside the viral core. When more viral cores are made, those cores begin replication and transcription. This continues until the cell is lysed, releasing all of the new mimiviruses.

Crazy, right? This is one of the only known viruses that replicate in this manner!

If you want to know more about how the mimvirus works and how scientists discovered it, you should read this article:

http://www.pnas.org/content/107/13/5978.full

I love the name! And I have noticed that the Arthrobacter phage tend to have more angular heads while the M. smeg phage have more round heads. I love how you can see the true morphology of the phage from the electron microscopy. It is really interesting to compare pictures of our phage and note the differences from phage to phage.

Awww! Thanks Abby! I am so thankful I have you too. It makes it a lot easier when there is someone else there to check and make sure you are doing things right. This lab would definitely be a struggle without you and I on the same page.

I think this area of science is so interesting! I don’t know a lot about what it entails to make such a robot, but I know that they are trying to develop a similar type of robot to be used in the medical field. The idea is that every doctor would get this robot where they could enter in symptoms and facts about the patient and the robot would scan through all the medical records and science article regarding the symptoms and make a recommendation for the course of treatment for the patient. I think once it is fully functional, it would be a great asset to physicians who are constantly pressed for time. Hopefully, though, physicians will still be adept and not rely solely on the robot to make decisions.

Ugh! That must have been so frustrating! I will definitely take your word for it. Kirby was just saying today how glad she was that she kept her flood solution (she has used it three times since then). I will keep the advice in mind for when I get to that step.