Today we found a much more efficient method of merging our annotation work.  We got in our groups and discussed our reasoning for extending, inserting, deleting the genes.  This process actually worked wonderfully!  We almost finished and came to a consensus on the entire genome.  However, one thing I learned was just the uncertainty of science.  The importance of educated guessing and asking stupid questions became so much clearer to me in this lab. There were many points in lab today where no of us had any idea of what we were doing.  There was no evidence either way, and we simply had to make an educated guess in one direction.  Because this genome has never been annotated, we are exploring totally unchartered territory.  We are researchers asking stupid questions and making educated guesses, hoping it will lead to further understanding!

Hey guys! Check this out. Its super cool.

Evolutionary and developmental biologist Ulrich Technau and his team at the University of Vienna have discovered that sea anemones display a genomic landscape with a complexity of regulatory elements similar to that of fruit flies or other animal model systems. This suggests that this principle of gene regulation is already 600 million years old and dates back to the common ancestor of human, fly and sea anemone. On the other hand, sea anemones are more similar to plants rather to vertebrates or insects in their regulation of gene expression by short regulatory RNAs called microRNAs. It assumed that plant microRNAs arose independently from animal microRNAs, but their evolutionary origins, as they state in the article, is unclear. This is the first qualitative difference found between Cnidaria and “higher” animals and the findings provide insight on how important levels of gene regulation can evolve independently.

http://www.sciencedaily.com/releases/2014/03/140318113816.htm

I was looking at my twitter account the other day and found this article posted by Scientific American. Being the nerdy person I am, this is basically the only stuff on my twitter feed.

While the end of this article does point out possible selection bias on the part of the researchers, I found this to be extremely interesting. Until reading this article, it had never occurred to me that all of the autistic individuals I know or have heard of are male. This is definitely something good to read if you are interested in genetics!

http://www.scientificamerican.com/article/females-are-genetically-protected-from-autism/?utm_source=twitterfeed&utm_medium=twitter

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!

Yesterday, an article was posted on a biology news site concerning research done on lentiviruses.  Lentiviruses are retroviruses that are used as vectors.  They are used as vectors to exchange/replace certain genetic material in cells.  One issue they were confronted with concerned the target cells with these lentiviruses.  How do they minimize the amount of virus cells used, while making sure the viruses attach to target cells alone?  Research was done at an institution in Germany concerning these questions, and major developments were made.  The scientists at the research institution covered the surface of the viruses with specific glycoproteins fused with an antibody.  When facilitated by the glycoproteins, the viruses  attached only to the target cells.  This, in turn, resolved the second question raised.  Because the viruses only attached to the target cells now, the rate of “infection” was much quicker, therefore less lentiviruses were needed.  This research has great medical significance.  This more efficient procedure can be used in gene therapy now to treat specific genetic disorders!

This is just a brief/quick post about the research being done all around us everyday!

So this week and last week, my group had so much fun annotating Amigo’s genes. Our group finally finished on Monday. On Monday, we found the major tail protein for Amigo. It is so cool to find genes that code for proteins that are structurally important to our phage. We did find a gene between gene 20 and 21. It coded for a hypothetical protein, and it had good coding potential. I can’t wait to see what you guys found when we collaborate together

Since we are currently studying evolution, I thought I would post about some recent discovers in our own lineage. Recently, some scientists from the University of Washington put the mystery of the Neanderthal extinction to rest. By sequencing modern human genomes, the scientists discovered that more than 20% of the Neanderthal genome survives today through contemporary humans. This proves that humans and Neanderthals interbred somewhere along the line. What I find most interesting is the selection from these genes. It appears that the Neanderthal genes for skin pigmentation were more fit for local conditions at the time (due to the high amount of Neanderthal DNA present in the genes known to contribute to skin pigmentation). Moreover, the genomes appeared to have been mismatched at certain points, due to the low concentration of Neanderthal DNA in other parts of the contemporary human genome. For example, a strong depletion of Neanderthal DNA was found in a gene that is thought to play an important role in human speech and language. If you wish to read the article, it is linked below.

Neanderthal lineages excavated from modern human genomes

As many of you know, our class has finally begun to annotate Amigo’s genome!  I learned two things really fast.  Firstly, Dr. Gibbon and Dr. Adair were right – you eventually get the hang of what you are doing.  A few posts ago I was complaining about how confused I was in lab.  However, I am pretty sure that I finally got the hang of what I was doing today!  It is an exciting feeling not being totally confused in lab:)  Secondly, I am learning that a lot of scientific research is educated guessing.  For example, Yasmene and I are annotating part of the genome together.  There was one section where we thought a potential tiny gene could be inserted.  A few classmates said no.  A few classmates said yes.  One teacher said no.  One teacher said yes.  In the end we decided to insert the gene because of the high coding potential.  However, all of that goes to say that a lot of what we are doing is opinion based.  It is totally up to our decision making if we insert, delete, or extend a gene – that is a lot of pressure it feels like!

Hey Guys,

I can not wait to start on our genome tomorrow. I have been anticipating this day all semester. To celebrate this milestone, I found an article on the history of phages, and how phages are used in phage therapy. We have read some of this stuff before, but there is some new information dealing with how we found phages. I would look specifically at the “Discovery of Bacteriophages and Early Phage Therapy Research” part of the article. This part has some neat history.

http://aac.asm.org/content/45/3/649.short

As we speak on the topic of human evolution, a recent study has shown that nearly 20% of the Neanderthal DNA is matched in the human genome, including numerous skin genes that may have contributed to our adaptation to the ancient environment. Benjamin Vernot, a population geneticist at the University of Washington, speaks on the importance of technology in making such discoveries: “I think it’s really interesting how careful application of the correct statistical and computational tools can uncover important aspects of health, biology and human history.” This is applicable to both our topics in class and in lab – the very techniques we are utilizing in lab are very much alike to those that other genetic scientists are using! From studying molecular trends we can attribute those findings to larger forms of life, and how they are all interconnected. He also stated that in the future, scientists may be able to examine and determine hominid ancestors just by studying human DNA: “…the “fossil free” method of sequencing archaic genomes… holds promise in revealing aspects of the evolution of now-extinct archaic humans and their characteristic population genetics…scientists will be able to identify DNA from other extinct hominid, just by analyzing modern human genomes.” This is both very exciting for in shedding new light on human evolution, but also emphasizes that the research we are performing on bacteriophages can relate to the data analyzation that scientists are using in their own labs, and that it is indeed the future of science. Pretty cool!

It finally hit me this morning: we are actually doing research.  This sounds like a horrible fact to just realize.  Firstly, it sounds stupid.  And secondly, you would think that I would have figured this out by then.  However, it finally hit me just today that the research we are doing has not been done before.  All throughout high school I just repeated experiments given to me by my teachers.  However, we are now entering the area of science/research, where we actually have freedom.  We can research what we want convening phages, and we will have to present on it!  Our class has the potential of noticing something that has never been noticed before.  We are not just repeating experiments that other scientists already have the answers to.  Our research is actually being used for research by scientists!  This just finally hit me today – so I figured I should post about it:)

As you all write your papers, maybe think about these ideas

Did God Create Earth with an Appearance of Age?

Maybe I am the only one who gets like this, but many times as I am studying something, I lose sight of its importance.  After investing hours of time into something I get fed up with it and ask myself, “Why should I even care about this?”  Therefore, today as I was thinking about biology lab, I stepped back and asked myself, “What is so important about phages anyway?  Why do we care so much about them?”  In my opinion, if there is no real purpose to studying something, why study it?  Now I could probably convince myself that the study of phages is important solely for the fact that it enhances my research and learning abilities, and knowledge learned in this field can apply in other fields.  However, those reasons are not very satisfying to me.  So I, as any student in the modern era would, googled why phages were so important.  What resettled actually surprised me.  Therefore, if you are in the place that I was and felt a little discouraged with the study of phages, read on!  Maybe we already knew this, and I forgot about it, but either way I am going to restate it.  Phages have much importance to humans!  In fact, there is a method called phage therapy that can help humans fight against bacterial infections.  Yes, we do have antibiotics to help fight these infections.  However, scientists are encountering numerous problems with antibiotics.  Bacterial cells are “evolving” and becoming resistant to these antibiotics.  One may say that the cells may soon become resistant to the phages as well.  However, there is a much lower likelihood of this happening, and based on the development of phages, the phages should be able to combat against any resistance.  This is only one of the many applications of phages!  Therefore, do not lose hope!  Our study of phages is not for nothing.  There are many advantages and possible applications with the study of phages!