Archive for March, 2014

Mar 05 2014

Amigo is annotated!

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downloadAfter four straight lab periods of staring at “No known functions” and 1200 bp gaps with no coding potential, we are finally done! I don’t know about any of you guys but I know that I certainly did not expect there to be so many genes with no matches or known functions. It really helps show just how little is known about these little guys and how much new information can be derived from a single phage’s DNA. While it may have been frustrating for us to have so little definitive knowledge as to what the genes do, what we just did will help connect puzzle pieces so that in the future these gene’s functions can be determined and the database can be expanded. Yay us, go team!

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Mar 05 2014

Adipose fins

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Some researchers are looking at another morphological structure of modern day fish to investigate fish evolution.

“Adipose fins are small, fleshy and usually not as elaborately structured as other fins. Although some 6,000 species of fish—including trout, catfish, and salmon—have them, relatively few researchers have studied these structures in the last half-century.”

They plan to explore early changes that may be linked to the transition to tetrapods.  The beauty of cience is there is always another question!


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Mar 05 2014


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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!

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Mar 05 2014

Amigo’s Genome

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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

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Mar 04 2014

Genome Gap

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Mar 02 2014

Neanderthal Lineages

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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

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