INTERNSHIP CANCELLED- WEATHER

Jan 12th 2012,

The internship was cancelled today because of weather; my mentors Mr. Adams and Ms. Urban couldn't drive to the museum therefore I couldn't go in as I won't have anyone to work with.
With the new free time I am reviewing the basic concepts of the research such as the Eukaryotic Cell, the Mitochondrial DNA, Sequencing and the phylum Lepidoptera.

MITOCHONDRIAL DNA BRIEFING

Jan 05th 2012,

I went to the NY State Museum in Albany to get started on my Internship. Unfortunately due to miscommunication Mr. Adams was not expecting me therefore he did not have anything for me to do in the lab. However I did get the chance to finally meet my second Mentor Ms. Urban, she briefed me on what she panned to do next week-Mitochondrial DNA.

She explained the most basic part of the research, the DNA. She went back a far as to the structure of the Eukaryotic cell to make sure I  understood what exactly I will working with. With the very short briefing I found out that the most of all DNA are from the Mitochondria. Ms. Urban also explained to me that they are conducting the research because they already know that Centuries ago what we now know as different species ( Of Moths in this situation) used to be one thing. The Mitochondrial DNA changed and mutated over the years to produce different species; but because the Mitochondrial DNA changes very slowly over time one can still tell which species are related by sequencing the DNA thus the research.

Ms. Urban also showed me a website that contains all the papers ever written about the research I will working on and many others "Genbank.com" she said. She showed me results they got from the research they had done in the past, and what to look for to know whether or not the experiment showed any relation or results.

I couldn't stay long at the Museum because Mr. Adams had to leave early since he was not expecting me. I left an hour earlier than I usually do, but as usual with new very interesting information that makes me even more excited to start collecting the DNA.

Multilocus Resolution of Phylogeny DURING X-MAS BREAK

Dec 22nd and Dec 29th

I didn't go to the Museum at all these two weeks because I am on Winter break.
I will go back after break on Jan 05th 2012.
Meanwhile Mr. Adams gave me a paper about butterflies to read so that I can familiarize myself with the name used for the insects. The paper is titled: Multilocus Resolution of Phylogeny and Timescale in the Extact Adaptive Radiation of Hawaiian Honeycreepers. 
I have not yet began reading the paper but I am excited to learn more about the genome and the phylum in general.

LENGTH VARIATION AND BARCODING, SEQUENCING

Dec 08^th 2011

The paper that I read from the first meeting really helped me understand a lot about the research. The paper is in extensive detail of what the research is about, how it is done and the expected results.

I learned that what I will be doing is sequencing and length variation of the Moths. Sequencing is used to identify species and the relationship they have with other species. In this research I will be sequencing entire mitogenome of a specific species of Moth and determine whether or not different species are related or were once related. In the paper they worked with the mitogenome, Agehama Maharo[1] that is said to be the longest mitogenome found in any Lepidoptera. And like Mr. Adams and Ms. Urban research they are determining this particulars species’ relationship with other species of its kind.

To be able to sequence one must use the bar coding system, which is simply a method that analyses the way DNA materials are arranged. So far particular parts of the genome are said to be best with Sequencing/ Bar coding; cox1 and cox 2 [2]. The research with Agehama Maharo also used other parts of the mitogenome like atp 8 and 6, nad 3 and 6, cob to nad 6 that are strong alternatives to cox 1 in identifying closely related species[3].

In the paper I also learned the meaning of a couple of things that I didn’t understand before. Phylogeny is the study of history of an organism or evolution of genetically related group of organisms.

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[1] The Complete Mitochondrial Genome of the Near-Threatened Swallowtail,
Agehama Maharo (Lepidoptera: Papilionidae): Evaluating Sequence Variability and Sustainable Markers for Conservation Genetic Studies.

[2] The Study from Taiwan (the paper above)

[3] The Complete Mitochondrial Genome of the Near-Threatened Swallowtail,
Agehama Maharo (Lepidoptera: Papilionidae): Evaluating Sequence Variability and Sustainable Markers for Conservation Genetic Studies

REVELS WEEK. INTERNSHIP POSTPONED

Dec 15th 2011

The meeting this week and of next week have been cancelled because I am rehearsing for Revels.
Next week I will be in Thanksgiving break so I can't make the internship. I start again on Dec 01st 2011.

LEPIDOPTERA: PAPILIOMIDAE RESEARCH FROM TAIWAN

Dec 02nd 2011

The Internship was cancelled today because Ms. Julie Urban still couldn't make it and Mr. Adams needs her to be around for me to start working in the lab.
However I am reading the paper Mr. Adams gave me on our first meeting. The paper is very long and is titled: "The Complete Mitochodrial Genome Of The Near-Threatened Swallowtail, Agehana Maraha (Lepidoptera: Papiliomidae): Evaluating Sequence Variability and  Suitable Markers for Conversation Genetic Studies".

I have read 1/4 of the paper and it helps me understand the research a little better and I get the idea of what I will be doing in the lab.

INTRODUCTION TO INTERNSHIP AND MOTH RESEARCH

Nov 17th 2011. 

FIRST MEETING WITH MENTORS:

Mr. Calos and I went to the NY State Museum in Albany to meet one of my mentors, Mr. Sam Adams for the Science Internship. I had an agenda for the meeting and I was to be introduced to what exactly Mr. Adams and Ms. Urban are working on and what my role will be for the next few weeks. 

Upon arrival my mentor Mr. Adams took us upstairs where the labs are located and where I will be doing my internship. He also showed me ID cards that I must soon have to have access to the lab and how they work. Mr. Adams explained that his partner, Ms. Julie Urban was on a trip therefore couldn't make it to the first meeting. In the meeting we reviewed the Research program with Mr. Adams and Mr. Calos; I was to have a 2-hour session every week and take on small projects in my mentor's lab. The goal of the Internship is to deepen and authenticate my experience in the laboratory. In addition I am expected to present my work at the end of the year to the school. There will also be an evaluation by mentors in May. After going through the scheduling and review of the program Mr. Adams gave me a short introduction to what exactly the Research I will be working on is about.

The research that Mr. Adams and Ms. Julie are working on, which I will be working on as well in about Moth Evolution. He explained that the research is on Genomics particularly on the Mitochondrial set of the Moths depending on the host cell.  After collecting data from the Moth DNA and reading the results, a “Bar Code” method of decoding to see if they get the results they expecting.

My job in the lab will be to collect the DNA from the Moth then from it design Primers to start the chain reaction of duplicating the DNA. Mr. Adams also mentioned that the Moths I will be using are old and delicate and so their DNA might not work, but hopefully with the methods they’re trying on it will. I am also expected to put the Moths in families and make the genome robust and inclusive.

This first meeting was very interesting must was mostly confusing on my part. I had so many questions at the end of the day, I didn’t know what Primers were, or the Bar code method, and above all the family of the Moths I might be working with.