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Archive for September, 2009

Debora Afezolli

Hello everyone,

My name is Debora Afezolli and I am 1/4 of Team Origins. I was born on April 17, 1989, and I’m currently a senior at WPI majoring in Bio/Biotechnology.

I love music, clothes, my friends, my family, and everything else that’s wonderful in the world.

Debora Afezolli

Debora Afezolli

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Project Proposal Draft

Our project proposal draft can be found here:

http://docs.google.com/fileview?id=0B2qobUpVF8neNWVkOTczZGYtYmFkNC00ODQ4LWI2OWEtZmI0ODRjOTYzMzhh&hl=en

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Family Tree DNA is a service that provides the latest technology for genealogical research. They offer one of the largest DNA databases out of any company in the DNA business, with a total of 263,316 to date. Of these, 166,100 are Y-DNA records (what we will be collecting in Venice!) and 97,216 are mtDNA records.

They work in association with a scientific advisory board and also the University of Arizona Research Labs. The Family Tree’s chief scientist is Dr. Michael Hammer, whose expertise lies in the study of the variations of the Y chromosome as a model system to explore human evolution.

Population geneticist are able to use variations on the Y chromosome to create a phylogenetic family tree. The changes in the genetic code are known as Single Nucleotide Polymorphisms  (SNPs), or simply base pair variations. Scientists are able to determine when these changes diverged from one another, and can subsequently create these elaborate family trees.

Human migration pattern according to Y-chromosome variations

Human migration pattern according to Y-chromosome variations

An SNP marks the a branch in the y-chromosome phylogenetic tree, and the branch points are known as haplogroups. These are named as A-T. The sub-branches are further known as subclades, which can also be tested by the Deep Clade Testing offered by the Family Tree DNA.

Origins are determined by the haplogroup: for example, Haplogroup E originated 50,000 years ago and has been linked to Neolithic expansion of peoples into Southern Europe.

Family Tree DNA actually provides the DNA tests to the Genographic Project, one of our sponsors. It might be worth our time to start a Venetian project with them, to specifically focus on the origins of its inhabitants.

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This is a general outline of the methodology used by the B08 Origins Team, when performing their DNA testing.

Before testing can begin, permission to use humans as subjects must be obtained. The B08 group received this clearance from the WPI Institutional Review Board, by filling out the appropriate paperwork and submitting it for review.

Dr. David Comas outlined a general protocol for the collection of DNA samples in and around Venice. He stipulated that all of the participants should be male, and above the age of 18. They should not be related, directly (no siblings, fathers/sons, uncles/nephews, etc), and the grandparents of the participants should be from the same geographical area. Once these stipulations were met, each individual was to read and sign the informed consent paperwork. He also suggested that neighboring regions, such as Friuli Venezia Giulia, Trentino Alto, Adige, Lombarida and Emilia Romagna (etc.) be tested as well.  

The informed consent paperwork outlines the purpose of the project, collection procedure, storage of the sample, potential risks and benefits for the individual, and declaration of confidentiality.

Once the paperwork is signed, the individual is then subject to the cheek swab, administered by one of the IQP group members. The swab is opened, and removed, carefully, so as not to touch the collection tip. The collection tip is then scraped firmly against the inside of the participant’s cheek (roughly about 5-6 times, or 10 seconds). The tip is then ejected, using the plunger at the end of the handle, into the appropriately labeled 2mL microcentrifuge tube. Each participant then receives an information card that has their sample number and directions to obtain information on their sample via the Genographic website.

There is not much mention of how they targeted their subjects. Further research must be done to determine the best way to do so.

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All of the records of the ancient city of Venice are kept in the Venice State Archives. It was established in 1822 in order to “reconstruct the constitutional make-up of the Venetian Republic bringing together all the records produced by the Venetian magistrate back to the 7th century A.D.” The State Archives is the former convent of the Minor Friars at “I Frari.” It is one of the oldest archives in Italy. All of the documents housed at the archives are related to Venetian history, more than 1,o00 years of records. The shelves are about cover a combined distance of about 90km.

The Venice State Archives are important for three, very important reasons (among others!). The first is that they allow for the preservation of the entire history of the Venetian Republic, in document form. They also give historians an understanding of what it was like to be a Venetian, in a given time period. These documents explain things such as Venetian “boat-building, navigation techniques, knowledge of accounting…and warehousing methods.” Additionally, they show the close “network of linkages” between the famous Venetian artists and their many patrons. The art around the city can be greater understood with a deeper knowledge of the creators. One last reason is that these handwritten pages are important for the study of writing and for the study of writing mediums.

There was a project that lasted from 1995 to 1998 called the VENetIan Virtual Archive. It seems relatively similar to the Uscript program started by WPI IQP groups. Its main goal is to preserve and improve the system of consultation of all historical documents in the Venice State Archive, in addition to the Marciana National Library of Venice, the Cephalonia CounThis is one of the documents used on the VENIVA site, when talking about the War for Candiaty Archive and the Austrian State Archive. This program was to make an internet application that utilizes remote access to make these documents readily available to the public. Additionally, various “cultural institutions,” which includes libraries and other archives, will be able to access the application without charge, or a minimal fee for additional services. A paper published in 1997 talks about the software used to create this application. After perusing the site, it seems like an interactive history lesson that is based off of maps, letters and drawings (similar to the one shown) from was the participating archives.

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Uscript

Uscript is a web application that was created in an attempt to automatically transcribe the Venetian manuscripts.  Previous MQP’s have worked on this and have set up a system that allows for easy access and transcription of the manuscripts.  The system also allows for historians to add translations to the data.

This system allows for the manuscripts, that Venice has treasured and that hold the Venetian history, to be preserved digitally for future generations.  By using Uscript the historians can also organize and classify each manuscript as they traVenetian Manuscriptnslate them.

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Simtable

The newest generation of a Simtable is a Sandtable.  A Simtable is used to simulate possible situations and view the outcomes, such as natural disasters including forest fires and flooding.  The Sandtable is a new generation of Simtable that allows the user to control and view the outcomes of different situations.newTable2

In the online demonstration, the Sandtable shows how much faster and easier it is to use then previous simtables.  It allows for easier setup and it is automated, which allows for real time data viewing.  The simulation that was run demonstrated contouring the sand into a landscape then adding foliage and simulating a forest fire.  The program also allows the user to change the wind direction, which in the simulation has a large effect on the forest fire.

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