Max Win's Genomics Page

This web page was produced as an assignment for an undergraduate course at Davidson College.

The "Longevity" gene: Mass Media Vs. Scientific Writing

In recent years, researchers began to unlock the secret of some of the mechanisms that may prolong lives. One such mechanism is calorie restriction. By reducing the amount the food intake of animals such as worms, yeasts, and mice, researchers had increased their life spans significantly. How does dietary- restriction induced longevity work? What are the genes involved? Is there a gene that plays a key role for dietary restriction induced longevity? The following scientific article from Nature provides some insights into these questions...

Paper Review One

The researchers studied lactic acid-producing bacteria called Lactobacillus delbrueckii ssp. bulgaricus (L. bulgaricus). L.bulgaricus. L.bulgaricus is important because of its application in yogurt production. The environment that L.bulgaricus currently lives in contains abundant lactose-rich milk and stable proteins. L.bulgaricus have been living in this environment for at least 5000 years because "the first records of yogurt (kisim) were 3200 before Christ". The benefits of consuming yogurt containing L.bulgaricus include attenuation of lactose intolerance, immune modulation and diarrhea-alleviation. The assembled genomic sequence of L.bulgaricus is about 1,864,998 bp.The researchers claimed that there is an "extensive and ongoing reductive evolution" in the complete genome sequence of L.bulgaricus...

Paper Review Two

HTLV-1 Tax protein plays an important role in the development of Adult T-cell Leukemia (ATL). Because of its involvement in ATL, a significant amount of research projects has been conducted to study Tax’s functions and its protein interactions. According to the authors, a system for analysis and validation of these interactions is required to identify protein-protein interactions of no functional consequences. Thus, they have proposed two methods to indentify functionally significant Tax-protein interactions. One is the wet lab approach using affinity isolation of Tax complexes coupled to MS/MS analysis to construct a physical Tax interactome map and the other is the in silico approach using computer modeling and node graph visualization techniques to create Tax interactome node graphs of first and second neighbors of known Tax-binding proteins...

Perl Tutorial

The tutorial is for non-programmers who want to learn the basics of perl programming in order to solve problems related to biology.In this tutorial, I will use "SubEthaEdit" as the perl editor. If you have a Mac computer, you can download "SubEthaEdit" for a one-month free trial at http://www.codingmonkeys.de/subethaedit/ . This tutorial is divided into eight parts. For each part, there is an "Overview" section summarising which perl commands will be learned, an example including the source code and output, and a detailed explanation of the perl commands presented in the example...