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Undergraduate Research

Undergraduate Research. Nicholas Celms Undergraduate BioMath Program, San Diego State University. Nicholas Celms. Computer Science major, graduating after this semester. Involved with UBM for approx. 2 years. Research: College kids that don’t care need not apply.

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Undergraduate Research

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  1. Undergraduate Research Nicholas Celms Undergraduate BioMath Program, San Diego State University

  2. Nicholas Celms Computer Science major, graduating after this semester. Involved with UBM for approx. 2 years

  3. Research: College kids that don’t care need not apply Undergraduate Biomath Program @ SDSU

  4. History on the relationship between mathematics and biology The Need for ubm

  5. History “The interplay between mathematics and physics has, in recent years, become so profound that the lines have been blurred. The two disciplines, long complementary, have begun a deep and fundamental relationship...” ~ Eric Zaslow

  6. History “Mathematics is biology's next microscope, only better; biology is mathematics' next physics, only better” ~J.E. Cohen

  7. “The lack of real contact between mathematics and biology is either a tragedy, a scandal, or a challenge, it is hard to decide which” ~ Gian-Carlo Rota History

  8. Presentation Overview

  9. Splits Graph of 45 Strains 22 strains of Escherichia, 15 strains of Salmonella, 8 strains of Shigella.

  10. Splits Graph of 3 Genuses Shigella and Escherichia Salmonella

  11. Presentation Overview I want all of you to understand my project, but I don’t expect that to happen in one day, or in one presentation. We will get as far as we can, but these conversations will continue this semester, so there is plenty of time for you to get it. Please ask questions and slow me down as much as you’d like, we’ll get through it by December!

  12. Biology: Background

  13. Biology: Background Salmonella, viruses, etc Us, plants, etc

  14. Biology: Background

  15. Reverse transcription transcription translation Biology: Central dogma of biology DNA mRNA Protein

  16. Biology: Background Every 3 base pairs of DNA encodes for one of the 20 amino acids Amino Acids form proteins, which are structured groups of amino acids that operate as the building blocks of life.

  17. Biology: Background Shorter sequences longer sequences

  18. Math: Graphs • Nodes/vertices are connected by paths/edges • They are a central concept in computer science

  19. Math: Graphs: Cliques A clique is a subset of a graph in which for every two vertices in the clique, there exists an edge connecting them.

  20. Math: Graphs: Cliques For example, vertices 1, 2, and 5 form a clique A clique is a subset of a graph in which for every two vertices in the clique, there exists an edge connecting them.

  21. Math: Matrices A Matrix is a rectangular array of numbers

  22. Math: Matrices Rows are strains, and columns are proteins in our matrices ai,j= 1 if strain i contains protein j , and 0 otherwise.

  23. Math: Matrices: Distance Matrix

  24. Math: Hamming Space: Metrics A metric defines “distance” between elements in a set. A metric for the set of US cities might define distance in miles, as the physical distance between the cities. In our case, we define a metric on a set of strains, and define distance as dissimilarity in proteins. For example, two identical strains have distance = 0.

  25. Bacterial dataset and viral dataset Data

  26. Bacterial dataset Escherichia, shigella, and salmonella

  27. Escherichia

  28. Shigella

  29. Salmonella

  30. Math: Graphs: Cliques For example, vertices 1, 2, and 5 form a clique A clique is a subset of a graph in which for every two vertices in the clique, there exists an edge connecting them.

  31. Finding Cliques

  32. Splits Graph of 45 Strains 22 strains of Escherichia, 15 strains of Salmonella, 8 strains of Shigella.

  33. Splits Graph of 3 Genuses Shigella and Escherichia Salmonella

  34. Applying This To Phages: What is a Phage? Short for bacteriophage, “bacteria eater” Viruses that infect bacteria Typically have a head/capsid, tail, and a base plate (image next slide) Usually 24-200 nm long Attach to a bacteria, inject DNA, and either kill the cell, releasing hundreds of new phages (Lytic), or lay dormant in the bacteria, with the potential to become Lytic in the future (Lysogenic) (video will help!)

  35. Applying This To Phages: What is a Phage?

  36. Applying This To Phages: What is a Phage?

  37. Applying This To Phages: What is a Phage?

  38. Applying This To Phages: Why is that hard? Horizontal Gene Transfer

  39. Applying this to Phages: Early Results

  40. Undergraduate Research Nicholas Celms Undergraduate BioMath Program, San Diego State University Questions?

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