Undergrad Research Experience

Fall 2020

Participants

• 'Eamen Ho': Volunteer research assistant
• 'Ramandeep Singh': BIOL 48002
• 'Desiree Pante': BIOL 48001
• 'Afsana Rahman': Volunteer research assistant
• 'Roman Shimonov': BIOL 48002
• 'Justin Hiraldo': BIOL 48002
• 'Zaheen Hossain': Volunteer research assistant

Schedule

• Tuesdays at 12 noon - 2pm by Zoom
• Sept 1, 2020. Week 1. Meet & Greet; Intro to projects
• Sept 8, 2020. Week 2. Presentations (background, data, and methods), based on assigned readings

Project 1. Structure & evolution of multipartite genome of Lyme disease bacteria

• Participants: Desiree & Ramon
• Readings
  • Review: deCenzo & Finan (2017).
• Data set: lp54 & cp26 plasmids
• TO DO:
  • Week 1. 9/8/2020, 12 noon: 5-slides presentation on multipartite bacterial genome evolution (based on the paper above)
  • Week 2. 9/15, 12 noon: Use prorgram codonO to calculate codon bias (SCUO) for replicons (n=23) on Borrelia burgdorferi B31 genome

Project 2. OspC Cross-reactivity analysis

• Participants: Justin, Roman
• Readings: Ivanova et al (2009)
• Tool: ImageJ
• Data set (to be sent)
• To Do
  • 9/8/2020 12 noon: 5-slide presentation on background, material & methods, and data capture using ImageJ

Project 3. Clostridium transcriptome analysis

• Participants: Eaman, Zaheen
• Readings
  • SPARTA pipeline
  • Fletcher et al (2018).
  • Gu et al (2018)
• Data set: posted on "genometracker.org"
  • Wild type transcriptome at 12 hour, paired-end read files:
  • /home/azureuser/18134XR-29-01_S0_L001_R1_001.fastq.gz
  • /home/azureuser/18134XR-29-01_S0_L001_R2_001.fastq.gz
• To Do
  • 9/8/2020 12 noon:
    • A short presentation on C. diff transcriptome (one of the 2 papers above)
    • Demo on read quality using FastQC and mapping reads to reference genomes with bowtie

Project 4. Protein classification using natural language processing

• Participants: Afsana
• Goal: Classify protein sequences
• Readings:
  • Rives et al (2019)
  • Lan et al (2019)