Welcome to Dynamic Genome! This repository contains tutorials, molecular methods and other materials we will be utilizing in the Biol 020 Dynamic Genome Class. If you have questions and/or comments, please post them in the issues section of this reposoitory.
Your instructor for this until will be Dr. Holly Bik, an Assistant Professor in the Department of Nematology at UC Riverside. Her lab website is here: https://biklab.github.io
Before we get started on Week 5, please complete this pre-class assessment survey (it will only take 5 minutes!): https://goo.gl/forms/8Ct1Solza2oGglAE3
Mon Oct 29th - Begin DNA extractions of Nematodes (Click here for DNA extraction protocol), followed by introductory lecture on nematode research in the Bik Lab.
Wed Oct 31st - start PCR of three 18S rRNA gene fragments, using three different primer sets to be used per worm (Click here for nematode PCR protocol)
Mon Nov 5 - Run Electrophoresis Gels for PCR products generated last Wednesday (check for ~800bp gel bands and postive/negative controls worked as expected; Follow Electrophoresis Gel protocol here). Redo PCRs as needed for worms and primer sets that didn't work (Redo this same PCR protocol from last week). Short discussion on Botanic Gardens sampling - how to collect samples and location metadata.
Wed Nov 7 - Field Trip to UCR Botanic Gardens to collect soil samples for nematoe extractions. Click here for sampling guielines and procedures.
Mon Nov 12 - No Class (Veteran's Day)
Wed Nov 14 - Soil/Sediment extraction demo, portable SEM demo and begin nematode microscopy (taxonomic identifications and drawings). Redo any futher PCRs as needed to obtain good gel bands for all three primer sets for one nematode worm.
Mon Nov 19th - Continue nematode microscopy - picking and identifications. Use this Warwick & Platt pictorial key to morphologically identify your namatodes. By the end of class you need to 1) pick and mount a live soil nematode on a slide with a coverslip, and 2) use a permanent slide to make a taxonmy drawing of a nematode, identifying all the relevant natomical parts.
Wed Nov 21 Update lab noteboks (annotate gel images, fill in protocol steps), work on paper, and make sure all successful PCR products have been handed over for sequencing before Thanksgiving break.
Mon Nov 26th - Begin basecalling of Sanger sequences (quality checking and assembling sequences). Click here for DNA basecalling instructions for today's class Introduce BLAST and begin identifications of nematodes (using video capture images and web searches for morphology). Once finished with class nematodes, complete this extended exercise on morphology vs. DNA seqeunces
Wed Nov 28th - Finish basecalling of Sanger sequences. Link DNA seqeunces with nematode morphology. Find the images of the nematode you used for DNA sequencing and PCR in classs (Click here for the folder of images) - describe the morphological features you see and use the Warwick & Platt taxonomic keys (link listed above) to try and identify your nematode down to genus level.
Mon Dec 3rd Fill out iEval asssessments (click the link on Blackboard) as well as this post-course Google Doc survey
Section 25
Section 26
