Molecular Ecology

ISSR Analysis/Concatenating Alignment/Inferred Phylogenetic Tree

In lab we set up a ISSR reaction on a large gel for the Lupinus arboreus. First, we directly added loading 1μL dye to the PCR tubes because we were not going to sequence the PCR reactions. Next, 5μL of… Continue Reading →


To begin the protocol we made two sets of 1:10 dilutions of our plant samples form the previous week. Each Lupinus arboreus sample was placed in a labeled 1.5 mL tube with its unique label. 45 μL of water and… Continue Reading →

Plant Samples: Analysis of EPIC Markers

We did not successfully sequence forward and reverse reads of EPIC makers for approximately 25 individuals of Mimulus cardinalis from various locations. Instead of using our own data for the protocol we used the sequences of previous classes. The first… Continue Reading →

Plant DNA PCR-EPIC markers

Before beginning the protocol for the October 24, 2018 lab, we ran gels of the three DNA plant samples we extracted the week before. The gels were loaded with the samples of an entire lab table. The loading dye was… Continue Reading →

DNA Extraction with modified Alexander et al. tube protocol

For the Plant DNA extraction lab a modified Alexander et al. tube protocol was followed. Filtered tips were used throughout the entire lab. Form the distributed samples, each person was assigned three different plant samples. Along with the samples 2.0… Continue Reading →

Phylogenetic Inference Lab- October 10th

On the day the lab pertained to phylogenetic inferences we arrived with an alignment of COI sequences including our own sushi DNA and 25 sequences form NCBI obtained through Geneious. The protocol instructed us to clean up all the sequences… Continue Reading →

Introduction to Geneious

On October 3rd we were introduced to the Geneious software program. The lab revolved around the interpretation of the sushi sequence we collected the durning the last laboratory session. Since we had already downloaded the program onto out laptops before… Continue Reading →

Molecular Ecology Field Trip to see the Purple-flowered Lupine and Mimulus Cardinals

On September 26, 2018 the class took a trip to Mt. Tamalpais to see the  Purple-flowered Lupine and Mimulus Cardinals. The first stop to led us to hike down a steep hill to a small stream. Unfortunately we did not… Continue Reading →

Lupinus Arboreus Plant Field Trip

On the 19th of September the class took a trip to the coast south of USF to see the Lupinus arboreus population. The first stop was on atop a hill side parallel to the ocean. There the class observed a… Continue Reading →

Lab #3: PCR Clean Up Protocol

First the PCR products from lab two were run through electrophoresis. The content in the five sample tubes were pipetted onto a row with five dots of Loading Dye. When each sample was pipetted the pipette tip was exchanged for… Continue Reading →

« Older posts

© 2019 LEXLY'S LAB NOTEBOOK — Powered by WordPress

Theme by Anders NorenUp ↑

Skip to toolbar