New Evolution Lab 7

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Modesto Junior College *

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Biology

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Dec 6, 2023

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Lab 7 Worksheet Bacterial Evolution Name: TPS 1 : Are changes to colony morphology heritable? What do you think would happen if you inoculated a new culture with a wrinkly colony, grew the culture overnight, and then plated a sample of the bacteria? Changes to colony morphology are heritable because morphological changes are due to changes in bacterial DNA which is passed to offsprings. If we introduced a wrinkly colony into the plate then we would see more individuals with this morphology because these bacteria would reproduce overnight. This worksheet is organized by how a research article is setup. It will ask introductory questions, methods questions, results questions and discussion questions. In today’s lab, you will be doing a scientific exploration using bioinformatic tools ☺! Bioinformatics is an important growing field that does not require wet lab work. Instead, you can answer scientific questions using publicly available data and your very own computer. As a newly appointed bioinformatic researcher, you have been tasked in investigating what gene mutant causes the different phenotypic variations below. Additionally, you will also be choosing your own mutant to look at. Introduction: Q1: What are some benefits and drawbacks of using bacterial genomes to study evolution? (Name at least two benefits and one drawback)
If we are only using one genome to study evolution then it makes our study easier as it is easy to interpret genetic variation which makes it easier to study complex traits. Another benefit is that it can reduce the costs we need to study the evolution of target traits as we can keep the genome in the lab. One drawback to this is that since we would only use one genome, it can introduce biases which would make us believe that a complex trait is mutated a certain way when in fact it occurs through a different mechanism in our genome of study. Methods: Q2: Bowtie2 is called an “aligner” in bioinformatic tools. It “aligns” sequences to a reference genome. Using google scholar (or another article finder), find another aligner tool [hint: you can use the key words “bioinformatics aligner”] a. What is the name of the aligner? TM-Alinger b. What type of data does it use (DNA, RNA, single cell etc.)? Transmembrane proteins c. Cite the aligner’s article (in correct format, points will be removed if cited incorrectly). Example: Langmead, B. and Salzberg, S.L., 2012. Fast gapped-read alignment with Bowtie 2. Nature methods , 9 (4), p.357 . Bhat, B., Ganai, N.A., Andrabi, S.M. 2017. TM-Alinger: Multiple sequence alignment tool for transmembrane proteins with reduced time and improved accuracy. Sci Rep, 7. https://doi.org/10.1038/s41598-017-13083-y Now it’s time to find out your mutants! Using the mutant 1, mutant 3, mutant 5 and mutant 4 files, follow the slides starting from “downloading the all.var.tsv files” for each mutant. Results: Q3: For each mutant below answer ALL questions: How many mutations did you find? For each mutant: what is the “old” reference nucleotide and what base pair did it mutate into? What “type” of mutation is this? What is the function of each mutant? Paste the locus tag of each mutant (will be used later). i.e. Number of mutations: Base pair mutation: Type of mutation: Function of mutation: Locus tag: - If there is more than 1 mutation, fill this table out for each mutant. a. Mutant 1? Number of mutations: 2 Base pair mutations: C and T Type of mutation: single nucleotide change, nonsynonymous Function of protein: Sensory box/GGDEF domain/EAL domain protein
Locus tag: PFLU5329 Number of mutations: 2 Base pair mutations: G and T Type of mutation: single nucleotide change, nonsynonymous Function of protein: Chemotaxis response regulatory protein-glutamate methylesterase CheB Locus tag: PFLU1224 b. Mutant 3? Number of mutations: 2 Base pair mutations: C to T Type of mutation: single nucleotide change, nonsynonymous Function of protein: methyl-accepting chemotaxis protein Locus tag: PFLU1219 Number of mutations: 2 Base pair mutations: C to T Type of mutation: single nucleotide change, nonsynonymous Function of protein: Sensory box/GGDEF domain/EAL domain protein Locus tag: PFLU5329 c. Mutant 5? Number of mutations: 2 Base pair mutations: C to T Type of mutation: single nucleotide change, nonsynonymous Function of protein: Sensory box/GGDEF domain/EAL domain protein Locus tag: PFLU5329 Number of mutations: 2 Base pair mutations: CCCTGGAGCGCC to CCC Type of mutation: single nucleotide change, nonsynonymous Function of protein: Sensory box/GGDEF domain/EAL domain protein Locus tag: PFLU5329 d. Mutant 4? Number of mutations: 1 Base pair mutations: A and C Type of mutation: single nucleotide change, nonsynonymous Function of protein: Uncharacterized protein YfiR Locus tag: PFLU5211 Q4: What does the star at the end of Glu319* indicate? The star at the end indicates that this is a stop codon so the mutant should have a stop codon at the end. Discussion:
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