Week 3 Lecture 29JAN2024 - Plant Anatomy & Stomata Regulation - PDF

PMB 3005W Jan 29, 2024 Reminders: - click ‘Complete’ on your eLabJournal journal entry before the assignment due date. - Add a new section for the assignment answers. - Either embed your images or attach them as a single PDF to eLabJournal. - After Thursdays lab I will post the papers for Writing As...

PMB 3005W Jan 29, 2024 Reminders: - click ‘Complete’ on your eLabJournal journal entry before the assignment due date. - Add a new section for the assignment answers. - Either embed your images or attach them as a single PDF to eLabJournal. - After Thursdays lab I will post the papers for Writing Assignment #1. What We Learned Lab 1 – Plant Anatomy Recap Shoot apex Stem Root Endodermis Pericycle Int. J. Mol. Sci. 2015, 16(8), 19195-19224; https://doi.org/10.3390/ijms160819195 Cortex Epidermis Phloem Xylem Flower Two main reproductive structures: ○ Carpel - female organ with ovules or egg cells ○ Stamen - male organ containing anthers that shed pollen Dicots and Monocots Dicot seeds contain an embryo with two embryonic leaves (cotyledons) Monocot seeds have one cotyledon. https://courses.lumenlearning.com/wm-biology2/chapter/development-seeds-and-fruit/ Dicots and Monocots Dicot seeds contain an embryo with two embryonic leaves (cotyledons) Monocot seeds have one cotyledon. Seed Leaf Leaf Epidermis Lab 2 Stomatal Regulation SCIENTIST OF THE WEEK Stomata as a model for studying cell fate and stem cell renewal Dominique C. Bergmann Professor of Biology – Stanford University Associate of the Stanford Institute for Stem Cell Biology and Regenerative Medicine HHMI Development 2012 139: 3683-3692; doi: 10.1242/dev.080523 Making a difference: stem cells, asymmetries, and stomata https://youtu.be/C66MFIl_Y6k Stomata are the site of gas exchange in the leaf Stoma are: - located on the leaf epidermis. - formed by 2 guard cells. - needed for uptake of carbon dioxide that will be made into sugars and release of oxygen, which is a byproduct of photosynthesis. - openings are required for the release of water vapor through a process called transpiration, this is what drives the transport of nutrients from the roots to the shoot. - critical to control for plant survival. Stomata are the sites of gas exchange in the leaf Stoma – singular Stomata – plural stomate – singular stomates – plural Each stoma or stomate contains two guard cells Opening between two guard cells is called stomatal aperture H2O is smaller than CO2 so more water leaves than CO2 enters, CO2 has to travel further from the atmosphere to the chloroplast but water just moves from the leaf cell surface to the atmosphere Stoma are considered to be either open or closed Opening and closing of stoma depends on the shape of the guard cells Turgid guard cell Vacuoles filled with water Stoma open Flaccid guard cell Stoma closed Expansion is driven by the influx of water 1. Blue light perception by the photoreceptor activates proton pumps 2. K+ channels open and K+ enters passively 3. Energy of proton gradient used to bring in anions such as Cl- into the cell 4. Water potential decreases in cell causing water to enter 5. Turgor pressure increases 6. Cells change shape and open stoma Lab 2 - Goals Determine the effects of: ○ Light ○ The plant hormone ABA ○ The plant toxin fusicoccin ○ Increasing the osmotic pressure of the guard cell environment (1M sucrose) on stoma opening and closing It is important for everyone to measure the aperture width in the same fashion. *Plant seeds for abiotic stress lab! Use the provided cameras to maintain the same scale for every image. Hypothesis testing For this lab assignment you will make testable hypotheses concerning the effects of various treatments. - example: I hypothesize that stomata will be more open after 2 hours in the light compared to 2 hours in the dark. You will use an ANOVA and student’s t-test to compare the data to determine if your hypothesis is reasonable (acceptable) or can be rejected For conducting the statistical tests, restructure your hypothesis into the form of a null hypothesis: “There is no difference between the 2 hour light and dark treated stomata” Student’s t-test - - The t-test gives you the probability (P) that the two datasets are the same. You need both the mean value of the two populations and the P value to test your hypothesis. By convention, if the probability is above 0.05 then the null hypothesis is accepted and thus the data don’t support a difference in the two means. This does not mean that the null is true! If the probability is 0.05 or below then the hypothesis is rejected. Example: p.value = 0.002 Dark mean 3.5 Light mean 6.2 The data supports (but does not prove) our hypothesis that light promotes the opening of stomata Student’s t-test - Most t-test calculators consider variance – the spread of the data around the mean. - t-test assumes that the groups are sampled from normal distributions with equal variance. - We will use the F-test to test whether the variance is the same for the groups being compared. Student’s t-test vs Anova Experiment #1 Compare Control vs Light Control Light Student’s t-test vs Anova Experiment #1 Compare Control vs Light Control Light When comparing 2 population means = t-test Student’s t-test vs Anova Experiment #1 Compare Control vs Light Control Light When comparing 2 population means = t-test Experiment #2 Compare Control vs Light, ABA and Fusicoccin Control Light ABA Fusicoccin Experiment #1 Compare Control vs Light Control Student’s t-test vs Anova Light Experiment #2 Compare Control vs Light, ABA and Fusicoccin Control Light ABA Fusicoccin When comparing 2 population means = t-test When comparing more than 2 population means = ANOVA Statistical Analysis in R We will be running all our statistical tests in R. Please download and install R and R studio onto your computer before lab See the Lab2-Introduction to R protocol on eLabJournal The R Project for Statistical Computing https://www.r-project.org/ Integrated Development Environment for R https://rstudio.com/products/rstudio/#rstudio-desktop ANOVA – Analysis of Variance - One-way ANOVA compares means of multiple groups simultaneously Estimates the amount of variation due to sampling error Null hypothesis: All population means are the same for all treatments Alternative hypothesis: At least one mean is different. ANOVA – Analysis of Variance - One-way ANOVA compares means of multiple groups simultaneously Estimates the amount of variation due to sampling error Null hypothesis: All population means are the same for all treatments Alternative hypothesis: At least one mean is different. ANOVA Table Df Sum Sq Mean Sq F value Pr(>F) CONDITION 6 410.8 68.47 33.51