The Baker Lab
Overview
To introduce students to a broad spectrum of field and laboratory methods for data collection in environmental science. Through exposure to environmental data collection, experimental design, data analysis, interpretation and reporting, students will gain a deeper appreciation of the process that underlies environmental science research and it's relevancy to critical thinking and future careers in the sciences.
This course will involve environmental data collection in both field and laboratory settings. In-class lectures will cover basic principles of specific methodologies and relevant applications in preparation for laboratory and field-based experiential learning. Having an interdisciplinary focus, the course will cover topics relevant to the study of the biosphere, encompassing terrestrial, aquatic, and atmospheric systems. Students will gain hands-on experience with the operation of standard and advanced sampling and analytical equipment, quality control, basic data analysis and reporting.
ENVS2001/2014 Field and Lab Methods
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References:
Project Materials:
Week 11: DNA Techniques (Nov. 11th)
Tutorial: PCR Reaction
This Nobel Prize winning bichemical reaction is the foundation of modern DNA analyses. It permits the exponential amplification of DNA sequences which can be useful for identifying organisms, including microbial pathogens, from the environment. With myriad uses in Environmental Science, PCR is an important technique that any scientist should know about.
This week we will learn one of the most important techniques in molecular biology; DNA extraction and the PCR reaction. As a group, you will use a MoBio PowerSoil DNA Extraction kit to extract and purify DNA from our SWIMS coral's symbiotic algae (Symbiodinium) that we isolated on Saturday. The cell pellets will be transfered to a "beat beating" tube, to help to burst the cells to release their DNA. After that, the detailed protocol is like a cook book and explains the entire process and what each solution is doing to your sample. Remember to maintain good pipetting techniques!
Tutorial: DNA Extraction
Using the MoBio PowerSoil DNA isolation kit. We will use the same kit in our laboratory today.
Tutorial: Gel Electrophoresis
How to separate and visualize DNA and PCR products.
Week 9: Air Pollution (Oct. 27th)
This week we will learn about the problem of atmospheric pollution and how to measure important air quality metrics including total suspended particulates (TSP), PM10 and PM2.5. We will demonstrate our new (and very cool) MiniVol TAS portable air samplers. We'll use this issue to discuss considerations for field sampling designs and break out into groups to present different case studies for field sampling.
Tutorial: Ground level ozone
Not only are suspended particulates a concern for human and environmental health, but reactions with gaseous emissions of nitrogen and hydrocarbons can produce highly reactive ozone, which is a major emerging threat to the biosphere.
References:
Overview of Atmospheric Pollution, Effects, and Thresholds:
Fenn et al. (2011) Issues in Ecology
Stable isotope analysis of wet and dry atmospheric deposition:
Elliot et al. (2009) J Geophys Res
The bane of ecologists, the dreaded pitfalls of PSEUDOREPLICATION!! Hurlbert (1984) Ecological Monographs
Designing Environmental Field Studies (must read!)
Week 8: Marine Sediment Analyses & Heavy Metals (Oct. 20)
This week we will discuss the important environmental problem of heavy metal pollution. We welcome Dr. Christelle Not to the class to lecture on sediment records of pollution and environmental change, with some examples from her research. Later, we will take a look at a sediment core from Victoria Harbour, provided by Dr. Yasuhara. We will discuss sampling equipment, and demonstrate the process of acid digestion of sediments for heavy metals determination using AA-Spectrophotometer in the Central Facilities of the School of Biological Sciences.
Lab Tutorial: ICP-AES (OES) for heavy metals analysis
References:
Lab Tutorial: Sediment Sampling
Dr. Yasuhara's team samples a sediment core from Victoria Harbour. A simlar core will be on display for examination during our class.
Lab Tutorial: Flame AA Spectroscopy
Lab Tutorial: How it works ICP-OES
In this tutorial you can get an atomized view of how the ICP-OES measures cations in samples at very small concentrations. This unit is similar to the one in the SBS Central Facilities.
Week 7: Stable Isotope Analysis (Oct. 6)
References:
This week we will discuss the use of stable isotope analysis in environmental science. The technique allows us to trace the flow of matter through ecosystems and assess human-impacts on those processes. Many examples will be covered with an emphasis on the isotopes of two very important elements for life: carbon and nitrogen.
In class, we will also have group meetings to discuss your progress with team projects.
Lecture: Stable Isotope Analysis
Week 6: Terrestrial Ecology (Sept. 29)
This week we will meet Dr. Luke Gibson, who will show us some field techniques for sampling populations in the field, and share with us the power of camera traps for documenting rare and nocturnal animals.
Lecture 1: Ecological Sampling
This video covers techniques commonly used to quantify species abundance and distribution, and thus is vital for estimating total biodiversity in an ecosystem.
Lecture 2: Quadrats
This lecture discusses the use of quadrats in ecological sampling. Quadrats are one of the most widely used tools by an ecologist both in terrestrial and aquatic habitats.
Week 5: Soil Analysis (Sept. 22)
This week we move from the sea to the land where we will apply some new sampling skills with familiar chemical assays. You will learn how to sample soil using different devices. We will demonstrate how to prepare soils for % moisture and organic composition, texture, and phosphate concentration.
Lecture #4: Soil Analysis
References:
Lab Tutorial: Sieve & Texture
This detailed video explains how to sort soil particles and then characterize soil texture and composition which is important for soil classification. We will use the sieve together in a demonstration. Each group will use the hydrometer method for soil texture analysis.
Assignment:
References:
Now you know how to sample some water using a Van Dorn sampler, why don't we use it to test some real samples from Victoria harbor? This week we will begin our lesson with a quick field trip to the waterfront. There, we will sample water from 4 depths, from the surface to the seafloor. We'll bring our samples back to the lab, and learn some new tools and methods for measuring other water quality parameters, like pH, salinity, nutrient concentration, and microbial indicators.
To prepare for the lab, please review the following video tutorials, and familiarize yourself with the laboratory protocol.
NOTE: WE WILL MEET THE COACH BEHIND THE MAIN BUILDING AT 1:30pm SHARP!!! DON'T BE LATE!!!
Week 4: Water Quality (Sept. 15)
Lecture #3: water quality
Lab Tutorial: Water Quality
A walkthrough of Tuesday's practical. Please review.
Week 2: Photosynthesis & respiration (Sept. 8)
The objectives of this week's lab are to 1) learn how to sample water, 2) learn how to measure oxygen and carbon dioxide in water, 3) see how this is related to photosynthesis and respiration, and 4) appreciate the difference between chemistry and electro-chemical or optical probes. You will contrast the use of the classic "Winkler" titration for dissolved oxygen determination with the now common use of probes. This week we will use 2 different probes made by YSI.
To prepare for the lab, please review the following video tutorials, and familiarize yourself with the laboratory protocol.
Lecture #2: Oxygen & CO2
References:
Video Tutorial #3: How to pipette
Learn how to pipette accurately, without damaging the pipette!
Lab Tutorial: Dissolved Gasses
A walkthrough of Tuesday's practical. Please review.
Course Materials
Week 1: course intro, safety, science, & team projects
(Sept. 1st)
Welcome to the course! This week we will overview the course objectives and discuss matters of safety and assessments. This week I will introduce the group projects which you must review in order to form project teams. This year we are doing this on Week 1 so that groups have the maximium time to research and prepare for their projects!
SIGN UP!!:
Below you will find the course syllabus and schedule and team project details under "course materials". Assignments for this week are also below. Supplementary information is given under "references" which may be useful if you have never taken a lab course before.