PER Project Descriptions (2018–19)

DIRECTIONS:

Step 1:  Read the list of mentors and brief research descriptions in the table below. To see a more detailed description of a mentor's project, click on their name or scroll past the table. It is strongly recommended that you look up the labs of each of the mentors to gain more information about their research. It is important to take the time to carefully review the projects and lab websites because you may soon be engaging in this work through a one-year research experience.

Step 2:  Identify 3 “unique” mentors that have project(s) that interest you. For example, if a mentor has more than one project that interests you, you will indicate Koskella 1 & 3. This “counts” as one mentor only, but signals to us that you are interested in projects 1 and 3 that are offered by Koskella. At this point, you are still required to select two more mentors, for a grand total of 3 mentors. As an example, your final selection may look like this: (1) Koskella 1 & 3, (2) Kremen 2, (3) Weisblat 1.

**DO NOT CONTACT THESE MENTORS DIRECTLY ABOUT THE PROGRAM**

Detailed Research Descriptions

Dennis Baldocchi

(Biometeorology Lab)

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Project Description: Investigating plant litter decomposition rates in restored wetlands:Wetlands are associated with deep organic carbon rich soils due to their high water table. Where land subsidence has resulted in elevations below sea level, wetlands are crucial in helping to reverse this effect by building carbon rich soils from plant litter. The rate at which this process occurs is of prime interest, especially with rising sea levels threatening to flood agriculturally important areas, and therefore the rate of decomposition of plant biomass needs to be quantified. The student will design and implement an experiment to measure decomposition rates of plant litter in a restored wetland using litter bags. They will be responsible for producing the litter bags, harvesting and processing plant material for the experiment, deploying and collecting them in the field, as well as analyzing and presenting the data with support from the lab technicians and myself. The results from this project will support the Lab's ongoing monitoring work at multiple wetland sites and provide important information on the efficacy of using wetlands to reverse land subsidence

Learning Outcome or Skills Students Will Learn: Understand and apply the scientific method (incl. experimental design, critical literature review, basic data analysis, statistics, and presentation and discussion of the results), develop safety awareness for field and lab work settings, demonstrate knowledge of carbon and nutrient cycling in ecosystems using the example of wetlands, name the main drivers of litter decomposition, acquire and apply basic statistical and data analysis skills (with the possibility of learning script-based software for analyses), ability to critically evaluate data and assess data quality, and present and communicate the results effectively.

Rauri Bowie

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Project Description:  Learning to DNA and complete analyses for a bird or insect phylogeny/phylogeography project.

Learning Outcome or Skills Students Will Learn: DNA sequencing, project design, molecular DNA analyses, writing, and if things go well conference poster/oral.

Stephanie Carlson

Ecology of intermittent streams.We have a variety of ongoing projects in the Carlson Lab generally related to our studies of intermittent streams that cease to flow during the summer dry season.

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Project Description:  We continue our field data collection through ~Nov 15th, and there may  be opportunities for the BSP student to join us in the field. Following our summer 2018 field campaigns, we will have data to enter, error check, visualize, and analyze.

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Project Description:  We will collect macroinvertebrate samples from isolated pools, and there will be opportunities to help sort and identify these organisms (after proper training).

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Project Description:  Finally, if the student is interested in terrestrial vertebrates and their dependence on streams, we will have some critter camera footage to process.

Learning Outcome or Skills Students Will Learn: We anticipate that the BSP student would participate in a variety of activities that would help introduce the student to intermittent streams (which represent > 60% of the streams in California) as well as standard methods in stream ecology. Through participation with a series of related projects, the student will learn about the ecology of intermittent streams that cease to flow during dry seasons and dry years.Past BSP students in the lab have carved out small independent projects and many of these students have gone on to present their results at meetings such as SACNAS.In terms of practical and transferable skills, the student will gain exposure with MS Excel by entering data from our summer 2018 field campaigns, QA/QC'ing those data, and learning how to create exploratory plots and summary tables. Depending on the student's interest, there will also be opportunities to link in with ongoing work on stream macroinvertebrates (sorting and identifying) and processing video footage from critter cameras deployed at our field research sites. There may also be opportunities to participate with field data collection in early fall.

Britt Glaunsinger

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Project Description:  How is the host gene expression machinery affected by viral infection? We study a type of herpesvirus that takes over many aspects of the host gene expression machinery upon infection. However, viral gene production is also dependent on certain aspects of these same pathways. I'm trying to understand how specific proteins like PABPC1 and Xrn1 are important for for both host and viral gene expression.

Learning Outcome or Skills Students Will Learn: Many molecular biology skills including cloning. Also cell culture including passaging cells, transfection, extraction of DNA, profiling cells for gene expression changes. The student will also gain presentation skills, read papers, think about data presentation, basic statistics and potentially some coding and sequence analysis depending on interest.

Britt Koskella

We have numerous projects that a BSP student could join, and each would have an independent component that the student would have complete ownership over.  Each project has both a wet lab component and a molecular component. We use both culture independent sequencing and droplet digital PCR methods to measure host-microbiome and bacteria-phage dynamics.

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Project Description:  First, we have a new experimental evolution study of plant-associated microbiomes that will examine how transmission from parent to offspring plant affects how well-adapted a given microbiome is to its host.

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Project Description:  Next we have a projects examining the role of bacteriophages in shaping the microbiome of pear trees, with a focus on their role during fire blight disease.

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Project Description:  And finally, we have a project examining the role of non-infectious phage particles in shaping the outcome of phage infection of a plant pathogenic bacterium.

Learning Outcome or Skills Students Will Learn: Critical thinking skills, molecular an microbiology techniques, experimental design, and statistical analysis of data. We would also hope the student would be keen to be involved in any publication resulting from the work in which they were involved.

Claire Kremen

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Project Description: Species respond differently to habitat conversion—even species in the same family or genus that share many functional traits (e.g. breeding strategy, diet, coloration). For example, in the family Centrolenidae (glass frogs), some species are extremely disturbance-adverse (e.g. Centrolene heloderma and C. lynchi) while others (e.g. Espadarana prosoblepon) are found in many habitat types along a disturbance gradient, from primary forest to pastures. These three species are all arboreal, have extremely similar coloration and body size, lay a similar number of eggs on leaves above streams, and are found at similar elevations and climate profiles. These response differences may be driven by functional traits that are rarely considered, such as vocalization characteristics. The conversion of forest to agriculture changes not only the microhabitat suitability for a species, but its acoustic space as well. I am looking for a student to help 1) compile a dataset of traditional functional traits (e.g. body size, breeding strategy);

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Project Description:  and 2) call characteristics across amphibian species in Ecuador. Functional traits and disturbance tolerance profiles will be compiled from a field guide of Ecuadorian frogs (pre-release access from Tropical Herping Group) as well as from primary literature. Vocalizations for each species will be collected (when possible) from recording databases such as the Cornell Lab of Ornithology’s Macaulay Library of Natural Sounds, natural history museums, and personal recordings). Spectrogram analysis will be performed in Raven Software 2.0 (Cornell Lab of Ornithology). For each species, the student and I will categorize/bin each call characteristic (e.g. dominant frequency, diversity of notes, number of pulses per note) to create a call profile for each species. The student can work on the functional traits, vocalization analysis, or both depending on their interests.

Learning Outcome or Skills Students Will Learn: Experience with wildlife acoustics, database generation, amphibian natural history, conservation biology, mining scientific papers and field guides for information. Help with professional development if interested.

Krishna Niyogi

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Project Description:  Efficient photosynthesis is essential for productive food crops. However, natural light is highly dynamic and often in excess, resulting in damage to pigments, proteins, and lipids within the chloroplast. To cope with saturating light, plants dissipate excess energy through a process called nonphotochemical quenching (NPQ). NPQ mechanisms are important photoprotective responses that compete with light harvesting and limit photosynthetic efficiency. Previous work to improve relaxation of the fast-acting components of NPQ has increased growth in the field-grown model crop Nicotiana tabacum by 15%. Given this success, the Niyogi lab is interested in improving the recovery of slowly-relaxing photoinhibitory quenching – caused by high light damage to core photosynthetic machinery and subsequent sustained reduction in CO2 assimilation. However, the mechanisms underlying photoinhibition are poorly understood. First-time undergraduate researchers will work alongside graduate student Dhruv Patel to apply a variety of molecular biological techniques to address this gap in the literature. Students with an interest in plant biology, molecular biology, and/or genetics are highly encouraged to apply.

Learning Outcome or Skills Students Will Learn: The researcher will apply the scientific method firsthand and will have the freedom to address independent questions, under the guidance of their mentor, if desired. At the end of their program, the student will have the opportunity to present their contribution to the work at a lab meeting. Students will learn molecular biology techniques applicable to a variety of disciplines. Namely, the researcher will learn and apply 1) PCR for cloning candidate genes, assembling transformation vectors, and genotyping 2) Protein analysis techniques such as SDS-PAGE and western blotting and 3) Analysis of photosynthetic efficiency by chlorophyll fluorescence. Additional analysis techniques such as HPLC and mass spectrometry may also be applied as projects develop.

Jose Pablo Vazquez-Medina

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Project Description:  Ferroptosis is a recently described type of cell death characterized by the accumulation of lipid peroxides. Glutathione peroxidase 4 (GPx4), an enzyme that reduces lipid hydroperoxides, has been identified as a critical regulator of ferroptosis. GPx4 expression, however, is modest in several tissues such as the lung. We are studying alternative enzymatic regulators of ferroptosis in lung cells.

Learning Outcome or Skills Students Will Learn: Students will learn primary cell culture and basic biochemistry and molecular biology techniques including fluorescence microscopy, RT-qPCR and western blotting. Students will also learn about non-technical aspects of research such as experimental design, scientific article reading, data interpretation and oral presentation of results.

David Weisblat

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Project Description:  Working with postdoc Chris Winchell and other lab members to understand cellular and molecular mechanisms of anterior-posterior patterning in leech embryos.

Learning Outcome or Skills Students Will Learn: Basic molecular biology techniques that are used in most areas of molecular & cell biology; exposure to developmental biology and the rationale of evolutionary developmental biology (Evo-Devo).