Noah Whiteman, Professor

Closed (1) Reproductive trait evolution and the invasion of novel habitats

Closed. This professor is continuing with Spring 2017 apprentices on this project; no new apprentices needed for Fall 2017.

Drosophila suzukii is an invasive fruit fly that lays its eggs in small ripening fruits that include caneberries, strawberries, cherries, and grapes. This fly uses its sawing ovipositor to create a hole in the fruit skin, and larvae develop in the fruit. Since its invasion in 2008 in Santa Cruz raspberry fields, D. suzukii has cost the state of California hundreds of millions of dollars in agricultural damage. This project seeks to find the ovipositor traits that have allowed the fly to establish in such diverse fruit environments. For example, the possession of more or larger ovipositor pegs, or a longer ovipositor, might enable the fly to saw into fruits with thicker skins. The primary goals of this project are to identify traits of adaptive significance during invasion. Ultimately we hope to identify the genetic basis of these traits using next generation sequencing technology. We hope that this work will also have agricultural application, although this work will focus on evolutionary questions.



The URAP apprentice should expect to perform the following tasks:

1. Microscope dissection of fly ovipositors
2. Use of ImageJ or other image processing software to measure quantitative traits
3. Data entry and simple statistical analyses
4. Establish fly crosses and maintain colonies

Other tasks may include molecular lab work and some introductory bioinformatics, conducting choice tests on female flies, or other duties as interest arises.

Benefits: The apprentice will gain extensive experience in data collection and project design, which will be of broad use in the field of evolutionary genetics. Data generation is a crucial step in conducting scientific research, and Drosophila is a model system for evolutionary biology. This experience will serve as an excellent foundation for any student interested in evolutionary biology.

Day-to-day supervisor: Cathy Rushworth, postdoctoral researcher

Weekly hours: 10-15

Related website: www.noahwhiteman.org


Day-to-day supervisor for this project: Cathy Rushworth, Post-Doc

Qualifications: Qualifications: Detail-oriented, responsible, mature individuals who are capable of careful and meticulous data collection.

Weekly Hours: 9-12 hrs

Related website: http://www.noahwhiteman.org

Closed (2) Multimodal chemosensory reception in herbivorous insects

Applications for Fall 2017 are now closed for this project.

During the evolutionary transition from one feeding guild to another, such as microbe- to plant-feeding, it is hypothesized that behavioral adaptations are among the first to evolve. In insects, changes to the chemosensory systems that determine host preference are necessary, not only for finding an appropriate host, but in deciding at a fine spatial scale within an individual host where to feed and lay eggs. Understanding the functional genetic changes that underlie these complex behavioral shifts is a long-term goal in evolutionary biology. Scaptomyza flava, a small leaf-mining fly lends itself to be an ideal study system because (1) they evolved herbivory within the last 20 million years (relatively recent compared to other well-studied herbivores), (2) they can be collected on the UC Berkeley campus and are easily grown in culture on the model plant Arabidopsis thaliana, and (3) we can leverage the genetic tools of the model organism Drosophila melanogaster, its close relative.

S. flava has a number of body parts involved in chemoreception, which include the proboscis, maxillary palps, antennae, tarsi, wings, and ovipositor, the organ used for depositing eggs. This project aims to characterize the chemosensory receptors and other necessary proteins located in some of these regions, particularly the ovipositor, which is highly modified in S. flava and its other herbivorous relatives.

The URAP student will:
1. Perform fine skilled dissections on flies
2. Maintain fly colonies
3. Learn RNase-free techniques, RNA extractions, and cDNA library preparation

Day-to-day supervisor for this project: Julianne Pelaez, Graduate Student

Qualifications: We are looking for a curious, highly motivated, and detail oriented student, who can operate independently but seek guidance when necessary. Steady hands and a positive attitude are a must.

Weekly Hours: 6-9 hrs

Related website: http://www.noahwhiteman.org

Closed (3) The consequences of hybridization on plant defenses and herbivory

Applications for Fall 2017 are now closed for this project.

Hybridization between reproductively isolated species has numerous downstream consequences. In plants, hybridization can alter the production of defensive compounds, which can in turn alter patterns of herbivory and even the assembly of herbivore communities. At the same time, outcrossing (which may include hybridization) can relieve genetic load of inbred organisms. Thus hybridization can have both positive and negative consequences for fitness in the field. This project uses the mustard genus Boechera, a close relative of the model plant Arabidopsis thaliana, as a system to ask what specific alterations in defensive chemistry (glucosinolates) occur following recent hybridization, how these alterations may influence patterns of herbivory, and whether or not putatively detrimental alterations in defensive chemistry are associated with growth benefits in hybrid plants.

In the genus Boechera, hybridization is rampant and often results in asexual lineages where all offspring are identical to the parent. These asexual lineages are common across the native range of the plant, and a previous large-scale field experiment showed that asexuals experience increased herbivory when compared to their sexual progenitors. However, asexuals also experience a large survival advantage, and this fitness advantage is consistent across years and sites. When sexual, Boechera is highly self-fertilizing. Thus this system offers a well-characterized natural context for addressing questions of growth/defense tradeoffs and the fitness consequences of inbreeding and outcrossing.

In this experiment, we will 1) assess germination rate and proportion of sexual and asexual plants; 2) assess growth rate of ~1000 plants 3x/week for 6-8 weeks; 3) collect leaf tissue for RNAseq; 4) apply an insect or insect-mimic chemical to plants and re-collect leaf tissue for RNAseq; 5) collect leaf tissue and prepare for glucosinolate profiling. This design will permit downstream focus on expression differences in glucosinolate pathway genes, allowing us to pinpoint the effects of hybridization on both constitutive and induced defenses. This experiment will allow us to ask which alterations in defensive chemistry have established in asexual plants, and whether or not there is a growth/defense trade-off that explains both the survivorship advantage and herbivory disadvantage of asexuality in nature.


The URAP apprentice should expect to perform the following tasks:

1. Plant growth and maintenance
2. Data collection for greenhouse experiments (growth rate, to be measured on ~1000 plants 3x/week; germination rate)
3. Data entry and simple statistical analyses
4. Tissue collection for DNA and RNA extraction as well as glucosinolate profiling

Other tasks may include RNA extraction and transcriptome analysis, as time allows.


Day-to-day supervisor for this project: Cathy Rushworth, Post-Doc

Qualifications: Benefits: The apprentice will gain extensive experience in data collection and project design, which will be of broad use in the field of evolutionary genetics. Data generation is a crucial step in conducting scientific research, and Boechera is an emerging ecological model system for evolutionary biology. This experience will serve as an excellent foundation for any student interested in evolutionary biology. Day-to-day supervisor: Cathy Rushworth, postdoctoral researcher Qualifications (required): Detail-oriented, responsible, mature individuals who are capable of careful and meticulous data collection, and work in wet or dirty conditions. We also hope to find a student who has flexibility in hours so that we can collect data Mondays, Wednesdays, and Fridays of each week. Weekly hours: estimated 5-10

Weekly Hours: 6-9 hrs

Related website: www.noahwhiteman.org
Related website: cathyrushworth.weebly.com

Closed (4) The effects of herbivore gut bacteria on plant defenses to herbivore attack

Applications for Fall 2017 are now closed for this project.

Plants have complex immune systems that respond differently based on cues from different attackers. For example, plant defenses against herbivore attackers are induced by the phytohormone Jasmoinic Acid (JA), whereas defenses against pathogenic bacteria are induced by Salicylic Acid (SA). Interestingly, JA and SA signaling are mutually antagonistic, which can result in plants being defended against one type of attacker while being susceptible to another type of attacker. This mutually antagonistic JA/SA crosstalk provides an opportunity for herbivorous insects to use their associated bacteria to manipulate host plant defenses in their favor.

The emerging model herbivorous fly, Scaptomyza flava, produced a leaf-mining larva with curious behavior that may be involved in modulating plant defenses through JA/SA crosstalk: As the larva tunnels through the leaf, it periodically returns to parts of the mine where it defecated and continues to feed, possibly taking advantage of suppressed JA signaling from bacteria in its frass. This project will investigate the role of bacteria in S. flava frass in suppressing host plant defenses against the fly. By using the model plant Arabidopsis thaliana as the S. flava host plant, we will leverage transgenic reporter lines to monitor SA and JA signaling and test whether frass bacteria serve to suppress host plant defenses against S. flava.

The URAP student will:

1) Work with supervisor to design experiments
2) Use light microscopy to monitor JA and SA signaling in A. thaliana reporter lines
3) Maintain a S. flava colony for experimental use
4) Plant and maintain A. thaliana plants for S. flava colony maintenance and for experiments
5) Perform basic data analysis and statistics

Day-to-day supervisor for this project: Rebecca Duncan, Post-Doc

Qualifications: Qualifications: We are looking for a student who is curious, independent, detail-oriented, and can collect/record data in an organized fashion. This project is meant to be an independent project driven by the URAP student and the supervisor will be available for guidance. The student will gain hands on experience being a scientist in a lab.

Weekly Hours: to be negotiated

Related website: www.noahwhiteman.org